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Bruschi M, Angeletti A, Prunotto M, Meroni PL, Ghiggeri GM, Moroni G, Sinico RA, Franceschini F, Fredi M, Vaglio A, Cavalli A, Scapozza L, Patel JJ, Tan JC, Lo KC, Cavagna L, Petretto A, Pratesi F, Migliorini P, Locatelli F, Pazzola G, Pesce G, Giannese D, Manfredi A, Ramirez GA, Esposito P, Murdaca G, Negrini S, Bui F, Trezzi B, Emmi G, Cavazzana I, Binda V, Fenaroli P, Pisan I, Montecucco C, Santoro D, Scolari F, Mescia F, Volpi S, Mosca M, Tincani A, Ravelli A, Murtas C, Candiano G, Caridi G, La Porta E, Verrina E. A critical view on autoantibodies in lupus nephritis: Concrete knowledge based on evidence. Autoimmun Rev 2024; 23:103535. [PMID: 38552995 DOI: 10.1016/j.autrev.2024.103535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/07/2024]
Abstract
Deposition of autoantibodies in glomeruli is a key factor in the development of lupus nephritis (LN). For a long time, anti-dsDNA and anti-C1q antibodies were thought to be the main cause of the kidney damage. However, recent studies have shown that the list of autoantibidies that have renal tropism and deposit in the kidney in LN is increasing and the link between anti-dsDNA and renal pathology is weak due to potential confounders. Aspecific bindings of dsDNA with cationic antibodies and of anti-dsDNA with several renal antigens such as actinin, laminin, entactin, and annexinA2 raised doubts about the specific target of these antibodies in the kidney. Moreover, the isotype of anti-dsDNA in SLE and LN has never received adequate interest until the recent observation that IgG2 are preponderant over IgG1, IgG3 and IgG4. Based on the above background, recent studies investigated the involvement of anti-dsDNA IgG2 and of other antibodies in LN. It was concluded that circulating anti-dsDNA IgG2 levels do not distinguish between LN versus non-renal SLE, and, in patients with LN, their levels do not change over time. Circulating levels of other antibodies such as anti-ENO1 and anti-H2 IgG2 were, instead, higher in LN vs non-renal SLE at the time of diagnosis and decreased following therapies. Finally, new classes of renal antibodies that potentially modify the anti-inflammatory response in the kidney are emerging as new co-actors in the pathogenetic scenario. They have been defined as 'second wave antibodies' for the link with detoxifying mechanisms limiting the oxidative stress in glomeruli that are classically stimulated in a second phase of inflammation. These findings have important clinical implications that may modify the laboratory approach to LN. Serum levels of anti-ENO1 and anti-H2 IgG2 should be measured in the follow up of patients for designing the length of therapies and identify those patients who respond to treatments. Anti-SOD2 could help to monitor and potentiate the anti-inflammatory response in the kidney.
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Affiliation(s)
- Maurizio Bruschi
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Andrea Angeletti
- Division of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marco Prunotto
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Pier Luigi Meroni
- Experimental Laboratory of Immunological and Rheumatologic Researches, Istituto Auxologico Italiano-Istituto di Ricovero e Cura a Carattere Scientifico, Milano, Italy.
