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Plöger R, Tsikolia N, Viebahn C. A network of transient domains for breaking symmetry during anterior-posterior axis formation in the porcine embryo. Dev Dyn 2024. [PMID: 39377464 DOI: 10.1002/dvdy.739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 10/09/2024] Open
Abstract
Breaking radial symmetry for anterior-posterior axis formation is one of the key developmental steps of vertebrate gastrulation and is established through a succession of transient domains defined by morphology or gene expression. Three such domains were interpreted recently in the rabbit to be part of a "three-anchor-point model" for axis formation. To answer the question as to whether the model is generally applicable to mammals, the dynamic expression patterns of four marker genes were analyzed in the pig, where gastrulating epiblast forms from half the inner cell mass: EOMES and PKDCC transcripts display decreasing expression intensities in the anterior hypoblast and-together with WNT3-increasing intensity in the anterior streak domain and the node; TBX6 expression changes from an initial central expression to exclusive expression in the posterior extremity of the primitive streak. The anterior streak domain has thus a molecular footprint similar to the one in the rabbit, the end node shares TBX6 between the species, while the anterior hypoblast-mirroring specific porcine epiblast derivation and fate-is marked by PKDCC instead of WNT3. The molecular similarities in transient domains point to conserved mechanisms for establishing the mammalian anterior-posterior axis and, possibly, breaking radial symmetry.
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Affiliation(s)
- Ruben Plöger
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Göttingen, Germany
| | - Nikoloz Tsikolia
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Göttingen, Germany
| | - Christoph Viebahn
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Göttingen, Germany
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2
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Wang J, Yu H, Zhang X, Zhou X, Tan Y, Li Z, Gu Y, Lin L. Prenatal diagnosis of a skeletal disorder characterized by rhizomelic shortening of limbs caused by compound heterozygous variants in the PKDCC gene: Case report and literature review. Mol Genet Genomic Med 2024; 12:e2477. [PMID: 38860479 PMCID: PMC11165336 DOI: 10.1002/mgg3.2477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 04/04/2024] [Accepted: 05/21/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND The protein kinase domain containing cytoplasmic (PKDCC) gene (OMIM#618821) is associated with bone development. Biallelic variants in the PKDCC gene can cause rhizomelic limb shortening with dysmorphic features. CASE REPORT A fetus was found to be rhizomelic limb shortening at 16 weeks of gestation and amniocentesis was performed at 19 weeks of gestation. Genomic DNA extracted from the amniotic fluid was subjected to chromosomal microarray analysis (CMA), and Trio-total whole-exome sequencing (Trio-WES). Sanger sequencing was used to verify the candidate pathogenic variants. CMA was normal, while Trio-WES identified two compound heterozygous variants in the PKDCC gene, namely c.417_c.423delCGGCGCG insTCATGGGCTCAGTACAC(p.G140fs*35) and c.345G>A (p.W115*,379). Then the fetus was aborted and the development of its bone cells were compared with that of a normal fetus of similar gestational age by histopathological examination. Clinical findings of the fetus were shortening humerus and femur, synophrys, much hair on the side face, simian line on the right palm, etc. Histopathological examination showed that the affected fetus had increased proliferative chondrocytes, widened proliferative bands, and delayed bone mineralization. CONCLUSIONS We reported a prenatal case of rhizomelic shortening of limbs caused by compound heterozygous variants in the PKDCC gene, which emphasized the important role of Trio-WES for diagnosis of skeletal dysplasia in fetuses.
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Affiliation(s)
- Jing Wang
- Department of Obstetrics and GynecologyPeking University International HospitalBeijingChina
| | - Huijun Yu
- Department of Obstetrics and GynecologyPeking University International HospitalBeijingChina
| | - Xiaoying Zhang
- Department of PathologyPeking University International HospitalBeijingChina
| | - Xiuyun Zhou
- Department of Obstetrics and GynecologyPeking University International HospitalBeijingChina
| | - Ya Tan
- Department of Obstetrics and GynecologyPeking University International HospitalBeijingChina
| | - Zhi Li
- Department of Obstetrics and GynecologyPeking University International HospitalBeijingChina
| | - Ying Gu
- Department of Obstetrics and GynecologyPeking University International HospitalBeijingChina
| | - Li Lin
- Department of Obstetrics and GynecologyPeking University International HospitalBeijingChina
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3
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Srikanth KD, Elahi H, Chander P, Washburn HR, Hassler S, Mwirigi JM, Kume M, Loucks J, Arjarapu R, Hodge R, Shiers SI, Sankaranarayanan I, Erdjument-Bromage H, Neubert TA, Campbell ZT, Paik R, Price TJ, Dalva MB. VLK drives extracellular phosphorylation of EphB2 to govern the EphB2-NMDAR interaction and injury-induced pain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585314. [PMID: 38562765 PMCID: PMC10983893 DOI: 10.1101/2024.03.18.585314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Phosphorylation of hundreds of protein extracellular domains is mediated by two kinase families, yet the significance of these kinases is underexplored. Here, we find that the presynaptic release of the tyrosine directed-ectokinase, Vertebrate Lonesome Kinase (VLK/Pkdcc), is necessary and sufficient for the direct extracellular interaction between EphB2 and GluN1 at synapses, for phosphorylation of the ectodomain of EphB2, and for injury-induced pain. Pkdcc is an essential gene in the nervous system, and VLK is found in synaptic vesicles, and is released from neurons in a SNARE-dependent fashion. VLK is expressed by nociceptive sensory neurons where presynaptic sensory neuron-specific knockout renders mice impervious to post-surgical pain, without changing proprioception. VLK defines an extracellular mechanism that regulates protein-protein interaction and non-opioid-dependent pain in response to injury.
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Affiliation(s)
- Kolluru D. Srikanth
- Tulane Brain Institute, Department of Cell and Molecular Biology, Tulane University; New Orleans, LA 70118, USA
- Jefferson Synaptic Biology Center, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
| | - Hajira Elahi
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Praveen Chander
- Tulane Brain Institute, Department of Cell and Molecular Biology, Tulane University; New Orleans, LA 70118, USA
- Jefferson Synaptic Biology Center, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
| | - Halley R. Washburn
- Jefferson Synaptic Biology Center, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
- Department of Molecular Biology, Princeton University; Princeton, NJ 08544, USA
| | - Shayne Hassler
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- College of Medicine, University of Houston; Houston, TX 77004, USA
| | - Juliet M. Mwirigi
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Moeno Kume
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Jessica Loucks
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
| | - Rohita Arjarapu
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
| | - Rachel Hodge
- Jefferson Synaptic Biology Center, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
| | - Stephanie I. Shiers
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Ishwarya Sankaranarayanan
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Hediye Erdjument-Bromage
- Department of Neuroscience and Physiology and Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Thomas A. Neubert
- Department of Neuroscience and Physiology and Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Zachary T. Campbell
- Department of Anesthesiology, University of Wisconsin-Madison; Madison, WI 53792, USA
| | - Raehum Paik
- Department of Anesthesiology, University of Wisconsin-Madison; Madison, WI 53792, USA
- Department of Genetics, University of Texas Health Science Center at San Antonio; San Antonio, TX 78229, USA
| | - Theodore J. Price
- Department of Neuroscience, The University of Texas at Dallas; Richardson, TX 75080, USA
- Center for Advanced Pain Studies, University of Texas at Dallas; Richardson, TX 75080, USA
| | - Matthew B. Dalva
- Tulane Brain Institute, Department of Cell and Molecular Biology, Tulane University; New Orleans, LA 70118, USA
- Jefferson Synaptic Biology Center, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107
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4
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Mohammed J, Arora N, Matthews HS, Hansen K, Bader M, Walsh S, Shaffer JR, Weinberg SM, Swigut T, Claes P, Selleri L, Wysocka J. A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis. eLife 2024; 13:e82564. [PMID: 38483448 PMCID: PMC10939500 DOI: 10.7554/elife.82564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/18/2024] [Indexed: 03/17/2024] Open
Abstract
Genome-wide association studies (GWAS) identified thousands of genetic variants linked to phenotypic traits and disease risk. However, mechanistic understanding of how GWAS variants influence complex morphological traits and can, in certain cases, simultaneously confer normal-range phenotypic variation and disease predisposition, is still largely lacking. Here, we focus on rs6740960, a single nucleotide polymorphism (SNP) at the 2p21 locus, which in GWAS studies has been associated both with normal-range variation in jaw shape and with an increased risk of non-syndromic orofacial clefting. Using in vitro derived embryonic cell types relevant for human facial morphogenesis, we show that this SNP resides in an enhancer that regulates chondrocytic expression of PKDCC - a gene encoding a tyrosine kinase involved in chondrogenesis and skeletal development. In agreement, we demonstrate that the rs6740960 SNP is sufficient to confer chondrocyte-specific differences in PKDCC expression. By deploying dense landmark morphometric analysis of skull elements in mice, we show that changes in Pkdcc dosage are associated with quantitative changes in the maxilla, mandible, and palatine bone shape that are concordant with the facial phenotypes and disease predisposition seen in humans. We further demonstrate that the frequency of the rs6740960 variant strongly deviated among different human populations, and that the activity of its cognate enhancer diverged in hominids. Our study provides a mechanistic explanation of how a common SNP can mediate normal-range and disease-associated morphological variation, with implications for the evolution of human facial features.
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Affiliation(s)
- Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Neha Arora
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Harold S Matthews
- Department of Human Genetics, KU LeuvenLeuvenBelgium
- Medical Imaging Research Center, University Hospitals LeuvenLeuvenBelgium
| | - Karissa Hansen
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Susan Walsh
- Department of Biology, Indiana University IndianapolisIndianapolisUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of PittsburghPittsburghUnited States
- Department of Human Genetics, University of PittsburghPittsburghUnited States
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of PittsburghPittsburghUnited States
- Department of Human Genetics, University of PittsburghPittsburghUnited States
- Department of Anthropology, University of PittsburghPittsburghUnited States
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Peter Claes
- Department of Human Genetics, KU LeuvenLeuvenBelgium
- Medical Imaging Research Center, University Hospitals LeuvenLeuvenBelgium
- Department of Electrical Engineering, ESAT/PSI, KU LeuvenLeuvenBelgium
- Murdoch Children’s Research InstituteMelbourneAustralia
| | - Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
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5
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Luján-Amoraga L, Delgado-Martín B, Lourenço-Marques C, Gavaia PJ, Bravo J, Bandarra NM, Dominguez D, Izquierdo MS, Pousão-Ferreira P, Ribeiro L. Exploring Omega-3's Impact on the Expression of Bone-Related Genes in Meagre ( Argyrosomus regius). Biomolecules 2023; 14:56. [PMID: 38254657 PMCID: PMC10813611 DOI: 10.3390/biom14010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Dietary supplementation with Omega-3 fatty acids seems to promote skeletal health. Therefore, their consumption at imbalanced or excessive levels has offered less beneficial or even prejudicial effects. Fish produced in aquaculture regimes are prone to develop abnormal skeletons. Although larval cultures are usually fed with diets supplemented with Omega-3 Long Chain Polyunsaturated fatty acids (LC-PUFAs), the lack of knowledge about the optimal requirements for fatty acids or about their impact on mechanisms that regulate skeletal development has impeded the design of diets that could improve bone formation during larval stages when the majority of skeletal anomalies appear. In this study, Argyrosomus regius larvae were fed different levels of Omega-3s (2.6% and 3.6% DW on diet) compared to a commercial diet. At 28 days after hatching (DAH), their transcriptomes were analyzed to study the modulation exerted in gene expression dynamics during larval development and identify impacted genes that can contribute to skeletal formation. Mainly, both levels of supplementation modulated bone-cell proliferation, the synthesis of bone components such as the extracellular matrix, and molecules involved in the interaction and signaling between bone components or in important cellular processes. The 2.6% level impacted several genes related to cartilage development, denoting a special impact on endochondral ossification, delaying this process. However, the 3.6% level seemed to accelerate this process by enhancing skeletal development. These results offered important insights into the impact of dietary Omega-3 LC-PUFAs on genes involved in the main molecular mechanism and cellular processes involved in skeletal development.
