Rab family of small GTPases: an updated view on their regulation and functions

ERK activation by Rab2B in the early secretory pathway impacts the ERGIC-Golgi interface

The Golgi complex is a hub for several signal transduction networks that regulate Golgi morphology, membrane transport, and glycosylation. The Rab2 (A, B isoforms) protein participates in membrane trafficking to and from the Golgi and is also linked to signaling molecules. In that regard, Rab2A in breast cancer stem cells binds and blocks (p)ERK1/2 inactivation by MAP kinase phosphatase 3. However, the cellular role of Rab2B in ERK1/2 signaling activity at the endoplasmic reticulum-Golgi intermediate compartment (ERGIC/IC) and cis Golgi where Rab2B immunolocalizes and functions is unknown. To address this question, normal rat kidney (NRK) cells were transfected with Rab2B cDNA to mimic Rab2 overexpression as found in cancer cells. Rab2B overexpressing NRK cells had a significant increase in steady state activated ERK. Studies were then performed to identify the Rab2-ERK1/2 substrate(s) that locate and function in the early secretory pathway. To that end, GRASP65 was identified as a target of ERK1/2 phosphorylation. In Rab2B overexpressing NRK cells, GRASP65 co-distributed with GM130 on membranes of the ERGIC/IC that increased in size and number with the concomitant appearance of unlinked cis Golgi elements. Additionally, we observed GRASP65 labeled ERGIC/IC membranes that accumulated at 15°C and remained prominent after temperature shift to 37 °C to promote transport. However, addition of a MEK inhibitor reversed the transport block indicating that ERK1/2 phosphorylation of GRASP65 effected ERGIC/IC redistribution to the cis Golgi. Since several glycosyltransferases cycle between the Golgi and ERGIC/IC, a potential consequence of Golgi structural changes is modification of protein glycosylation. Indeed, we found changes in total and cell surface O-glycosylation in Rab2B overexpressing cells. These results suggest that phosphoGRASP65 plays an important role in the protein sorting and recycling process from the ERGIC/IC to cis Golgi: Dysregulation results in cis Golgi discontinuities and aberrant glycosylated proteins that are potentially pro-oncogenic.

Non-coding RNA RMRP governs RAB31-dependent MMP secretion, enhancing ovarian cancer invasion

Non-coding RNAs (ncRNAs) are frequently dysregulated in various cancers and have been implicated in the etiology and progression of cancer. Ovarian cancer, the most fatal gynecological cancer, has a poor prognosis and a high patient fatality rate due to metastases. In this study, we classified patients with ovarian cancer into three groups based on their ncRNA expression levels. Notably, an ncRNA transcribed by RNA polymerase III, RNA component of mitochondrial RNA processing endoribonuclease (RMRP), is highly expressed in a group with a poor prognosis. Functional assays using SKOV3 and HeyA8 human ovarian cancer cell lines revealed that while RMRP modulation had no significant effect on cell viability, it markedly enhanced cell invasion. Knockdown and ectopic expression experiments demonstrated that RMRP promotes the secretion of matrix metalloproteinase (MMP)-2 and -9, thereby facilitating ovarian cancer cell invasiveness. Transcriptomic analysis further revealed a positive correlation between RMRP expression and genes involved in cellular localization, including RAB31, a member of the Ras-related protein family. Notably, RAB31 knockdown abrogated the pro-invasive effects of RMRP, identifying it as a key downstream effector in SKOV3 and HeyA8 cells. In addition, MechRNA analysis identified RAB31 as a putative RMRP-interacting transcript. These findings establish RMRP as a critical regulator of RAB31-dependent MMP secretion and ovarian cancer cell invasion. Moreover, our results suggest that RMRP could serve as a promising prognostic biomarker for ovarian cancer.

Diplonemid protists possess exotic endomembrane machinery, impacting models of membrane trafficking in modern and ancient eukaryotes

Diplonemids are among the most abundant and species-rich protists in the oceans. Marine heterotrophic flagellates, including diplonemids, have been suggested to play important roles in global biogeochemical cycles. Diplonemids are also the sister taxon of kinetoplastids, home to trypanosomatid parasites of global health importance, and thus are informative about the evolution of kinetoplastid biology. However, the genomic and cellular complement that underpins diplonemids' highly successful lifestyle is underexplored. At the same time, our framework describing cellular processes may not be as broadly applicable as presumed, as it is largely derived from animal and fungal model organisms, a small subset of extant eukaryotic diversity. In addition to uniquely evolved machinery in animals and fungi, there exist components with sporadic (i.e., "patchy") distributions across other eukaryotes. A most intriguing subset are components ("jötnarlogs") stochastically present in a wide range of eukaryotes but lost in animal and/or fungal models. Such components are considered exotic curiosities but may be relevant to inferences about the complexity of the last eukaryotic common ancestor (LECA) and frameworks of modern cell biology. Here, we use comparative genomics and phylogenetics to comprehensively assess the membrane-trafficking system of diplonemids. They possess several proteins thought of as kinetoplastid specific, as well as an extensive set of patchy proteins, including jötnarlogs. Diplonemids apparently function with endomembrane machinery distinct from existing cell biological models but comparable with other free-living heterotrophic protists, highlighting the importance of including such exotic components when considering different models of ancient eukaryotic genomic complexity and the cell biology of non-opisthokont organisms.

TBC1D20 coordinates vesicle transport and actin remodeling to regulate ciliogenesis

TBC1D20 deficiency causes Warburg Micro Syndrome in humans, characterized by multiple eye abnormalities, severe intellectual disability, and abnormal sexual development, but the molecular mechanisms remain unknown. Here, we identify TBC1D20 as a novel Rab11 GTPase-activating protein that coordinates vesicle transport and actin remodeling to regulate ciliogenesis. Depletion of TBC1D20 promotes Rab11 vesicle accumulation and actin deconstruction around the centrosome, facilitating the initiation of ciliogenesis even in cycling cells. Further investigations reveal enhanced Rab11-MICAL1 interaction upon TBC1D20 loss, activating the monooxygenase domain of MICAL1 and inducing F-actin depolymerization around the centrosome. This actin network reorganization facilitates vesicle trafficking and docking, ultimately promoting ciliogenesis. In summary, our work uncovers a coordinated ciliogenesis initiation mechanism via Rab11 activation. These findings underscore a pivotal role for TBC1D20 in early ciliogenesis, advancing our understanding of its spatiotemporal regulation and offering insights into the disease pathogenesis associated with TBC1D20 mutations.

Retromer promotes the lysosomal turnover of mtDNA

Mitochondrial DNA (mtDNA) is exposed to multiple insults produced by normal cellular function. Upon mtDNA replication stress, the mitochondrial genome transfers to endosomes for degradation. Using proximity biotinylation, we found that mtDNA stress leads to the rewiring of the mitochondrial proximity proteome, increasing mitochondria's association with lysosomal and vesicle-related proteins. Among these, the retromer complex, particularly VPS35, plays a pivotal role by extracting mitochondrial components. The retromer promotes the formation of mitochondrial-derived vesicles shuttled to lysosomes. The mtDNA, however, directly shuttles to a recycling organelle in a BAX-dependent manner. Moreover, using a Drosophila model carrying a long deletion on the mtDNA (ΔmtDNA), we found that ΔmtDNA activates a specific transcriptome profile to counteract mitochondrial damage. Here, Vps35 expression restores mtDNA homoplasmy and alleviates associated defects. Hence, we demonstrate the existence of a previously unknown quality control mechanism for the mitochondrial matrix and the essential role of lysosomes in mtDNA turnover to relieve mtDNA damage.

Sculpting excitable membranes: voltage-gated ion channel delivery and distribution

The polarized and domain-specific distribution of membrane ion channels is essential for neuronal homeostasis, but delivery of these proteins to distal neuronal compartments (such as the axonal ends of peripheral sensory neurons) presents a logistical challenge. Recent developments have enabled the real-time imaging of single protein trafficking and the investigation of the life cycle of ion channels across neuronal compartments. These studies have revealed a highly regulated process involving post-translational modifications, vesicular sorting, motor protein-driven transport and targeted membrane insertion. Emerging evidence suggests that neuronal activity and disease states can dynamically modulate ion channel localization, directly influencing excitability. This Review synthesizes current knowledge on the spatiotemporal regulation of ion channel trafficking in both central and peripheral nervous system neurons. Understanding these processes not only advances our fundamental knowledge of neuronal excitability, but also reveals potential therapeutic targets for disorders involving aberrant ion channel distribution, such as chronic pain and neurodegenerative diseases.

