Toll-Like Receptors 1/2/4/6 and Nucleotide-Binding Oligomerization
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Genetic Diagnosis in First Or Second Trimester Pregnancy Loss Using Exome Sequencing: a Systematic Review of Human Essential Genes
Journal of Assisted Reproduction and Genetics (2019) 36:1539–1548 https://doi.org/10.1007/s10815-019-01499-6 REVIEW Genetic diagnosis in first or second trimester pregnancy loss using exome sequencing: a systematic review of human essential genes Sarah M. Robbins1,2 & Matthew A. Thimm3 & David Valle1 & Angie C. Jelin4 Received: 18 December 2018 /Accepted: 29 May 2019 /Published online: 4 July 2019 # Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract Purpose Non-aneuploid recurrent pregnancy loss (RPL) affects approximately 100,000 pregnancies worldwide annually. Exome sequencing (ES) may help uncover the genetic etiology of RPL and, more generally, pregnancy loss as a whole. Previous studies have attempted to predict the genes that, when disrupted, may cause human embryonic lethality. However, predictions by these early studies rarely point to the same genes. Case reports of pathogenic variants identified in RPL cases offer another clue. We evaluated known genetic etiologies of RPL identified by ES. Methods We gathered primary research articles from PubMed and Embase involving case reports of RPL reporting variants identified by ES. Two authors independently reviewed all articles for eligibility and extracted data based on predetermined criteria. Preliminary and amended analysis isolated 380 articles; 15 met all inclusion criteria. Results These 15 articles described 74 families with 279 reported RPLs with 34 candidate pathogenic variants in 19 genes (NOP14, FOXP3, APAF1, CASP9, CHRNA1, NLRP5, MMP10, FGA, FLT1, EPAS1, IDO2, STIL, DYNC2H1, IFT122, PA DI6, CAPS, MUSK, NLRP2, NLRP7) and 26 variants of unknown significance in 25 genes. These genes cluster in four essential pathways: (1) gene expression, (2) embryonic development, (3) mitosis and cell cycle progression, and (4) inflammation and immunity. -
Post-Transcriptional Inhibition of Luciferase Reporter Assays
THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 34, pp. 28705–28716, August 17, 2012 © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Post-transcriptional Inhibition of Luciferase Reporter Assays by the Nod-like Receptor Proteins NLRX1 and NLRC3* Received for publication, December 12, 2011, and in revised form, June 18, 2012 Published, JBC Papers in Press, June 20, 2012, DOI 10.1074/jbc.M111.333146 Arthur Ling‡1,2, Fraser Soares‡1,2, David O. Croitoru‡1,3, Ivan Tattoli‡§, Leticia A. M. Carneiro‡4, Michele Boniotto¶, Szilvia Benko‡5, Dana J. Philpott§, and Stephen E. Girardin‡6 From the Departments of ‡Laboratory Medicine and Pathobiology and §Immunology, University of Toronto, Toronto M6G 2T6, Canada, and the ¶Modulation of Innate Immune Response, INSERM U1012, Paris South University School of Medicine, 63, rue Gabriel Peri, 94276 Le Kremlin-Bicêtre, France Background: A number of Nod-like receptors (NLRs) have been shown to inhibit signal transduction pathways using luciferase reporter assays (LRAs). Results: Overexpression of NLRX1 and NLRC3 results in nonspecific post-transcriptional inhibition of LRAs. Conclusion: LRAs are not a reliable technique to assess the inhibitory function of NLRs. Downloaded from Significance: The inhibitory role of NLRs on specific signal transduction pathways needs to be reevaluated. Luciferase reporter assays (LRAs) are widely used to assess the Nod-like receptors (NLRs)7 represent an important class of activity of specific signal transduction pathways. Although pow- intracellular pattern recognition molecules (PRMs), which are erful, rapid and convenient, this technique can also generate implicated in the detection and response to microbe- and dan- www.jbc.org artifactual results, as revealed for instance in the case of high ger-associated molecular patterns (MAMPs and DAMPs), throughput screens of inhibitory molecules. -
ATP-Binding and Hydrolysis in Inflammasome Activation