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Affiliation(s)
- Leticia Luján-Amoraga
- Aquaculture Research Station (EPPO), Portuguese Institute for the Ocean and Atmosphere (IPMA), 8700-194 Olhão, Portugal; (L.L.-A.); (C.L.-M.); (P.P.-F.)
| | - Belén Delgado-Martín
- Department of Microbiology and Crop Protection, Institute of Subtropical and Mediterranean Horticulture (IHSM-UMA-CSIC), 29010 Malaga, Spain;
| | - Cátia Lourenço-Marques
- Aquaculture Research Station (EPPO), Portuguese Institute for the Ocean and Atmosphere (IPMA), 8700-194 Olhão, Portugal; (L.L.-A.); (C.L.-M.); (P.P.-F.)
- Collaborative Laboratory on Sustainable and Smart Aquaculture (S2AQUACOLAB) Av. Parque Natural da Ria Formosa s/n, 8700-194 Olhão, Portugal
| | - Paulo J. Gavaia
- Centre of Marine Sciences (CCMAR), University of Algarve (UALG), 8005-139 Faro, Portugal;
| | - Jimena Bravo
- Aquaculture Research Group (GIA), University of Las Palmas de Gran Canaria (ULPGC) Crta. Taliarte s/n, 35214 Telde, Spain; (J.B.); (D.D.); (M.S.I.)
| | - Narcisa M. Bandarra
- Division of Aquaculture, Upgrading, and Bioprospection (DivAV), Portuguese Institute for the Sea and Atmosphere (IPMA, IP), Rua Alfredo Magalhães Ramalho, 7, 1495-006 Lisbon, Portugal;
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - David Dominguez
- Aquaculture Research Group (GIA), University of Las Palmas de Gran Canaria (ULPGC) Crta. Taliarte s/n, 35214 Telde, Spain; (J.B.); (D.D.); (M.S.I.)
| | - Marisol S. Izquierdo
- Aquaculture Research Group (GIA), University of Las Palmas de Gran Canaria (ULPGC) Crta. Taliarte s/n, 35214 Telde, Spain; (J.B.); (D.D.); (M.S.I.)
| | - Pedro Pousão-Ferreira
- Aquaculture Research Station (EPPO), Portuguese Institute for the Ocean and Atmosphere (IPMA), 8700-194 Olhão, Portugal; (L.L.-A.); (C.L.-M.); (P.P.-F.)
- Collaborative Laboratory on Sustainable and Smart Aquaculture (S2AQUACOLAB) Av. Parque Natural da Ria Formosa s/n, 8700-194 Olhão, Portugal
| | - Laura Ribeiro
- Aquaculture Research Station (EPPO), Portuguese Institute for the Ocean and Atmosphere (IPMA), 8700-194 Olhão, Portugal; (L.L.-A.); (C.L.-M.); (P.P.-F.)
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6
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Konstantinidis I, Sætrom P, Brieuc S, Jakobsen KS, Liedtke H, Pohlmann C, Tsoulia T, Fernandes JMO. DNA hydroxymethylation differences underlie phenotypic divergence of somatic growth in Nile tilapia reared in common garden. Epigenetics 2023; 18:2282323. [PMID: 38010265 PMCID: PMC10732659 DOI: 10.1080/15592294.2023.2282323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the underlying mechanisms are poorly understood, especially in the case of hydroxymethylation. Using reduced representation 5-hydroxymethylcytosine profiling, we compared the liver hydroxymethylomes in full-sib Nile tilapia with distinct growth rates (3.8-fold difference) and demonstrated that DNA hydroxymethylation is strongly associated with phenotypic divergence of somatic growth during the early stages of domestication. The 2677 differentially hydroxymethylated cytosines between fast- and slow-growing fish were enriched within gene bodies (79%), indicating a pertinent role in transcriptional regulation. Moreover, they were found in genes involved in biological processes related to skeletal system and muscle structure development, and there was a positive association between somatic growth and 5hmC levels in genes coding for growth factors, kinases and receptors linked to myogenesis. Single nucleotide polymorphism analysis revealed no genetic differentiation between fast- and slow-growing fish. In addition to unveiling a new link between DNA hydroxymethylation and epigenetic regulation of growth in fish during the initial stages of domestication, this study suggests that epimarkers may be applied in selective breeding programmes for superior phenotypes.
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Affiliation(s)
| | - Pål Sætrom
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
- Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - S.O. Brieuc
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S. Jakobsen
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Hannes Liedtke
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Caroline Pohlmann
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Thomais Tsoulia
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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7
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Yan L, Cao J, Zhang Y, Liu Y, Zou J, Lou B, Zhuang D, Li H. Prenatal diagnosis to identify compound heterozygous variants in PKDCC that causes rhizomelic limb shortening with dysmorphic features in a fetus from China. BMC Med Genomics 2023; 16:190. [PMID: 37592254 PMCID: PMC10433562 DOI: 10.1186/s12920-023-01631-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/11/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Rhizomelic limb shortening with dysmorphic features (RLSDF) has already been a disorder of the rare autosomal recessive skeletal dysplasia, just having a few reported cases. RLSDF is caused by protein kinase domain containing, cytoplasmic(PKDCC)gene variants. In this study, we describe the clinical features and potential RLSDF molecular etiology in a fetus from China. METHODS Genomic DNA (gDNA) extracted from the fetal muscle tissue and parents' peripheral blood was subjected to chromosomal microarray analysis (CMA) and trio-based whole exome sequencing (Trio-WES). The candidate pathogenic variants were verified by using Sanger sequencing. RESULTS Trio-WES identified two compound heterozygous variants in PKDCC, c.346delC (p.Pro117Argfs*113) and c.994G > T (p.Glu332Ter), inherited from the father and mother, respectively. Both variants are classified as pathogenic according to American College of Medical Genetics and Genomics guidelines. CONCLUSIONS We reported the first prenatal case of RLSDF caused by PKDCC in the Chinese population. Our findings extended the variation spectrum of PKDCC and emphasized the necessity of WES for the early diagnosis of skeletal dysplasia and other ultrasound structural abnormalities in fetuses.
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Affiliation(s)
- Lulu Yan
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Juan Cao
- Department of Obstetrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Yuxin Zhang
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Yingwen Liu
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Jinghui Zou
- Department of Obstetrics, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, 315000, China
| | - Biying Lou
- Ningbo University School of Medicine, Ningbo, Zhejiang, 315000, China
| | - Danyan Zhuang
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Haibo Li
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China.
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8
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Pagnamenta AT, Belles RS, Salbert BA, Wentzensen IM, Guillen Sacoto MJ, Santos FJR, Caffo A, Ferla M, Banos‐Pinero B, Pawliczak K, Makvand M, Najmabadi H, Maroofian R, Lester T, Yanez‐Felix AL, Villarroel‐Cortes CE, Xia F, Al Fayez K, Al Hashem A, Shears D, Irving M, Offiah AC, Kariminejad A, Taylor JC. The prevalence and phenotypic range associated with biallelic PKDCC variants. Clin Genet 2023; 104:121-126. [PMID: 36896672 PMCID: PMC10952701 DOI: 10.1111/cge.14324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/08/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023]
Abstract
PKDCC encodes a component of Hedgehog signalling required for normal chondrogenesis and skeletal development. Although biallelic PKDCC variants have been implicated in rhizomelic shortening of limbs with variable dysmorphic features, this association was based on just two patients. In this study, data from the 100 000 Genomes Project was used in conjunction with exome sequencing and panel-testing results accessed via international collaboration to assemble a cohort of eight individuals from seven independent families with biallelic PKDCC variants. The allelic series included six frameshifts, a previously described splice-donor site variant and a likely pathogenic missense variant observed in two families that was supported by in silico structural modelling. Database queries suggested that the prevalence of this condition is between 1 of 127 and 1 of 721 in clinical cohorts with skeletal dysplasia of unknown aetiology. Clinical assessments, combined with data from previously published cases, indicate a predominantly upper limb involvement. Micrognathia, hypertelorism and hearing loss appear to be commonly co-occurring features. In conclusion, this study strengthens the link between biallelic inactivation of PKDCC and rhizomelic limb-shortening and will enable clinical testing laboratories to better interpret variants in this gene.
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Affiliation(s)
- Alistair T. Pagnamenta
- NIHR Biomedical Research Centre, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | | | | | | | | | - Francis Jeshira Reynoso Santos
- Joe DiMaggio Children's HospitalHollywoodFloridaUSA
- Division of Human GeneticsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Alesky Caffo
- Joe DiMaggio Children's HospitalHollywoodFloridaUSA
| | - Matteo Ferla
- NIHR Biomedical Research Centre, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Benito Banos‐Pinero
- Oxford Genetics LaboratoriesOxford University Hospitals NHS Foundation Trust, The Churchill HospitalOxfordUK
| | | | - Mina Makvand
- Kariminejad‐Najmabadi Pathology & Genetics CenterTehranIran
| | - Hossein Najmabadi
- Kariminejad‐Najmabadi Pathology & Genetics CenterTehranIran
- Genetics Research CenterUniversity of Social Welfare & Rehabilitation ScienceTehranIran
| | | | - Reza Maroofian
- Department of Neuromuscular DiseasesUCL Queen Square Institute of Neurology, University College LondonLondonUK
| | - Tracy Lester
- Oxford Genetics LaboratoriesOxford University Hospitals NHS Foundation Trust, The Churchill HospitalOxfordUK
| | | | | | - Fan Xia
- Baylor GeneticsHoustonTexasUSA
| | - Khowla Al Fayez
- Department of Pediatrics, Division of Clinical Genetic and Metabolic MedicinePrince Sultan Medical Military CityRiyadhSaudi Arabia
| | - Amal Al Hashem
- Department of Pediatrics, Division of Clinical Genetic and Metabolic MedicinePrince Sultan Medical Military CityRiyadhSaudi Arabia
| | - Deborah Shears
- Oxford Centre for Genomic MedicineOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Melita Irving
- Department of Clinical GeneticsGuy's and St Thomas' NHS Foundation TrustLondonUK
| | - Amaka C. Offiah
- Department of Oncology & MetabolismUniversity of SheffieldSheffieldUK
| | | | - Jenny C. Taylor
- NIHR Biomedical Research Centre, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
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9
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Brütsch SM, Madzharova E, Pantasis S, Wüstemann T, Gurri S, Steenbock H, Gazdhar A, Kuhn G, Angel P, Bellusci S, Brinckmann J, Auf dem Keller U, Werner S, Bordoli MR. Mesenchyme-derived vertebrate lonesome kinase controls lung organogenesis by altering the matrisome. Cell Mol Life Sci 2023; 80:89. [PMID: 36920550 PMCID: PMC10017657 DOI: 10.1007/s00018-023-04735-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/29/2023] [Accepted: 02/21/2023] [Indexed: 03/16/2023]
Abstract
Vertebrate lonesome kinase (VLK) is the only known secreted tyrosine kinase and responsible for the phosphorylation of a broad range of secretory pathway-resident and extracellular matrix proteins. However, its cell-type specific functions in vivo are still largely unknown. Therefore, we generated mice lacking the VLK gene (protein kinase domain containing, cytoplasmic (Pkdcc)) in mesenchymal cells. Most of the homozygous mice died shortly after birth, most likely as a consequence of their lung abnormalities and consequent respiratory failure. E18.5 embryonic lungs showed a reduction of alveolar type II cells, smaller bronchi, and an increased lung tissue density. Global mass spectrometry-based quantitative proteomics identified 97 proteins with significantly and at least 1.5-fold differential abundance between genotypes. Twenty-five of these had been assigned to the extracellular region and 15 to the mouse matrisome. Specifically, fibromodulin and matrilin-4, which are involved in extracellular matrix organization, were significantly more abundant in lungs from Pkdcc knockout embryos. These results support a role for mesenchyme-derived VLK in lung development through regulation of matrix dynamics and the resulting modulation of alveolar epithelial cell differentiation.
