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1.
Dis Model Mech ; 15(10)2022 10 01.
Article in English | MEDLINE | ID: mdl-36004645

ABSTRACT

Ureter obstruction is a highly prevalent event during embryonic development and is a major cause of pediatric kidney disease. We have previously reported that ureteric bud-specific ablation of the gene expressing the exocyst subunit EXOC5 in late murine gestation results in failure of urothelial stratification, cell death and complete ureter obstruction. However, the mechanistic connection between disrupted exocyst activity, urothelial cell death and subsequent ureter obstruction was unclear. Here, we report that inhibited urothelial stratification does not drive cell death during ureter development. Instead, we demonstrate that the exocyst plays a critical role in autophagy in urothelial cells, and that disruption of autophagy activates a urothelial NF-κB stress response. Impaired autophagy first provokes canonical NF-κB activity, which is progressively followed by increasing levels of non-canonical NF-κB activity and cell death if the stress remains unresolved. Furthermore, we demonstrate that ureter obstructions can be completely rescued in Exoc5 conditional knockout mice by administering a single dose of the pan-caspase inhibitor z-VAD-FMK at embryonic day 16.5 prior to urothelial cell death. Taken together, ablation of Exoc5 disrupts autophagic stress response and activates progressive NF-κB signaling, which promotes obstructive uropathy.


Subject(s)
Autophagy , NF-kappa B , Animals , Caspases/metabolism , Female , Mice , Mice, Knockout , NF-kappa B/metabolism , Pregnancy , Signal Transduction , Vesicular Transport Proteins/genetics
2.
Biol Reprod ; 106(4): 730-740, 2022 04 26.
Article in English | MEDLINE | ID: mdl-34977916

ABSTRACT

Origin recognition complex subunit 4 (ORC4) is a DNA-binding protein required for DNA replication. During oocyte maturation, after the last oocyte DNA replication step and before zygotic DNA replication, the oocyte undergoes two meiotic cell divisions in which half the DNA is ejected in much smaller polar bodies. We previously demonstrated that ORC4 forms a cytoplasmic cage around the DNA that is ejected in both polar body extrusion (PBE) events. Here, we used ZP3 activated Cre to delete exon 7 of Orc4 during oogenesis to test how it affected both predicted functions of ORC4: its recently discovered role in PBE and its well-known role in DNA synthesis. Orc4 deletion severely reduced PBE. Almost half of Orc4-depleted germinal vesicle (GV) oocytes cultured in vitro were arrested before anaphase I (48%), and only 25% produced normal first polar bodies. This supports the role of ORC4 in PBE and suggests that transcription of the full-length Orc4 during oogenesis is required for efficient PBE. Orc4 deletion also abolished zygotic DNA synthesis. Fewer Orc4-depleted oocytes developed to the metaphase II (MII) stage, and after activation these oocytes were arrested at the two-cell stage without undergoing DNA synthesis. This confirms that transcription of full-length Orc4 after the primary follicle stage is required for zygotic DNA replication. The data also suggest that MII oocytes do not have a replication licensing checkpoint as cytokinesis progressed without DNA synthesis. Together, the data confirm that oocyte ORC4 is important for both PBE and zygotic DNA synthesis.


Subject(s)
Origin Recognition Complex , Polar Bodies , DNA Replication , Meiosis/genetics , Oogenesis/genetics , Origin Recognition Complex/genetics , Origin Recognition Complex/metabolism
3.
Int J Mol Sci ; 22(10)2021 May 11.
Article in English | MEDLINE | ID: mdl-34064901

ABSTRACT

To characterize the mechanisms by which the highly conserved exocyst trafficking complex regulates eye physiology in zebrafish and mice, we focused on Exoc5 (also known as sec10), a central exocyst component. We analyzed both exoc5 zebrafish mutants and retinal pigmented epithelium (RPE)-specific Exoc5 knockout mice. Exoc5 is present in both the non-pigmented epithelium of the ciliary body and in the RPE. In this study, we set out to establish an animal model to study the mechanisms underlying the ocular phenotype and to establish if loss of visual function is induced by postnatal RPE Exoc5-deficiency. Exoc5-/- zebrafish had smaller eyes, with decreased number of melanocytes in the RPE and shorter photoreceptor outer segments. At 3.5 days post-fertilization, loss of rod and cone opsins were observed in zebrafish exoc5 mutants. Mice with postnatal RPE-specific loss of Exoc5 showed retinal thinning associated with compromised visual function and loss of visual photoreceptor pigments. Abnormal levels of RPE65 together with a reduced c-wave amplitude indicate a dysfunctional RPE. The retinal phenotype in Exoc5-/- mice was present at 20 weeks, but was more pronounced at 27 weeks, indicating progressive disease phenotype. We previously showed that the exocyst is necessary for photoreceptor ciliogenesis and retinal development. Here, we report that exoc5 mutant zebrafish and mice with RPE-specific genetic ablation of Exoc5 develop abnormal RPE pigmentation, resulting in retinal cell dystrophy and loss of visual pigments associated with compromised vision. Together, these data suggest that exocyst-mediated signaling in the RPE is required for RPE structure and function, indirectly leading to photoreceptor degeneration.