Rab27b Promotes Lysosomal Function and Alpha-Synuclein Clearance in Neurons

Alpha-synuclein (αsyn) is the key pathogenic protein implicated in synucleinopathies including Parkinson's disease (PD) and dementia with Lewy bodies (DLB). In these diseases, αsyn is thought to spread between cells where it accumulates and induces pathology; however, mechanisms that drive its propagation or aggregation are poorly understood. We have previously reported that the small GTPase Rab27b is elevated in human PD and DLB and that it can mediate the autophagic clearance and toxicity of αsyn in a paracrine αsyn cell culture model. Here, we expanded our previous work and characterized the role of Rab27b in neuronal lysosomal processing and αsyn clearance. We found that Rab27b KD in this αsyn-inducible neuronal model resulted in lysosomal dysfunction and increased αsyn levels in lysosomes. Similar lysosomal proteolytic defects and enzymatic dysfunction were observed in both primary neuronal cultures and brain lysates from male and female Rab27b knock-out (KO) mice. αSyn aggregation was exacerbated in Rab27b KO neurons upon treatment with αsyn preformed fibrils. We found no changes in lysosomal counts or lysosomal pH in either model, but we did identify changes in acidic vesicle trafficking and in lysosomal enzyme maturation and localization, which may drive lysosomal dysfunction and promote αsyn aggregation. Rab27b OE enhanced lysosomal activity and reduced insoluble αsyn accumulation. Finally we found elevated Rab27b levels in human postmortem incidental Lewy body disease subjects relative to healthy controls. These data suggest the role of Rab27b in neuronal lysosomal activity and identify it as a potential therapeutic target in synucleinopathies.

Rab10 regulates neuropeptide release by maintaining Ca2+ homeostasis and protein synthesis

Dense core vesicles (DCVs) transport and release various neuropeptides and neurotrophins that control diverse brain functions, but the DCV secretory pathway remains poorly understood. Here, we tested a prediction emerging from invertebrate studies about the crucial role of the intracellular trafficking GTPase Rab10, by assessing DCV exocytosis at single-cell resolution upon acute Rab10 depletion in mature mouse hippocampal neurons, to circumvent potential confounding effects of Rab10's established role in neurite outgrowth. We observed a significant inhibition of DCV exocytosis in Rab10-depleted neurons, whereas synaptic vesicle exocytosis was unaffected. However, rather than a direct involvement in DCV trafficking, this effect was attributed to two ER-dependent processes, ER-regulated intracellular Ca2+ dynamics, and protein synthesis. Gene Ontology analysis of differentially expressed proteins upon Rab10 depletion identified substantial alterations in synaptic and ER/ribosomal proteins, including the Ca2+ pump SERCA2. In addition, ER morphology and dynamics were altered, ER Ca2+ levels were depleted, and Ca2+ homeostasis was impaired in Rab10-depleted neurons. However, Ca2+ entry using a Ca2+ ionophore still triggered less DCV exocytosis. Instead, leucine supplementation, which enhances protein synthesis, largely rescued DCV exocytosis deficiency. We conclude that Rab10 is required for neuropeptide release by maintaining Ca2+ dynamics and regulating protein synthesis. Furthermore, DCV exocytosis appeared more dependent on (acute) protein synthesis than synaptic vesicle exocytosis.

Moving the fat: Emerging roles of rab GTPases in the regulation of lipid droplet contact sites

Lipid droplets (LDs) play crucial roles in lipid metabolism, energy homeostasis, and cellular stress. Throughout their lifecycle, LDs establish membrane contact sites (MCSs) with the endoplasmic reticulum, mitochondria, peroxisomes, endosomes, lysosomes, and phagosomes. LD MCSs are dynamically generated in response to metabolic or immune cues to ensure that LD lipids (and proteins) are timely delivered to optimize valuable substrates and avoid lipotoxicity. It is increasingly evident that many Rab GTPases are involved in LD dynamics. Here, we summarize our current understanding of how and when Rab proteins dynamically drive the generation of LD MCSs and regulate a variety of LD functions.

GDP-bound Rab37 modulates M2-like tumor-associated macrophage polarization by attenuating STAT1 translocation to downregulate the type I IFN pathway

BACKGROUND

Tumor-associated macrophages (TAMs) in the tumor microenvironment (TME) primarily polarize into the M2-phenotype. Our previous study showed that the small GTPase Rab37 mediates IL-6 trafficking in macrophages for M2 polarization. Here, we uncover an unconventional role of Rab37, independent of vesicle trafficking, in promoting M2 polarization of TAMs.

METHODS

The gene profiles in wild-type and Rab37 knockout (KO) bone marrow-derived macrophages (BMDMs) were analyzed using cDNA microarray. The mechanism of Rab37 in regulating the interferon (IFN) pathway was confirmed through in vitro/vivo assays and clinical studies.

RESULTS

Type I IFN signaling was highly enriched in BMDMs from Rab37 KO mice. Moreover, Rab37 induction and decreased type I IFN genes were observed in macrophages treated with lung cancer-conditioned medium and epigenetic drugs, indicating an epigenetic regulation of Rab37 in TAMs. Mechanistically, GDP-bound Rab37 interacted with the nuclear localization sequence of STAT1 to sequest it in the cytosol from its transcription activities, thus leading to the downregulation of IFN genes. Clinically, CD163+/Rab37+/STAT1cytosol in TAMs expression signature correlated with advanced tumor stages and poor survival of lung cancer patients.

CONCLUSIONS

Our findings highlight the cytosolic interaction of Rab37-STAT1 in M2 TAM polarization, with CD163+/Rab37+/STAT1cytosol TAMs as a lung cancer prognosis biomarker.

Growth, fusion and degradation of lipid droplets: advances in lipid droplet regulatory protein

Context: An adequate supply of energy is essential for the proper functioning of all life activities in living organisms. As organelles that store neutral lipids, lipid droplets (LDs) are involved in the synthesis and metabolism of lipids in cells and are also an important source of energy supply.

Methods and mechanisms: A comprehensive summary of the literature was first carried out to screen for relevant proteins affecting the morphological size of LDs. The size of milk fat globules (MFGs) is directly influenced by the morphological size of LDs, which also controls the energy storage capacity of LDs. In this review, we detail the progress of research into the role of some protein in regulating the morphological size of LDs.

Conclusion: It has been discovered that the number of protein are involved in the control of LD growth and degradation, such as Rab18-mediated local synthesis of triacylglycerol (TAG), cell death-inducing DFF45-like effector family proteins (CIDEs)-mediated atypical fusion between LDs, Stomatin protein-mediated LD fusion and autophagy-related proteins (ATGs)-mediated autophagic degradation of LDs. However, more studies are needed in the future to enrich the network of mechanisms that regulate the morphological size of LDs.

Insights into the renal pathophysiology in Hermansky-Pudlak syndrome-1 from urinary extracellular vesicle proteomics and a new mouse model

Hermansky-Pudlak syndrome type 1 (HPS-1) is a rare, autosomal recessive disorder caused by defects in the biogenesis of lysosome-related organelles complex-3 (BLOC-3). Impaired kidney function is among its clinical manifestations. To investigate HPS-1 renal involvement, we employed 1D-gel-LC-MS/MS and compared the protein composition of urinary extracellular vesicles (uEVs) from HPS-1 patients to normal control individuals. We identified 1029 proteins, 149 of which were altered in HPS-1 uEVs. Ingenuity Pathway Analysis revealed disruptions in mitochondrial function and the LXR/RXR pathway that regulates lipid metabolism, which is supported by our novel Hps1 knockout mouse. Serum concentration of the LXR/RXR pathway protein ApoA1 in our patient cohort was positively correlated with kidney function (with the estimated glomerular filtration rate or eGFR). uEVs can be used to study epithelial cell protein trafficking in HPS-1 and may provide outcome measures for HPS-1 therapeutic interventions.

PI(3,4,5)P3-mediated Cdc42 activation regulates macrophage podosome assembly

Podosomes are adhesion structures with densely-polymerized F-actin. While PI(3,4,5)P3 and Cdc42-GTP are known factors to trigger WASP-mediated actin polymerization at the macrophage podosome, their causal mechanism to activate WASP remains unclear. Here, we demonstrate that spatially elevated Cdc42-GTP is a downstream effector of local PI(3,4,5)P3 production at the podosome. We further examine the expression and distribution of 19 Cdc42 guanine exchange factors (GEFs) and identify VAV1 as the key PI(3,4,5)P3-dependent Cdc42 GEF. VAV1 is spatially enriched at the macrophage podosome, and the association of VAV1 with the membrane plays a critical role in upregulating its GEF activity. Reintroduction of wildtype VAV1, rather than the PI(3,4,5)P3-binding deficient or catalytically dead mutants restores the matrix degradation and chemotactic migration of VAV1-knockdown macrophage. Thus, the biogenesis of PI(3,4,5)P3 acts as an upstream signal to locally recruit VAV1 and in turn triggers the guanine nucleotide exchange of Cdc42. Elevated levels of Cdc42-GTP then promote WASP-mediated podosome assembly and macrophage chemotaxis.