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Affiliation(s)
- Salome M Brütsch
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093, Zurich, Switzerland
| | - Elizabeta Madzharova
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), 2800, Kongens Lyngby, Denmark
| | - Sophia Pantasis
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093, Zurich, Switzerland
| | - Till Wüstemann
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093, Zurich, Switzerland
| | - Selina Gurri
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093, Zurich, Switzerland
| | - Heiko Steenbock
- Institute of Virology and Cell Biology, University of Lübeck, 23562, Lübeck, Germany
| | - Amiq Gazdhar
- Department of Pulmonary Medicine, University Hospital Bern, 3010, Bern, Switzerland.,Department of Biomedical Research, University of Bern, 3010, Bern, Switzerland
| | - Gisela Kuhn
- Department of Health Sciences and Technology, Institute of Biomechanics, ETH Zurich, 8093, Zurich, Switzerland
| | - Peter Angel
- Division of Signal Transduction and Growth Control, DKFZ/ZMBH Alliance, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Saverio Bellusci
- German Lung Research Center (DCL), Giessen, Germany.,Department of Internal Medicine II, Universities of Giessen and Marburg Lung Center (UGMLC), Cardio-Pulmonary Institute (CPI), Aulweg 130, 35392, Giessen, Germany
| | - Jürgen Brinckmann
- Institute of Virology and Cell Biology, University of Lübeck, 23562, Lübeck, Germany.,Department of Dermatology, University of Lübeck, 23562, Lübeck, Germany
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), 2800, Kongens Lyngby, Denmark.
| | - Sabine Werner
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093, Zurich, Switzerland.
| | - Mattia R Bordoli
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093, Zurich, Switzerland.
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10
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Gao M, Liu X, Guo P, Wang J, Li J, Wang W, Stoddart MJ, Grad S, Li Z, Wu H, Li B, He Z, Zhou G, Liu S, Zhu W, Chen D, Zou X, Zhou Z. Deciphering postnatal limb development at single-cell resolution. iScience 2023; 26:105808. [PMID: 36619982 PMCID: PMC9813795 DOI: 10.1016/j.isci.2022.105808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 08/22/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
The early postnatal limb developmental progression bridges embryonic and mature stages and mirrors the pathological remodeling of articular cartilage. However, compared with multitudinous research on embryonic limb development, the early postnatal stage seems relatively unnoticed. Here, a systematic work to portray the postnatal limb developmental landscape was carried out by characterization of 19,952 single cells from murine hindlimbs at 4 postnatal stages using single-cell RNA sequencing technique. By delineation of cell heterogeneity, the candidate progenitor sub-clusters marked by Cd34 and Ly6e were discovered in articular cartilage and enthesis, and three cellular developmental branches marked by Col10a1, Spp1, and Tnni2 were reflected in growth plate. The representative transcriptomes and developmental patterns were intensively explored, and the key regulation mechanisms as well as evolvement in osteoarthritis were discussed. Above all, these results expand horizons of postnatal limb developmental biology and reach the interconnections between limb development, remodeling, and regeneration.
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Affiliation(s)
- Manman Gao
- Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
- Department of Sport Medicine, Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen 518035, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
- Shenzhen Key Laboratory of Anti-aging and Regenerative Medicine, Department of Medical Cell Biology and Genetics, Health Sciences Center, Shenzhen University, Shenzhen 518071, China
| | - Xizhe Liu
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Peng Guo
- Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Jianmin Wang
- Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Junhong Li
- Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Wentao Wang
- Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | | | - Sibylle Grad
- AO Research Institute Davos, Davos 7270, Switzerland
| | - Zhen Li
- AO Research Institute Davos, Davos 7270, Switzerland
| | - Huachuan Wu
- Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Baoliang Li
- Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Zhongyuan He
- Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Guangqian Zhou
- Shenzhen Key Laboratory of Anti-aging and Regenerative Medicine, Department of Medical Cell Biology and Genetics, Health Sciences Center, Shenzhen University, Shenzhen 518071, China
| | - Shaoyu Liu
- Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Weimin Zhu
- Department of Sport Medicine, Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen 518035, China
- Shenzhen Key Laboratory of Anti-aging and Regenerative Medicine, Department of Medical Cell Biology and Genetics, Health Sciences Center, Shenzhen University, Shenzhen 518071, China
| | - Dafu Chen
- Laboratory of Bone Tissue Engineering, Beijing Laboratory of Biomedical Materials, Beijing Research Institute of Orthopaedics and Traumatology, Beijing JiShuiTan Hospital, Beijing 100035, China
| | - Xuenong Zou
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Zhiyu Zhou
- Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
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11
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Zieger HK, Weinhold L, Schmidt A, Holtgrewe M, Juranek SA, Siewert A, Scheer AB, Thieme F, Mangold E, Ishorst N, Brand FU, Welzenbach J, Beule D, Paeschke K, Krawitz PM, Ludwig KU. Prioritization of non-coding elements involved in non-syndromic cleft lip with/without cleft palate through genome-wide analysis of de novo mutations. HGG ADVANCES 2023; 4:100166. [PMID: 36589413 PMCID: PMC9795529 DOI: 10.1016/j.xhgg.2022.100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Non-syndromic cleft lip with/without cleft palate (nsCL/P) is a highly heritable facial disorder. To date, systematic investigations of the contribution of rare variants in non-coding regions to nsCL/P etiology are sparse. Here, we re-analyzed available whole-genome sequence (WGS) data from 211 European case-parent trios with nsCL/P and identified 13,522 de novo mutations (DNMs) in nsCL/P cases, 13,055 of which mapped to non-coding regions. We integrated these data with DNMs from a reference cohort, with results of previous genome-wide association studies (GWASs), and functional and epigenetic datasets of relevance to embryonic facial development. A significant enrichment of nsCL/P DNMs was observed at two GWAS risk loci (4q28.1 (p = 8 × 10-4) and 2p21 (p = 0.02)), suggesting a convergence of both common and rare variants at these loci. We also mapped the DNMs to 810 position weight matrices indicative of transcription factor (TF) binding, and quantified the effect of the allelic changes in silico. This revealed a nominally significant overrepresentation of DNMs (p = 0.037), and a stronger effect on binding strength, for DNMs located in the sequence of the core binding region of the TF Musculin (MSC). Notably, MSC is involved in facial muscle development, together with a set of nsCL/P genes located at GWAS loci. Supported by additional results from single-cell transcriptomic data and molecular binding assays, this suggests that variation in MSC binding sites contributes to nsCL/P etiology. Our study describes a set of approaches that can be applied to increase the added value of WGS data.
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Affiliation(s)
- Hanna K. Zieger
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Leonie Weinhold
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn 53127, Germany
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
| | - Stefan A. Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn 53127, Germany
| | - Anna Siewert
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Annika B. Scheer
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Fabian U. Brand
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn 53127, Germany
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn 53127, Germany
| | - Peter M. Krawitz
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn 53127, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
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12
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Bai J, Shi J, Zhang Y, Li C, Xiong Y, Koka H, Wang D, Zhang T, Song L, Luo W, Zhu B, Hicks B, Hutchinson A, Kirk E, Troester MA, Li M, Shen Y, Ma T, Wang J, Liu X, Wang S, Gui S, McMaster ML, Chanock SJ, Parry DM, Goldstein AM, Yang XR. Gene Expression Profiling Identifies Two Chordoma Subtypes Associated with Distinct Molecular Mechanisms and Clinical Outcomes. Clin Cancer Res 2023; 29:261-270. [PMID: 36260525 PMCID: PMC11293090 DOI: 10.1158/1078-0432.ccr-22-1865] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/30/2022] [Accepted: 10/17/2022] [Indexed: 02/07/2023]
Abstract
PURPOSE Chordoma is a rare bone tumor with a high recurrence rate and limited treatment options. The aim of this study was to identify molecular subtypes of chordoma that may improve clinical management. EXPERIMENTAL DESIGN We conducted RNA sequencing in 48 tumors from patients with Chinese skull-base chordoma and identified two major molecular subtypes. We then replicated the classification using a NanoString panel in 48 patients with chordoma from North America. RESULTS Tumors in one subtype were more likely to have somatic mutations and reduced expression in chromatin remodeling genes, such as PBRM1 and SETD2, whereas the other subtype was characterized by the upregulation of genes in epithelial-mesenchymal transition and Sonic Hedgehog pathways. IHC staining of top differentially expressed genes between the two subtypes in 312 patients with Chinese chordoma with long-term follow-up data showed that the expression of some markers such as PTCH1 was significantly associated with survival outcomes. CONCLUSIONS Our findings may improve the understanding of subtype-specific tumorigenesis of chordoma and inform clinical prognostication and targeted options.
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Affiliation(s)
- Jiwei Bai
- Beijing Neurosurgery Institute, Capital Medical University, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Yazhuo Zhang
- Beijing Neurosurgery Institute, Capital Medical University, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China
| | - Chuzhong Li
- Beijing Neurosurgery Institute, Capital Medical University, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China
| | - Yujia Xiong
- Beijing Neurosurgery Institute, Capital Medical University, Beijing, 100070, China
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Wen Luo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Erin Kirk
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Melissa A. Troester
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Mingxuan Li
- Beijing Neurosurgery Institute, Capital Medical University, Beijing, 100070, China
| | - Yutao Shen
- Beijing Neurosurgery Institute, Capital Medical University, Beijing, 100070, China
| | - Tianshun Ma
- Beijing Neurosurgery Institute, Capital Medical University, Beijing, 100070, China
| | - Junmei Wang
- Beijing Neurosurgery Institute, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China
| | - Xing Liu
- Beijing Neurosurgery Institute, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China
| | - Shuai Wang
- Beijing Neurosurgery Institute, Capital Medical University, Beijing, 100070, China
| | - Songbai Gui
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Mary L. McMaster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Dilys M. Parry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
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13
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Du S, Zhu C, Ren X, Chen X, Cui X, Guan S. Regulation of secretory pathway kinase or kinase-like proteins in human cancers. Front Immunol 2023; 14:942849. [PMID: 36825005 PMCID: PMC9941534 DOI: 10.3389/fimmu.2023.942849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Secretory pathway kinase or kinase-like proteins (SPKKPs) are effective in the lumen of the endoplasmic reticulum (ER), Golgi apparatus (GA), and extracellular space. These proteins are involved in secretory signaling pathways and are distinctive from typical protein kinases. Various reports have shown that SPKKPs regulate the tumorigenesis and progression of human cancer via the phosphorylation of various substrates, which is essential in physiological and pathological processes. Emerging evidence has revealed that the expression of SPKKPs in human cancers is regulated by multiple factors. This review summarizes the current understanding of the contribution of SPKKPs in tumorigenesis and the progression of immunity. With the epidemic trend of immunotherapy, targeting SPKKPs may be a novel approach to anticancer therapy. This study briefly discusses the recent advances regarding SPKKPs.