Subject(s)
Photoreceptor Cells/pathology , Retinal Degeneration , Retinal Pigment Epithelium/pathology , Vesicular Transport Proteins/physiology , Vision Disorders/pathology , Animals , Mice , Mice, Inbred C57BL , Mice, Knockout , Photoreceptor Cells/metabolism , Retinal Pigment Epithelium/metabolism , Vision Disorders/metabolism , Zebrafish
4.
J Biol Chem ; 294(50): 19099-19110, 2019 12 13.
Article in English | MEDLINE | ID: mdl-31694916

ABSTRACT

The recently proposed idea of "urocrine signaling" hypothesizes that small secreted extracellular vesicles (EVs) contain proteins that transmit signals to distant cells. However, the role of renal primary cilia in EV production and content is unclear. We previously showed that the exocyst, a highly conserved trafficking complex, is necessary for ciliogenesis; that it is present in human urinary EVs; that knockdown (KD) of exocyst complex component 5 (EXOC5), a central exocyst component, results in very short or absent cilia; and that human EXOC5 overexpression results in longer cilia. Here, we show that compared with control Madin-Darby canine kidney (MDCK) cells, EXOC5 overexpression increases and KD decreases EV numbers. Proteomic analyses of isolated EVs from EXOC5 control, KD, and EXOC5-overexpressing MDCK cells revealed significant alterations in protein composition. Using immunoblotting to specifically examine the expression levels of ADP-ribosylation factor 6 (ARF6) and EPS8-like 2 (EPS8L2) in EVs, we found that EXOC5 KD increases ARF6 levels and decreases EPS8L2 levels, and that EXOC5 overexpression increases EPS8L2. Knockout of intraflagellar transport 88 (IFT88) confirmed that the changes in EV number/content were due to cilia loss: similar to EXOC5, the IFT88 loss resulted in very short or absent cilia, decreased EV numbers, increased EV ARF6 levels, and decreased Eps8L2 levels compared with IFT88-rescued EVs. Compared with control animals, urine from proximal tubule-specific EXOC5-KO mice contained fewer EVs and had increased ARF6 levels. These results indicate that perturbations in exocyst and primary cilia affect EV number and protein content.


Subject(s)
Cilia/metabolism , Exocytosis , Extracellular Vesicles/metabolism , Kidney/metabolism , Vesicular Transport Proteins/metabolism , ADP-Ribosylation Factor 6 , Animals , Cells, Cultured , Dogs , Humans , Madin Darby Canine Kidney Cells/metabolism , Mice , Mice, Knockout , Vesicular Transport Proteins/deficiency
5.
Am J Physiol Endocrinol Metab ; 317(6): E957-E972, 2019 12 01.
Article in English | MEDLINE | ID: mdl-31593505

ABSTRACT

Skeletal muscle handles ~80-90% of the insulin-induced glucose uptake. In skeletal muscle, insulin binding to its cell surface receptor triggers redistribution of intracellular glucose transporter GLUT4 protein to the cell surface, enabling facilitated glucose uptake. In adipocytes, the eight-protein exocyst complex is an indispensable constituent in insulin-induced glucose uptake, as it is responsible for the targeted trafficking and plasma membrane-delivery of GLUT4. However, the role of the exocyst in skeletal muscle glucose uptake has never been investigated. Here we demonstrate that the exocyst is a necessary factor in insulin-induced glucose uptake in skeletal muscle cells as well. The exocyst complex colocalizes with GLUT4 storage vesicles in L6-GLUT4myc myoblasts at a basal state and associates with these vesicles during their translocation to the plasma membrane after insulin signaling. Moreover, we show that the exocyst inhibitor endosidin-2 and a heterozygous knockout of Exoc5 in skeletal myoblast cells both lead to impaired GLUT4 trafficking to the plasma membrane and hinder glucose uptake in response to an insulin stimulus. Our research is the first to establish that the exocyst complex regulates insulin-induced GLUT4 exocytosis and glucose metabolism in muscle cells. A deeper knowledge of the role of the exocyst complex in skeletal muscle tissue may help our understanding of insulin resistance in type 2 diabetes.


Subject(s)
Exocytosis/genetics , Glucose Transporter Type 4/metabolism , Glucose/metabolism , Insulin/metabolism , Muscle Fibers, Skeletal/metabolism , Transport Vesicles/metabolism , Animals , Cell Line , Cell Membrane/metabolism , Exocytosis/drug effects , Gene Knockout Techniques , Insulin Resistance , Limonins/pharmacology , Myoblasts, Skeletal , Protein Transport/genetics , Rats , Vesicular Transport Proteins/genetics
6.
Circulation ; 140(16): 1331-1341, 2019 10 15.
Article in English | MEDLINE | ID: mdl-31387361