The Rab3 GTPase cycle modulates cardiomyocyte exocytosis and atrial natriuretic peptide release

Natriuretic peptides are produced predominantly by atrial cardiomyocytes in response to cardiovascular stress and attenuate cardiac maladaptation by reducing blood pressure, blood volume, and cardiac workload primarily through activation of natriuretic peptide receptors in the kidney and vasculature. However, mechanisms underlying cardiomyocyte exocytosis and natriuretic peptide secretion remain poorly defined. Manipulation of Rab3a GTPase activity by Rab3gap1 was recently found to modulate atrial natriuretic peptide (ANP) release by cardiomyocytes. Here, we examined upstream signaling mechanisms and the role of the Rab3a GTPase cycle in exocytosis and ANP secretion by cardiomyocytes. Pharmacological inhibition of the heterotrimeric G protein subunit G⍺q suppressed ANP secretion at baseline and prevented GTP loading of Rab3a and ANP release in neonatal rat cardiomyocytes in response to phenylephrine (PE). Similar to agonist-induced activation of ANP secretion, genetic overexpression of a constitutively active, GTP-loaded Rab3a mutant (Q81L) in neonatal rat cardiomyocytes resulted in enhanced intracellular distribution of Rab3a at endomembranes peripheral to the Golgi and promotion of ANP release, indicating that enhancement of Rab3a activity is sufficient to elicit ANP secretion by cardiomyocytes. Collectively, these data indicate G⍺q signaling downstream of receptor activation and Rab3a-regulated secretory pathway activity and exocytosis facilitate ANP release by cardiomyocytes that could potentially be harnessed to antagonize hypertension and adverse cardiac remodeling in cardiovascular disease.

TAT-1, a phosphatidylserine flippase, affects molting and regulates membrane trafficking in the epidermis of Caenorhabditis elegans

Membrane trafficking is a conserved process required for the import, export, movement, and distribution of proteins and other macromolecules within cells. The Caenorhabditis elegans NIMA-related kinases NEKL-2 (human NEK8/9) and NEKL-3 (human NEK6/7) are conserved regulators of membrane trafficking and are required for the completion of molting. Using a genetic approach, we identified reduction-of-function mutations in tat-1 that suppress nekl-associated molting defects. tat-1 encodes the C. elegans ortholog of mammalian ATP8A1/2, a phosphatidylserine flippase that promotes the asymmetric distribution of phosphatidylserine on the cytosolic leaflet of lipid membrane bilayers. CHAT-1 (human CDC50), a conserved chaperone, was required for the correct localization of TAT-1, and chat-1 inhibition strongly suppressed nekl defects. Using a phosphatidylserine sensor, we found that TAT-1 was required for the normal localization of phosphatidylserine at apical endosomes and that loss of TAT-1 led to aberrant endosomal morphologies. Consistent with these data, TAT-1 localized to early endosomes and to recycling endosomes marked with RME-1, the C. elegans ortholog of the human EPS15 homology domain-containing protein, EHD1. TAT-1, phosphatidylserine biosynthesis, and the phosphatidylserine-binding protein RFIP-2 (human RAB11-FIP2) were all required for the normal localization of RME-1 to apical endosomes. Consistent with these proteins functioning together, inhibition of RFIP-2 or RME-1 led to the partial suppression of nekl molting defects, as did inhibition of phosphatidylserine biosynthesis. We propose that TAT-1 flippase activity, in conjunction with RFIP-2, promotes the recruitment of RME-1 to apical recycling endosomes and that inhibition of TAT-1-RFIP-2-RME-1 can compensate for a reduction in NEKL activities.

Targeting uPARAP Modifies Lymphatic Vessel Architecture and Attenuates Lymphedema

BACKGROUND

Lymphedema is an incurable disease associated with lymphatic dysfunction that causes tissue swelling and fibrosis. We investigated whether lymphedema could be attenuated by interfering with uPARAP (urokinase plasminogen activator receptor-associated protein; Mrc2 gene), an endocytic receptor involved in fibrosis and lymphangiogenesis.

METHODS

We generated mice with lymphatic endothelial cell (LEC)-specific uPARAP deficiency and compared them with constitutive knockout mice by applying a preclinical model of secondary lymphedema (SL). Computerized methods were applied for 2-dimensional and 3-dimensional image quantifications. Cellular effects of uPARAP deletion on lymphatic permeability were assessed by small interfering RNA-mediated silencing in human dermal LECs and a pharmacologic treatment targeting ROCK (rho-associated coiled coil containing kinase), an established regulator of cell junctions. The uPARAP and vascular endothelial cadherin partnership was investigated through proximity ligation assay, coimmunoprecipitation, and immunostaining. An in silico model was generated to analyze the fluid-absorbing function of the lymphatic vasculature. To interfere with uPARAP, its downregulation was achieved in vivo through a gapmer approach.

RESULTS

uPARAP deficiency mitigated several key pathologic features of SL, including hindlimb swelling, epidermal thickening, and the accumulation and size of adipocytes. In both global and LEC-conditional uPARAP-deficient mice, induction of SL led to a distinctive labyrinthine vasculature, defined herein by twisted and hyperbranched vessels with overlapping cells. This topology, mainly composed of pre-collecting vessels, correlated with reduced SL, but not with change in fibrosis, highlighting the importance of uPARAP in regulating LEC functions in a lymphedematous context. In vitro, uPARAP knockdown in LECs impaired vascular endothelial growth factor C-mediated endosomal trafficking of vascular endothelial cadherin and induced overlapping cell junctions. The pharmacologic inhibition of ROCK recapitulated cell superimposition in vitro and the labyrinthine vasculature in vivo with attenuated SL. Computational modeling of labyrinthine lymphatic vasculature supported the observation on their improved fluid-absorbing function in comparison with a normal hierarchic network. These data provide proof of concept of inducing a labyrinthine topology to treat SL. For therapeutic purposes, we validated the use of an anti-uPARAP gapmer to induce a labyrinthine vasculature and attenuate SL formation.

CONCLUSIONS

Our findings provide evidence that downregulating uPARAP expression can induce a beneficial remodeling of lymphatic vasculature that attenuates lymphedema through a cell junction-based mechanism, offering a novel therapeutic pathway for lymphedema.

AKT activation triggers Rab14-mediated ADAM10 translocation to the cell surface in human aortic endothelial cells

AKT (protein kinase B) activation reduces the harmful effects of advanced glycation end products (AGEs); however, the protective mechanisms remain unknown. In cultured human aortic endothelial cells (HAECs), we investigated how AKT signaling suppresses AGEs-induced intercellular adhesion molecule-1 (ICAM-1) expression. AGEs of bovine serum albumin (AGE-BSA) increased ICAM-1 expression, but this effect was abolished by pretreatment with the AKT activator SC79. SC79 activated AKT1, AKT2, and AKT3, translocated a disintegrin and metalloprotease 10 (ADAM10) to the cell surface, and induced ectodomain shedding of the receptor for AGEs (RAGE). In contrast, GI 254023X-mediated ADAM10 inhibition and siRNA-mediated ADAM10 knockdown both prevented SC79-induced RAGE ectodomain shedding. On the other hand, MK-2206, a pan-AKT inhibitor, and siRNA-mediated knockdown of AKT1, AKT2, or AKT3 prevented SC79-induced ADAM10 cell surface translocation and RAGE ectodomain shedding. Notably, Rab14 was co-immunoprecipitated with ADAM10. Following SC79 treatment, Rab14 moved to the cell surface, whereas siRNA-mediated Rab14 knockdown prevented SC79 from promoting ADAM10 cell surface translocation and RAGE ectodomain shedding and abolished SC79's ability to inhibit AGE-BSA-induced ICAM-1 expression. In conclusion, upon activation of all three isoforms, AKT suppresses AGE-BSA-induced ICAM-1 expression by inducing ADAM10-mediated RAGE ectodomain shedding. This occurs because AKT signaling boosts Rab14-dependent ADAM10 cell surface translocation.