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Affiliation(s)
- Shaonan Du
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chen Zhu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Xiaolin Ren
- Department of Neurosurgery, Shenyang Red Cross Hospital, Shenyang, China
| | - Xin Chen
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiao Cui
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Shu Guan
- Department of Surgical Oncology and Breast Surgery, The First Hospital of China Medical University, Shenyang, China
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14
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Maridas DE, Gamer L, Moore ER, Doedens AM, Yu Y, Ionescu A, Revollo L, Whitman M, Rosen V. Loss of Vlk in Prx1 + Cells Delays the Initial Steps of Endochondral Bone Formation and Fracture Repair in the Limb. J Bone Miner Res 2022; 37:764-775. [PMID: 35080046 DOI: 10.1002/jbmr.4514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/29/2021] [Accepted: 01/21/2022] [Indexed: 11/10/2022]
Abstract
Vertebrate lonesome kinase (Vlk) is a secreted tyrosine kinase important for normal skeletogenesis during embryonic development. Vlk null mice (Vlk-/- ) are born with severe craniofacial and limb skeletal defects and die shortly after birth. We used a conditional deletion model to remove Vlk in limb bud mesenchyme (Vlk-Prx1 cKO) to assess the specific requirement for Vlk expression by skeletal progenitor cells during endochondral ossification, and an inducible global deletion model (Vlk-Ubq iKO) to address the role of Vlk during fracture repair. Deletion of Vlk with Prx1-Cre recapitulated the limb skeletal phenotype of the Vlk-/- mice and enabled us to study the postnatal skeleton as Vlk-Prx1 cKO mice survived to adulthood. In Vlk-Prx1 cKO adult mice, limbs remained shorter with decreased trabecular and cortical bone volumes. Both Vlk-Prx1 cKO and Vlk-Ubq iKO mice had a delayed fracture repair response but eventually formed bridging calluses. Furthermore, levels of phosphorylated osteopontin (OPN) were decreased in tibias of Vlk-Ubq iKO, establishing OPN as a Vlk substrate in bone. In summary, our data indicate that Vlk produced by skeletal progenitor cells influences the timing and extent of chondrogenesis during endochondral bone formation and fracture repair. © 2022 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- David E Maridas
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Laura Gamer
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Emily R Moore
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Annemiek M Doedens
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Yunqing Yu
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | | | - Leila Revollo
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Vicki Rosen
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
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15
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Pantasis S, Friemel J, Brütsch SM, Hu Z, Krautbauer S, Liebisch G, Dengjel J, Weber A, Werner S, Bordoli MR. Vertebrate lonesome kinase modulates the hepatocyte secretome to prevent perivascular liver fibrosis and inflammation. J Cell Sci 2022; 135:275016. [PMID: 35293576 PMCID: PMC9016620 DOI: 10.1242/jcs.259243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/08/2022] [Indexed: 11/20/2022] Open
Abstract
Vertebrate lonesome kinase (VLK) is the only known extracellular tyrosine kinase, but its physiological functions are largely unknown. We show that VLK is highly expressed in hepatocytes of neonatal mice, but downregulated during adulthood. To determine the role of VLK in liver homeostasis and regeneration, we generated mice with a hepatocyte-specific knockout of the VLK gene (Pkdcc). Cultured progenitor cells established from primary hepatocytes of Pkdcc knockout mice produced a secretome, which promoted their own proliferation in 3D spheroids and proliferation of cultured fibroblasts. In vivo, Pkdcc knockout mice developed liver steatosis with signs of inflammation and perivascular fibrosis upon aging, combined with expansion of liver progenitor cells. In response to chronic CCl4-induced liver injury, the pattern of deposited collagen was significantly altered in these mice. The liver injury marker alpha-fetoprotein (AFP) was increased in the secretome of VLK-deficient cultured progenitor cells and in liver tissues of aged or CCl4-treated knockout mice. These results support a key role for VLK and extracellular protein phosphorylation in liver homeostasis and repair through paracrine control of liver cell function and regulation of appropriate collagen deposition. This article has an associated First Person interview with the first author of the paper. Summary: The secreted protein kinase VLK is released from hepatocytes and protects the liver from perivascular fibrosis and inflammation.
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Affiliation(s)
- Sophia Pantasis
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology ETH, Otto-Stern Weg 7, CH-8093, Zurich, Switzerland
| | - Juliane Friemel
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Salome Mirjam Brütsch
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology ETH, Otto-Stern Weg 7, CH-8093, Zurich, Switzerland
| | - Zehan Hu
- Department of Biology, Université de Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Sabrina Krautbauer
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany
| | - Joern Dengjel
- Department of Biology, Université de Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Sabine Werner
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology ETH, Otto-Stern Weg 7, CH-8093, Zurich, Switzerland
| | - Mattia Renato Bordoli
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology ETH, Otto-Stern Weg 7, CH-8093, Zurich, Switzerland
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16
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Dubey A, Saint-Jeannet JP. Anterior patterning genes induced by Zic1 are sensitive to retinoic acid and its metabolite, 4-oxo-RA. Dev Dyn 2022; 251:498-512. [PMID: 34536327 PMCID: PMC8891028 DOI: 10.1002/dvdy.420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Development of paired sensory organs is a highly complex and coordinated process. These organs arise from ectodermal thickenings in the cephalic region known as cranial placodes. We have previously shown that Zic1 is a critical regulator for the formation of the pre-placodal region (PPR), the common territory for the development of all cranial placodes in Xenopus laevis. RESULTS In this study, we have analyzed a number of Zic1 targets for their expression during PPR patterning, as well as their regulation by retinoic acid (RA) and one of its major metabolites, 4-oxo-RA. Our findings show that anteriorly Zic1 regulates several transcription factors, Crx, Fezf2, Nkx3-1, and Xanf1 as well as a serine/threonine/tyrosine kinase, Pkdcc.2. These factors are all expressed in the vicinity of the PPR and as such are candidate regulators of placode formation downstream of Zic1. In addition to their differential regulation by RA, we find that 4-oxo-RA is also capable of modulating the expression of these genes, as well as a broad array of RA-regulated genes. CONCLUSION Our data highlight the complexity of retinoid-mediated regulation required for Zic1-activated anterior structure specification in Xenopus, and the potential physiological role of 4-oxo-RA in cranial placode development.
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Affiliation(s)
| | - Jean-Pierre Saint-Jeannet
- Correspondence: Jean-Pierre Saint-Jeannet, Department of Molecular Pathobiology, New York University, College of Dentistry, 345 East 24 Street, New York, NY 10010 – USA, tel: 212-998-9978,
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17
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Revollo L, Merrill-Skoloff G, De Ceunynck K, Dilks JR, Guo S, Bordoli MR, Peters CG, Noetzli L, Ionescu A, Rosen V, Italiano JE, Whitman M, Flaumenhaft R. The secreted tyrosine kinase VLK is essential for normal platelet activation and thrombus formation. Blood 2022; 139:104-117. [PMID: 34329392 PMCID: PMC8718620 DOI: 10.1182/blood.2020010342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 07/22/2021] [Indexed: 01/09/2023] Open
Abstract
Tyrosine phosphorylation of extracellular proteins is observed in cell cultures and in vivo, but little is known about the functional roles of tyrosine phosphorylation of extracellular proteins. Vertebrate lonesome kinase (VLK) is a broadly expressed secretory pathway tyrosine kinase present in platelet α-granules. It is released from platelets upon activation and phosphorylates substrates extracellularly. Its role in platelet function, however, has not been previously studied. In human platelets, we identified phosphorylated tyrosines mapped to luminal or extracellular domains of transmembrane and secreted proteins implicated in the regulation of platelet activation. To determine the role of VLK in extracellular tyrosine phosphorylation and platelet function, we generated mice with a megakaryocyte/platelet-specific deficiency of VLK. Platelets from these mice are normal in abundance and morphology but have significant changes in function both in vitro and in vivo. Resting and thrombin-stimulated VLK-deficient platelets exhibit a significant decrease in several tyrosine phosphobands. Results of functional testing of VLK-deficient platelets show decreased protease-activated receptor 4-mediated and collagen-mediated platelet aggregation but normal responses to adenosine 5'-diphosphate. Dense granule and α-granule release are reduced in these platelets. Furthermore, VLK-deficient platelets exhibit decreased protease-activated receptor 4-mediated Akt (S473) and Erk1/2 (T202/Y204) phosphorylation, indicating altered proximal signaling. In vivo, mice lacking VLK in megakaryocytes/platelets display strongly reduced platelet accumulation and fibrin formation after laser-induced injury of cremaster arterioles compared with control mice but with normal bleeding times. These studies show that the secretory pathway tyrosine kinase VLK is critical for stimulus-dependent platelet activation and thrombus formation, providing the first evidence that a secreted protein kinase is required for normal platelet function.
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Affiliation(s)
- Leila Revollo
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA
| | - Glenn Merrill-Skoloff
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Karen De Ceunynck
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - James R Dilks
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Shihui Guo
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Mattia R Bordoli
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA
| | - Christian G Peters
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Leila Noetzli
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Vascular Biology Program, Boston Children's Hospital and Department of Surgery, Harvard Medical School, Boston, MA; and
| | | | - Vicki Rosen
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA
| | - Joseph E Italiano
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Vascular Biology Program, Boston Children's Hospital and Department of Surgery, Harvard Medical School, Boston, MA; and
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
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18
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Zhang G, Deighan A, Raj A, Robinson L, Donato HJ, Garland G, Leland M, Martin-McNulty B, Kolumam GA, Riegler J, Freund A, Wright KM, Churchill GA. Intermittent fasting and caloric restriction interact with genetics to shape physiological health in mice. Genetics 2022; 220:iyab157. [PMID: 34791228 PMCID: PMC8733459 DOI: 10.1093/genetics/iyab157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/10/2021] [Indexed: 11/20/2022] Open
Abstract
Dietary interventions can dramatically affect physiological health and organismal lifespan. The degree to which organismal health is improved depends upon genotype and the severity of dietary intervention, but neither the effects of these factors, nor their interaction, have been quantified in an outbred population. Moreover, it is not well understood what physiological changes occur shortly after dietary change and how these may affect the health of an adult population. In this article, we investigated the effect of 6-month exposure of either caloric restriction (CR) or intermittent fasting (IF) on a broad range of physiological traits in 960 1-year old Diversity Outbred mice. We found CR and IF affected distinct aspects of physiology and neither the magnitude nor the direction (beneficial or detrimental) of effects were concordant with the severity of the intervention. In addition to the effects of diet, genetic variation significantly affected 31 of 36 traits (heritabilities ranged from 0.04 to 0.65). We observed significant covariation between many traits that was due to both diet and genetics and quantified these effects with phenotypic and genetic correlations. We genetically mapped 16 diet-independent and 2 diet-dependent significant quantitative trait loci, both of which were associated with cardiac physiology. Collectively, these results demonstrate the degree to which diet and genetics interact to shape the physiological health of adult mice following 6 months of dietary intervention.
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Affiliation(s)
- Guozhu Zhang
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | - Anil Raj
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | | | | | | | | | | | | | - Adam Freund
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Kevin M Wright
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
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19
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Gamart J, Barozzi I, Laurent F, Reinhardt R, Martins LR, Oberholzer T, Visel A, Zeller R, Zuniga A. SMAD4 target genes are part of a transcriptional network that integrates the response to BMP and SHH signaling during early limb bud patterning. Development 2021; 148:273522. [PMID: 34822715 PMCID: PMC8714076 DOI: 10.1242/dev.200182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022]
Abstract
SMAD4 regulates gene expression in response to BMP and TGFβ signal transduction, and is required for diverse morphogenetic processes, but its target genes have remained largely elusive. Here, we identify the SMAD4 target genes in mouse limb buds using an epitope-tagged Smad4 allele for ChIP-seq analysis in combination with transcription profiling. This analysis shows that SMAD4 predominantly mediates BMP signal transduction during early limb bud development. Unexpectedly, the expression of cholesterol biosynthesis enzymes is precociously downregulated and intracellular cholesterol levels are reduced in Smad4-deficient limb bud mesenchymal progenitors. Most importantly, our analysis reveals a predominant function of SMAD4 in upregulating target genes in the anterior limb bud mesenchyme. Analysis of differentially expressed genes shared between Smad4- and Shh-deficient limb buds corroborates this function of SMAD4 and also reveals the repressive effect of SMAD4 on posterior genes that are upregulated in response to SHH signaling. This analysis uncovers opposing trans-regulatory inputs from SHH- and SMAD4-mediated BMP signal transduction on anterior and posterior gene expression during the digit patterning and outgrowth in early limb buds. Summary: The transcriptional targets of SMAD4 in early limb buds are identified and the largely opposing impact of BMP and SHH signaling on early digit patterning and outgrowth is revealed.
