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1.
Sci Rep ; 13(1): 17647, 2023 10 17.
Article in English | MEDLINE | ID: mdl-37848494

ABSTRACT

CLIC5 belongs to a family of ion channels with six members reported so far. In vertebrates, the CLIC5 gene encodes two different isoforms, CLIC5A and CLIC5B. In addition to its ion channel activity, there is evidence for further functions of CLIC5A, such as the remodeling of the actin cytoskeleton during the formation of a functional glomerulus in the vertebrate kidney. However, its specific role is still incompletely understood and a specific functional role for CLIC5B has not been described yet. Here we report our findings on the differential expression and functions of Clic5a and Clic5b during zebrafish kidney development. Whole-mount in situ hybridization studies revealed specific expression of clic5a in the eye and pronephric glomerulus, and clic5b is expressed in the gut, liver and the pronephric tubules. Clic5 immunostainings revealed that Clic5b is localized in the cilia. Whereas knockdown of Clic5a resulted in leakiness of the glomerular filtration barrier, Clic5b deficient embryos displayed defective ciliogenesis, leading to ciliopathy-associated phenotypes such as ventral body curvature, otolith deposition defects, altered left-right asymmetry and formation of hydrocephalus and pronephric cysts. In addition, Clic5 deficiency resulted in dysregulation of cilia-dependent Wnt signalling pathway components. Mechanistically, we identified a Clic5-dependent activation of the membrane-cytoskeletal linker proteins Ezrin/Radixin/Moesin (ERM) in the pronephric tubules of zebrafish. In conclusion, our in vivo data demonstrates a novel role for Clic5 in regulating essential ciliary functions and identified Clic5 as a positive regulator of ERM phosphorylation.


Subject(s)
Chloride Channels , Chlorides , Cilia , Kidney Glomerulus , Microfilament Proteins , Zebrafish , Animals , Actin Cytoskeleton/metabolism , Chloride Channels/genetics , Chloride Channels/metabolism , Chlorides/metabolism , Cilia/genetics , Cilia/metabolism , Kidney Glomerulus/metabolism , Microfilament Proteins/genetics , Microfilament Proteins/metabolism , Zebrafish/genetics , Zebrafish/metabolism
2.
Am J Hum Genet ; 109(5): 928-943, 2022 05 05.
Article in English | MEDLINE | ID: mdl-35397207

ABSTRACT

Organ fibrosis is a shared endpoint of many diseases, yet underlying mechanisms are not well understood. Several pathways governed by the primary cilium, a sensory antenna present on most vertebrate cells, have been linked with fibrosis. Ciliopathies usually start early in life and represent a considerable disease burden. We performed massively parallel sequencing by using cohorts of genetically unsolved individuals with unexplained liver and kidney failure and correlated this with clinical, imaging, and histopathological analyses. Mechanistic studies were conducted with a vertebrate model and primary cells. We detected bi-allelic deleterious variants in TULP3, encoding a critical adaptor protein for ciliary trafficking, in a total of 15 mostly adult individuals, originating from eight unrelated families, with progressive degenerative liver fibrosis, fibrocystic kidney disease, and hypertrophic cardiomyopathy with atypical fibrotic patterns on histopathology. We recapitulated the human phenotype in adult zebrafish and confirmed disruption of critical ciliary cargo composition in several primary cell lines derived from affected individuals. Further, we show interaction between TULP3 and the nuclear deacetylase SIRT1, with roles in DNA damage repair and fibrosis, and report increased DNA damage ex vivo. Transcriptomic studies demonstrated upregulation of profibrotic pathways with gene clusters for hypertrophic cardiomyopathy and WNT and TGF-ß signaling. These findings identify variants in TULP3 as a monogenic cause for progressive degenerative disease of major organs in which affected individuals benefit from early detection and improved clinical management. Elucidation of mechanisms crucial for DNA damage repair and tissue maintenance will guide novel therapeutic avenues for this and similar genetic and non-genomic diseases.


Subject(s)
Cardiomyopathy, Hypertrophic , Cilia , Adult , Animals , Cardiomyopathy, Hypertrophic/metabolism , Child , Cilia/genetics , Cilia/metabolism , Fibrosis , Humans , Intracellular Signaling Peptides and Proteins/genetics , Kidney , Liver , Mutation/genetics , Zebrafish/genetics
3.
Hum Mol Genet ; 31(14): 2295-2306, 2022 07 21.
Article in English | MEDLINE | ID: mdl-35137054

ABSTRACT

Mutations in genes that lead to dysfunctional cilia can cause a broad spectrum of human disease phenotypes referred to as ciliopathies. Many ciliopathy-associated proteins are localized to the evolutionary conserved ciliary transition zone (TZ) subdomain. We identified biallelic missense and nonsense mutations in the gene encoding the transmembrane protein TMEM218 in unrelated patients with features related to Bardet-Biedl, Joubert and Meckel-Gruber syndrome (MKS) and characterized TMEM218 as a major component of the ciliary TZ module. Co-immunoprecipitation assays resulted in the physical interaction of TMEM218 with the MKS module member TMEM67/Meckelin that was significantly reduced by the TMEM218 missense change harboured by one of our patients. We could further validate its pathogenicity by functional in vivo analysis in zebrafish (Danio rerio) as a well-established vertebrate model for ciliopathies. Notably, ciliopathy-related phenotypes were most prominent by genetic interactions with the NPHP module component Nphp4. Conclusively, we describe TMEM218 as a new disease gene for patients with a wide spectrum of syndromic ciliopathy phenotypes and provide evidence for a synergistic interaction of TMEM218 and the NPHP module crucial for proper ciliary function.