ABSTRACT

BACKGROUND: Bicuspid aortic valve (BAV) disease is a congenital defect that affects 0.5% to 1.2% of the population and is associated with comorbidities including ascending aortic dilation and calcific aortic valve stenosis. To date, although a few causal genes have been identified, the genetic basis for the vast majority of BAV cases remains unknown, likely pointing to complex genetic heterogeneity underlying this phenotype. Identifying genetic pathways versus individual gene variants may provide an avenue for uncovering additional BAV causes and consequent comorbidities. METHODS: We performed genome-wide association Discovery and Replication Studies using cohorts of 2131 patients with BAV and 2728 control patients, respectively, which identified primary cilia genes as associated with the BAV phenotype. Genome-wide association study hits were prioritized based on P value and validated through in vivo loss of function and rescue experiments, 3-dimensional immunohistochemistry, histology, and morphometric analyses during aortic valve morphogenesis and in aged animals in multiple species. Consequences of these genetic perturbations on cilia-dependent pathways were analyzed by Western and immunohistochemistry analyses, and assessment of aortic valve and cardiac function were determined by echocardiography. RESULTS: Genome-wide association study hits revealed an association between BAV and genetic variation in human primary cilia. The most associated single-nucleotide polymorphisms were identified in or near genes that are important in regulating ciliogenesis through the exocyst, a shuttling complex that chaperones cilia cargo to the membrane. Genetic dismantling of the exocyst resulted in impaired ciliogenesis, disrupted ciliogenic signaling and a spectrum of cardiac defects in zebrafish, and aortic valve defects including BAV, valvular stenosis, and valvular calcification in murine models. CONCLUSIONS: These data support the exocyst as required for normal ciliogenesis during aortic valve morphogenesis and implicate disruption of ciliogenesis and its downstream pathways as contributory to BAV and associated comorbidities in humans.


Subject(s)
Aortic Valve Stenosis/pathology , Aortic Valve/abnormalities , Cilia/physiology , Heart Defects, Congenital/pathology , Heart Valve Diseases/pathology , Animals , Aortic Valve/metabolism , Aortic Valve/pathology , Aortic Valve Stenosis/genetics , Bicuspid Aortic Valve Disease , Case-Control Studies , Cilia/pathology , Gene Frequency , Genome-Wide Association Study , Genotype , Heart Defects, Congenital/genetics , Heart Valve Diseases/genetics , Heart Valve Diseases/metabolism , Humans , Mice , Mice, Knockout , Polymorphism, Single Nucleotide , Vesicular Transport Proteins/genetics , Vesicular Transport Proteins/metabolism , Zebrafish , Zebrafish Proteins/genetics , Zebrafish Proteins/metabolism
7.
J Biol Chem ; 294(26): 10104-10119, 2019 06 28.
Article in English | MEDLINE | ID: mdl-31073028

ABSTRACT

Although the slit diaphragm proteins in podocytes are uniquely organized to maintain glomerular filtration assembly and function, little is known about the underlying mechanisms that participate in trafficking these proteins to the correct location for development and homeostasis. Identifying these mechanisms will likely provide novel targets for therapeutic intervention to preserve podocyte function following glomerular injury. Analysis of structural variation in cases of human nephrotic syndrome identified rare heterozygous deletions of EXOC4 in two patients. This suggested that disruption of the highly-conserved eight-protein exocyst trafficking complex could have a role in podocyte dysfunction. Indeed, mRNA profiling of injured podocytes identified significant exocyst down-regulation. To test the hypothesis that the exocyst is centrally involved in podocyte development/function, we generated homozygous podocyte-specific Exoc5 (a central exocyst component that interacts with Exoc4) knockout mice that showed massive proteinuria and died within 4 weeks of birth. Histological and ultrastructural analysis of these mice showed severe glomerular defects with increased fibrosis, proteinaceous casts, effaced podocytes, and loss of the slit diaphragm. Immunofluorescence analysis revealed that Neph1 and Nephrin, major slit diaphragm constituents, were mislocalized and/or lost. mRNA profiling of Exoc5 knockdown podocytes showed that vesicular trafficking was the most affected cellular event. Mapping of signaling pathways and Western blot analysis revealed significant up-regulation of the mitogen-activated protein kinase and transforming growth factor-ß pathways in Exoc5 knockdown podocytes and in the glomeruli of podocyte-specific Exoc5 KO mice. Based on these data, we propose that exocyst-based mechanisms regulate Neph1 and Nephrin signaling and trafficking, and thus podocyte development and function.


Subject(s)
Gene Deletion , Kidney Glomerulus/pathology , Nephrotic Syndrome/pathology , Podocytes/pathology , Vesicular Transport Proteins/physiology , Animals , Apoptosis , Cell Movement , Exocytosis , Humans , Kidney Glomerulus/metabolism , Membrane Proteins/genetics , Membrane Proteins/metabolism , Mice , Mice, Inbred C57BL , Mice, Knockout , Nephrotic Syndrome/genetics , Phosphorylation , Podocytes/metabolism , Protein Transport , Proteinuria/etiology , Proteinuria/pathology , Signal Transduction
9.
Mol Neurobiol ; 55(8): 6518-6532, 2018 Aug.
Article in English | MEDLINE | ID: mdl-29327200