molecules Review ATP-Binding and Hydrolysis in Inflammasome Activation Christina F. Sandall, Bjoern K. Ziehr and Justin A. MacDonald * Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada; [email protected] (C.F.S.); [email protected] (B.K.Z.) * Correspondence: [email protected]; Tel.: +1-403-210-8433 Academic Editor: Massimo Bertinaria Received: 15 September 2020; Accepted: 3 October 2020; Published: 7 October 2020 Abstract: The prototypical model for NOD-like receptor (NLR) inflammasome assembly includes nucleotide-dependent activation of the NLR downstream of pathogen- or danger-associated molecular pattern (PAMP or DAMP) recognition, followed by nucleation of hetero-oligomeric platforms that lie upstream of inflammatory responses associated with innate immunity. As members of the STAND ATPases, the NLRs are generally thought to share a similar model of ATP-dependent activation and effect. However, recent observations have challenged this paradigm to reveal novel and complex biochemical processes to discern NLRs from other STAND proteins. In this review, we highlight past findings that identify the regulatory importance of conserved ATP-binding and hydrolysis motifs within the nucleotide-binding NACHT domain of NLRs and explore recent breakthroughs that generate connections between NLR protein structure and function. Indeed, newly deposited NLR structures for NLRC4 and NLRP3 have provided unique perspectives on the ATP-dependency of inflammasome activation. Novel molecular dynamic simulations of NLRP3 examined the active site of ADP- and ATP-bound models. The findings support distinctions in nucleotide-binding domain topology with occupancy of ATP or ADP that are in turn disseminated on to the global protein structure. -
The Landscape of Genomic Imprinting Across Diverse Adult Human Tissues
Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Research The landscape of genomic imprinting across diverse adult human tissues Yael Baran,1 Meena Subramaniam,2 Anne Biton,2 Taru Tukiainen,3,4 Emily K. Tsang,5,6 Manuel A. Rivas,7 Matti Pirinen,8 Maria Gutierrez-Arcelus,9 Kevin S. Smith,5,10 Kim R. Kukurba,5,10 Rui Zhang,10 Celeste Eng,2 Dara G. Torgerson,2 Cydney Urbanek,11 the GTEx Consortium, Jin Billy Li,10 Jose R. Rodriguez-Santana,12 Esteban G. Burchard,2,13 Max A. Seibold,11,14,15 Daniel G. MacArthur,3,4,16 Stephen B. Montgomery,5,10 Noah A. Zaitlen,2,19 and Tuuli Lappalainen17,18,19 1The Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel; 2Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA; 3Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA; 5Department of Pathology, Stanford University, Stanford, California 94305, USA; 6Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA; 7Wellcome Trust Center for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, United Kingdom; 8Institute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland; 9Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; -
NLRP2 and FAF1 Deficiency Blocks Early Embryogenesis in the Mouse
REPRODUCTIONRESEARCH NLRP2 and FAF1 deficiency blocks early embryogenesis in the mouse Hui Peng1,*, Haijun Liu2,*, Fang Liu1, Yuyun Gao1, Jing Chen1, Jianchao Huo1, Jinglin Han1, Tianfang Xiao1 and Wenchang Zhang1 1College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, People’s Republic of China and 2Tianjin Institute of Animal Science and Veterinary Medicine, Tianjin, People’s Republic of China Correspondence should be addressed to W Zhang; Email: [email protected] *(H Peng and H Liu contributed equally to this work) Abstract Nlrp2 is a maternal effect gene specifically expressed by mouse ovaries; deletion of this gene from zygotes is known to result in early embryonic arrest. In the present study, we identified FAF1 protein as a specific binding partner of the NLRP2 protein in both mouse oocytes and preimplantation embryos. In addition to early embryos, both Faf1 mRNA and protein were detected in multiple tissues. NLRP2 and FAF1 proteins were co-localized to both the cytoplasm and nucleus during the development of oocytes and preimplantation embryos. Co-immunoprecipitation assays were used to confirm the specific interaction between NLRP2 and FAF1 proteins. Knockdown of the Nlrp2 or Faf1 gene in zygotes interfered with the formation of a NLRP2–FAF1 complex and led to developmental arrest during early embryogenesis. We therefore conclude that NLRP2 interacts with FAF1 under normal physiological conditions and that this interaction is probably essential for the successful development of cleavage-stage mouse embryos. Our data therefore indicated a potential role for NLRP2 in regulating early embryo development in the mouse. Reproduction (2017) 154 245–251 Introduction (Peng et al. -