Rab3B Proteins: Cellular Functions, Regulatory Mechanisms, and Potential as a Cancer Therapy Target

RAB3 proteins, a pivotal subgroup within the Rab protein family, are known to be highly expressed in brain and endocrine gland tissues, with detectable levels also observed in exocrine glands, adipose tissue, and other peripheral tissues. They play an indispensable role in the trafficking of cellular products from the endoplasmic reticulum (ER) to the Golgi apparatus and ultimately to secretory vesicles, participating in vesicle transport, mediating cell membrane adhesion, and facilitating membrane fusion during exocytosis. Among these, Rab3B, a specific subtype of RAB3, is a low-molecular-weight (approximately 25 kD) GTP-binding protein (GTPase) characterized by its typical GTPase fold, composed of seven β-strands (six parallel and one antiparallel) surrounded by six α-helices. Previous studies have proved the significant roles of Rab3B in vesicle transport and hormone trafficking. However, its involvement in cancer remains largely unexplored. This review aims to dig into the potential mechanisms of Rab3B in various cancers, including hepatocellular cancer, lung adenocarcinoma, pancreatic cancer, breast cancer, prostate cancer, neuroblastoma and cervical cancer. Given its pivotal functions and underexplored status in oncology, Rab3B stands out as a promising target for both diagnosis and therapy in cancer treatment, with investigations into its biological mechanisms in tumorigenesis offering significant potential to advance future diagnostic and therapeutic strategies across various malignancies.

Exploring the ncRNA landscape in exosomes: Insights into wound healing mechanisms and therapeutic applications

Exosomal non-coding RNAs (ncRNAs), including miRNAs, lncRNAs, and circRNAs, have emerged as crucial modulators in cellular signaling, influencing wound healing processes. Stem cell-derived exosomes, which serve as vehicles for these ncRNAs, show remarkable therapeutic potential due to their ability to modulate wound healing stages, from initial inflammation to collagen formation. These ncRNAs act as molecular signals, regulating gene expression and protein synthesis necessary for cellular responses in healing. Wound healing is a complex, staged process involving inflammation, hemostasis, fibroblast proliferation, angiogenesis, and tissue remodeling. Stem cell-derived exosomal ncRNAs enhance these stages by reducing excessive inflammation, promoting anti-inflammatory responses, guiding fibroblast and keratinocyte maturation, enhancing vascularization, and ensuring organized collagen deposition. Their molecular cargo, particularly ncRNAs, specifically targets pathways to aid chronic wound repair and support scarless regeneration. This review delves into the unique composition and signaling roles of Stem cell-derived exosomes and ncRNAs, highlighting their impact across wound healing stages and their potential as innovative therapeutics. Understanding the interaction between exosomal ncRNAs and cellular signaling pathways opens new avenues in regenerative medicine, positioning Stem cell-derived exosomes and their ncRNAs as promising molecular-level interventions in wound healing.

Phosphorylated Eriocheir sinensis Rab10 regulates apoptosis and phagocytosis to defense Spiroplasma eriocheiris infection

The Rab GTPases play a crucial role in the regulation of immune responses towards viruses and bacteria infection in invertebrates. The proteomic data revealed Eriocheir sinensis Rab10 (EsRab10) phosphorylation was strongly decreased following Spiroplasma eriocheiris infection. However, the regulatory mechanism by which Rab10 modulates the innate immunity of E. sinensis against S. eriocheiris infection remains to be elucidated. In the present study, the coding sequence of EsRab10 identified as 609 bp, encoding a protein of 203 amino acids. EsRab10 was highly transcribed in diverse immune-related tissues of crab, including hepatopancreas, gills, and hemocytes, with a notable downregulation observed after S. eriocheiris infection. Knockdown of EsRab10 via RNA interference (RNAi) led to a significant increase in hemocyte apoptosis and a marked reduction in the phagocytic capacity of hemocytes against S. eriocheiris. Furthermore, EsRab10 RNAi resulted in an elevated S. eriocheiris load in hemocytes and a significant decrease in crab survival rates. Overexpression of EsRab10 in Drosophila Schneider 2 (S2) cells demonstrated that phosphorylation of EsRab10 enhanced cell viability, reduced apoptosis, increased phagocytic activity, and decreased the S. eriocheiris load in S2 cells. Conversely, dephosphorylation of EsRab10 exerted opposite effects. In summary, these results demonstrated that EsRab10 played a crucial role in the resistance of E. sinensis to S. eriocheiris infection by modulating apoptosis and phagocytosis through phosphorylation.

RAB4B and Japanese encephalitis virus E protein interaction is essential for viral entry in early endosomes

RAB4B (Ras-Related GTP-Binding Protein 4b) is essential for intracellular trafficking and endosomal recycling processes. Our previous study, we demonstrated that RAB4B promotes Japanese encephalitis virus (JEV) replication in PK15 cells. However, the exact mechanisms underlying the role of RAB4B in JEV internalization remain unclear. Here, a genome-wide CRISPR/Cas9 library screen was performed, which identified RAB4B, along with other significant hits like ST8SIA4 and ELAVL1, as essential mediators of JEV replication. In vitro validation using RAB4B knockout in U251 and BV2 cells showed a significant reduction in JEV genome copies and viral titers, which were restored upon reintroducing RAB4B, confirming its pivotal role in viral propagation. Further mechanistic investigation revealed that RAB4B is required for JEV internalization into early endosomes. Co-immunoprecipitation and in vitro binding assays demonstrated a direct interaction between RAB4B and the JEV E protein, highlighting the functional importance of this interaction. In vivo experiments with RAB4B knockout mice showed a reduction in viral load in the brain and improved survival rates compared to wild-type mice. Taken together, these findings provide compelling evidence that RAB4B is indispensable for JEV entry and replication.

LRRK2, lysosome damage, and Parkinson's disease

Limited understanding of regulatory mechanisms controlling LRRK2 kinase activity has hindered insights into both its normal biology and how its dysregulation contributes to Parkinson's disease. Fortunately, recent years have yielded an increased understanding of how LRRK2 kinase activity is dynamically regulated by recruitment to endolysosomal membranes. Notably, multiple small GTPases from the Rab family act as both activators and substrates of LRRK2. Additionally, it was recently discovered that LRRK2 is recruited to, and activated at, stressed or damaged lysosomes through an interaction with GABARAP via the CASM (conjugation of ATG8 to single membranes) pathway. These discoveries position LRRK2 within the rapidly growing field of lysosomal damage and repair mechanisms, offering important insights into lysosome biology and the pathogenesis of Parkinson's disease.

Rab3gap1 palmitoylation cycling modulates cardiomyocyte exocytosis and atrial natriuretic peptide release

Rab3 GTPase-activating protein 1 (Rab3gap1) hydrolyzes GTP on Rab3 to inactivate it and reinitiate the Rab3 cycle, which regulates exocytic release of neuropeptides and hormones from neuroendocrine cells and atrial natriuretic peptide (ANP) secretion by cardiomyocytes. Cysteine palmitoylation of Rab3gap1 by the Golgi-localized S-acyltransferase zDHHC9 was recently shown to hinder ANP release by impairing Rab3gap1-mediated nucleotide cycling on Rab3a. Here, we interrogate the cysteine residues of Rab3gap1 modified by palmitoylation and impacts on ANP secretion in cardiomyocytes. Although mutation of the previously identified cysteine (Cys)-678 site of Rab3gap1 alone was insufficient to elicit complete loss of Rab3gap1 palmitoylation in cardiomyocytes, combinatorial mutation of Cys-509, 510, 521, 522, and 678 (Rab3gap15CS) dramatically reduced Rab3gap1 palmitoylation. Notably, total cellular GTPase-activating protein (GAP) activity in cardiomyocytes was maintained with mutation of the Rab3gap1 palmitoylation sites as the Rab3gap15CS mutant substantially reduced steady-state Rab3a-GTP levels in cardiomyocytes similar to wild-type Rab3gap1. However, although expression of wild-type Rab3gap1 induced robust secretion of ANP and greatly enhanced phenylephrine-stimulated ANP release, the Rab3gap15CS palmitoylation-deficient mutant was incapable of promoting exocytosis and ANP release by cardiomyocytes. These data suggest Rab3gap1 cysteine palmitoylation may target Rab3gap1 to Rab3a for regulated GAP-mediated inactivation at specific intracellular membrane domains to modulate the Rab3 cycle and exocytosis. Collectively, these data support a role for Rab3gap1 palmitoylation cycling in spatiotemporal control of the Rab3 cycle to regulate exocytosis and ANP secretion by cardiomyocytes.

EndoMAP.v1, a Structural Protein Complex Landscape of Human Endosomes

Early/sorting endosomes are dynamic organelles that play key roles in proteome control by triaging plasma membrane proteins for either recycling or degradation in the lysosome1,2,3. These events are coordinated by numerous transiently-associated regulatory complexes and integral membrane components that contribute to organelle identity during endosome maturation4. While a subset of the several hundred protein components and cargoes known to associate with endosomes have been studied at the biochemical and/or structural level, interaction partners and higher order molecular assemblies for many endosomal components remain unknown. Here, we combine cross-linking and native gel mass spectrometry5-8 of purified early endosomes with AlphaFold9,10 and computational analysis to create a systematic human endosomal structural interactome. We present dozens of structural models for endosomal protein pairs and higher order assemblies supported by experimental cross-links from their native subcellular context, suggesting structural mechanisms for previously reported regulatory processes. Using induced neurons, we validate two candidate complexes whose interactions are supported by crosslinks and structural predictions: TMEM230 as a subunit of ATP8/11 lipid flippases11 and TMEM9/9B as subunits of CLCN3/4/5 chloride-proton antiporters12. This resource and its accompanying structural network viewer provide an experimental framework for understanding organellar structural interactomes and large-scale validation of structural predictions.