Subject(s)
Abnormalities, Multiple , Ciliopathies , Polycystic Kidney Diseases , Abnormalities, Multiple/genetics , Abnormalities, Multiple/metabolism , Animals , Caenorhabditis elegans/genetics , Cilia/genetics , Cilia/metabolism , Ciliary Motility Disorders , Ciliopathies/genetics , Ciliopathies/metabolism , Encephalocele , Humans , Mutation , Polycystic Kidney Diseases/genetics , Retinitis Pigmentosa , Zebrafish/genetics
4.
Hum Mutat ; 41(12): 2179-2194, 2020 12.
Article in English | MEDLINE | ID: mdl-33131181

ABSTRACT

Ciliopathies are clinically and genetically heterogeneous diseases. We studied three patients from two independent families presenting with features of Joubert syndrome: abnormal breathing pattern during infancy, developmental delay/intellectual disability, cerebellar ataxia, molar tooth sign on magnetic resonance imaging scans, and polydactyly. We identified biallelic loss-of-function (LOF) variants in CBY1, segregating with the clinical features of Joubert syndrome in the families. CBY1 localizes to the distal end of the mother centriole, contributing to the formation and function of cilia. In accordance with the clinical and mutational findings in the affected individuals, we demonstrated that depletion of Cby1 in zebrafish causes ciliopathy-related phenotypes. Levels of CBY1 transcript were found reduced in the patients compared with controls, suggesting degradation of the mutated transcript through nonsense-mediated messenger RNA decay. Accordingly, we could detect CBY1 protein in fibroblasts from controls, but not from patients by immunofluorescence. Furthermore, we observed reduced ability to ciliate, increased ciliary length, and reduced levels of the ciliary proteins AHI1 and ARL13B in patient fibroblasts. Our data show that CBY1 LOF-variants cause a ciliopathy with features of Joubert syndrome.


Subject(s)
Abnormalities, Multiple/genetics , Carrier Proteins/genetics , Cerebellum/abnormalities , Ciliopathies/genetics , Eye Abnormalities/genetics , Kidney Diseases, Cystic/genetics , Mutation/genetics , Nuclear Proteins/genetics , Retina/abnormalities , Abnormalities, Multiple/diagnostic imaging , Abnormalities, Multiple/pathology , Adolescent , Animals , Cerebellum/diagnostic imaging , Cerebellum/pathology , Child , Child, Preschool , Cilia/metabolism , Cilia/pathology , Ciliopathies/diagnostic imaging , Ciliopathies/pathology , Eye Abnormalities/diagnostic imaging , Eye Abnormalities/pathology , Female , Fibroblasts/metabolism , Fibroblasts/pathology , Homozygote , Humans , Infant , Infant, Newborn , Kidney Diseases, Cystic/diagnostic imaging , Kidney Diseases, Cystic/pathology , Magnetic Resonance Imaging , Male , Pedigree , Phenotype , Retina/diagnostic imaging , Retina/pathology , Smoothened Receptor/metabolism , Young Adult , Zebrafish/genetics
5.
Nat Genet ; 49(7): 1025-1034, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28530676

ABSTRACT

Autosomal recessive polycystic kidney disease (ARPKD), usually considered to be a genetically homogeneous disease caused by mutations in PKHD1, has been associated with ciliary dysfunction. Here, we describe mutations in DZIP1L, which encodes DAZ interacting protein 1-like, in patients with ARPKD. We further validated these findings through loss-of-function studies in mice and zebrafish. DZIP1L localizes to centrioles and to the distal ends of basal bodies, and interacts with septin2, a protein implicated in maintenance of the periciliary diffusion barrier at the ciliary transition zone. In agreement with a defect in the diffusion barrier, we found that the ciliary-membrane translocation of the PKD proteins polycystin-1 and polycystin-2 is compromised in DZIP1L-mutant cells. Together, these data provide what is, to our knowledge, the first conclusive evidence that ARPKD is not a homogeneous disorder and further establish DZIP1L as a second gene involved in ARPKD pathogenesis.