| | - Gian Marco Ghiggeri
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Division of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - Gabriella Moroni
- Department of Biomedical Sciences, Humanitas University and IRCCS Humanitas Research Hospital, Milan, Italy
| | | | - Franco Franceschini
- Rheumatology and Clinical Immunology, ASST SpedaliCivili and Università of Brescia, Italy
| | - Micaela Fredi
- Rheumatology and Clinical Immunology, ASST SpedaliCivili and Università of Brescia, Italy
| | - Augusto Vaglio
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Firenze, and Nephrology and Dialysis Unit, Meyer Children's Hospital, Firenze, Italy
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Leonardo Scapozza
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | | | | | - Ken C Lo
- Nimble Therapeutics, Madison, WI, USA
| | - Lorenzo Cavagna
- Division of Rheumatology, University and IRCCS Policlinico S. Matteo, Pavia, Italy
| | - Andrea Petretto
- Core Facilities-Proteomics Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Federico Pratesi
- Clinical Immunology Unit, Department of Internal Medicine, University of Pisa, Italy
| | - Paola Migliorini
- Clinical Immunology Unit, Department of Internal Medicine, University of Pisa, Italy
| | - Francesco Locatelli
- Division of Rheumatology, University and IRCCS Policlinico S. Matteo, Pavia, Italy
| | - Giulia Pazzola
- Nephrology and Dialysis, Arciospedale Santa Maria nuova, Reggio Emilia, Italy
| | - Giampaola Pesce
- Nephrology and Dialysis, Arciospedale Santa Maria nuova, Reggio Emilia, Italy
| | | | - Angelo Manfredi
- Unit of Internal Medicine and Immunology, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Giuseppe A Ramirez
- Unit of Internal Medicine and Immunology, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Pasquale Esposito
- Division of Nephrology, University of Genoa and Policlinico San Martino, Genova, Italy
| | | | - Simone Negrini
- Department of Internal Medicine, University of Genoa, Italy
| | - Federica Bui
- Division of Nephrology, University of Genoa and Policlinico San Martino, Genova, Italy
| | - Barbara Trezzi
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Giacomo Emmi
- Lupus Clinic Department of biomedicine, University of Florence, University Hospital Careggi, Florence, Italy
| | - Ilaria Cavazzana
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Valentina Binda
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Firenze, and Nephrology and Dialysis Unit, Meyer Children's Hospital, Firenze, Italy
| | - Paride Fenaroli
- Nephrology Unit, University Hospital, University of Parma, Parma, Italy
| | - Isabella Pisan
- Nephrology Unit, University Hospital, University of Parma, Parma, Italy
| | | | - Domenico Santoro
- Nephrology and Dialysis Unit, University of Messina and G Martino Hospital, Messina, Italy
| | - Francesco Scolari
- Division of Nephrology and Dialysis, ASST SpedaliCivili and Università of Brescia, Brescia, Italy
| | - Federica Mescia
- Division of Nephrology and Dialysis, ASST SpedaliCivili and Università of Brescia, Brescia, Italy
| | - Stefano Volpi
- Division of Paediatric Rheumatology and Scientific Institute for Research and Health Care, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marta Mosca
- Rheumatologu Unit, Department of Clinical and Experimental Medicine, University of Pisa, Italy
| | - Angela Tincani
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Angelo Ravelli
- Division of Paediatric Rheumatology and Scientific Institute for Research and Health Care, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Corrado Murtas
- Nephrology and Dialysis Unit, Ospedale Belcolle, 01100 Viterbo, Italy
| | - Giovanni Candiano
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Gianluca Caridi
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Edoardo La Porta
- Division of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Enrico Verrina
- Division of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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Bach E, Fitzgerald SF, Williams-MacDonald SE, Mitchell M, Golde WT, Longbottom D, Nisbet AJ, Dinkla A, Sullivan E, Pinapati RS, Tan JC, Joosten LAB, Roest HJ, Østerbye T, Koets AP, Buus S, McNeilly TN. Genome-wide epitope mapping across multiple host species reveals significant diversity in antibody responses to Coxiella burnetii vaccination and infection. Front Immunol 2023; 14:1257722. [PMID: 37954609 PMCID: PMC10637584 DOI: 10.3389/fimmu.2023.1257722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/19/2023] [Indexed: 11/14/2023] Open
Abstract
Coxiella burnetii is an important zoonotic bacterial pathogen of global importance, causing the disease Q fever in a wide range of animal hosts. Ruminant livestock, in particular sheep and goats, are considered the main reservoir of human infection. Vaccination is a key control measure, and two commercial vaccines based on formalin-inactivated C. burnetii bacterins are currently available for use in livestock and humans. However, their deployment is limited due to significant reactogenicity in individuals previously sensitized to C. burnetii antigens. Furthermore, these vaccines interfere with available serodiagnostic tests which are also based on C. burnetii bacterin antigens. Defined subunit antigen vaccines offer significant advantages, as they can be engineered to reduce reactogenicity and co-designed with serodiagnostic tests to allow discrimination between vaccinated and infected individuals. This study aimed to investigate the diversity of antibody responses to C. burnetii vaccination and/or infection in cattle, goats, humans, and sheep through genome-wide linear epitope mapping to identify candidate vaccine and diagnostic antigens within the predicted bacterial proteome. Using high-density peptide microarrays, we analyzed the seroreactivity in 156 serum samples from vaccinated and infected individuals to peptides derived from 2,092 open-reading frames in the C. burnetii genome. We found significant diversity in the antibody responses within and between species and across different types of C. burnetii exposure. Through the implementation of three different vaccine candidate selection methods, we identified 493 candidate protein antigens for protein subunit vaccine design or serodiagnostic evaluation, of which 65 have been previously described. This is the first study to investigate multi-species seroreactivity against the entire C. burnetii proteome presented as overlapping linear peptides and provides the basis for the selection of antigen targets for next-generation Q fever vaccines and diagnostic tests.