The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics

The evolution of eukaryotes is a fundamental event in the history of life. The closest prokaryotic lineage to eukaryotes, the Asgardarchaeota, encode proteins previously found only in eukaryotes, providing insight into their archaeal ancestor. Eukaryotic cells are characterized by endomembrane organelles, and the Arf family GTPases regulate organelle dynamics by recruiting effector proteins to membranes upon activation. The Arf family is ubiquitous among eukaryotes, but its origins remain elusive. Here we report a group of prokaryotic GTPases, the ArfRs, which are widely present in Asgardarchaeota. Phylogenetic analyses reveal that eukaryotic Arf family proteins arose from the ArfR group. Expression of representative Asgardarchaeota ArfR proteins in yeast and X-ray crystallographic studies show that ArfR GTPases possess the mechanism of membrane binding and structural features unique to Arf family proteins. Our results indicate that Arf family GTPases originated in the archaeal ancestor of eukaryotes, consistent with aspects of the endomembrane system evolving early in eukaryogenesis.

The Diverse Pathways for Cell Surface MT1-MMP Localization in Migratory Cells

Controlled cell migration is an essential biological process in health, while uncontrolled cell migration contributes to disease progression. For cells to migrate through tissue, they must first degrade the extracellular matrix (ECM), which acts as a physical barrier to cell migration. A type I transmembrane-type matrix metalloproteinase, MT1-MMP, is the key enzyme involved in this process. It has been extensively shown that MT1-MMP promotes the migration of different cell types in tissue, including fibroblasts, epithelial cells, endothelial cells, macrophages, mesenchymal stem cells, and cancer cells. MT1-MMP is tightly regulated at different levels, and its localization to leading-edge membrane structures is an essential process for MT1-MMP to promote cellular invasion. Different cells display different motility-associated membrane structures, which contribute to their invasive ability, and there are diverse mechanisms of MT1-MMP localization to these structures. In this article, we will discuss the current understanding of MT1-MMP regulation, in particular, localization mechanisms to these different motility-associated membrane structures.

Loss of Arhgap39 facilitates cell migration and invasion in murine hepatocellular cancer cells

Background

Rho GTPases are essential regulators for cellular movement and intracellular membrane trafficking. Their enzymatic activities fluctuate between active GTP-bound and inactive GDP-bound states regulated by GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs). Arhgap39/Vilse/Porf-2 is a newly identified GAP. The role of Arhgap39 in migration and invasion has not been addressed thoroughly.

Methods

The Arhgap39 gene was knocked out by Crispr-Cas9 gene editing in mouse Hepa1-6 and Hepa-1c1c7 cells to analyze the impact of Arhgap39 depletion on migration and invasion.

Results

Loss of Arhgap39 noticeably increased the migration and invasive potential. Purified Arhgap39 recombinant protein facilitated the hydrolysis of GTP in RhoA and Rac1 in vitro. RNA-seq analysis revealed that matrix metalloproteinase 13 (MMP13) and Laminin subunit beta 1 (LAMB1) were increased in Arhgap39-/- cells. We further crossed Arhgap39fl/fl with KrasLSL-G12D and p53fl/fl mice under the control of albumin-Cre recombinase to induce the spontaneous development of hepatocellular carcinomas. Intriguingly, the expression levels of MMP13 and the overall survival in Alb-Cre_KrasLSL-G12D_p53fl/fl_Arhgap39fl/fl (KPA) mice were comparable to control Alb-Cre_KrasLSL-G12D_p53fl/fl (KP) mice. The cell migration and invasion of KPA mice were also similar to those of control KP mice.

Conclusion

Arhgap39 loss could modulate the migration and invasion in some hepatocellular cancer cells, but not in those isolated from KPA mice.

Rab10-associated tubulation as an early marker for biogenesis of the assembly compartment in cytomegalovirus-infected cells

Introduction

Cytomegalovirus (CMV) infection reorganizes early endosomes (EE), recycling endosome (RE), and trans-Golgi network (TGN) and expands their intermediates into a large perinuclear structure that forms the inner part of the cytoplasmic assembly complex (AC). The reorganization begins and results with the basic configuration (known as pre-AC) in the early (E) phase of infection, but the sequence of developmental steps is not yet well understood. One of the first signs of the establishment of the inner pre-AC, which can be observed by immunofluorescence, is the accumulation of Rab10. This study aims to investigate whether Rab10-positive domain (Rab10-PD) is expanded during the E phase of infection.

Methods

We performed long-term live imaging of EGFP-Rab10 with epifluorescence imaging-enhanced digital holotomographic microscopy (DHTM), confocal imaging of known Rab10 interactors and identification of important Rab10 interactors with the proximity-dependent biotin identification assay (BioID). The accumulation of Rab10-PD was analyzed after knock-down of EHBP1 and Rabin8, two proteins that facilitate Rab10 recruitment to membranes, and after blocking of PI(4,5)P2 by PI(4,5)P2-binding protein domains.

Results

Our study shows the gradual expansion of Rab10-PD in the inner pre-AC, the association of Rab10 with EHBP1 and MICAL-L1, and the dependence of Rab10-PD expansion on EHBP1 and PI(4,5)P2 but not Rabin8, indicating the expansion of EE-derived tubular recycling endosome-like membranes in the pre-AC. Silencing of Rab10 and EHBP1 suggests that Rab10-PD expansion is not required for the establishment of the inner pre-AC nor for the expansion of downstream tubular domains.

Conclusion

The present work characterizes one of the earliest sequences in the establishment of pre-AC and suggests that subsets of EE-derived tubular membranes may serve as the earliest biomarkers in pre-AC biogenesis. Our study also indicates that the pre-AC biogenesis is complex and likely involves multiple parallel processes, of which Rab10-PD expansion is one. Our experiments, particularly our silencing experiments, show that Rab10 and EHBP-1 do not play a significant role in the later stages of inner pre-AC biogenesis or in the expansion of downstream tubular domains. A more comprehensive understanding of the tubular domain expansion remains to be established.

Structural basis of human VANGL-PRICKLE interaction

Planar cell polarity (PCP) is an evolutionarily conserved process for development and morphogenesis in metazoans. The well-organized polarity pattern in cells is established by the asymmetric distribution of two core protein complexes on opposite sides of the cell membrane. The Van Gogh-like (VANGL)-PRICKLE (PK) pair is one of these two key regulators; however, their structural information and detailed functions have been unclear. Here, we present five cryo-electron microscopy structures of human VANGL1, VANGL2, and their complexes with PK1 at resolutions of 2.2-3.0 Å. Through biochemical and cell imaging experiments, we decipher the molecular details of the VANGL-PK interaction. Furthermore, we reveal that PK1 can target VANGL-containing intracellular vesicles to the peripheral cell membrane. These findings provide a solid foundation to understand the explicit interaction between VANGL and PK while opening new avenues for subsequent studies of the PCP pathway.

Known and unknown: Exosome secretion in tumor microenvironment needs more exploration

Exosomes, extracellular vesicles originating from endosomes, were discovered in the late 1980s and their function in intercellular communication has since garnered considerable interest. Exosomes are lipid bilayer-coated vesicles that range in size from 30 to 150 nm and appear as sacs under the electron microscope. Exosome secretion is crucial for cell-to-cell contact in both normal physiology and the development and spread of tumors. Furthermore, cancer cells can secrete more exosomes than normal cells. Scientists believe that intercellular communication in the complex tissue environment of the human body is an important reason for cancer cell invasion and metastasis. For example, some particles containing regulatory molecules are secreted in the tumor microenvironment, including exosomes. Then the contents of exosomes can be released by donor cells into the environment and interact with recipient cells to promote the migration and invasion of tumor cells. Therefore, in this review, we summarized the biogenesis of exosome, as well as exosome cargo and related roles. More importantly, this review introduces and discusses the factors that have been reported to affect exosome secretion in tumors and highlights the important role of exosomes in tumors.