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Affiliation(s)
- Julie Gamart
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Iros Barozzi
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Frédéric Laurent
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Robert Reinhardt
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Laurène Ramos Martins
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Thomas Oberholzer
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Axel Visel
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.,School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
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20
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Greenbaum J, Su KJ, Zhang X, Liu Y, Liu A, Zhao LJ, Luo Z, Tian Q, Shen H, Deng HW. A multiethnic whole genome sequencing study to identify novel loci for bone mineral density. Hum Mol Genet 2021; 31:1067-1081. [PMID: 34673960 PMCID: PMC8976433 DOI: 10.1093/hmg/ddab305] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
At present, there have only been a few DNA sequencing-based studies to explore the genetic determinants of bone mineral density (BMD). We carried out the largest whole genome sequencing analysis to date for femoral neck and spine BMD (n = 4981), with one of the highest average sequencing depths implemented thus far at 22×, in a multiethnic sample (58% Caucasian and 42% African American) from the Louisiana Osteoporosis Study (LOS). The LOS samples were combined with summary statistics from the GEFOS consortium and several independent samples of various ethnicities to perform GWAS meta-analysis (n = 44 506). We identified 31 and 30 genomic risk loci for femoral neck and spine BMD, respectively. The findings substantiate many previously reported susceptibility loci (e.g. WNT16 and ESR1) and reveal several others that are either novel or have not been widely replicated in GWAS for BMD, including two for femoral neck (IGF2 and ZNF423) and one for spine (SIPA1). Although we were not able to uncover ethnicity specific differences in the genetic determinants of BMD, we did identify several loci which demonstrated sex-specific associations, including two for women (PDE4D and PIGN) and three for men (TRAF3IP2, NFIB and LYSMD4). Gene-based rare variant association testing detected MAML2, a regulator of the Notch signaling pathway, which has not previously been suggested, for association with spine BMD. The findings provide novel insights into the pathophysiological mechanisms of osteoporosis.
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Affiliation(s)
- Jonathan Greenbaum
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Kuan-Jui Su
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Xiao Zhang
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Yong Liu
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA,School of Basic Medical Science, Central South University, Changsha 410013, Hunan Province, PR China
| | - Anqi Liu
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Lan-Juan Zhao
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Zhe Luo
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Qing Tian
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hui Shen
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hong-Wen Deng
- To whom correspondence should be addressed at: Section of Biomedical Informatics and Genomics, Director, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, 1440 Canal St., RM 1619F, New Orleans, LA 70112, USA.
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21
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Abraham SP, Nita A, Krejci P, Bosakova M. Cilia kinases in skeletal development and homeostasis. Dev Dyn 2021; 251:577-608. [PMID: 34582081 DOI: 10.1002/dvdy.426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 11/08/2022] Open
Abstract
Primary cilia are dynamic compartments that regulate multiple aspects of cellular signaling. The production, maintenance, and function of cilia involve more than 1000 genes in mammals, and their mutations disrupt the ciliary signaling which manifests in a plethora of pathological conditions-the ciliopathies. Skeletal ciliopathies are genetic disorders affecting the development and homeostasis of the skeleton, and encompass a broad spectrum of pathologies ranging from isolated polydactyly to lethal syndromic dysplasias. The recent advances in forward genetics allowed for the identification of novel regulators of skeletogenesis, and revealed a growing list of ciliary proteins that are critical for signaling pathways implicated in bone physiology. Among these, a group of protein kinases involved in cilia assembly, maintenance, signaling, and disassembly has emerged. In this review, we summarize the functions of cilia kinases in skeletal development and disease, and discuss the available and upcoming treatment options.
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Affiliation(s)
- Sara P Abraham
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Alexandru Nita
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Institute of Animal Physiology and Genetics of the CAS, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Michaela Bosakova
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Institute of Animal Physiology and Genetics of the CAS, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
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22
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Plöger R, Viebahn C. Expression patterns of signalling molecules and transcription factors in the early rabbit embryo and their significance for modelling amniote axis formation. Dev Genes Evol 2021; 231:73-83. [PMID: 34100128 PMCID: PMC8213660 DOI: 10.1007/s00427-021-00677-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 11/25/2022]
Abstract
The anterior-posterior axis is a central element of the body plan and, during amniote gastrulation, forms through several transient domains with specific morphogenetic activities. In the chick, experimentally proven activity of signalling molecules and transcription factors lead to the concept of a 'global positioning system' for initial axis formation whereas in the (mammotypical) rabbit embryo, a series of morphological or molecular domains are part of a putative 'three-anchor-point model'. Because circular expression patterns of genes involved in axis formation exist in both amniote groups prior to, and during, gastrulation and may thus be suited to reconcile these models, the expression patterns of selected genes known in the chick, namely the ones coding for the transcription factors eomes and tbx6, the signalling molecule wnt3 and the wnt inhibitor pkdcc, were analysed in the rabbit embryonic disc using in situ hybridisation and placing emphasis on their germ layer location. Peripheral wnt3 and eomes expression in all layers is found initially to be complementary to central pkdcc expression in the hypoblast during early axis formation. Pkdcc then appears - together with a posterior-anterior gradient in wnt3 and eomes domains - in the epiblast posteriorly before the emerging primitive streak is marked by pkdcc and tbx6 at its anterior and posterior extremities, respectively. Conserved circular expression patterns deduced from some of this data may point to shared mechanisms in amniote axis formation while the reshaping of localised gene expression patterns is discussed as part of the 'three-anchor-point model' for establishing the mammalian body plan.
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Affiliation(s)
- Ruben Plöger
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Göttingen, Germany
| | - Christoph Viebahn
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Göttingen, Germany
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23
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Secreted tyrosine kinase Vlk negatively regulates Hedgehog signaling by inducing lysosomal degradation of Smoothened. Biochem J 2020; 477:121-136. [PMID: 31845979 DOI: 10.1042/bcj20190784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/19/2022]
Abstract
Vlk is a secreted tyrosine kinase that plays crucial roles during vertebrate embryonic development including skeletal formation. Genetic studies suggest that Vlk can modulate the Hedgehog signaling pathway during skeletal development. Despite its potential roles as an extracellular regulator of signaling pathways, little is known regarding the molecular functions of Vlk. Here we show that Vlk can negatively regulate the Hedgehog signaling pathway. We found that Vlk can induce lysosomal degradation of Smoothened, a crucial transmembrane signal transducer of the Hedgehog pathway, through the interaction with the extracellular domain of Smoothened (Smo-ECD). In addition, we observed that Vlk can attenuate Hedgehog signaling-induced ciliary localization of Smoothened. Furthermore, Vlk-mediated suppression of Hedgehog signaling can be diminished by tyrosine-to-phenylalanine substitutions in Smo-ECD. Taken together, these results suggest that Vlk may function as a signaling regulator in extracellular space to modulate the Hedgehog pathway.
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24
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Park BC, Reese M, Tagliabracci VS. Thinking outside of the cell: Secreted protein kinases in bacteria, parasites, and mammals. IUBMB Life 2019; 71:749-759. [PMID: 30941842 DOI: 10.1002/iub.2040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 01/02/2023]
Abstract
Previous decades have seen an explosion in our understanding of protein kinase function in human health and disease. Hundreds of unique kinase structures have been solved, allowing us to create generalized rules for catalysis, assign roles of communities within the catalytic core, and develop specific drugs for targeting various pathways. Although our understanding of intracellular kinases has developed at a fast rate, our exploration into extracellular kinases has just begun. In this review, we will cover the secreted protein kinase families found in humans, bacteria, and parasites. © 2019 IUBMB Life, 71(6):749-759, 2019.
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Affiliation(s)
- Brenden C Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Reese
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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25
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Sajan SA, Ganesh J, Shinde DN, Powis Z, Scarano MI, Stone J, Winter S, Tang S. Biallelic disruption of PKDCC is associated with a skeletal disorder characterised by rhizomelic shortening of extremities and dysmorphic features. J Med Genet 2018; 56:850-854. [PMID: 30478137 DOI: 10.1136/jmedgenet-2018-105639] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/17/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND During mouse embryonic development the protein kinase domain containing, cytoplasmic (Pkdcc) gene, also known as Vlk, is expressed in several tissues including the ventral midbrain, with particularly strong expression in branchial arches and limb buds. Homozygous Pkdcc knockout mice have dysmorphic features and shortened long bones as the most obvious morphological abnormalities. The human PKDCC gene has currently not been associated with any disorders. OBJECTIVE To use clinical diagnostic exome sequencing (DES) for providing genetic diagnoses to two apparently unrelated patients with similar skeletal abnormalities comprising rhizomelic shortening of limbs and dysmorphic features. METHODS Patient-parents trio DES was carried out and the identified candidate variants were confirmed by Sanger sequencing. RESULTS Each patient had a homozygous gene disrupting variant in PKDCC considered to explain the skeletal phenotypes shared by both. The first patient was homozygous for the nonsense variant p.(Tyr217*) (NM_1 38 370 c.651C>A) expected to result in nonsense-mediated decay of the mutant transcripts, whereas the second patient was homozygous for the splice donor variant c.639+1G>T predicted to abolish the donor splice site by three in silico splice prediction algorithms. CONCLUSIONS Biallelic gene disrupting variants in PKDCC in humans, just like in mice, cause dysmorphic features and rhizomelic shortening of limbs.
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Affiliation(s)
- Samin A Sajan
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Jaya Ganesh
- Division of Genetics, Cooper University Hospital, Camden, New Jersey, USA
| | - Deepali N Shinde
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Zöe Powis
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Maria I Scarano
- Division of Genetics, Cooper University Hospital, Camden, New Jersey, USA
| | - Jennifer Stone
- Division of Genetics, Cooper University Hospital, Camden, New Jersey, USA
| | - Susan Winter
- Valley Children's Hospital, Madera, California, USA
| | - Sha Tang
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
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26
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Maddala R, Skiba NP, Rao PV. Vertebrate Lonesome Kinase Regulated Extracellular Matrix Protein Phosphorylation, Cell Shape, and Adhesion in Trabecular Meshwork Cells. J Cell Physiol 2017; 232:2447-2460. [PMID: 27591737 PMCID: PMC5462548 DOI: 10.1002/jcp.25582] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/01/2016] [Indexed: 12/11/2022]
Abstract
Glaucoma, a leading cause of irreversible blindness, is commonly associated with elevated intraocular pressure (IOP) due to impaired aqueous humor (AH) drainage through the trabecular meshwork (TM). Although dysregulated production and organization of extracellular matrix (ECM) is presumed to increase resistance to AH outflow and elevate IOP by altering TM cell contractile and adhesive properties, it is not known whether regulation of ECM protein phosphorylation via the secretory vertebrate lonesome kinase (VLK) influences TM cellular characteristics. Here, we tested this possibility. Experiments carried out in this study reveal that the 32 kDa protein is a prominent VLK isoform detectable in lysates and conditioned media (CM) of human TM cells. Increased levels of VLK were observed in CM of TM cells subjected to cyclic mechanical stretch, or treated with dexamethasone, TGF-β2, and TM cells expressing constitutively active RhoA GTPase. Downregulation of VLK expression in TM cells using siRNA decreased tyrosine phosphorylation (TyrP) of ECM proteins and focal adhesions, and induced changes in cell shape in association with reduced levels of actin stress fibers and phospho-paxillin. VLK was also demonstrated to regulate TGF-β2-induced TyrP of ECM proteins. Taken together, these results suggest that VLK secretion can be regulated by external cues, intracellular signal proteins, and mechanical stretch, and VLK can in turn regulate TyrP of ECM proteins secreted by TM cells and control cell shape, actin stress fibers, and focal adhesions. These observations indicate a potential role for VLK in homeostasis of AH outflow and IOP, and in the pathobiology of glaucoma. J. Cell. Physiol. 232: 2447-2460, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rupalatha Maddala
- Department of Ophthalmology, Duke University School of Medicine. Durham, NC. USA. 27710
| | - Nikolai P. Skiba
- Department of Ophthalmology, Duke University School of Medicine. Durham, NC. USA. 27710
| | - Ponugoti Vasantha Rao
- Department of Ophthalmology, Duke University School of Medicine. Durham, NC. USA. 27710
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine. Durham, NC. USA. 27710
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27
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Ludwig KU, Böhmer AC, Bowes J, Nikolic M, Ishorst N, Wyatt N, Hammond NL, Gölz L, Thieme F, Barth S, Schuenke H, Klamt J, Spielmann M, Aldhorae K, Rojas-Martinez A, Nöthen MM, Rada-Iglesias A, Dixon MJ, Knapp M, Mangold E. Imputation of orofacial clefting data identifies novel risk loci and sheds light on the genetic background of cleft lip ± cleft palate and cleft palate only. Hum Mol Genet 2017; 26:829-842. [PMID: 28087736 PMCID: PMC5409059 DOI: 10.1093/hmg/ddx012] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/09/2017] [Indexed: 12/22/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is among the most common human birth defects with multifactorial etiology. Here, we present results from a genome-wide imputation study of nsCL/P in which, after adding replication cohort data, four novel risk loci for nsCL/P are identified (at chromosomal regions 2p21, 14q22, 15q24 and 19p13). On a systematic level, we show that the association signals within this high-density dataset are enriched in functionally-relevant genomic regions that are active in both human neural crest cells (hNCC) and mouse embryonic craniofacial tissue. This enrichment is also detectable in hNCC regions primed for later activity. Using GCTA analyses, we suggest that 30% of the estimated variance in risk for nsCL/P in the European population can be attributed to common variants, with 25.5% contributed to by the 24 risk loci known to date. For each of these, we identify credible SNPs using a Bayesian refinement approach, with two loci harbouring only one probable causal variant. Finally, we demonstrate that there is no polygenic component of nsCL/P detectable that is shared with nonsyndromic cleft palate only (nsCPO). Our data suggest that, while common variants are strongly contributing to risk for nsCL/P, they do not seem to be involved in nsCPO which might be more often caused by rare deleterious variants. Our study generates novel insights into both nsCL/P and nsCPO etiology and provides a systematic framework for research into craniofacial development and malformation.