Subject(s)
Polycystic Kidney, Autosomal Recessive/genetics , Abnormalities, Multiple/embryology , Abnormalities, Multiple/genetics , Adaptor Proteins, Signal Transducing/deficiency , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/physiology , Animals , Centrioles/metabolism , Chromosomes, Human, Pair 3/genetics , Cilia/metabolism , Consanguinity , Disease Models, Animal , Embryo, Nonmammalian/abnormalities , Female , Gene Knockdown Techniques , Genetic Linkage , Humans , Male , Membrane Proteins/metabolism , Mice , Mice, Inbred C57BL , Pedigree , Polycystic Kidney, Autosomal Recessive/embryology , Protein Transport , Septins/metabolism , TRPP Cation Channels/metabolism , Zebrafish/embryology , Zebrafish/genetics , Zebrafish Proteins/deficiency , Zebrafish Proteins/genetics , Zebrafish Proteins/physiology
6.
Dev Biol ; 411(1): 101-14, 2016 Mar 01.
Article in English | MEDLINE | ID: mdl-26472045

ABSTRACT

Mutations in the homeobox transcription factor MNX1 are the major cause of dominantly inherited sacral agenesis. Studies in model organisms revealed conserved mnx gene requirements in neuronal and pancreatic development while Mnx activities that could explain the caudal mesoderm specific agenesis phenotype remain elusive. Here we use the zebrafish pronephros as a simple yet genetically conserved model for kidney formation to uncover a novel role of Mnx factors in nephron morphogenesis. Pronephros formation can formally be divided in four stages, the specification of nephric mesoderm from the intermediate mesoderm (IM), growth and epithelialisation, segmentation and formation of the glomerular capillary tuft. Two of the three mnx genes in zebrafish are dynamically transcribed in caudal IM in a time window that proceeds segmentation. We show that expression of one mnx gene, mnx2b, is restricted to the pronephric lineage and that mnx2b knock-down causes proximal pronephric tubule dilation and impaired pronephric excretion. Using expression profiling of embryos transgenic for conditional activation and repression of Mnx regulated genes, we further identified irx1b as a direct target of Mnx factors. Consistent with a repression of irx1b by Mnx factors, the transcripts of irx1b and mnx genes are found in mutual exclusive regions in the IM, and blocking of Mnx functions results in a caudal expansion of the IM-specific irx1b expression. Finally, we find that knock-down of irx1b is sufficient to rescue proximal pronephric tubule dilation and impaired nephron function in mnx-morpholino injected embryos. Our data revealed a first caudal mesoderm specific requirement of Mnx factors in a non-human system and they demonstrate that Mnx-dependent restriction of IM-specific irx1b activation is required for the morphogenesis and function of the zebrafish pronephros.


Subject(s)
Homeodomain Proteins/genetics , Homeodomain Proteins/physiology , Kidney Tubules/embryology , Organogenesis/genetics , Pronephros/embryology , Transcription Factors/genetics , Zebrafish Proteins/genetics , Zebrafish Proteins/physiology , Zebrafish/embryology , Abnormalities, Multiple/genetics , Animals , Animals, Genetically Modified , Body Patterning/physiology , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Enzyme Activation , Gene Expression Profiling , Gene Expression Regulation, Developmental , Gene Knockdown Techniques , Homeodomain Proteins/biosynthesis , Meningocele/genetics , Mesoderm/embryology , Models, Animal , Morpholinos/genetics , Organogenesis/physiology , Sacrococcygeal Region/abnormalities , Transcription Factors/biosynthesis , Zebrafish Proteins/biosynthesis
7.
PLoS One ; 6(5): e18609, 2011.
Article in English | MEDLINE | ID: mdl-21603652

ABSTRACT

OriP, the latent origin of Epstein-Barr virus (EBV), consists of two essential elements: the dyad symmetry (DS) and the family of repeats (FR). The function of these elements has been predominantly analyzed in plasmids transfected into transformed cells. Here, we examined the molecular functions of DS in its native genomic context and at an ectopic position in the mini-EBV episome. Mini-EBV plasmids contain 41% of the EBV genome including all information required for the proliferation of human B cells. Both FR and DS function independently of their genomic context. We show that DS is the most active origin of replication present in the mini-EBV genome regardless of its location, and it is characterized by the binding of the origin recognition complex (ORC) allowing subsequent replication initiation. Surprisingly, the integrity of oriP is not required for the formation of the pre-replicative complex (pre-RC) at or near DS. In addition we show that initiation events occurring at sites other than the DS are also limited to once per cell cycle and that they are ORC-dependent. The deletion of DS increases initiation from alternative origins, which are normally used very infrequently in the mini-EBV genome. The sequence-independent distribution of ORC-binding, pre-RC-assembly, and initiation patterns indicates that a large number of silent origins are present in the mini-EBV genome. We conclude that, in mini-EBV genomes lacking the DS element, the absence of a strong ORC binding site results in an increase of ORC binding at dispersed sites.


Subject(s)
Genome, Viral , Herpesvirus 4, Human/genetics , Origin Recognition Complex/metabolism , Replication Origin/genetics , B-Lymphocytes/pathology , B-Lymphocytes/virology , Binding Sites , Cell Proliferation , Cells, Cultured , Humans , Plasmids
8.
J Virol ; 84(5): 2533-46, 2010 Mar.
Article in English | MEDLINE | ID: mdl-20032186