Rab11b promotes M1-like macrophage polarization by restraining autophagic degradation of NLRP3 in alcohol-associated liver disease

Macrophage polarization is vital to mounting a host defense or repairing tissue in various liver diseases. Excessive activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome is related to the orchestration of inflammation and alcohol-associated liver disease (ALD) pathology. Rab GTPases play critical roles in regulating vesicular transport. In this study we investigated the role of Rab11b in ALD, aiming to identify effective therapeutic targets. Here, we first demonstrated a decreased expression of Rab11b in macrophages from ALD mice. Knockdown of Rab11b by macrophage-specific adeno-associated virus can alleviate alcohol induced liver inflammation, injury and steatosis. We found that LPS and alcohol stimulation promoted Rab11b transferring from the nucleus to the cytoplasm in bone marrow-derived macrophages (BMDM) cells. Rab11b specifically activated the NLRP3 inflammasome in BMDMs and RAW264.7 cells to induce M1 macrophage polarization. Rab11b overexpression in BMDMs inhibited autophagic flux, leading to the suppression of LC3B-mediated NLRP3 degradation. We conclude that impaired Rab11b could alleviate alcohol-induced liver injury via autophagy-mediated NLRP3 degradation.

Comprehensive knockout analysis of the RAB family small GTPases reveals an overlapping role of RAB2 and RAB14 in autophagosome maturation

Macroautophagy, simply referred to below as autophagy, is an intracellular degradation system that is highly conserved in eukaryotes. Since the processes involved in autophagy are accompanied by membrane dynamics, RAB small GTPases, key regulators of membrane trafficking, are generally thought to regulate the membrane dynamics of autophagy. Although more than half of the mammalian RABs have been reported to be involved in canonical and selective autophagy, no consensus has been reached in regard to the role of RABs in mammalian autophagy. Here, we comprehensively analyzed a rab-knockout (KO) library of MDCK cells to reevaluate the requirement for each RAB isoform in basal and starvation-induced autophagy. The results revealed clear alteration of the MAP1LC3/LC3-II level in only four rab-KO cells (rab1-KO, rab2-KO, rab7a-KO, and rab14-KO cells) and identified RAB14 as a new regulator of autophagy, specifically at the autophagosome maturation step. The autophagy-defective phenotype of two of these rab-KO cells, rab2-KO and rab14-KO cells, was very mild, but double KO of rab2 and rab14 caused a severer autophagy-defective phenotype (greater LC3 accumulation than in single-KO cells, indicating an overlapping role of RAB2 and RAB14 during autophagosome maturation. We also found that RAB14 is phylogenetically similar to RAB2 and that it possesses the same properties as RAB2, i.e. autophagosome localization and interaction with the HOPS subunits VPS39 and VPS41. Our findings suggest that RAB2 and RAB14 overlappingly regulate the autophagosome maturation step through recruitment of the HOPS complex to the autophagosome.Abbreviation: AID2: auxin-inducible degron 2; ATG: autophagy related; BafA1: bafilomycin A1; CKO: conditional knockout; EBSS: Earle's balanced salt solution; EEA1: early endosome antigen 1; HOPS: homotypic fusion and protein sorting; HRP: horseradish peroxidase; IP: immunoprecipitation; KD: knockdown; KO: knockout; LAMP2: lysosomal-associated membrane protein 2; MDCK: Madin-Darby canine kidney; mAb: monoclonal antibody; MEF: mouse embryonic fibroblast; MTORC1: mechanistic target of rapamycin kinase complex 1; 5-Ph-IAA: 5-phenyl-indole-3-acetic acid; pAb: polyclonal antibody; siRNA: small interfering RNA; SNARE: soluble NSF-attachment protein receptor; TF: transferrin; WT: wild-type.

The Genomic Signature and Transcriptional Response of Metal Tolerance in Brown Trout Inhabiting Metal-Polluted Rivers

Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.

The emerging role of Rab proteins in osteoclast organelle biogenesis and function

Rab GTPase proteins have been extensively studied for their roles in regulating vesicle and organelle dynamics. Among the ∼60 subtypes in mammalian cells, several Rabs have been reported to play crucial roles in osteoclast biogenesis and function. In this review, we aim to provide an update on recently described Rab GTPases, Rab11, Rab32, Rab44, and Rab38, as well as Rab7, Rab3D and Rab27A in osteoclast formation and function.

FMR1 Disorders: Basics of Biology and Therapeutics in Development

Fragile X Syndrome (FXS) presents with a constellation of phenotypes, including trouble regulating emotion and aggressive behaviors, disordered sleep, intellectual impairments, and atypical physical development. Genetic study of the X chromosome revealed that substantial repeat expansion of the 5' end of the gene fragile X messenger ribonucleoprotein 1 (FMR1) promoted DNA methylation and, consequently, silenced expression of FMR1. Further analysis proved that shorter repeat expansions in FMR1 also manifested in disease at later stages in life. Treatment and therapy options do exist, but they only manage symptoms. Up to now, no cure for FMR1 disorders exists. In this review, we aim to provide an overview of FMR1 biology and the latest research focused on developing therapeutic interventions that can potentially prevent and/or reverse FXS.

Exploring the role of the Rab network in epithelial-to-mesenchymal transition

Motivation

Rab GTPases (Rabs) are crucial for membrane trafficking within mammalian cells, and their dysfunction is implicated in many diseases. This gene family plays a role in several crucial cellular processes. Network analyses can uncover the complete repertoire of interaction patterns across the Rab network, informing disease research, opening new opportunities for therapeutic interventions.

Results

We examined Rabs and their interactors in the context of epithelial-to-mesenchymal transition (EMT), an indicator of cancer metastasizing to distant organs. A Rab network was first established from analysis of literature and was gradually expanded. Our Python module, resnet, assessed its network resilience and selected an optimally sized, resilient Rab network for further analyses. Pathway enrichment confirmed its role in EMT. We then identified 73 candidate genes showing a strong up-/down-regulation, across 10 cancer types, in patients with metastasized tumours compared to only primary-site tumours. We suggest that their encoded proteins might play a critical role in EMT, and further in vitro studies are needed to confirm their role as predictive markers of cancer metastasis. The use of resnet within the systematic analysis approach described here can be easily applied to assess other gene families and their role in biological events of interest.

Availability and implementation

Source code for resnet is freely available at https://github.com/Unmani199/resnet.

Histone deacetylase inhibition disrupts the molecular signature of the glioblastoma secretome related to extracellular vesicle-associated proteins and targets RAB7a and RAB14 in vitro

Glioblastoma (GBM) is the most aggressive brain tumor with a poor prognosis. While Histone Deacetylase inhibitors have shown promising results in inhibiting cancer cell invasion and promoting apoptosis, their effects on GBM secretion, specifically focusing on extracellular vesicles (EVs) secretion, remain largely unexplored. Using label-free NANOLC-MS/MS methodology, we identified significant changes in the abundance of membrane traffic regulatory proteins in the secretome of U87MG cells after the treatment with the HDAC inhibitor Trichostatin A (TSA). In silico analysis showed that TSA treatment disrupted the secretion pattern of EVs-associated proteins and cellular signaling pathways, both qualitatively and quantitatively. Notably, RAB14/RAB7a interaction was only observed in the secretome of cells treated with TSA. In vitro assays revealed that TSA treatment of glioma cells increased EVs secretion and intracellular protein levels of RAB7a and RAB14 without affecting gene expression, suggesting a role of these two EVs-associated proteins in grade IV glioma cells. Additionally, an integrative approach using clinical data highlighted a correlation between DNA mutations affecting vesicle traffic coding-genes and clinical and phenotypic outcomes in glioma patients. These findings provide insights into the interplay between epigenetics and GBM intracellular trafficking, potentially leading to improved strategies for targeting and modifying the complex signaling network established between GBM cells and the tumor cell microenvironment.

Proteomic Profiling of Pre- and Post-Surgery Saliva of Glioblastoma Patients: A Pilot Investigation

Glioblastoma multiforme (GBM) is an extremely aggressive brain tumor characterized by a high infiltration capability and recurrence rate. Early diagnosis is crucial to improve the prognosis and to personalize the therapeutic approach. This research explored, by LC-MS proteomic analysis after proteolytic digestion, the molecular profile of pre- and post-operative saliva pools from newly diagnosed (ND) GBM patients by comparing different times of collection and tumor recurrence (R). CYCS, PRDX2, RAB1C, PSMB1, KLK6, TMOD3, PAI2, PLBD1, CAST, and AHNAK, all involved in processes of tumor invasiveness and chemo- and radio-resistance, were found to depict the pre-surgery saliva of both ND and R GBM. PADI4 and CRYAB proteins, identified among the most abundant proteins exclusive of ND GBM pre-surgery saliva and classified as proteins elevated in glioma, could have a potential role as disease biomarkers. Selected panels of S100 proteins were found to potentially differentiate ND from R GBM patient saliva. TPD52 and IGKV3, exclusively identified in R GBM saliva, could be additionally distinctive of tumor relapse. Among the proteins identified in all pools, label-free relative quantitation showed statistically significant different levels of TXN, SERPINB5, FABP5, and S100A11 proteins between the pools. All of these proteins showed higher levels in both ND_ and R_T0 pre-surgery saliva with respect to CTRL and different modulation after surgery or chemo-radiotherapy combined treatment, suggesting a role as a potential panel of GBM predictive and prognostic biomarkers. These results highlight and confirm that saliva, a biofluid featured for an easily accessible and low invasiveness collection, is a promising source of GBM biomarkers, showing new potential opportunities for the development of targeted therapies and diagnostic tools.