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Affiliation(s)
- Emil Bach
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | - Annemieke Dinkla
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostic Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Eric Sullivan
- Nimble Therapeutics, Inc., Madison, WI, United States
| | | | - John C. Tan
- Nimble Therapeutics, Inc., Madison, WI, United States
| | - Leo A. B. Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hendrik-Jan Roest
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostic Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
- Ministry of Agriculture, Nature and Food Quality, Den Haag, Netherlands
- Department of Infection and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Thomas Østerbye
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ad P. Koets
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostic Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Søren Buus
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
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Tewey MA, Coulibaly D, Lawton JG, Stucke EM, Zhou AE, Berry AA, Bailey JA, Pike A, Dara A, Ouattara A, Lyke KE, Ifeonu O, Laurens MB, Adams M, Takala-Harrison S, Niangaly A, Kouriba B, Koné AK, Rowe JA, Doumbo OK, Patel JJ, Tan JC, Felgner PL, Plowe CV, Thera MA, Travassos MA. Natural immunity to malaria preferentially targets the endothelial protein C receptor-binding regions of PfEMP1s. mSphere 2023; 8:e0045123. [PMID: 37791774 PMCID: PMC10597466 DOI: 10.1128/msphere.00451-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 10/05/2023] Open
Abstract
Antibody responses to variant surface antigens (VSAs) produced by the malaria parasite Plasmodium falciparum may contribute to age-related natural immunity to severe malaria. One VSA family, P. falciparum erythrocyte membrane protein-1 (PfEMP1), includes a subset of proteins that binds endothelial protein C receptor (EPCR) in human hosts and potentially disrupts the regulation of inflammatory responses, which may lead to the development of severe malaria. We probed peptide microarrays containing segments spanning five PfEMP1 EPCR-binding domain variants with sera from 10 Malian adults and 10 children to determine the differences between adult and pediatric immune responses. We defined serorecognized peptides and amino acid residues as those that elicited a significantly higher antibody response than malaria-naïve controls. We aimed to identify regions consistently serorecognized among adults but not among children across PfEMP1 variants, potentially indicating regions that drive the development of immunity to severe malaria. Adult sera consistently demonstrated broader and more intense serologic responses to constitutive PfEMP1 peptides than pediatric sera, including peptides in EPCR-binding domains. Both adults and children serorecognized a significantly higher proportion of EPCR-binding peptides than peptides that do not directly participate in receptor binding, indicating a preferential development of serologic responses at functional residues. Over the course of a single malaria transmission season, pediatric serological responses increased between the start and the peak of the season, but waned as the transmission season ended. IMPORTANCE Severe malaria and death related to malaria disproportionately affect sub-Saharan children under 5 years of age, commonly manifesting as cerebral malaria and/or severe malarial anemia. In contrast, adults in malaria-endemic regions tend to experience asymptomatic or mild disease. Our findings indicate that natural immunity to malaria targets specific regions within the EPCR-binding domain, particularly peptides containing EPCR-binding residues. Epitopes containing these residues may be promising targets for vaccines or therapeutics directed against severe malaria. Our approach provides insight into the development of natural immunity to a binding target linked to severe malaria by characterizing an "adult-like" response as recognizing a proportion of epitopes within the PfEMP1 protein, particularly regions that mediate EPCR binding. This "adult-like" response likely requires multiple years of malaria exposure, as increases in pediatric serologic response over a single malaria transmission season do not appear significant.