ABSTRACT

The Epstein-Barr virus efficiently infects human B cells. The EBV genome is maintained extrachromosomally and replicates synchronously with the host's chromosomes. The latent origin of replication (oriP) guarantees plasmid stability by mediating two basic functions: replication and segregation of the viral genome. While the segregation process of EBV genomes is well understood, little is known about its chromatin association and nuclear distribution during interphase. Here, we analyzed the nuclear localization of EBV genomes and the role of functional oriP domains FR and DS for basic functions such as the transformation of primary cells, their role in targeting EBV genomes to distinct nuclear regions, and their association with epigenetic domains. Fluorescence in situ hybridization visualized the localization of extrachromosomal EBV genomes in the regions adjacent to chromatin-dense territories called the perichromatin. Further, immunofluorescence experiments demonstrated a preference of the viral genome for histone 3 lysine 4-trimethylated (H3K4me3) and histone 3 lysine 9-acetylated (H3K9ac) nuclear regions. To determine the role of FR and DS for establishment and subnuclear localization of EBV genomes, we transformed primary human B lymphocytes with recombinant mini-EBV genomes containing different oriP mutants. The loss of DS results in a slightly increased association in H3K27me3 domains. This study demonstrates that EBV genomes or oriP-based extrachromosomal vector systems are integrated into the higher order nuclear organization. We found that viral genomes are not randomly distributed in the nucleus. FR but not DS is crucial for the localization of EBV in perichromatic regions that are enriched for H3K4me3 and H3K9ac, which are hallmarks of transcriptionally active regions.


Subject(s)
Cell Nucleus/genetics , Cell Nucleus/virology , Genome, Viral , Herpesvirus 4, Human/genetics , Replication Origin , Virus Replication/genetics , Animals , B-Lymphocytes/cytology , B-Lymphocytes/immunology , B-Lymphocytes/virology , Cell Nucleus/metabolism , Cell Nucleus/ultrastructure , Cells, Cultured , Chromatin/metabolism , Chromatin/ultrastructure , Epstein-Barr Virus Nuclear Antigens/genetics , Epstein-Barr Virus Nuclear Antigens/metabolism , Herpesvirus 4, Human/metabolism , Histones/genetics , Histones/metabolism , Humans , In Situ Hybridization, Fluorescence , Plasmids/genetics , Plasmids/metabolism
9.
Int J Dev Biol ; 53(4): 517-24, 2009.
Article in English | MEDLINE | ID: mdl-19378255

ABSTRACT

The globin family, including hemoglobin, myoglobin, neuroglobin and cytoglobin, plays an important role in oxygen storage and delivery. Myoglobin has been shown to be necessary for cardiac function during development, but no information is currently available on the developmental regulation of myoglobin gene expression during embryogenesis. In this study, we used whole mount in situ hybridization to visualize myoglobin mRNA expression during zebrafish development. Our results show for the first time the spatial and temporal gene expression pattern of myoglobin during embryogenesis. Myoglobin was expressed as a maternal RNA and ubiquitous expression was observed until the end of gastrulation. At later stages of development, we discovered novel expression domains for myoglobin, including several non-muscular ones. Environmental stresses, like low oxygen tension (hypoxia) can lead to a developmental delay in zebrafish embryos. We show here that hypoxic stress induces myoglobin expression in skeletal muscle cells of anterior somites and in the dorsal aorta of zebrafish larvae. Finally, we analyzed the role of myoglobins in development by targeted gene knock-down. Silencing myoglobin in zebrafish embryos with gene-specific morpholinos led to a dose dependent curvature, vascular defects, enlarged pericardia and reduction of the gut. In conclusion, our results indicate that myoglobin plays a crucial role in zebrafish development and is important for angiogenesis and gut development.


Subject(s)
Myoglobin/metabolism , Zebrafish/embryology , Zebrafish/metabolism , Animals , Embryo, Nonmammalian/blood supply , Embryo, Nonmammalian/embryology , Embryo, Nonmammalian/metabolism , Gene Expression Regulation, Developmental , Genome/genetics , Humans , Myoglobin/genetics , Phylogeny , Zebrafish/genetics
11.
Dev Dyn ; 237(12): 3940-52, 2008 Dec.
Article in English | MEDLINE | ID: mdl-19035355

ABSTRACT

The LIM domain only protein 7 (LMO7), a member of the PDZ and LIM domain-containing protein family is a candidate gene with possible roles in embryonic development and breast cancer progression. LMO7 has been linked to actin cytoskeleton organization through nectin/afadin and to cell-cell adhesion by means of E-cadherin/catenin. In addition, LMO7 has been shown to regulate transcription of the nuclear membrane protein Emerin and other muscle relevant genes. In this study, we used in situ hybridization to investigate LMO7 expression during embryonic development in three widely used vertebrate model species: the zebrafish, the chicken and the mouse. Our temporal and spatial gene expression analysis revealed both common and distinct patterns between these species. In mouse and chicken embryos we found expression in the outflow tract, the inflow tract, the pro-epicardial organ and the second heart field, structures highly important in the developing heart. Furthermore, gene knockdown experiments in zebrafish embryos resulted in severe defects in heart development with effects on the conduction system and on heart localization. In summary, we present here the first developmental study of LMO7. We reveal the temporal and spatial expression patterns of this important gene during mouse, chicken and fish development and our findings suggest essential functions for LMO7 during vertebrate heart development.