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Affiliation(s)
- Kerstin U Ludwig
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Anne C Böhmer
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - John Bowes
- Arthritis Research UK Centre for Genetics and Genomics, The University of Manchester, Manchester M13 9PT, UK
| | - Miloš Nikolic
- Center for Molecular Medicine Cologne.,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Nina Ishorst
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Niki Wyatt
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Nigel L Hammond
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn 53111, Germany
| | - Frederic Thieme
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Sandra Barth
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Hannah Schuenke
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Johanna Klamt
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, RG Development and Disease, Berlin 14195, Germany.,Institute for Medical and Human Genetics.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Khalid Aldhorae
- Orthodontic Department, College of Dentistry, Thamar University, Thamar, Yemen
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, School of Medicine, and Universidad Autonoma de Nuevo Leon, Centro de Investigación y Desarrollo en Ciencias de la Salud, Monterrey 64460, Mexico
| | - Markus M Nöthen
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne.,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Michael J Dixon
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn 53127, Germany
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Mahas A, Potluri K, Kent MN, Naik S, Markey M. Copy number variation in archival melanoma biopsies versus benign melanocytic lesions. Cancer Biomark 2017; 16:575-97. [PMID: 27002761 DOI: 10.3233/cbm-160600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Skin melanocytes can give rise to benign and malignant neoplasms. Discrimination of an early melanoma from an unusual/atypical benign nevus can represent a significant challenge. However, previous studies have shown that in contrast to benign nevi, melanoma demonstrates pervasive chromosomal aberrations. OBJECTIVE This substantial difference between melanoma and benign nevi can be exploited to discriminate between melanoma and benign nevi. METHODS Array-comparative genomic hybridization (aCGH) is an approach that can be used on DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues to assess the entire genome for the presence of changes in DNA copy number. In this study, high resolution, genome-wide single-nucleotide polymorphism (SNP) arrays were utilized to perform comprehensive and detailed analyses of recurrent copy number aberrations in 41 melanoma samples in comparison with 21 benign nevi. RESULTS We found statistically significant copy number gains and losses within melanoma samples. Some of the identified aberrations are previously implicated in melanoma. Moreover, novel regions of copy number alterations were identified, revealing new candidate genes potentially involved in melanoma pathogenesis. CONCLUSIONS Taken together, these findings can help improve melanoma diagnosis and introduce novel melanoma therapeutic targets.
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Affiliation(s)
- Ahmed Mahas
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Keerti Potluri
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Michael N Kent
- Department of Dermatology, Wright State University Boonshoft School of Medicine, Dayton, OH, USA.,Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Sameep Naik
- Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Michael Markey
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
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29
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Genetic risk score based on the prevalence of vertebral fracture in Japanese women with osteoporosis. Bone Rep 2016; 5:168-172. [PMID: 28580384 PMCID: PMC5440966 DOI: 10.1016/j.bonr.2016.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 06/22/2016] [Accepted: 07/11/2016] [Indexed: 12/02/2022] Open
Abstract
A genetic risk score (GRS) was developed for predicting fracture risk based on the prevalence of vertebral fractures in 441 Japanese females with osteoporosis. A total of 979 (858 nonsynonymous and 121 silent) single-nucleotide polymorphisms (SNPs) located in 74 osteoporosis-susceptibility genes were genotyped and evaluated for their association with fracture prevalence. Four SNPs (protein kinase domain containing, cytoplasmic [PKDCC; rs4952590], CDK5-regulatory subunit-associated protein 1-like 1 [CDKAL1; rs4712556], wingless-type MMTV-integration site family member 16 [WNT16; rs2707466], and G-patch domain-containing gene 1 [GPATCH1; rs10416265]) showed a significant association (p < 0.05) with the fracture, in which the minor allele of the former two SNPs was the protective allele and that of the latter two SNPs was the risk allele. Applying a dominant-genetic model, we allotted − 1 point each to the protective-allele carriers and 1 point each to the risk-allele carriers, and GRS values were calculated as the sum of the points. The receiver-operating characteristic curves showed that GRS adequately predicted vertebral fracture. For the model predicted by the GRS with and without the effect of age, areas under the curves were 0.788 (95% confidence interval [CI]: 0.736–0.840) and 0.667 (95% CI: 0.599–0.735), respectively. Multiple logistic regression analysis revealed that the odds ratio for the association between fracture prevalence and GRS was 3.27 (95% CI: 1.36–7.87, p = 0.008) for scores of − 1 to 0 (n = 303) and 12.12 (95% CI: 4.19–35.07, p < 0.001) for scores of 1 to 2 (n = 35) relative to a score of − 2 (n = 103). The GRS based on the four SNPs could help identify at-risk individuals and enable implementation of preventive measures for vertebral fracture. A genetic risk score to predict fracture risk based on vertebral fracture prevalence is proposed. Four single-nucleotide polymorphisms showed significant association with fracture. This method helps identify at-risk individuals and promotes preventive measures for fractures.
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Key Words
- AUC, area under the curve
- BMD, bone mineral density
- CDKAL1, CDK5-regulatory subunit-associated protein 1-like 1
- CI, confidence interval
- GPATCH1, G-patch domain-containing gene 1
- GRS, genetic risk score
- GWAS, genome-wide association studies
- Genetic risk score
- OR, odds ratio
- Osteoporosis
- PKDCC, protein kinase domain containing, cytoplasmic
- ROC, receiver-operating characteristics
- SNP, single-nucleotide polymorphism
- Single-nucleotide polymorphism
- Vertebral fracture
- WNT16, wingless-type MMTV-integration site family member 16
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30
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Machado JP, Johnson WE, Gilbert MTP, Zhang G, Jarvis ED, O'Brien SJ, Antunes A. Bone-associated gene evolution and the origin of flight in birds. BMC Genomics 2016; 17:371. [PMID: 27193938 PMCID: PMC4870793 DOI: 10.1186/s12864-016-2681-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 04/28/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Bones have been subjected to considerable selective pressure throughout vertebrate evolution, such as occurred during the adaptations associated with the development of powered flight. Powered flight evolved independently in two extant clades of vertebrates, birds and bats. While this trait provided advantages such as in aerial foraging habits, escape from predators or long-distance travels, it also imposed great challenges, namely in the bone structure. RESULTS We performed comparative genomic analyses of 89 bone-associated genes from 47 avian genomes (including 45 new), 39 mammalian, and 20 reptilian genomes, and demonstrate that birds, after correcting for multiple testing, have an almost two-fold increase in the number of bone-associated genes with evidence of positive selection (~52.8 %) compared with mammals (~30.3 %). Most of the positive-selected genes in birds are linked with bone regulation and remodeling and thirteen have been linked with functional pathways relevant to powered flight, including bone metabolism, bone fusion, muscle development and hyperglycemia levels. Genes encoding proteins involved in bone resorption, such as TPP1, had a high number of sites under Darwinian selection in birds. CONCLUSIONS Patterns of positive selection observed in bird ossification genes suggest that there was a period of intense selective pressure to improve flight efficiency that was closely linked with constraints on body size.
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Affiliation(s)
- João Paulo Machado
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Porto, Portugal
- Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350, Copenhagen, Denmark
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzen, 518083, China
- Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Erich D Jarvis
- Department of Neurobiology Box 3209, Duke University Medical Center, Durham, NC, 27710, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia
- Oceanographic Center, 8000 N. Ocean Drive, Nova Southeastern University, Ft Lauderdale, FL, 33004, USA
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
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Identification of new regulators of embryonic patterning and morphogenesis in Xenopus gastrulae by RNA sequencing. Dev Biol 2016; 426:429-441. [PMID: 27209239 DOI: 10.1016/j.ydbio.2016.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/11/2016] [Accepted: 05/11/2016] [Indexed: 12/19/2022]
Abstract
During early vertebrate embryogenesis, cell fate specification is often coupled with cell acquisition of specific adhesive, polar and/or motile behaviors. In Xenopus gastrulae, tissues fated to form different axial structures display distinct motility. The cells in the early organizer move collectively and directionally toward the animal pole and contribute to anterior mesendoderm, whereas the dorsal and the ventral-posterior trunk tissues surrounding the blastopore of mid-gastrula embryos undergo convergent extension and convergent thickening movements, respectively. While factors regulating cell lineage specification have been described in some detail, the molecular machinery that controls cell motility is not understood in depth. To gain insight into the gene battery that regulates both cell fates and motility in particular embryonic tissues, we performed RNA sequencing (RNA-seq) to investigate differentially expressed genes in the early organizer, the dorsal and the ventral marginal zone of Xenopus gastrulae. We uncovered many known signaling and transcription factors that have been reported to play roles in embryonic patterning during gastrulation. We also identified many uncharacterized genes as well as genes that encoded extracellular matrix (ECM) proteins or potential regulators of actin cytoskeleton. Co-expression of a selected subset of the differentially expressed genes with activin in animal caps revealed that they had distinct ability to block activin-induced animal cap elongation. Most of these factors did not interfere with mesodermal induction by activin, but an ECM protein, EFEMP2, inhibited activin signaling and acted downstream of the activated type I receptor. By focusing on a secreted protein kinase PKDCC1, we showed with overexpression and knockdown experiments that PKDCC1 regulated gastrulation movements as well as anterior neural patterning during early Xenopus development. Overall, our studies identify many differentially expressed signaling and cytoskeleton regulators in different embryonic regions of Xenopus gastrulae and imply their functions in regulating cell fates and/or behaviors during gastrulation.
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32
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Ding Y, Colozza G, Zhang K, Moriyama Y, Ploper D, Sosa EA, Benitez MDJ, De Robertis EM. Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula. Dev Biol 2016; 426:176-187. [PMID: 27016259 PMCID: PMC5033668 DOI: 10.1016/j.ydbio.2016.02.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/14/2016] [Accepted: 02/26/2016] [Indexed: 12/31/2022]
Abstract
RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and Bambi. Complete transcriptome-wide tables of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ β-catenin signaling independently of its kinase activity. We conclude that RNA-Seq in combination with the X. laevis complete genome now available provides a powerful tool for unraveling cell-cell signaling pathways during embryonic induction.
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Affiliation(s)
- Yi Ding
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Gabriele Colozza
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Kelvin Zhang
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
| | - Yuki Moriyama
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Diego Ploper
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Eric A Sosa
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Maria D J Benitez
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Edward M De Robertis
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA.