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Affiliation(s)
- Madison A. Tewey
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Drissa Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Jonathan G. Lawton
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Emily M. Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Albert E. Zhou
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrea A. Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jason A. Bailey
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pike
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Antoine Dara
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Amed Ouattara
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kirsten E. Lyke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Olukemi Ifeonu
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Matthew B. Laurens
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Matthew Adams
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Abdoulaye K. Koné
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - J. Alexandra Rowe
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ogobara K. Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | | | - John C. Tan
- Roche NimbleGen, Inc., Madison, Wisconsin, USA
| | - Philip L. Felgner
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, California, USA
| | - Christopher V. Plowe
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Mahamadou A. Thera
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Mark A. Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Krabbe NP, Razo E, Abraham HJ, Spanton RV, Shi Y, Bhattacharya S, Bohm EK, Pritchard JC, Weiler AM, Mitzey AM, Eickhoff JC, Sullivan E, Tan JC, Aliota MT, Friedrich TC, O’Connor DH, Golos TG, Mohr EL. Control of maternal Zika virus infection during pregnancy is associated with lower antibody titers in a macaque model. Front Immunol 2023; 14:1267638. [PMID: 37809089 PMCID: PMC10556460 DOI: 10.3389/fimmu.2023.1267638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Zika virus (ZIKV) infection during pregnancy results in a spectrum of birth defects and neurodevelopmental deficits in prenatally exposed infants, with no clear understanding of why some pregnancies are more severely affected. Differential control of maternal ZIKV infection may explain the spectrum of adverse outcomes. Methods Here, we investigated whether the magnitude and breadth of the maternal ZIKV-specific antibody response is associated with better virologic control using a rhesus macaque model of prenatal ZIKV infection. We inoculated 18 dams with an Asian-lineage ZIKV isolate (PRVABC59) at 30-45 gestational days. Plasma vRNA and infectious virus kinetics were determined over the course of pregnancy, as well as vRNA burden in the maternal-fetal interface (MFI) at delivery. Binding and neutralizing antibody assays were performed to determine the magnitude of the ZIKV-specific IgM and IgG antibody responses throughout pregnancy, along with peptide microarray assays to define the breadth of linear ZIKV epitopes recognized. Results Dams with better virologic control (n= 9) cleared detectable infectious virus and vRNA from the plasma by 7 days post-infection (DPI) and had a lower vRNA burden in the MFI at delivery. In comparison, dams with worse virologic control (n= 9) still cleared detectable infectious virus from the plasma by 7 DPI but had vRNA that persisted longer, and had higher vRNA burden in the MFI at delivery. The magnitudes of the ZIKV-specific antibody responses were significantly lower in the dams with better virologic control, suggesting that higher antibody titers are not associated with better control of ZIKV infection. Additionally, the breadth of the ZIKV linear epitopes recognized did not differ between the dams with better and worse control of ZIKV infection. Discussion Thus, the magnitude and breadth of the maternal antibody responses do not seem to impact maternal virologic control. This may be because control of maternal infection is determined in the first 7 DPI, when detectable infectious virus is present and before robust antibody responses are generated. However, the presence of higher ZIKV-specific antibody titers in dams with worse virologic control suggests that these could be used as a biomarker of poor maternal control of infection and should be explored further.
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Affiliation(s)
- Nicholas P. Krabbe
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Elaina Razo
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Hunter J. Abraham
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Rachel V. Spanton
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Yujia Shi
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Saswati Bhattacharya
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, United States
| | - Julia C. Pritchard
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, United States
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Ann M. Mitzey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Jens C. Eickhoff
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Healthy, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric Sullivan
- Nimble Therapeutics, Inc, Madison, WI, United States
| | - John C. Tan
- Nimble Therapeutics, Inc, Madison, WI, United States
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, United States
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - David H. O’Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Thaddeus G. Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
- Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Emma L. Mohr
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
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Ho MT, Tan JC. The association between foot posture, single leg balance and running biomechanics of the foot. Foot (Edinb) 2022; 53:101946. [PMID: 36463612 DOI: 10.1016/j.foot.2022.101946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/05/2022] [Accepted: 10/28/2022] [Indexed: 12/04/2022]
Abstract
OBJECTIVES A mal-aligned foot posture (high-arched and flat feet) and poor single leg balance ability have been separately associated with foot injuries during running. Therefore, clinicians assess these routinely. However, the extent to which foot posture and single-leg balance ability affect actual foot biomechanics during running is not known. This study aims to investigate the association of foot posture, single-leg balance ability, and foot biomechanics during running. METHOD This is a cross sectional study of sixty-nine participants who had their foot postures and single-leg balance ability assessed. The Foot Posture Index and Balance Error Scoring System were used. Their foot kinetics was measured as they ran on an instrumented treadmill and foot kinematics was processed using a 3D motion capture system. Multiple-regression was used to analyse the variance of foot biomechanics explained by foot posture and single-leg balance ability. RESULTS Foot posture and single-leg balance ability were found to account significantly for the variance in rearfoot eversion (24%) and forefoot dorsiflexion (7%). Two regression equations were derived, where rearfoot eversion and forefoot dorsiflexion during running may be predicted. CONCLUSION Foot posture and single-leg balance ability can predict rearfoot eversion and forefoot dorsiflexion only during running. Based on the regression equations, individuals with the same foot posture but different single-leg balance ability may exhibit different foot kinematics. However, the angular differences are small. The equations may be useful for clinicians working in places where running gait analysis equipment are not readily accessible. Further studies with larger sample sizes are required to validate these equations. In addition, further studies are necessary to investigate the effect of these two variables under different running conditions e.g. with footwear and with orthoses.