ABSTRACT

The exocyst, an octameric protein complex consisting of Exoc1 through Exoc8, was first determined to regulate exocytosis by targeting vesicles to the plasma membrane in yeast to mice. In addition to this fundamental role, the exocyst complex has been implicated in other cellular processes. In this study, we investigated the role of the exocyst in cochlear development and hearing by targeting EXOC5, a central exocyst component. Deleting Exoc5 in the otic epithelium with widely used Cre lines resulted in early lethality. Thus, we generated two different inner ear-specific Exoc5 knockout models by crossing Gfi1Cre mice with Exoc5f/f mice for hair cell-specific deletion (Gfi1Cre/+;Exoc5f/f) and by in utero delivery of rAAV-iCre into the otocyst of embryonic day 12.5 for deletion throughout the otic epithelium (rAAV2/1-iCre;Exoc5f/f). Gfi1Cre/+;Exoc5f/f mice showed relatively normal hair cell morphology until postnatal day 20, after which hair cells underwent apoptosis accompanied by disorganization of stereociliary bundles, resulting in progressive hearing loss. rAAV2/1-iCre;Exoc5f/f mice exhibited abnormal neurite morphology, followed by apoptotic degeneration of spiral ganglion neurons (SGNs) and hair cells, which led to profound and early-onset hearing loss. These results demonstrate that Exoc5 is essential for the normal development and survival of cochlear hair cells and SGNs, as well as the functional maintenance of hearing.


Subject(s)
Hair Cells, Auditory/metabolism , Hair Cells, Auditory/pathology , Hearing , Neurons/pathology , Spiral Ganglion/pathology , Vesicular Transport Proteins/metabolism , Animals , Apoptosis , Cell Survival , DNA-Binding Proteins/metabolism , Dependovirus/metabolism , Epithelium/pathology , Hair Cells, Auditory/ultrastructure , Hearing Loss/metabolism , Hearing Loss/pathology , Integrases/metabolism , Mice, Inbred C57BL , Nerve Degeneration/pathology , Neurites/metabolism , Neurons/metabolism , Organ of Corti/metabolism , Organ of Corti/ultrastructure , Stereocilia/metabolism , Stereocilia/ultrastructure , Transcription Factors/metabolism , Vesicular Transport Proteins/deficiency
10.
PLoS Genet ; 14(1): e1007181, 2018 01.
Article in English | MEDLINE | ID: mdl-29377931

ABSTRACT

Nephron progenitor number determines nephron endowment; a reduced nephron count is linked to the onset of kidney disease. Several transcriptional regulators including Six2, Wt1, Osr1, Sall1, Eya1, Pax2, and Hox11 paralogues are required for specification and/or maintenance of nephron progenitors. However, little is known about the regulatory intersection of these players. Here, we have mapped nephron progenitor-specific transcriptional networks of Six2, Hoxd11, Osr1, and Wt1. We identified 373 multi-factor associated 'regulatory hotspots' around genes closely associated with progenitor programs. To examine their functional significance, we deleted 'hotspot' enhancer elements for Six2 and Wnt4. Removal of the distal enhancer for Six2 leads to a ~40% reduction in Six2 expression. When combined with a Six2 null allele, progeny display a premature depletion of nephron progenitors. Loss of the Wnt4 enhancer led to a significant reduction of Wnt4 expression in renal vesicles and a mildly hypoplastic kidney, a phenotype also enhanced in combination with a Wnt4 null mutation. To explore the regulatory landscape that supports proper target gene expression, we performed CTCF ChIP-seq to identify insulator-boundary regions. One such putative boundary lies between the Six2 and Six3 loci. Evidence for the functional significance of this boundary was obtained by deep sequencing of the radiation-induced Brachyrrhine (Br) mutant allele. We identified an inversion of the Six2/Six3 locus around the CTCF-bound boundary, removing Six2 from its distal enhancer regulation, but placed next to Six3 enhancer elements which support ectopic Six2 expression in the lens where Six3 is normally expressed. Six3 is now predicted to fall under control of the Six2 distal enhancer. Consistent with this view, we observed ectopic Six3 in nephron progenitors. 4C-seq supports the model for Six2 distal enhancer interactions in wild-type and Br/+ mouse kidneys. Together, these data expand our view of the regulatory genome and regulatory landscape underpinning mammalian nephrogenesis.


Subject(s)
Cell Differentiation/genetics , Gene Regulatory Networks , Nephrons/embryology , Organogenesis/genetics , Stem Cells/physiology , Transcription Factors/physiology , Animals , Embryo, Mammalian , Female , Gene Expression Regulation, Developmental , Homeodomain Proteins/genetics , Homeodomain Proteins/physiology , Male , Mice , Mice, Inbred C57BL , Mice, Transgenic , Transcription Factors/genetics , Transcription Factors/isolation & purification , Wnt4 Protein/genetics , Wnt4 Protein/physiology
11.
Article in English | MEDLINE | ID: mdl-28264817