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Costello I, Nowotschin S, Sun X, Mould AW, Hadjantonakis AK, Bikoff EK, Robertson EJ. Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern anterior mesendoderm, node, and midline development. Genes Dev 2016; 29:2108-22. [PMID: 26494787 PMCID: PMC4617976 DOI: 10.1101/gad.268979.115] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Costello et al. demonstrate that Smad4/Eomes-dependent Lhx1 expression in the epiblast marks the entire definitive endoderm lineage, the anterior mesendoderm, and midline progenitors. In proteomic experiments, they characterize a complex comprised of Lhx1, Otx2, and Foxa2 as well as the chromatin-looping protein Ldb1. Gene regulatory networks controlling functional activities of spatially and temporally distinct endodermal cell populations in the early mouse embryo remain ill defined. The T-box transcription factor Eomes, acting downstream from Nodal/Smad signals, directly activates the LIM domain homeobox transcription factor Lhx1 in the visceral endoderm. Here we demonstrate Smad4/Eomes-dependent Lhx1 expression in the epiblast marks the entire definitive endoderm lineage, the anterior mesendoderm, and midline progenitors. Conditional inactivation of Lhx1 disrupts anterior definitive endoderm development and impedes node and midline morphogenesis in part due to severe disturbances in visceral endoderm displacement. Transcriptional profiling and ChIP-seq (chromatin immunoprecipitation [ChIP] followed by high-throughput sequencing) experiments identified Lhx1 target genes, including numerous anterior definitive endoderm markers and components of the Wnt signaling pathway. Interestingly, Lhx1-binding sites were enriched at enhancers, including the Nodal-proximal epiblast enhancer element and enhancer regions controlling Otx2 and Foxa2 expression. Moreover, in proteomic experiments, we characterized a complex comprised of Lhx1, Otx2, and Foxa2 as well as the chromatin-looping protein Ldb1. These partnerships cooperatively regulate development of the anterior mesendoderm, node, and midline cell populations responsible for establishment of the left–right body axis and head formation.
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Affiliation(s)
- Ita Costello
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Xin Sun
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Arne W Mould
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | | | - Elizabeth K Bikoff
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Elizabeth J Robertson
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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Patthey C, Clifford H, Haerty W, Ponting CP, Shimeld SM, Begbie J. Identification of molecular signatures specific for distinct cranial sensory ganglia in the developing chick. Neural Dev 2016; 11:3. [PMID: 26819088 PMCID: PMC4730756 DOI: 10.1186/s13064-016-0057-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/08/2016] [Indexed: 11/22/2022] Open
Abstract
Background The cranial sensory ganglia represent populations of neurons with distinct functions, or sensory modalities. The production of individual ganglia from distinct neurogenic placodes with different developmental pathways provides a powerful model to investigate the acquisition of specific sensory modalities. To date there is a limited range of gene markers available to examine the molecular pathways underlying this process. Results Transcriptional profiles were generated for populations of differentiated neurons purified from distinct cranial sensory ganglia using microdissection in embryonic chicken followed by FAC-sorting and RNAseq. Whole transcriptome analysis confirmed the division into somato- versus viscerosensory neurons, with additional evidence for subdivision of the somatic class into general and special somatosensory neurons. Cross-comparison of distinct ganglia transcriptomes identified a total of 134 markers, 113 of which are novel, which can be used to distinguish trigeminal, vestibulo-acoustic and epibranchial neuronal populations. In situ hybridisation analysis provided validation for 20/26 tested markers, and showed related expression in the target region of the hindbrain in many cases. Conclusions One hundred thirty-four high-confidence markers have been identified for placode-derived cranial sensory ganglia which can now be used to address the acquisition of specific cranial sensory modalities. Electronic supplementary material The online version of this article (doi:10.1186/s13064-016-0057-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cedric Patthey
- Department of Zoology, University of Oxford, Oxford, UK. .,Umeå Center for Molecular Medicine, Umeå University, Umeå, Sweden.
| | - Harry Clifford
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. .,MRC Functional Genomics, University of Oxford, Oxford, UK.
| | - Wilfried Haerty
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. .,MRC Functional Genomics, University of Oxford, Oxford, UK.
| | - Chris P Ponting
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. .,MRC Functional Genomics, University of Oxford, Oxford, UK.
| | | | - Jo Begbie
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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35
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Funato N, Nakamura M, Yanagisawa H. Molecular basis of cleft palates in mice. World J Biol Chem 2015; 6:121-138. [PMID: 26322171 PMCID: PMC4549757 DOI: 10.4331/wjbc.v6.i3.121] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 05/26/2015] [Accepted: 07/14/2015] [Indexed: 02/05/2023] Open
Abstract
Cleft palate, including complete or incomplete cleft palates, soft palate clefts, and submucosal cleft palates, is the most frequent congenital craniofacial anomaly in humans. Multifactorial conditions, including genetic and environmental factors, induce the formation of cleft palates. The process of palatogenesis is temporospatially regulated by transcription factors, growth factors, extracellular matrix proteins, and membranous molecules; a single ablation of these molecules can result in a cleft palate in vivo. Studies on knockout mice were reviewed in order to identify genetic errors that lead to cleft palates. In this review, we systematically describe these mutant mice and discuss the molecular mechanisms of palatogenesis.
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Vitorino M, Silva AC, Inácio JM, Ramalho JS, Gur M, Fainsod A, Steinbeisser H, Belo JA. Xenopus Pkdcc1 and Pkdcc2 Are Two New Tyrosine Kinases Involved in the Regulation of JNK Dependent Wnt/PCP Signaling Pathway. PLoS One 2015; 10:e0135504. [PMID: 26270962 PMCID: PMC4536202 DOI: 10.1371/journal.pone.0135504] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 07/22/2015] [Indexed: 12/28/2022] Open
Abstract
Protein Kinase Domain Containing, Cytoplasmic (PKDCC) is a protein kinase which has been implicated in longitudinal bone growth through regulation of chondrocytes formation. Nevertheless, the mechanism by which this occurs remains unknown. Here, we identified two new members of the PKDCC family, Pkdcc1 and Pkdcc2 from Xenopus laevis. Interestingly, our knockdown experiments revealed that these two proteins are both involved on blastopore and neural tube closure during gastrula and neurula stages, respectively. In vertebrates, tissue polarity and cell movement observed during gastrulation and neural tube closure are controlled by Wnt/Planar Cell Polarity (PCP) molecular pathway. Our results showed that Pkdcc1 and Pkdcc2 promote the recruitment of Dvl to the plasma membrane. But surprisingly, they revealed different roles in the induction of a luciferase reporter under the control of Atf2 promoter. While Pkdcc1 induces Atf2 expression, Pkdcc2 does not, and furthermore inhibits its normal induction by Wnt11 and Wnt5a. Altogether our data show, for the first time, that members of the PKDCC family are involved in the regulation of JNK dependent Wnt/PCP signaling pathway.
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Affiliation(s)
- Marta Vitorino
- Regenerative Medicine Program, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Faro, Portugal
- Center for Biomedical Research (CBMR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Ana Cristina Silva
- Center for Biomedical Research (CBMR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - José Manuel Inácio
- Regenerative Medicine Program, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Faro, Portugal
- Center for Biomedical Research (CBMR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- CEDOC, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - José Silva Ramalho
- CEDOC, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Michal Gur
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University, P.O. Box 12272, Jerusalem, 91120, Israel
| | - Abraham Fainsod
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University, P.O. Box 12272, Jerusalem, 91120, Israel
| | | | - José António Belo
- Regenerative Medicine Program, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Faro, Portugal
- Center for Biomedical Research (CBMR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- CEDOC, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
- * E-mail:
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Yalak G, Olsen BR. Proteomic database mining opens up avenues utilizing extracellular protein phosphorylation for novel therapeutic applications. J Transl Med 2015; 13:125. [PMID: 25927841 PMCID: PMC4427915 DOI: 10.1186/s12967-015-0482-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/07/2015] [Indexed: 02/07/2023] Open
Abstract
Recent advances in extracellular signaling suggest that extracellular protein phosphorylation is a regulatory mechanism outside the cell. The list of reported active extracellular protein kinases and phosphatases is growing, and phosphorylation of an increasing number of extracellular matrix molecules and extracellular domains of trans-membrane proteins is being documented. Here, we use public proteomic databases, collagens – the major components of the extracellular matrix, extracellular signaling molecules and proteolytic enzymes as examples to assess what the roles of extracellular protein phosphorylation may be in health and disease. We propose that novel tools be developed to help assess the role of extracellular protein phosphorylation and translate the findings for biomedical applications. Furthermore, we suggest that the phosphorylation state of extracellular matrix components as well as the presence of extracellular kinases be taken into account when designing translational medical applications.
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Affiliation(s)
- Garif Yalak
- Department of Developmental Biology, Harvard Medical School/Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA, 02115, USA.
| | - Bjorn R Olsen
- Department of Developmental Biology, Harvard Medical School/Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA, 02115, USA.
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Sreelatha A, Kinch LN, Tagliabracci VS. The secretory pathway kinases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1687-93. [PMID: 25862977 DOI: 10.1016/j.bbapap.2015.03.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 03/31/2015] [Indexed: 12/16/2022]
Abstract
Protein phosphorylation is a nearly universal post-translation modification involved in a plethora of cellular events. Even though phosphorylation of extracellular proteins had been observed, the identity of the kinases that phosphorylate secreted proteins remained a mystery until only recently. Advances in genome sequencing and genetic studies have paved the way for the discovery of a new class of kinases that localize within the endoplasmic reticulum, Golgi apparatus and the extracellular space. These novel kinases phosphorylate proteins and proteoglycans in the secretory pathway and appear to regulate various extracellular processes. Mutations in these kinases cause human disease, thus underscoring the biological importance of phosphorylation within the secretory pathway. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.
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Affiliation(s)
- Anju Sreelatha
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa N Kinch
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Bordoli MR, Yum J, Breitkopf SB, Thon JN, Italiano JE, Xiao J, Worby C, Wong SK, Lin G, Edenius M, Keller TL, Asara JM, Dixon JE, Yeo CY, Whitman M. A secreted tyrosine kinase acts in the extracellular environment. Cell 2014; 158:1033-1044. [PMID: 25171405 PMCID: PMC4149754 DOI: 10.1016/j.cell.2014.06.048] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/06/2014] [Accepted: 06/20/2014] [Indexed: 11/17/2022]
Abstract
Although tyrosine phosphorylation of extracellular proteins has been reported to occur extensively in vivo, no secreted protein tyrosine kinase has been identified. As a result, investigation of the potential role of extracellular tyrosine phosphorylation in physiological and pathological tissue regulation has not been possible. Here, we show that VLK, a putative protein kinase previously shown to be essential in embryonic development, is a secreted protein kinase, with preference for tyrosine, that phosphorylates a broad range of secreted and ER-resident substrate proteins. We find that VLK is rapidly and quantitatively secreted from platelets in response to stimuli and can tyrosine phosphorylate coreleased proteins utilizing endogenous as well as exogenous ATP sources. We propose that discovery of VLK activity provides an explanation for the extensive and conserved pattern of extracellular tyrosine phosphophorylation seen in vivo, and extends the importance of regulated tyrosine phosphorylation into the extracellular environment.
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Affiliation(s)
- Mattia R Bordoli
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Jina Yum
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA; Department of Life Science and Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan N Thon
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Joseph E Italiano
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Vascular Biology Program, Department of Surgery, Children's Hospital, Boston, MA 02115, USA
| | - Junyu Xiao
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Carolyn Worby
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Swee-Kee Wong
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Grace Lin
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Maja Edenius
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Tracy L Keller
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jack E Dixon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Chang-Yeol Yeo
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA; Department of Life Science and Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea.
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA.