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Affiliation(s)
- Malia T Ho
- Department of Podiatry, School of Health, Medical and Applied Sciences, CQUniversity Australia, Building 34, Bruce Highway, North Rockhampton, QLD 4701, Australia.
| | - John C Tan
- Physical Education and Sports Science Academic Group, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Singapore.
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Rettig TA, Tan JC, Nishiyama NC, Chapes SK, Pecaut MJ. An Analysis of the Effects of Spaceflight and Vaccination on Antibody Repertoire Diversity. Immunohorizons 2021; 5:675-686. [PMID: 34433623 PMCID: PMC10996920 DOI: 10.4049/immunohorizons.2100056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/26/2021] [Indexed: 11/19/2022] Open
Abstract
Ab repertoire diversity plays a critical role in the host's ability to fight pathogens. CDR3 is partially responsible for Ab-Ag binding and is a significant source of diversity in the repertoire. CDR3 diversity is generated during VDJ rearrangement because of gene segment selection, gene segment trimming and splicing, and the addition of nucleotides. We analyzed the Ab repertoire diversity across multiple experiments examining the effects of spaceflight on the Ab repertoire after vaccination. Five datasets from four experiments were analyzed using rank-abundance curves and Shannon indices as measures of diversity. We discovered a trend toward lower diversity as a result of spaceflight but did not find the same decrease in our physiological model of microgravity in either the spleen or bone marrow. However, the bone marrow repertoire showed a reduction in diversity after vaccination. We also detected differences in Shannon indices between experiments and tissues. We did not detect a pattern of CDR3 usage across the experiments. Overall, we were able to find differences in the Ab repertoire diversity across experimental groups and tissues.
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Affiliation(s)
- Trisha A Rettig
- Division of Biomedical Engineering Sciences, Department of Basic Sciences, Loma Linda University, Loma Linda, CA
- Division of Biology, Kansas State University, Manhattan, KS
| | - John C Tan
- Division of Biomedical Engineering Sciences, Department of Basic Sciences, Loma Linda University, Loma Linda, CA
| | - Nina C Nishiyama
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; and
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Michael J Pecaut
- Division of Biomedical Engineering Sciences, Department of Basic Sciences, Loma Linda University, Loma Linda, CA;
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Friedman-Klabanoff DJ, Travassos MA, Ifeonu OO, Agrawal S, Ouattara A, Pike A, Bailey JA, Adams M, Coulibaly D, Lyke KE, Laurens MB, Takala-Harrison S, Kouriba B, Kone AK, Doumbo OK, Patel JJ, Thera MA, Felgner PL, Tan JC, Plowe CV, Berry AA. Epitope-Specific Antibody Responses to a Plasmodium falciparum Subunit Vaccine Target in a Malaria-Endemic Population. J Infect Dis 2020; 223:1943-1947. [PMID: 32992328 DOI: 10.1093/infdis/jiaa611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/25/2020] [Indexed: 11/14/2022] Open
Abstract
Circumsporozoite protein (CSP) coats the Plasmodium falciparum sporozoite surface and is a major malaria subunit vaccine target. We measured epitope-specific reactivity to field-derived CSP haplotypes in serum samples from Malian adults and children on a custom peptide microarray. Compared to children, adults showed greater antibody responses and responses to more variants in regions proximal to and within the central repeat region. Children acquired short-lived immunity to an epitope proximal to the central repeat region but not to the central repeat region itself. This approach has the potential to differentiate immunodominant from protective epitope-specific responses when combined with longitudinal infection data.