Subject(s)
Heart/embryology , Myocardium/metabolism , Transcription Factors/metabolism , Zebrafish Proteins/metabolism , Zebrafish/embryology , Zebrafish/metabolism , Animals , Animals, Genetically Modified , Chickens , Embryo, Nonmammalian/embryology , Embryo, Nonmammalian/metabolism , Gene Expression Regulation, Developmental , Humans , LIM Domain Proteins , Mice , Transcription Factors/deficiency , Transcription Factors/genetics , Zebrafish/genetics , Zebrafish Proteins/deficiency , Zebrafish Proteins/genetics
12.
BMC Evol Biol ; 8: 166, 2008 Jun 02.
Article in English | MEDLINE | ID: mdl-18518953

ABSTRACT

BACKGROUND: Actin is a cytoskeletal protein which exerts a broad range of functions in almost all eukaryotic cells. In higher vertebrates, six primary actin isoforms can be distinguished: alpha-skeletal, alpha-cardiac, alpha-smooth muscle, gamma-smooth muscle, beta-cytoplasmic and gamma-cytoplasmic isoactin. Expression of these actin isoforms during vertebrate development is highly regulated in a temporal and tissue-specific manner, but the mechanisms and the specific differences are currently not well understood. All members of the actin multigene family are highly conserved, suggesting that there is a high selective pressure on these proteins. RESULTS: We present here a model for the evolution of the genomic organization of alpha-skeletal actin and by molecular modeling, illustrate the structural differences of actin proteins of different phyla. We further describe and compare alpha-skeletal actin expression in two developmental stages of five vertebrate species (mouse, chicken, snake, salamander and fish). Our findings confirm that alpha-skeletal actin is expressed in skeletal muscle and in the heart of all five species. In addition, we identify many novel non-muscular expression domains including several in the central nervous system. CONCLUSION: Our results show that the high sequence homology of alpha-skeletal actins is reflected by similarities of their 3 dimensional protein structures, as well as by conserved gene expression patterns during vertebrate development. Nonetheless, we find here important differences in 3D structures, in gene architectures and identify novel expression domains for this structural and functional important gene.


Subject(s)
Actins/genetics , Gene Expression Regulation, Developmental , Actins/chemistry , Amino Acid Sequence , Animals , In Situ Hybridization , Mice , Models, Molecular , Molecular Sequence Data , Muscle, Skeletal/embryology , Phylogeny , Sequence Alignment , Zebrafish
13.
Dev Dyn ; 236(11): 3144-54, 2007 Nov.
Article in English | MEDLINE | ID: mdl-17937393

ABSTRACT

The three Enigma subfamily proteins, Enigma, Enigma homologue, and Cypher/ZASP belong to the PDZ and LIM encoding protein family, which is characterized by the presence of a PDZ- and one or more LIM domains. PDZ/LIM proteins play important biological roles, and all members have been shown to associate with the actin cytoskeleton. We describe here the splice form specific expression patterns for the three Enigma subfamily members during zebrafish embryogenesis. Whole-mount in situ hybridization revealed common and distinct expression patterns for the different PDZ or LIM domain encoding splice variants. We further studied the role of enigma in zebrafish development. Enigma knockdown appeared to be embryonic lethal shortly after the end of gastrulation and in few surviving embryos led to elongation defects and disorganized somites. In summary, we show here the temporal and spatial expression patterns of the three Enigma family members and their PDZ and LIM domain encoding splice forms during zebrafish embryogenesis. Our results suggest that enigma is important for the formation and organization of somites and might play an important role for actin cytoskeleton organization during development.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Embryo, Nonmammalian/metabolism , Gene Expression Regulation, Developmental , Homeodomain Proteins/genetics , Zebrafish Proteins/genetics , Zebrafish/embryology , Animals , Cytoskeletal Proteins , Cytoskeleton/metabolism , Embryonic Development/genetics , Gene Expression Profiling , Humans , In Situ Hybridization , Intracellular Signaling Peptides and Proteins/genetics , LIM Domain Proteins , Protein Isoforms/genetics , Protein Isoforms/metabolism , Protein Structure, Tertiary , Somites/embryology , Somites/metabolism , Zebrafish/genetics , Zebrafish/metabolism , Zebrafish Proteins/metabolism
14.
J Thorac Cardiovasc Surg ; 133(5): 1242-51, 2007 May.
Article in English | MEDLINE | ID: mdl-17467436

ABSTRACT

OBJECTIVE: In an international, prospective, observational study, we contrasted adverse vascular outcomes among four countries and then assessed practice pattern differences that may have contributed to these outcomes. METHODS: A total of 5065 patients undergoing coronary artery bypass graft surgery were analyzed at 70 international medical centers, and from this pool, 3180 patients from the 4 highest enrolling countries were selected. Fatal and nonfatal postoperative ischemic complications related to the heart, brain, kidney, and gastrointestinal tract were assessed by blinded investigators. RESULTS: In-hospital mortality was 1.5% (9/619) in the United Kingdom, 2.0% (9/444) in Canada, 2.7% (34/1283) in the United States, and 3.8% (32/834) in Germany (P = .03). The rates of the composite outcome (morbidity and mortality) were 12% in the United Kingdom, 16% in Canada, 18% in the United States, and 24% in Germany (P < .001). After adjustment for difference in case-mix (using the European System for Cardiac Operative Risk Evaluation) and practice, country was not an independent predictor for mortality. However, there was an independent effect of country on composite outcome. The practices that were associated with adverse outcomes were the intraoperative use of aprotinin, intraoperative transfusion of fresh-frozen plasma or platelets, lack of use of early postoperative aspirin, and use of postoperative heparin. CONCLUSIONS: Significant between-country differences in perioperative outcome exist and appear to be related to hematologic practices, including administration of antifibrinolytics, fresh-frozen plasma, platelets, heparin, and aspirin. Understanding the mechanisms for these observations and selection of practices associated with improved outcomes may result in significant patient benefit.