Nervous necrosis virus induced vacuolization is a Rab5- and actin-dependent process

Cytoplasmic vacuolization is commonly induced by bacteria and viruses, reflecting the complex interactions between pathogens and the host. However, their characteristics and formation remain unclear. Nervous necrosis virus (NNV) infects more than 100 global fish species, causing enormous economic losses. Vacuolization is a hallmark of NNV infection in host cells, but remains a mystery. In this study, we developed a simple aptamer labelling technique to identify red-spotted grouper NNV (RGNNV) particles in fixed and live cells to explore RGNNV-induced vacuolization. We observed that RGNNV-induced vacuolization was positively associated with the infection time and virus uptake. During infection, most RGNNV particles, as well as viral genes, colocalized with vacuoles, but not giant vacuoles > 3 μm in diameter. Although the capsid protein (CP) is the only structural protein of RGNNV, its overexpression did not induce vacuolization, suggesting that vacuole formation probably requires virus entry and replication. Given that small Rab proteins and the cytoskeleton are key factors in regulating cellular vesicles, we further investigated their roles in RGNNV-induced vacuolization. Using live cell imaging, Rab5, a marker of early endosomes, was continuously located in vacuoles bearing RGNNV during giant vacuole formation. Rab5 is required for vacuole formation and interacts with CP according to siRNA interference and Co-IP analysis. Furthermore, actin formed distinct rings around small vacuoles, while vacuoles were located near microtubules. Actin, but not microtubules, plays an important role in vacuole formation using chemical inhibitors. These results provide valuable insights into the pathogenesis and control of RGNNV infections.

The small GTPase RAB-18 is involved in regulating development/diapause by recruiting the intestinal cholesterol transporter NCR-1 onto the apical side in Caenorhabditis elegans

RAB family proteins, which are small GTPases, are integral to the process of eukaryotic membrane trafficking. In the nematode, Caenorhabditis elegans, 31 RAB proteins have been identified through genome sequencing. Using an RNAi screen specifically targeting C. elegans rab genes, we identified multiple genes that are involved in the regulation of larval development, in particular, the rab-18 gene. Our molecular genetic studies resulted in several findings. First, RAB-18 predominantly functions in the intestine to regulate larval development by modulating steroid hormone signaling. Second, the C. elegans cholesterol transporter NCR-1 is a target of RAB-18 in the intestine. Third, the membrane trafficking of NCR-1 to the apical side in intestinal cells is particularly influenced by RAB-18. Finally, RAB-18 and NCR-1 possibly co-localize on membrane vesicles. Our study is the first to demonstrate the relationship between a RAB protein and a cholesterol transporter, in which the RAB protein probably drives the transporter to the apical membrane in the intestine to regulate cholesterol uptake. This study provides insight into the molecular mechanisms underlying human disease stemming from a transport defect of cholesterol and its derivative.

Rab6a enables BICD2/dynein-mediated trafficking of human papillomavirus from the trans-Golgi network during virus entry

Rab GTPases control intracellular vesicular transport, including retrograde trafficking of human papillomavirus (HPV) during cell entry, guiding the virus from the endosome to the trans-Golgi network (TGN), the Golgi apparatus, and eventually the nucleus. Rab proteins have been identified that act prior to the arrival of HPV at the TGN, but Rab proteins operating in later stages of entry remain elusive. Here, we report that knockdown of Rab6a impairs HPV entry by preventing HPV exit from the TGN and impeding intra-Golgi transport of the incoming virus. Rab6a supports HPV trafficking by facilitating the association of HPV with dynein, a motor protein complex, and BICD2, a dynein adaptor, in the TGN. L2 can bind directly to GTP-Rab6a in vitro, and excess of either GTP-Rab6a or GDP-Rab6 inhibits HPV entry, suggesting that cycling between GDP-Rab6 and GTP-Rab6 is critical. Notably, Rab6a is crucial for HPV-BICD2 and HPV-dynein association in the TGN of infected cells but not in the endosome. Our findings reveal important features of the molecular basis of HPV infection, including the discovery that HPV uses different mechanisms to engage dynein at different times during entry, and identify potential targets for therapeutic approaches to inhibit HPV infection.

IMPORTANCE

Human papillomaviruses (HPVs) are small, non-enveloped DNA viruses that cause approximately 5% of human cancer. Like most other DNA viruses, HPV traffics to the nucleus during virus entry to successfully infect cells. We show here that HPV utilizes a cellular enzyme, Rab6a, during virus entry to engage the dynein molecular motor for transport along microtubules. Rab6a is required for complex formation between the HPV L2 capsid protein, dynein, and the dynein adaptor BICD2 in the trans-Golgi network (TGN). This complex is required for transport of the incoming virus out of the TGN as it journeys to the nucleus. Our findings identify potential targets for therapeutic approaches.

An automated high-content screening and assay platform for the analysis of spheroids at subcellular resolution

The endomembrane system is essential for healthy cell function, with the various compartments carrying out a large number of specific biochemical reactions. To date, almost all of our understanding of the endomembrane system has come from the study of cultured cells growing as monolayers. However, monolayer-grown cells only poorly represent the environment encountered by cells in the human body. As a first step to address this disparity, we have developed a platform that allows us to investigate and quantify changes to the endomembrane system in three-dimensional (3D) cell models, in an automated and highly systematic manner. HeLa Kyoto cells were grown on custom-designed micropatterned 96-well plates to facilitate spheroid assembly in the form of highly uniform arrays. Fully automated high-content confocal imaging and analysis were then carried out, allowing us to measure various spheroid-, cellular- and subcellular-level parameters relating to size and morphology. Using two drugs known to perturb endomembrane function, we demonstrate that cell-based assays can be carried out in these spheroids, and that changes to the Golgi apparatus and endosomes can be quantified from individual cells within the spheroids. We also show that image texture measurements are useful tools to discriminate cellular phenotypes. The automated platform that we show here has the potential to be scaled up, thereby allowing large-scale robust screening to be carried out in 3D cell models.

A unique symbiosome in an anaerobic single-celled eukaryote

Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes - the vast majority of such hosts in nature - remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis.

Rab40 GTPases regulate AMBRA1-mediated transcription and cell migration

The Rab40 subfamily are unique small monomeric GTPases that form CRL5-based ubiquitin E3 ligase complex and regulate ubiquitylation of specific target proteins. Recent studies have shown that Rab40s play an important role in regulating cell migration, but the underlying mechanisms of Rab40/CRL5 complex function are still not fully understood. In this study we identified AMBRA1 as a novel binding partner of Rab40 GTPases and showed that this interaction mediates a bi-directional crosstalk between CRL4 and CRL5 E3 ligases. Importantly, we found that Rab40/CRL5 ubiquitylates AMBRA1, which does not result in AMBRA1 degradation, but instead it seems to induce AMBRA1-dependent regulation of gene transcription. The global transcriptional profiles identified by RNA-seq showed that AMBRA1 regulates transcription of genes related to cell adhesion and migration. Additionally, we have shown that AMBRA1-dependent transcription regulation does not require the enzymatic activity of AMBRA1/CRL4, and that Rab40-induced AMBRA1 ubiquitylation leads to dissociation of AMBRA1/CRL4 complex. Taken together, our findings reveal a novel function of Rab40/CRL5 complex as an important regulator for AMBRA1-dependent transcription of genes involved in cell migration.

Impaired Development of Collagen Antibody-Induced Arthritis in Rab44-Deficient Mice

BACKGROUND

Rheumatoid arthritis (RA) is an autoimmune disease characterized by immune cell-mediated joint inflammation and subsequent osteoclast-dependent bone destruction. Collagen antibody-induced arthritis (CAIA) is a useful mouse model for examining the inflammatory mechanisms in human RA. Previously, we identified the novel gene Rab44, which is a member of the large Rab GTPase family and is highly expressed in immune-related cells and osteoclasts.

METHODS

In this study, we induced CAIA in Rab44-knockout (KO) mice to investigate the effects of Rab44 on inflammation, cell filtration, and bone destruction.