NOD2 and Inflammation: Current Insights
Journal name: Journal of Inflammation Research Article Designation: REVIEW Year: 2018 Volume: 11 Journal of Inflammation Research Dovepress Running head verso: Negroni et al Running head recto: NOD2 and inflammation open access to scientific and medical research DOI: http://dx.doi.org/10.2147/JIR.S137606 Open Access Full Text Article REVIEW NOD2 and inflammation: current insights Anna Negroni1 Abstract: The nucleotide-binding oligomerization domain (NOD) protein, NOD2, belonging to Maria Pierdomenico2 the intracellular NOD-like receptor family, detects conserved motifs in bacterial peptidoglycan Salvatore Cucchiara2 and promotes their clearance through activation of a proinflammatory transcriptional program Laura Stronati3 and other innate immune pathways, including autophagy and endoplasmic reticulum stress. An inactive form due to mutations or a constitutive high expression of NOD2 is associated 1Division of Health Protection Technologies, Territorial and with several inflammatory diseases, suggesting that balanced NOD2 signaling is critical for Production Systems Sustainability the maintenance of immune homeostasis. In this review, we discuss recent developments about Department, ENEA, Rome, Italy; the pathway and mechanisms of regulation of NOD2 and illustrate the principal functions of 2Department of Pediatrics and Infantile Neuropsychiatry, Pediatric the gene, with particular emphasis on its central role in maintaining the equilibrium between Gastroenterology and Liver Unit, intestinal microbiota and host immune responses to control -
Mechanisms and Functions of Inflammasomes
Leading Edge Review Mechanisms and Functions of Inflammasomes Mohamed Lamkanfi1,2,* and Vishva M. Dixit3,* 1Department of Medical Protein Research, VIB, Ghent 9000, Belgium 2Department of Biochemistry, Ghent University, Ghent 9000, Belgium 3Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA *Correspondence: mohamed.lamkanfi@vib-ugent.be (M.L.), [email protected] (V.M.D.) http://dx.doi.org/10.1016/j.cell.2014.04.007 Recent studies have offered a glimpse into the sophisticated mechanisms by which inflamma- somes respond to danger and promote secretion of interleukin (IL)-1b and IL-18. Activation of cas- pases 1 and 11 in canonical and noncanonical inflammasomes, respectively, also protects against infection by triggering pyroptosis, a proinflammatory and lytic mode of cell death. The therapeutic potential of inhibiting these proinflammatory caspases in infectious and autoimmune diseases is raised by the successful deployment of anti-IL-1 therapies to control autoinflammatory diseases associated with aberrant inflammasome signaling. This Review summarizes recent insights into inflammasome biology and discusses the questions that remain in the field. Introduction DNA and trigger the production of type I interferon (Paludan From the primitive lamprey to humans, vertebrates use innate and Bowie, 2013). and adaptive immune systems to defend against pathogens Many PRRs encountering PAMPs and DAMPs trigger (Boehm et al., 2012). In mammals, the innate immune system signaling cascades that promote gene transcription by nuclear mounts the initial response to threats. Concomitantly, den- factor-kB (NF-kB), activator protein 1 (AP1), and interferon regu- dritic cells and other antigen-presenting cells (APCs) relay in- latory factors (IRFs). -
The Regulatory Network Behind MHC Class I Expression T ⁎ Marlieke L.M