Subject(s)
Coronary Artery Bypass/adverse effects , Postoperative Complications/epidemiology , Aged , Canada/epidemiology , Coronary Artery Bypass/mortality , Female , Germany/epidemiology , Hospital Mortality , Humans , Male , Middle Aged , Outcome and Process Assessment, Health Care , Risk Factors , Survival Rate , Treatment Outcome , United Kingdom/epidemiology , United States/epidemiology
15.
Gene Expr Patterns ; 7(5): 620-9, 2007 Apr.
Article in English | MEDLINE | ID: mdl-17300993

ABSTRACT

LIM Kinases (LIMK) are genes encoding multi-domain proteins that can contain up to two LIM domains, a single PDZ domain, and a tyrosine kinase domain. Alternative splicing is a source for different combinations of these domains. Two family members, LIMK1 and LIMK2 have been described in mammals and are important for organization of the actin cytoskeleton. We have cloned LIMK1 and LIMK2 from zebrafish and characterized their domain specific expression patterns during embryogenesis. The results on temporal and spatial expression of the LIM Kinases during embryogenesis indicate overlapping and distinct expression domains for LMK1 and LIMK2. Differences in expression during embryogenesis were observed for PDZ and LIM encoding splice forms for both LIM Kinases. To better understand the transcriptional regulation of LIM Kinases, we searched for conserved regulatory elements. We identified evolutionary conserved smad binding sites for LIMK2. In summary, we present here the splice-form specific temporal and spatial expression patterns for both LIMK1 and LIMK2 during zebrafish embryogenesis.


Subject(s)
Alternative Splicing , Gene Expression Regulation, Developmental , Protein Kinases/genetics , Zebrafish/genetics , Animals , Binding Sites , Cloning, Molecular , Lim Kinases , Protein Kinases/metabolism , Regulatory Elements, Transcriptional , Zebrafish/embryology , Zebrafish/metabolism
16.
JAMA ; 297(5): 471-9, 2007 Feb 07.
Article in English | MEDLINE | ID: mdl-17284697

ABSTRACT

CONTEXT: Acute safety concerns have been raised recently regarding certain hemorrhage-sparing medications commonly used in cardiac surgery. However, no comprehensive data exist regarding their associations with long-term mortality. OBJECTIVE: To contrast long-term all-cause mortality in patients undergoing coronary artery bypass graft (CABG) surgery according to use of 2 lysine analog antifibrinolytics (aminocaproic acid and tranexamic acid), the serine protease inhibitor aprotinin, or no antibleeding agent. DESIGN, SETTING, AND PARTICIPANTS: Observational study of mortality conducted between November 11, 1996, and December 7, 2006. Following index hospitalization (4374 patients; 69 medical centers), survival was prospectively assessed at 6 weeks, 6 months, and annually for 5 years after CABG surgery among 3876 patients enrolled in a 62-center international cohort study. The associations of survival with hemorrhage-sparing medications were compared using multivariable analyses including propensity adjustments. MAIN OUTCOME MEASURE: Death (all-cause) over 5 years. RESULTS: Aprotinin treatment (223 deaths among 1072 patients [20.8% 5-year mortality]) was associated with significantly increased mortality compared with control (128 deaths among 1009 patients [12.7%]; covariate adjusted hazard ratio for death, 1.48; 95% confidence interval, 1.19-1.85), whereas neither aminocaproic acid (132 deaths among 834 patients [15.8%]; adjusted hazard ratio for death, 1.03; 95% confidence interval, 0.80-1.33) nor tranexamic acid (65 deaths among 442 patients [14.7%]; adjusted hazard ratio for death, 1.07; 95% confidence interval, 0.80-1.45) was associated with increased mortality. In multivariable logistic regression, either with propensity adjustment or without, aprotinin was independently predictive of 5-year mortality (adjusted odds ratio with propensity adjustment, 1.48; 95% confidence interval, 1.13-1.93; P = .005) among patients with diverse risk profiles, as well as among those surviving their index hospitalization. Neither aminocaproic nor tranexamic acid was associated with increased risk of death. CONCLUSIONS: These findings indicate that in addition to the previously reported acute renal and vascular safety concerns, aprotinin use is associated with an increased risk of long-term mortality following CABG surgery. Use of aprotinin among patients undergoing CABG surgery does not appear prudent because safer and less expensive alternatives (ie, aminocaproic acid and tranexamic acid) are available.