ABSTRACT

One requirement for establishing polarity within a cell is the asymmetric trafficking of intracellular vesicles to the plasma membrane. This tightly regulated process creates spatial and temporal differences in both plasma membrane composition and the membrane-associated proteome. Asymmetric membrane trafficking is also a critical mechanism to regulate cell differentiation, signaling, and physiology. Many eukaryotic cell types use the eight-protein exocyst complex to orchestrate polarized vesicle trafficking to certain membrane locales. Members of the exocyst were originally discovered in yeast while screening for proteins required for the delivery of secretory vesicles to the budding daughter cell. The same eight exocyst genes are conserved in mammals, in which the specifics of exocyst-mediated trafficking are highly cell-type-dependent. Some exocyst members bind to certain Rab GTPases on intracellular vesicles, whereas others localize to the plasma membrane at the site of exocytosis. Assembly of the exocyst holocomplex is responsible for tethering these vesicles to the plasma membrane before their soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-mediated exocytosis. In this review, we will focus on the role and regulation of the exocyst complex in targeted vesicular trafficking as related to the establishment and maintenance of cellular polarity. We will contrast exocyst function in apicobasal epithelial polarity versus front-back mesenchymal polarity, and the dynamic regulation of exocyst-mediated trafficking during cell phenotype transitions.


Subject(s)
Cell Polarity , Exocytosis , Animals , Biological Transport , Cell Movement , Cytoskeleton/physiology , Epithelial-Mesenchymal Transition , Humans , Intercellular Junctions/physiology , Monomeric GTP-Binding Proteins/metabolism , Secretory Vesicles/physiology
12.
J Biol Chem ; 292(36): 14814-14826, 2017 09 08.
Article in English | MEDLINE | ID: mdl-28729419

ABSTRACT

We previously have shown that the highly conserved eight-protein exocyst trafficking complex is required for ciliogenesis in kidney tubule cells. We hypothesized here that ciliogenic programs are conserved across organs and species. To determine whether renal primary ciliogenic programs are conserved in the eye, and to characterize the function and mechanisms by which the exocyst regulates eye development in zebrafish, we focused on exoc5, a central component of the exocyst complex, by analyzing both exoc5 zebrafish mutants, and photoreceptor-specific Exoc5 knock-out mice. Two separate exoc5 mutant zebrafish lines phenocopied exoc5 morphants and, strikingly, exhibited a virtual absence of photoreceptors, along with abnormal retinal development and cell death. Because the zebrafish mutant was a global knockout, we also observed defects in several ciliated organs, including the brain (hydrocephalus), heart (cardiac edema), and kidney (disordered and shorter cilia). exoc5 knockout increased phosphorylation of the regulatory protein Mob1, consistent with Hippo pathway activation. exoc5 mutant zebrafish rescue with human EXOC5 mRNA completely reversed the mutant phenotype. We accomplished photoreceptor-specific knockout of Exoc5 with our Exoc5 fl/fl mouse line crossed with a rhodopsin-Cre driver line. In Exoc5 photoreceptor-specific knock-out mice, the photoreceptor outer segment structure was severely impaired at 4 weeks of age, although a full-field electroretinogram indicated a visual response was still present. However, by 6 weeks, visual responses were eliminated. In summary, we show that ciliogenesis programs are conserved in the kidneys and eyes of zebrafish and mice and that the exocyst is necessary for photoreceptor ciliogenesis and retinal development, most likely by trafficking cilia and outer-segment proteins.


Subject(s)
Cilia/metabolism , Exocytosis , Photoreceptor Cells, Vertebrate/metabolism , Retina/metabolism , Animals , Mice , Mice, Inbred C57BL , Mutation , Photoreceptor Cells, Vertebrate/pathology , Retina/pathology , Vesicular Transport Proteins/deficiency , Vesicular Transport Proteins/metabolism , Zebrafish
13.
Sci Rep ; 6: 31137, 2016 08 11.
Article in English | MEDLINE | ID: mdl-27511831

ABSTRACT

Congenital obstructive nephropathy (CON) is the most prevalent cause of pediatric chronic kidney disease and end-stage renal disease. The ureteropelvic junction (UPJ) region, where the renal pelvis transitions to the ureter, is the most commonly obstructed site in CON. The underlying causes of congenital UPJ obstructions remain poorly understood, especially when they occur in utero, in part due to the lack of genetic animal models. We previously showed that conditional inactivation of Sec10, a central subunit of the exocyst complex, in the epithelial cells of the ureter and renal collecting system resulted in late gestational bilateral UPJ obstructions with neonatal anuria and death. In this study, we show that without Sec10, the urothelial progenitor cells that line the ureter fail to differentiate into superficial cells, which are responsible for producing uroplakin plaques on the luminal surface. These Sec10-knockout urothelial cells undergo cell death by E17.5 and the urothelial barrier becomes leaky to luminal fluid. Also at E17.5, we measured increased expression of TGFß1 and genes associated with myofibroblast activation, with evidence of stromal remodeling. Our findings support the model that a defective urothelial barrier allows urine to induce a fibrotic wound healing mechanism, which may contribute to human prenatal UPJ obstructions.