Molecular Immunology 113 (2019) 16–21 Contents lists available at ScienceDirect Molecular Immunology journal homepage: www.elsevier.com/locate/molimm The regulatory network behind MHC class I expression T ⁎ Marlieke L.M. Jongsmaa, Greta Guardab, Robbert M. Spaapena, a Department of Immunopathology, Sanquin Research and Landsteiner Laboratory AMC/UvA, Plesmanlaan 125, 1066 CX Amsterdam, The Netherlands b Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland ARTICLE INFO ABSTRACT Keywords: The MHC class I pathway, presenting endogenously derived peptides to T lymphocytes, is hijacked in many MHC class I pathological conditions. This affects MHC class I levels and peptide presentation at the cell surface leading to NLRC5 immune escape of cancer cells or microbes. It is therefore important to identify the molecular mechanisms Transcription behind MHC class I expression, processing and antigen presentation. The identification of NLRC5 as regulator of Expression MHC class I transcription was a huge step forward in understanding the transcriptional mechanism involved. Regulation Nevertheless, many questions concerning MHC class I transcription are yet unsolved. Here we illuminate current Screen knowledge on MHC class I and NLRC5 transcription, we highlight some remaining questions and discuss the use of quickly developing high-content screening tools to reveal unknowns in MHC class I transcription in the near future. 1. Introduction family and acid domain containing) was identified in 1993 as the master regulator of MHC transcription (Steimle et al., 1993). However, The role of MHC (Major Histocompatibility Complex) molecules in it soon became clear that CIITA, though capable of activating both MHC adaptive immunity has been extensively studied since their discovery in class I and class II transcription in vitro (Martin et al., 1997), could not 1936 (Klein, 1986). -
NOD-Like Receptors (Nlrs) and Inflammasomes
International Edition www.adipogen.com NOD-like Receptors (NLRs) and Inflammasomes In mammals, germ-line encoded pattern recognition receptors (PRRs) detect the presence of pathogens through recognition of pathogen-associated molecular patterns (PAMPs) or endogenous danger signals through the sensing of danger-associated molecular patterns (DAMPs). The innate immune system comprises several classes of PRRs that allow the early detection of pathogens at the site of infection. The membrane-bound toll-like receptors (TLRs) and C-type lectin receptors (CTRs) detect PAMPs in extracellular milieu and endo- somal compartments. TRLs and CTRs cooperate with PRRs sensing the presence of cytosolic nucleic acids, like RNA-sensing RIG-I (retinoic acid-inducible gene I)-like receptors (RLRs; RLHs) or DNA-sensing AIM2, among others. Another set of intracellular sensing PRRs are the NOD-like receptors (NLRs; nucleotide-binding domain leucine-rich repeat containing receptors), which not only recognize PAMPs but also DAMPs. PAMPs FUNGI/PROTOZOA BACTERIA VIRUSES MOLECULES C. albicans A. hydrophila Adenovirus Bacillus anthracis lethal Plasmodium B. brevis Encephalomyo- toxin (LeTx) S. cerevisiae E. coli carditis virus Bacterial pore-forming L. monocytogenes Herpes simplex virus toxins L. pneumophila Influenza virus Cytosolic dsDNA N. gonorrhoeae Sendai virus P. aeruginosa Cytosolic flagellin S. aureus MDP S. flexneri meso-DAP S. hygroscopicus S. typhimurium DAMPs MOLECULES PARTICLES OTHERS DNA Uric acid UVB Extracellular ATP CPPD Mutations R837 Asbestos Cytosolic dsDNA Irritants Silica Glucose Alum Hyaluronan Amyloid-b Hemozoin Nanoparticles FIGURE 1: Overview on PAMPs and DAMPs recognized by NLRs. NOD-like Receptors [NLRs] The intracellular NLRs organize signaling complexes such as inflammasomes and NOD signalosomes. -
Human Leucine-Rich Repeat Proteins: a Genome-Wide Bioinformatic Categorization and Functional Analysis in Innate Immunity
Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity Aylwin C. Y. Nga,b,1, Jason M. Eisenberga,b,1, Robert J. W. Heatha, Alan Huetta, Cory M. Robinsonc, Gerard J. Nauc, and Ramnik J. Xaviera,b,2 aCenter for Computational and Integrative Biology, and Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114; bThe Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142; and cMicrobiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 Edited by Jeffrey I. Gordon, Washington University School of Medicine, St. Louis, MO, and approved June 11, 2010 (received for review February 17, 2010) In innate immune sensing, the detection of pathogen-associated proteins have been implicated in human diseases to date, notably molecular patterns by recognition receptors typically involve polymorphisms in NOD2 in Crohn disease (8, 9), CIITA in leucine-rich repeats (LRRs). We provide a categorization of 375 rheumatoid arthritis and multiple sclerosis (10), and TLR5 in human LRR-containing proteins, almost half of which lack other Legionnaire disease (11). identifiable functional domains. We clustered human LRR proteins Most LRR domains consist of a chain of between 2 and 45 by first assigning LRRs to LRR classes and then grouping the proteins LRRs (12). Each repeat in turn is typically 20 to 30 residues long based on these class assignments, revealing several of the resulting and can be divided into a highly conserved segment (HCS) fol- protein groups containing a large number of proteins with certain lowed by a variable segment (VS). -