Subject(s)
Aprotinin/adverse effects , Coronary Artery Bypass/mortality , Hemostatics/adverse effects , Serine Proteinase Inhibitors/adverse effects , Aged , Aminocaproates/therapeutic use , Antifibrinolytic Agents/therapeutic use , Aprotinin/therapeutic use , Cardiopulmonary Bypass , Female , Follow-Up Studies , Hemostatics/therapeutic use , Humans , Logistic Models , Lysine/analogs & derivatives , Male , Middle Aged , Proportional Hazards Models , Prospective Studies , Risk , Serine Proteinase Inhibitors/therapeutic use , Survival Analysis , Tranexamic Acid/therapeutic use
17.
Gene Expr Patterns ; 7(3): 297-305, 2007 Jan.
Article in English | MEDLINE | ID: mdl-17045553

ABSTRACT

The actinin-associated LIM protein (ALP) genes belong to the PDZ/LIM protein family which is characterized by the presence of both a PDZ and a LIM domain. The ALP subfamily in mammals has four members: ALP, Elfin, Mystique and RIL. In this study, we have annotated and cloned the zebrafish ALP gene family and identified a zebrafish-specific fifth member of the family, the alp-like gene. We compared the zebrafish sequences to their human and mouse orthologues. A phylogenetic analysis based on the amino acid sequences showed the overall high degree of conservation within the family. We describe here the expression patterns for all five ALP family genes during zebrafish development. Whole mount in situ hybridization results revealed common and distinct expression patterns for the five genes. With the exception of elfin, all genes were expressed as maternal RNAs at early developmental stages. Gene expression for all of them appeared regulated and localized in specific regions at the eight different developmental stages studied. Expression for all five genes was observed in the central nervous system (CNS), which led us to further investigate brain-specific expression in sections of embryos at 2 days of development. In summary, we identified the zebrafish orthologues of the ALP family and determined their gene expression patterns during zebrafish embryogenesis. Finally, we compare our results to the limited expression data available for this gene family during mammalian development.


Subject(s)
Gene Expression Regulation, Developmental , Microfilament Proteins/genetics , Zebrafish/embryology , Amino Acid Sequence , Animals , Cloning, Molecular , Embryonic Development , Gene Expression Profiling , Molecular Sequence Data , Phylogeny , Zebrafish/genetics
18.
Mol Cell Biol ; 26(20): 7731-46, 2006 Oct.
Article in English | MEDLINE | ID: mdl-16954389

ABSTRACT

Metazoan genomes contain thousands of replication origins, but only a limited number have been characterized so far. We developed a two-step origin-trapping assay in which human chromatin fragments associated with origin recognition complex (ORC) in vivo were first enriched by chromatin immunoprecipitation. In a second step, these fragments were screened for transient replication competence in a plasmid-based assay utilizing the Epstein-Barr virus latent origin oriP. oriP contains two elements, an origin (dyad symmetry element [DS]) and the family of repeats, that when associated with the viral protein EBNA1 facilitate extrachromosomal stability. Insertion of the ORC-binding human DNA fragments in oriP plasmids in place of DS enabled us to screen functionally for their abilities to restore replication. Using the origin-trapping assay, we isolated and characterized five previously unknown human origins. The assay was validated with nascent strand abundance assays that confirm these origins as active initiation sites in their native chromosomal contexts. Furthermore, ORC and MCM2-7 components localized at these origins during G(1) phase of the cell cycle but were not detected during mitosis. This finding extends the current understanding of origin-ORC dynamics by suggesting that replication origins must be reestablished during the early stages of each cell division cycle and that ORC itself participates in this process.


Subject(s)
DNA Replication/genetics , DNA/analysis , DNA/genetics , Genetic Techniques , Base Sequence , Cell Cycle , Cell Line , Chromosomes, Human/genetics , Epstein-Barr Virus Nuclear Antigens/genetics , Epstein-Barr Virus Nuclear Antigens/metabolism , Humans , Molecular Sequence Data , Origin Recognition Complex/genetics , Plasmids/genetics , Protein Binding , Protein Subunits/genetics , Protein Subunits/metabolism , Replication Origin/genetics
19.
J Cell Sci ; 116(Pt 19): 3971-84, 2003 Oct 01.
Article in English | MEDLINE | ID: mdl-12953058

ABSTRACT

The sequential binding of the origin recognition complex (ORC), Cdc6p and the minichromosome maintenance proteins (MCM2-7) mediates replication competence at eukaryotic origins of DNA replication. The latent origin of Epstein-Barr virus, oriP, is a viral origin known to recruit ORC. OriP also binds EBNA1, a virally encoded protein that lacks any activity predicted to be required for replication initiation. Here, we used chromatin immunoprecipitation and chromatin binding to compare the cell-cycle-dependent binding of pre-RC components and EBNA1 to oriP and to global cellular chromatin. Prereplicative-complex components such as the Mcm2p-Mcm7p proteins and HsOrc1p are regulated in a cell-cycle-dependent fashion, whereas other HsOrc subunits and EBNA1 remain constantly bound. In addition, HsOrc1p becomes sensitive to the 26S proteasome after release from DNA during S phase. These results show that the complex protein-DNA dynamics at the viral oriP are synchronized with the cell division cycle. Chromatin-binding and chromatin-immunoprecipitation experiments on G0 arrested cells indicated that the ORC core complex (ORC2-5) and EBNA1 remain bound to chromatin and oriP. HsOrc6p and the MCM2-7 complex are released in resting cells. HsOrc1p is partly liberated from chromatin. Our data suggest that origins remain marked in resting cells by the ORC core complex to ensure a rapid and regulated reentry into the cell cycle. These findings indicate that HsOrc is a dynamic complex and that its DNA binding activity is regulated differently in the various stages of the cell cycle.