Subject(s)
Disease Models, Animal , Kidney Diseases/pathology , Ureteral Obstruction/congenital , Animals , Mice , Microscopy, Electron, Transmission , Real-Time Polymerase Chain Reaction
14.
EBioMedicine ; 7: 62-72, 2016 May.
Article in English | MEDLINE | ID: mdl-27322459

ABSTRACT

Long intergenic noncoding RNAs (lincRNAs) are a relatively new class of non-coding RNAs that have the potential as cancer biomarkers. To seek a panel of lincRNAs as pan-cancer biomarkers, we have analyzed transcriptomes from over 3300 cancer samples with clinical information. Compared to mRNA, lincRNAs exhibit significantly higher tissue specificities that are then diminished in cancer tissues. Moreover, lincRNA clustering results accurately classify tumor subtypes. Using RNA-Seq data from thousands of paired tumor and adjacent normal samples in The Cancer Genome Atlas (TCGA), we identify six lincRNAs as potential pan-cancer diagnostic biomarkers (PCAN-1 to PCAN-6). These lincRNAs are robustly validated using cancer samples from four independent RNA-Seq data sets, and are verified by qPCR in both primary breast cancers and MCF-7 cell line. Interestingly, the expression levels of these six lincRNAs are also associated with prognosis in various cancers. We further experimentally explored the growth and migration dependence of breast and colon cancer cell lines on two of the identified lncRNAs. In summary, our study highlights the emerging role of lincRNAs as potentially powerful and biologically functional pan-cancer biomarkers and represents a significant leap forward in understanding the biological and clinical functions of lincRNAs in cancers.


Subject(s)
Biomarkers, Tumor/genetics , Breast Neoplasms/diagnosis , Gene Expression Profiling/methods , RNA, Long Noncoding/genetics , Sequence Analysis, RNA/methods , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Cell Line, Tumor , Cell Movement , Cell Proliferation , Female , Gene Expression Regulation, Neoplastic , Humans , MCF-7 Cells , Organ Specificity , Prognosis
15.
Dis Model Mech ; 9(5): 585-96, 2016 05 01.
Article in English | MEDLINE | ID: mdl-26989192

ABSTRACT

Genetic variations affecting neural tube closure along the head result in malformations of the face and brain. Neural tube defects (NTDs) are among the most common birth defects in humans. We previously reported a mouse mutant called tuft that arose spontaneously in our wild-type 3H1 colony. Adult tuft mice present midline craniofacial malformations with or without an anterior cephalocele. In addition, affected embryos presented neural tube closure defects resulting in insufficient closure of the anterior neuropore or exencephaly. Here, through whole-genome sequencing, we identified a nonsense mutation in the Tet1 gene, which encodes a methylcytosine dioxygenase (TET1), co-segregating with the tuft phenotype. This mutation resulted in premature termination that disrupts the catalytic domain that is involved in the demethylation of cytosine. We detected a significant loss of TET enzyme activity in the heads of tuft embryos that were homozygous for the mutation and had NTDs. RNA-Seq transcriptome analysis indicated that multiple gene pathways associated with neural tube closure were dysregulated in tuft embryo heads. Among them, the expressions of Cecr2, Epha7 and Grhl2 were significantly reduced in some embryos presenting neural tube closure defects, whereas one or more components of the non-canonical WNT signaling pathway mediating planar cell polarity and convergent extension were affected in others. We further show that the recombinant mutant TET1 protein was capable of entering the nucleus and affected the expression of endogenous Grhl2 in IMCD-3 (inner medullary collecting duct) cells. These results indicate that TET1 is an epigenetic determinant for regulating genes that are crucial to closure of the anterior neural tube and its mutation has implications to craniofacial development, as presented by the tuft mouse.


Subject(s)
Mutation/genetics , Animals , Body Size , Cell Polarity , Codon, Nonsense/genetics , DNA-Binding Proteins/genetics , Ectoderm/metabolism , Embryo, Mammalian/metabolism , Gene Expression Regulation, Developmental , Homozygote , Mice , Models, Biological , Neural Tube , Point Mutation , Proto-Oncogene Proteins/genetics , RNA/metabolism , Transcription Factors/metabolism , Wnt Signaling Pathway/genetics
16.
Mol Biol Cell ; 27(2): 308-20, 2016 Jan 15.
Article in English | MEDLINE | ID: mdl-26582389

ABSTRACT

Arl13b belongs to the ADP-ribosylation factor family within the Ras superfamily of regulatory GTPases. Mutations in Arl13b cause Joubert syndrome, which is characterized by congenital cerebellar ataxia, hypotonia, oculomotor apraxia, and mental retardation. Arl13b is highly enriched in cilia and is required for ciliogenesis in multiple organs. Nevertheless, the precise role of Arl13b remains elusive. Here we report that the exocyst subunits Sec8, Exo70, and Sec5 bind preferentially to the GTP-bound form of Arl13b, consistent with the exocyst being an effector of Arl13b. Moreover, we show that Arl13b binds directly to Sec8 and Sec5. In zebrafish, depletion of arl13b or the exocyst subunit sec10 causes phenotypes characteristic of defective cilia, such as curly tail up, edema, and abnormal pronephric kidney development. We explored this further and found a synergistic genetic interaction between arl13b and sec10 morphants in cilia-dependent phenotypes. Through conditional deletion of Arl13b or Sec10 in mice, we found kidney cysts and decreased ciliogenesis in cells surrounding the cysts. Moreover, we observed a decrease in Arl13b expression in the kidneys from Sec10 conditional knockout mice. Taken together, our results indicate that Arl13b and the exocyst function together in the same pathway leading to functional cilia.