NLRP2 Controls Age-Associated Maternal Fertility
Published November 23, 2016 Brief Definitive Report NLRP2 controls age-associated maternal fertility Anna A. Kuchmiy,1,2 Jinke D’Hont,1,3 Tino Hochepied,1,3 and Mohamed Lamkanfi1,2 1Inflammation Research Center, VIB, B-9052 Zwijnaarde, Belgium 2Department of Internal Medicine and 3Department of Biomedical Molecular Biology, Ghent University, B-9000 Ghent, Belgium Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are well-known for their key roles in the immune system. Ectopically expressed NLRP2 in immortalized cell lines assembles an inflammasome and inhibits activation of the proinflam- matory transcription factor NF-κB, but the physiological roles of NLRP2 are unknown. Here, we show that Nlrp2-deficient mice were born with expected Mendelian ratios and that Nlrp2 was dispensable for innate and adaptive immunity. The obser- vation that Nlrp2 was exclusively expressed in oocytes led us to explore the role of Nlrp2 in parthenogenetic activation of oocytes. Remarkably, unlike oocytes of young adult Nlrp2-deficient mice, activated oocytes of mature adult mice developed slower and largely failed to reach the blastocyst stage. In agreement, we noted strikingly declining reproductive rates in vivo with progressing age of female Nlrp2-deficient mice. This work identifies Nlrp2 as a critical regulator of oocyte quality and suggests that NLRP2 variants with reduced activity may contribute to maternal age-associated fertility loss in humans. Downloaded from INTRODUCTION Nucleotide-binding domain and leucine-rich repeat (NLR) Unlike the aforementioned NLRs, the roles of NLRP2 proteins are well-established hub proteins regulating a di- are ill-defined. Ectopically expressed NLRP2 was shown to versity of inflammatory and host defense responses in the regulate inflammasome signaling and to inhibit NF-κB ac- immune system. -
NOD2: Activation During Bacterial and Viral Infections, Polymorphisms
REVISTA DE INVESTIGACIÓN CLÍNICA Contents available at PubMed www.clinicalandtranslationalinvestigation.com PERMANYER Rev Inves Clin. 2018;70:18-28 IN-DEPTH REVIEW NOD2: Activation During Bacterial and Viral Infections, Polymorphisms and Potential as Therapeutic Target Diana Alhelí Domínguez-Martínez1, Daniel Núñez-Avellaneda1, Carlos Alberto Castañón-Sánchez2 and Ma Isabel Salazar3* 1Laboratorio de Inmunología Celular e Inmunopatogénesis, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City; 2Subdirección de Enseñanza e Investigación, Hospital Regional de Alta Especialidad de Oaxaca, San Bartolo Coyotepec, Oax.; 3Sección de Inmunovirología, Laboratorio de Virología, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico ABSTRACT Nucleotide-binding domain (NBD) leucine-rich repeat (LRR)-containing receptors or NLRs are a family of receptors that detect both, molecules associated to pathogens and alarmins, and are located mainly in the cytoplasm. NOD2 belongs to the NLR family and is a dynamic receptor capable of interacting with multiple proteins and modulate immune responses in a stimuli-dependent manner. The experimental evidence shows that interaction between NOD2 structural domains and the effector proteins shape the overall response against bacterial or viral infections. Other reports have focused on the importance of NOD2 not only in infection but also in maintaining tissue homeostasis. However, not only protein interactions relate to function but also certain polymorphisms in the gene that encodes NOD2 have been associated with inflammatory diseases, such as Crohn’s disease. Here, we review the importance and general characteristics of NOD2, discussing its participation in infections caused by bacteria and viruses as well as its interaction with other pathogen recognition receptors or effectors to induce antibacterial and antiviral responses.