Subject(s)
Chromatin/metabolism , DNA-Binding Proteins/metabolism , Epstein-Barr Virus Nuclear Antigens/metabolism , Herpesvirus 4, Human/physiology , Animals , Cell Cycle , Cells, Cultured , Chromatin/virology , Flow Cytometry , Humans , Origin Recognition Complex , Plasmids , Protein Binding , Resting Phase, Cell Cycle/physiology , S Phase/physiology , Viral Proteins/metabolism , Virus Replication/physiology
20.
J Thorac Cardiovasc Surg ; 125(6): 1481-92, 2003 Jun.
Article in English | MEDLINE | ID: mdl-12830070

ABSTRACT

OBJECTIVE: Inhibition of cyclooxygenase 2 provides analgesia in ambulatory patients. We prospectively evaluated the safety and efficacy of a newly introduced cyclooxygenase 2 inhibitor in patients undergoing coronary artery bypass grafting surgery through a median sternotomy in a randomized clinical trial. METHODS: A total of 462 patients with New York Heart Association classes I to III who were less than 77 years of age and were from 58 institutions in the United States, Canada, Germany, and the United Kingdom participated in this multicenter, phase III, placebo-controlled, double-blind, randomized, parallel-group trial. Patients were allocated at a ratio of 2:1 to parecoxib/valdecoxib or standard care (control) groups, respectively. Intravenous study drug (40 mg) was administered within 30 minutes after extubation and every 12 hours for a minimum of 3 days. Subsequently, oral treatment at a dose of 40 mg every 12 hours was initiated and administered for a combined total of 14 days. Patient-controlled analgesia with morphine, oral opioids, or acetaminophen was available as required. Assessment of the analgesic efficacy of the study drug was primarily based on morphine and morphine equivalent use. Additional efficacy evaluations included daily pain intensity, patient and physician global evaluation of study medication, and pain effect on quality of life. Clinical adverse events were assessed by the principal investigator at each site from the time of the first dose through the 30-day postdosing period. RESULTS: Patients in the parecoxib/valdecoxib group received significantly less morphine or morphine equivalents than patients in the control group during the 0- to 24-hour (P =.009), 24- to 48-hour (P =.017), 72- to 96-hour (P =.002), 96- to 120-hour (P =.004), and 120- to 144-hour (P =.037) periods. Both patients (P <.001) and physicians (P <.001) evaluated the study medication as significantly better than control therapy. The modified Brief Pain Inventory questionnaire used in the oral dosing period detected significant improvements in the parecoxib/valdecoxib treatment group in 6 of 8 domains tested (eg, current pain, worst pain, and mood) beginning on day 4 and continuing for at least 4 days. Although there were no differences between the groups in overall adverse events, serious adverse events occurred twice as frequently in parecoxib/valdecoxib-treated patients (19.0%, 59/311 patients) than in control patients (9.9%, 15/151 patients; P =.015). Regarding individual serious adverse events, a greater incidence in sternal wound infection was found in the parecoxib/valdecoxib patients (10 [3.2%]) versus control patients (0 [0%]) (P =.035). The incidences of other individual serious adverse events, including cerebrovascular complications, myocardial infarction, and renal dysfunction, were proportionally greater but not significantly different between the groups. CONCLUSIONS: In patients undergoing coronary artery bypass grafting surgery, the cyclooxygenase 2 inhibitor combination, parecoxib/valdecoxib, was effective for postoperative analgesia. However, the 14-day treatment regimen also was associated with an increased incidence of serious adverse events overall and sternal wound infections in particular. Therefore our study raises important concerns requiring their comprehensive evaluation in a large-scale trial before these cyclooxygenase 2 inhibitors are used in patients undergoing coronary artery bypass grafting surgery.


Subject(s)
Analgesia/methods , Coronary Artery Bypass , Cyclooxygenase Inhibitors/administration & dosage , Isoenzymes/antagonists & inhibitors , Isoxazoles/administration & dosage , Sulfonamides/administration & dosage , Administration, Oral , Adult , Aged , Analgesia, Patient-Controlled , Cyclooxygenase 2 , Cyclooxygenase 2 Inhibitors , Cyclooxygenase Inhibitors/adverse effects , Double-Blind Method , Drug Therapy, Combination , Female , Humans , Injections, Intravenous , Isoxazoles/adverse effects , Male , Membrane Proteins , Middle Aged , Morphine/administration & dosage , Pain Measurement , Prospective Studies , Prostaglandin-Endoperoxide Synthases , Safety , Sulfonamides/adverse effects
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