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Comes S, Gagliardi M, Laprano N, Fico A, Cimmino A, Palamidessi A, De Cesare D, De Falco S, Angelini C, Scita G, Patriarca EJ, Matarazzo MR, Minchiotti G. L-Proline induces a mesenchymal-like invasive program in embryonic stem cells by remodeling H3K9 and H3K36 methylation. Stem Cell Reports 2013; 1:307-21. [PMID: 24319666 PMCID: PMC3849245 DOI: 10.1016/j.stemcr.2013.09.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 09/11/2013] [Accepted: 09/12/2013] [Indexed: 12/25/2022] Open
Abstract
Metabolites are emerging as key mediators of crosstalk between metabolic flux, cellular signaling, and epigenetic regulation of cell fate. We found that the nonessential amino acid L-proline (L-Pro) acts as a signaling molecule that promotes the conversion of embryonic stem cells into mesenchymal-like, spindle-shaped, highly motile, invasive pluripotent stem cells. This embryonic-stem-cell-to-mesenchymal-like transition (esMT) is accompanied by a genome-wide remodeling of the H3K9 and H3K36 methylation status. Consistently, L-Pro-induced esMT is fully reversible either after L-Pro withdrawal or by addition of ascorbic acid (vitamin C), which in turn reduces H3K9 and H3K36 methylation, promoting a mesenchymal-like-to-embryonic-stem-cell transition (MesT). These findings suggest that L-Pro, which is produced by proteolytic remodeling of the extracellular matrix, may act as a microenvironmental cue to control stem cell behavior. L-Pro induces a reversible embryonic-stem-to-mesenchymal-like transition (esMT) The esMT is characterized by a dynamic redistribution of E-cadherin L-Pro acts as an epigenetic modifier remodeling H3K9 and H3K36 methylation L-Pro and vitamin C regulate esMT-MesT plasticity modulating H3K9/H3K36 methylation
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Affiliation(s)
- Stefania Comes
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso," CNR, 80131 Naples, Italy ; Institute of Genetics and Biophysics "A. Buzzati-Traverso," CNR, 80131 Naples, Italy
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A novel predicted calcium-regulated kinase family implicated in neurological disorders. PLoS One 2013; 8:e66427. [PMID: 23840464 PMCID: PMC3696010 DOI: 10.1371/journal.pone.0066427] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/08/2013] [Indexed: 12/03/2022] Open
Abstract
The catalogues of protein kinases, the essential effectors of cellular signaling, have been charted in Metazoan genomes for a decade now. Yet, surprisingly, using bioinformatics tools, we predicted protein kinase structure for proteins coded by five related human genes and their Metazoan homologues, the FAM69 family. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases present in four out of five human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. An EF-hand Ca2+-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase domain, suggests they may function as Ca2+-dependent kinases. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 (DIA1) and CXORF36 (DIA1R), are by large uncharacterised molecularly, yet linked to several neurological disorders in genetics studies. The C3ORF58 gene is found deleted in autism, and resides in the Golgi. Unusually high cysteine content and presence of signal peptides in some of the family members suggest that FAM69 proteins may be involved in phosphorylation of proteins in the secretory pathway and/or of extracellular proteins.
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Probst S, Zeller R, Zuniga A. The hedgehog target Vlk genetically interacts with Gli3 to regulate chondrocyte differentiation during mouse long bone development. Differentiation 2013; 85:121-30. [PMID: 23792766 DOI: 10.1016/j.diff.2013.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 02/08/2013] [Accepted: 03/05/2013] [Indexed: 10/26/2022]
Abstract
Endochondral bone development is orchestrated by the spatially and temporally coordinated differentiation of chondrocytes along the longitudinal axis of the cartilage anlage. Initially, the slowly proliferating, periarticular chondrocytes give rise to the pool of rapidly dividing columnar chondrocytes, whose expansion determines the length of the long bones. The Indian hedgehog (IHH) ligand regulates both the proliferation of columnar chondrocytes and their differentiation into post-mitotic hypertrophic chondrocytes in concert with GLI3, one of the main transcriptional effectors of HH signal transduction. In the absence of Hh signalling, the expression of Vlk (vertebrate lonesome kinase, also called Pkdcc) is increased. We now show that the shortening of limb long bones in Vlk-deficient mouse embryos is aggravated by additional inactivation of Gli3. Our analysis establishes that Vlk and Gli3 synergize to control the temporal kinetics of chondrocyte differentiation during long bone development. Whereas differentiation of limb mesenchymal progenitors into chondrocytes and the initial formation of the cartilage anlagen of the limb skeleton are not altered, Vlk and Gli3 are required for the temporally coordinated differentiation of periarticular into columnar and ultimately hypertrophic chondrocytes in long bones. In limbs lacking both Vlk and Gli3, the appearance of columnar and hypertrophic chondrocytes is severely delayed and zones of morphologically distinct chondrocytes are not established until E16.5. At the molecular level, these morphological alterations are reflected by delayed activation and lowered expression of Ihh, Pth1r and Col10a1 in long bone rudiments of double mutant limbs. In summary, our genetic analysis establishes that VLK plays a role in the IHH/GLI3 interactions and that Vlk and Gli3 cooperate to regulate long bone development by modulating the temporal kinetics of establishing columnar and hypertrophic chondrocyte domains.
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Affiliation(s)
- Simone Probst
- Developmental Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland
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Melvin VS, Feng W, Hernandez-Lagunas L, Artinger KB, Williams T. A morpholino-based screen to identify novel genes involved in craniofacial morphogenesis. Dev Dyn 2013; 242:817-31. [PMID: 23559552 DOI: 10.1002/dvdy.23969] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/11/2013] [Accepted: 03/24/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The regulatory mechanisms underpinning facial development are conserved between diverse species. Therefore, results from model systems provide insight into the genetic causes of human craniofacial defects. Previously, we generated a comprehensive dataset examining gene expression during development and fusion of the mouse facial prominences. Here, we used this resource to identify genes that have dynamic expression patterns in the facial prominences, but for which only limited information exists concerning developmental function. RESULTS This set of ∼80 genes was used for a high-throughput functional analysis in the zebrafish system using Morpholino gene knockdown technology. This screen revealed three classes of cranial cartilage phenotypes depending upon whether knockdown of the gene affected the neurocranium, viscerocranium, or both. The targeted genes that produced consistent phenotypes encoded proteins linked to transcription (meis1, meis2a, tshz2, vgll4l), signaling (pkdcc, vlk, macc1, wu:fb16h09), and extracellular matrix function (smoc2). The majority of these phenotypes were not altered by reduction of p53 levels, demonstrating that both p53-dependent and -independent mechanisms were involved in the craniofacial abnormalities. CONCLUSIONS This Morpholino-based screen highlights new genes involved in development of the zebrafish craniofacial skeleton with wider relevance to formation of the face in other species, particularly mouse and human.
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Affiliation(s)
- Vida Senkus Melvin
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Denver, Colorado, USA
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Bento M, Correia E, Tavares AT, Becker JD, Belo JA. Identification of differentially expressed genes in the heart precursor cells of the chick embryo. Gene Expr Patterns 2011; 11:437-47. [PMID: 21767665 DOI: 10.1016/j.gep.2011.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/19/2011] [Accepted: 07/04/2011] [Indexed: 02/04/2023]
Abstract
Genetic evidence has implicated several genes as being critical for heart development. However, the inducers of these genes as well as their targets and pathways they are involved with, remain largely unknown. Previous studies in the avian embryo showed that at HH4 Cerberus (cCer) transcripts are detected in the anterior endomesoderm including the heart precursor cells and later in the left lateral plate mesoderm. We have identified a promoter element of chick cCer able to drive EGFP expression in a population of cells that consistently exit from the anterior primitive streak region, from as early as stage HH3+, and that later will populate the heart. Using this promoter element as a tool allowed us to identify novel genes previously not known to potentially play a role in heart development. In order to identify and study genes expressed and involved in the correct development and differentiation of the vertebrate heart precursor cell (HPC) lineages, a differential screening using Affymetrix GeneChip system technologies was performed. Remarkably, this screening led to the identification of more than 700 transcripts differentially expressed in the heart forming regions (HFR). Bioinformatic tools allowed us to filter the large amount of data generated from this approach and to select a few transcripts for in vivo validation. Whole-mount in situ hybridization and sectioning of selected genes showed heart and vascular expression patterns for these transcripts during early chick development. We have developed an effective strategy to specifically identify genes that are differentially expressed in the HPC lineages. Within this set we have identified several genes that are expressed in the heart, blood and vascular lineages, which are likely to play a role in their development. These genes are potential candidates for future functional studies on early embryonic patterning.
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Affiliation(s)
- Margaret Bento
- Regenerative Medicine Program, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Portugal.
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Probst S, Kraemer C, Demougin P, Sheth R, Martin GR, Shiratori H, Hamada H, Iber D, Zeller R, Zuniga A. SHH propagates distal limb bud development by enhancing CYP26B1-mediated retinoic acid clearance via AER-FGF signalling. Development 2011; 138:1913-23. [PMID: 21471156 DOI: 10.1242/dev.063966] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The essential roles of SHH in anteroposterior (AP) and AER-FGF signalling in proximodistal (PD) limb bud development are well understood. In addition, these morphoregulatory signals are key components of the self-regulatory SHH/GREM1/AER-FGF feedback signalling system that regulates distal progression of limb bud development. This study uncovers an additional signalling module required for coordinated progression of limb bud axis development. Transcriptome analysis using Shh-deficient mouse limb buds revealed that the expression of proximal genes was distally extended from early stages onwards, which pointed to a more prominent involvement of SHH in PD limb axis development. In particular, retinoic acid (RA) target genes were upregulated proximally, while the expression of the RA-inactivating Cyp26b1 enzyme was downregulated distally, pointing to increased RA activity in Shh-deficient mouse limb buds. Further genetic and molecular analysis established that Cyp26b1 expression is regulated by AER-FGF signalling. During initiation of limb bud outgrowth, the activation of Cyp26b1 expression creates a distal 'RA-free' domain, as indicated by complementary downregulation of a transcriptional sensor of RA activity. Subsequently, Cyp26b1 expression increases as a consequence of SHH-dependent upregulation of AER-FGF signalling. To better understand the underlying signalling interactions, computational simulations of the spatiotemporal expression patterns and interactions were generated. These simulations predicted the existence of an antagonistic AER-FGF/CYP26B1/RA signalling module, which was verified experimentally. In summary, SHH promotes distal progression of limb development by enhancing CYP26B1-mediated RA clearance as part of a signalling network linking the SHH/GREM1/AER-FGF feedback loop to the newly identified AER-FGF/CYP26B1/RA module.
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Affiliation(s)
- Simone Probst
- Developmental Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland
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Castro-Giner F, Bustamante M, Ramon González J, Kogevinas M, Jarvis D, Heinrich J, Antó JM, Wjst M, Estivill X, de Cid R. A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS). BMC MEDICAL GENETICS 2009; 10:128. [PMID: 19961619 PMCID: PMC2797505 DOI: 10.1186/1471-2350-10-128] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 12/06/2009] [Indexed: 11/23/2022]
Abstract
Background Asthma and atopy are complex phenotypes with shared genetic component. In this study we attempt to identify genes related to these traits performing a two-stage DNA pooling genome-wide analysis in order to reduce costs. First, we assessed all markers in a subset of subjects using DNA pooling, and in a second stage we evaluated the most promising markers at an individual level. Methods For the genome-wide analysis, we constructed DNA pools from 75 subjects with atopy and asthma, 75 subjects with atopy and without asthma and 75 control subjects without atopy or asthma. In a second stage, the most promising regions surrounding significant markers after correction for false discovery rate were replicated with individual genotyping of samples included in the pools and an additional set of 429 atopic subjects and 222 controls from the same study centres. Results Homo sapiens protein kinase-like protein SgK493 (SGK493) was found to be associated with atopy. To lesser extent mitogen-activated protein kinase 5 (MAP3K5), collagen type XVIII alpha 1 (COL18A1) and collagen type XXIX alpha 1 (COL29A1) were also found to be associated with atopy. Functional evidences points out a role for MAP3K5, COL18A1 and COL29A1 but the function of SGK493 is unknown. Conclusion In this analysis we have identified new candidate regions related to atopy and suggest SGK493 as an atopy locus, although these results need further replication.
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