Subject(s)
ADP-Ribosylation Factors/metabolism , Cilia/metabolism , ADP-Ribosylation Factors/genetics , Abnormalities, Multiple , Animals , Cerebellum/abnormalities , Eye Abnormalities , Genetic Association Studies , HeLa Cells , Humans , Kidney/metabolism , Kidney Diseases, Cystic , Mice , Mice, Knockout , Microtubules/metabolism , Mutation , NIH 3T3 Cells , Retina/abnormalities , Vesicular Transport Proteins/metabolism , Zebrafish , Zebrafish Proteins/genetics , Zebrafish Proteins/metabolism
17.
Am J Physiol Cell Physiol ; 309(3): C190-201, 2015 Aug 01.
Article in English | MEDLINE | ID: mdl-26040895

ABSTRACT

The highly conserved exocyst protein complex regulates polarized exocytosis of subsets of secretory vesicles. A previous study reported that shRNA knockdown of an exocyst central subunit, Sec10 (Sec10-KD) in Madin-Darby canine kidney (MDCK) cells disrupted primary cilia assembly and 3D cyst formation. We used three-dimensional collagen cultures of MDCK cells to further investigate the mechanisms by which Sec10 and the exocyst regulate epithelial polarity, morphogenesis, and homeostasis. Sec10-KD cysts initially demonstrated undisturbed lumen formation although later displayed significantly fewer and shorter primary cilia than controls. Later in cystogenesis, control cells maintained normal homeostasis, while Sec10-KD cysts displayed numerous apoptotic cells extruded basally into the collagen matrix. Sec10-KD MDCK cells were also more sensitive to apoptotic triggers than controls. These phenotypes were reversed by restoring Sec10 expression with shRNA-resistant human Sec10. Apico-basal polarity appeared normal in Sec10-KD cysts, whereas mitotic spindle angles differed significantly from controls, suggesting a planar cell polarity defect. In addition, analysis of renal tubules in a newly generated kidney-specific Sec10-knockout mouse model revealed significant defects in primary cilia assembly and in the targeted renal tubules; abnormal epithelial cell extrusion was also observed, supporting our in vitro results. We hypothesize that, in Sec10-KD cells, the disrupted exocyst activity results in increased apoptotic sensitivity through defective primary cilia signaling and that, in combination with an increased basal cell extrusion rate, it affects epithelial barrier integrity and homeostasis.


Subject(s)
Apoptosis/physiology , Epithelial Cells/physiology , Homeostasis/physiology , Kidney/physiology , Vesicular Transport Proteins/physiology , Animals , Cell Proliferation/physiology , Dogs , Humans , Kidney/cytology , Madin Darby Canine Kidney Cells , Mice , Mice, Inbred C57BL , Mice, Knockout
18.
PLoS One ; 10(6): e0129346, 2015.
Article in English | MEDLINE | ID: mdl-26046524

ABSTRACT

Most cases of congenital obstructive nephropathy are the result of ureteropelvic junction obstructions, and despite their high prevalence, we have a poor understanding of their etiology and scarcity of genetic models. The eight-protein exocyst complex regulates polarized exocytosis of intracellular vesicles in a large variety of cell types. Here we report generation of a conditional knockout mouse for Sec10, a central component of the exocyst, which is the first conditional allele for any exocyst gene. Inactivation of Sec10 in ureteric bud-derived cells using Ksp1.3-Cre mice resulted in severe bilateral hydronephrosis and complete anuria in newborns, with death occurring 6-14 hours after birth. Sec10 FL/FL;Ksp-Cre embryos developed ureteropelvic junction obstructions between E17.5 and E18.5 as a result of degeneration of the urothelium and subsequent overgrowth by surrounding mesenchymal cells. The urothelial cell layer that lines the urinary tract must maintain a hydrophobic luminal barrier again urine while remaining highly stretchable. This barrier is largely established by production of uroplakin proteins that are transported to the apical surface to establish large plaques. By E16.5, Sec10 FL/FL;Ksp-Cre ureter and pelvic urothelium showed decreased uroplakin-3 protein at the luminal surface, and complete absence of uroplakin-3 by E17.5. Affected urothelium at the UPJ showed irregular barriers that exposed the smooth muscle layer to urine, suggesting this may trigger the surrounding mesenchymal cells to overgrow the lumen. Findings from this novel mouse model show Sec10 is critical for the development of the urothelium in ureters, and provides experimental evidence that failure of this urothelial barrier may contribute to human congenital urinary tract obstructions.