RESULTS

Compared with wild-type (WT) mice, Rab44-KO mice showed reduced inflammation in arthritis under CAIA-inducing conditions. Rab44-KO CAIA mice exhibited reduced cell filtration in the radiocarpal joints. Consistent with these findings, Rab44-KO CAIA mice showed decreased mRNA levels of arthritis-related marker genes including genes for inflammation, cartilage turnover, bone formation, and bone absorption markers. Rab44-KO CAIA mice exhibited predominant infiltration of M2-type macrophages at inflammatory sites and reduced bone loss compared to WT CAIA mice.

CONCLUSIONS

These results indicate that Rab44 deficiency reduces the progression of inflammation in CAIA in mice.

TBC1D4 antagonizes RAB2A-mediated autophagic and endocytic pathways

Macroautophagic/autophagic and endocytic pathways play essential roles in maintaining homeostasis at different levels. It remains poorly understood how both pathways are coordinated and fine-tuned for proper lysosomal degradation of diverse cargoes. We and others recently identified a Golgi-resident RAB GTPase, RAB2A, as a positive regulator that controls both autophagic and endocytic pathways. In the current study, we report that TBC1D4 (TBC1 domain family member 4), a TBC domain-containing protein that plays essential roles in glucose homeostasis, suppresses RAB2A-mediated autophagic and endocytic pathways. TBC1D4 bound to RAB2A through its N-terminal PTB2 domain, which impaired RAB2A-mediated autophagy at the early stage by preventing ULK1 complex activation. During the late stage of autophagy, TBC1D4 impeded the association of RUBCNL/PACER and RAB2A with STX17 on autophagosomes by direct interaction with RUBCNL via its N-terminal PTB1 domain. Disruption of the autophagosomal trimeric complex containing RAB2A, RUBCNL and STX17 resulted in defective HOPS recruitment and eventually abortive autophagosome-lysosome fusion. Furthermore, TBC1D4 inhibited RAB2A-mediated endocytic degradation independent of RUBCNL. Therefore, TBC1D4 and RAB2A form a dual molecular switch to modulate autophagic and endocytic pathways. Importantly, hepatocyte- or adipocyte-specific tbc1d4 knockout in mice led to elevated autophagic flux and endocytic degradation and tissue damage. Together, this work establishes TBC1D4 as a critical molecular brake in autophagic and endocytic pathways, providing further mechanistic insights into how these pathways are intertwined both in vitro and in vivo.Abbreviations: ACTB: actin beta; ATG9: autophagy related 9; ATG14: autophagy related 14; ATG16L1: autophagy related 16 like 1; CLEM: correlative light electron microscopy; Ctrl: control; DMSO: dimethyl sulfoxide; EGF: epidermal growth factor; EGFR: epidermal growth factor receptor; FL: full length; GAP: GTPase-activating protein; GFP: green fluorescent protein; HOPS: homotypic fusion and protein sorting; IP: immunoprecipitation; KD: knockdown; KO: knockout; LAMP1: lysosomal associated membrane protein 1; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; OE: overexpression; PG: phagophore; PtdIns3K: class III phosphatidylinositol 3-kinase; SLC2A4/GLUT4: solute carrier family 2 member 4; SQSTM1/p62: sequestosome 1; RUBCNL/PACER: rubicon like autophagy enhancer; STX17: syntaxin 17; TAP: tandem affinity purification; TBA: total bile acid; TBC1D4: TBC1 domain family member 4; TUBA1B: tubulin alpha 1b; ULK1: unc-51 like autophagy activating kinase 1; VPS39: VPS39 subunit of HOPS complex; WB: western blot; WT: wild type.

The GTPase RAB6 is required for stem cell maintenance and cell migration in the gut epithelium

Intestinal epithelial cells, which are instrumental in nutrient absorption, fluid regulation, and pathogen defense, undergo continuous proliferation and differentiation within the intestinal crypts, migrating towards the luminal surface where they are eventually shed. RAB GTPases are key regulators of intracellular vesicular trafficking and are involved in various cellular processes, including cell migration and polarity. Here, we investigated the role of RAB6 in the development and maintenance of the gut epithelium. We generated conditional knockout mice with RAB6 specifically deleted in the gut epithelium. We found that deletion of the Rab6a gene resulted in embryonic lethality. In adult mice, RAB6 depletion led to altered villus architecture and impaired junction integrity without affecting the segregation of apical and basolateral membrane domains. Further, RAB6 depletion slowed down cell migration and adversely affected both cell proliferation and stem cell maintenance. Notably, the absence of RAB6 resulted in a diminished number of functional stem cells, as evidenced by the rapid death of isolated crypts from Rab6a KO mice when cultured as 3D organoids. Together, these results underscore the essential role of RAB6 in maintaining gut epithelial homeostasis.

Genome-wide association study of salt tolerance at the seed germination stage in lettuce

Developing lettuce varieties with salt tolerance at the seed germination stage is essential since lettuce seeds are planted half an inch deep in soil where salt levels are often highest in the salinity-affected growing regions. Greater knowledge of genetics and genomics of salt tolerance in lettuce will facilitate breeding of improved lettuce varieties with salt tolerance. Accordingly, we conducted a genome-wide association study (GWAS) in lettuce to identify marker-trait association for salt tolerance at the seed germination stage. The study involved 445 diverse lettuce accessions and 56,820 single nucleotide polymorphism (SNP) markers obtained through genotype-by-sequencing technology using lettuce reference genome version v8. GWAS using two single-locus and three multi-locus models for germination rate (GR) under salinity stress, 5 days post seeding (GR5d_S) and a salinity susceptibility index (SSI) based on GR under salinity stress and control conditions, 5 days post seeding (SSI_GR5d) revealed 10 significant SNPs on lettuce chromosomes 2, 4, and 7. The 10 SNPs were associated with five novel QTLs for salt tolerance in lettuce, explaining phenotyping variations of 5.85%, 4.38%, 4.26%, 3.77%, and 1.80%, indicating the quantitative nature of these two salt tolerance-related traits. Using the basic local alignment search tool (BLAST) within 100 Kb upstream and downstream of each of the 10 SNPs, we identified 25 salt tolerance-related putative candidate genes including four genes encoding for major transcription factors. The 10 significant salt tolerance-related SNPs and the 25 candidate genes identified in the current study will be a valuable resource for molecular marker development and marker-assisted selection for breeding lettuce varieties with improved salt tolerance at the seed germination stage.

RABR-1, an atypical Rab-related GTPase, cell-nonautonomously restricts somatosensory dendrite branching

Neurons are highly polarized cells with dendrites and axons. Dendrites, which receive sensory information or input from other neurons, often display elaborately branched morphologies. While mechanisms that promote dendrite branching have been widely studied, less is known about the mechanisms that restrict branching. Using the nematode Caenorhabditis elegans, we identify rabr-1 (for Rab-related gene 1) as a factor that restricts branching of the elaborately branched dendritic trees of PVD and FLP somatosensory neurons. Animals mutant for rabr-1 show excessively branched dendrites throughout development and into adulthood in areas where the dendrites overlay epidermal tissues. Phylogenetic analyses show that RABR-1 displays similarity to small GTPases of the Rab-type, although based on sequence alone, no clear vertebrate ortholog of RABR-1 can be identified. We find that rabr-1 is expressed and can function in epidermal tissues, suggesting that rabr-1 restricts dendritic branching cell-nonautonomously. Genetic experiments further indicate that for the formation of ectopic branches rabr-1 mutants require the genes of the Menorin pathway, which have been previously shown to mediate dendrite morphogenesis of somatosensory neurons. A translational reporter for RABR-1 reveals a subcellular localization to punctate, perinuclear structures, which correlates with endosomal and autophagosomal markers, but anticorrelates with lysosomal markers suggesting an amphisomal character. Point mutations in rabr-1 analogous to key residues of small GTPases suggest that rabr-1 functions in a GTP-bound form independently of GTPase activity. Taken together, rabr-1 encodes for an atypical small GTPase of the Rab-type that cell-nonautonomously restricts dendritic branching of somatosensory neurons, likely independently of GTPase activity.

Cytokines on the way to secretion

The activation of immune cells by pro-inflammatory or immunosuppressive stimuli is followed by the secretion of immunoregulatory cytokines which serve as messengers to activate the immune response in target cells. Although the mechanisms that control the secretion of cytokines by immune cells are not yet fully understood, several key aspects of this process have recently emerged. This review focuses on cytokine release via exocytosis and highlights the routes of cytokine trafficking leading to constitutive and regulated secretion as well as the impact of sorting receptors on this process. We discuss the involvement of cytoskeletal rearrangements in vesicular transport, secretion, and formation of immunological synapses. Finally, we describe the non-classical pathways of cytokine release that are independent of vesicular ER-Golgi transport. Instead, these pathways are based on processing by inflammasome or autophagic mechanisms. Ultimately, understanding the molecular mechanisms behind cytokine release may help to identify potential therapeutic targets in diseases associated with altered immune responses.