Subject(s)
Kidney Pelvis/metabolism , Ureteral Obstruction/genetics , Urothelium/metabolism , Vesicular Transport Proteins/genetics , Animals , Animals, Newborn , Anuria/genetics , Anuria/metabolism , Blotting, Western , Disease Models, Animal , Gene Expression Regulation, Developmental , Humans , Hydronephrosis/genetics , Hydronephrosis/metabolism , Kidney Pelvis/embryology , Kidney Pelvis/pathology , Mice, Knockout , Mice, Transgenic , Microscopy, Fluorescence , Reverse Transcriptase Polymerase Chain Reaction , Time Factors , Ureteral Obstruction/metabolism , Urothelium/embryology , Urothelium/pathology , Vesicular Transport Proteins/metabolism
19.
Am J Physiol Renal Physiol ; 307(12): F1334-41, 2014 Dec 15.
Article in English | MEDLINE | ID: mdl-25298525

ABSTRACT

Acute kidney injury is common and has a high mortality rate, and no effective treatment exists other than supportive care. Using cell culture models, we previously demonstrated that exocyst Sec10 overexpression reduced damage to renal tubule cells and speeded recovery and that the protective effect was mediated by higher basal levels of mitogen-activated protein kinase (MAPK) signaling. The exocyst, a highly-conserved eight-protein complex, is known for regulating protein trafficking. Here we show that the exocyst biochemically interacts with the epidermal growth factor receptor (EGFR), which is upstream of MAPK, and Sec10-overexpressing cells express greater levels of phosphorylated (active) ERK, the final step in the MAPK pathway, in response to EGF stimulation. EGFR endocytosis, which has been linked to activation of the MAPK pathway, increases in Sec10-overexpressing cells, and gefitinib, a specific EGFR inhibitor, and Dynasore, a dynamin inhibitor, both reduce EGFR endocytosis. In turn, inhibition of the MAPK pathway reduces ligand-mediated EGFR endocytosis, suggesting a potential feedback of elevated ERK activity on EGFR endocytosis. Gefitinib also decreases MAPK signaling in Sec10-overexpressing cells to levels seen in control cells and, demonstrating a causal role for EGFR, reverses the protective effect of Sec10 overexpression following cell injury in vitro. Finally, using an in vivo zebrafish model of acute kidney injury, morpholino-induced knockdown of sec10 increases renal tubule cell susceptibility to injury. Taken together, these results suggest that the exocyst, acting through EGFR, endocytosis, and the MAPK pathway is a candidate therapeutic target for acute kidney injury.


Subject(s)
Acute Kidney Injury/prevention & control , Endocytosis , ErbB Receptors/metabolism , Kidney Tubules/enzymology , Mitogen-Activated Protein Kinases/metabolism , Vesicular Transport Proteins/metabolism , Zebrafish Proteins/metabolism , Acute Kidney Injury/enzymology , Acute Kidney Injury/genetics , Acute Kidney Injury/pathology , Animals , Animals, Genetically Modified , Disease Models, Animal , Dogs , Endocytosis/drug effects , Enzyme Activation , ErbB Receptors/antagonists & inhibitors , ErbB Receptors/genetics , Gene Knockdown Techniques , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Kidney Tubules/drug effects , Kidney Tubules/pathology , Madin Darby Canine Kidney Cells , Oxidative Stress , Phosphorylation , Protein Binding , Protein Kinase Inhibitors/pharmacology , Signal Transduction , Time Factors , Transfection , Vesicular Transport Proteins/genetics , Zebrafish/genetics , Zebrafish Proteins/genetics
20.
Nephron Exp Nephrol ; 120(4): e134-40, 2012.
Article in English | MEDLINE | ID: mdl-23037926

ABSTRACT

BACKGROUND: Protein translation and translocation at the rough endoplasmic reticulum (RER) are the first steps in the secretory pathway. The translocon through which newly made proteins are translocated into or across the RER membrane consists of three main subunits: Sec61α, -ß, and -γ. Sec61ß facilitates translocation, and we and others have shown that the highly conserved eight-protein exocyst complex interacts with Sec61ß. We have also shown that the exocyst is involved in basolateral, not apical, protein synthesis and delivery. Recently, however, exocyst involvement in apical protein delivery has been reported. Furthermore, we have shown that the exocyst is necessary for formation of primary cilia, organelles found on the apical surface. METHODS: GST pulldown was performed on lysate of renal tubule cells to investigate biochemical interactions. Cell-free assays consisting of cell-free extracts from rabbit reticulocytes, pancreatic endoplasmic reticulum (ER) microsomal membranes, transcripts of cDNA from apical and basolateral proteins, ATP/GTP, amino acids, and (35)S-methionine for protein detection were used to investigate the role of the exocyst in synthesis of polarized proteins. P(32)-orthophosphate and immunoprecipitation with antibody against Sec61ß was used to investigate Sec61ß phosphorylation in exocyst Sec10-overexpressing cells. RESULTS: Sec10 biochemically interacts with Sec61ß using GST pulldown. Using cell-free assays, there is enhanced exocyst recruitment to endoplasmic reticulum membranes following exocyst depletion and basolateral G protein of vesicular stomatitis virus protein translation, compared to apical hemagglutinin of influenza virus protein translation. Finally, Sec10 overexpression increases Sec61ß phosphorylation. CONCLUSION: These data confirm that the exocyst is preferentially involved in basolateral protein translation and translocation, and may well act through the phosphorylation of Sec61ß.


Subject(s)
Endoplasmic Reticulum/metabolism , Membrane Proteins/metabolism , Protein Biosynthesis/physiology , Protein Transport/physiology , Vesicular Transport Proteins/metabolism , Animals , Humans , Rabbits , SEC Translocation Channels
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