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Affiliation(s)
- DeAnna J Friedman-Klabanoff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Mark A Travassos
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Olukemi O Ifeonu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sonia Agrawal
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amed Ouattara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pike
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jason A Bailey
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Drissa Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Kirsten E Lyke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Matthew B Laurens
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Abdoulaye K Kone
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Ogobara K Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | | | - Mahamadou A Thera
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Philip L Felgner
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, California, USA
| | - John C Tan
- Roche Sequencing Solutions, Madison, Wisconsin, USA
| | - Christopher V Plowe
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrea A Berry
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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8
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Bailey JA, Berry AA, Travassos MA, Ouattara A, Boudova S, Dotsey EY, Pike A, Jacob CG, Adams M, Tan JC, Bannen RM, Patel JJ, Pablo J, Nakajima R, Jasinskas A, Dutta S, Takala-Harrison S, Lyke KE, Laurens MB, Niangaly A, Coulibaly D, Kouriba B, Doumbo OK, Thera MA, Felgner PL, Plowe CV. Microarray analyses reveal strain-specific antibody responses to Plasmodium falciparum apical membrane antigen 1 variants following natural infection and vaccination. Sci Rep 2020; 10:3952. [PMID: 32127565 PMCID: PMC7054363 DOI: 10.1038/s41598-020-60551-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 02/13/2020] [Indexed: 11/30/2022] Open
Abstract
Vaccines based on Plasmodium falciparum apical membrane antigen 1 (AMA1) have failed due to extensive polymorphism in AMA1. To assess the strain-specificity of antibody responses to malaria infection and AMA1 vaccination, we designed protein and peptide microarrays representing hundreds of unique AMA1 variants. Following clinical malaria episodes, children had short-lived, sequence-independent increases in average whole-protein seroreactivity, as well as strain-specific responses to peptides representing diverse epitopes. Vaccination resulted in dramatically increased seroreactivity to all 263 AMA1 whole-protein variants. High-density peptide analysis revealed that vaccinated children had increases in seroreactivity to four distinct epitopes that exceeded responses to natural infection. A single amino acid change was critical to seroreactivity to peptides in a region of AMA1 associated with strain-specific vaccine efficacy. Antibody measurements using whole antigens may be biased towards conserved, immunodominant epitopes. Peptide microarrays may help to identify immunogenic epitopes, define correlates of vaccine protection, and measure strain-specific vaccine-induced antibodies.
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Affiliation(s)
- Jason A Bailey
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrea A Berry
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark A Travassos
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amed Ouattara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sarah Boudova
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emmanuel Y Dotsey
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA
| | - Andrew Pike
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - John C Tan
- Previous address: Roche Sequencing Solutions, Madison, WI, USA
- Nimble Therapeutics, Madison, WI, USA
| | - Ryan M Bannen
- Previous address: Roche Sequencing Solutions, Madison, WI, USA
- Nimble Therapeutics, Madison, WI, USA
| | - Jigar J Patel
- Previous address: Roche Sequencing Solutions, Madison, WI, USA
- Nimble Therapeutics, Madison, WI, USA
| | - Jozelyn Pablo
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA
| | - Rie Nakajima
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA
| | - Algis Jasinskas
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA
| | - Sheetij Dutta
- U.S. Military Malaria Vaccine Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kirsten E Lyke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew B Laurens
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Drissa Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ogobara K Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou A Thera
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Philip L Felgner
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA
| | - Christopher V Plowe
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
- Duke Global Health Institute, Duke University, Durham, NC, USA.
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9
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Forde D, Deming DD, Tan JC, Phillips RM, Fry-Bowers EK, Barger MK, Bahjri K, Angeles DM, Boskovic DS. Oxidative Stress Biomarker Decreased in Preterm Neonates Treated With Kangaroo Mother Care. Biol Res Nurs 2020; 22:188-196. [PMID: 31973579 DOI: 10.1177/1099800419900231] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVE Due to physiological and metabolic immaturity, prematurely born infants are at increased risk because of maternal separation in many neonatal intensive care units (NICUs). The stress induced from maternal-infant separation can lead to well-documented short-term physiologic instability and potentially lifelong neurological, sociological, or psychological sequelae. Based on previous studies of kangaroo mother care (KMC) that demonstrated improvement in physiologic parameters, we examined the impact of KMC on physiologic measures of stress (abdominal temperature, heart rate, oxygen saturation, perfusion index, near-infrared spectrometry), oxidative stress, and energy utilization/conservation in preterm infants. METHODS In this randomized, stratified study of premature neonates, we compared the effects on urinary concentrations of biomarkers of energy utilization and oxidative stress of 1 hr of KMC versus incubator care on Day 3 of life in intervention-group babies (n = 26) and control-group babies (n = 25), respectively. On Day 4, both groups received 1 hr of KMC. Urinary samples were collected 3 hr before and 3 hr after intervention/incubator care on both days. Energy utilization was assessed by measures of adenosine triphosphate (ATP) degradation (i.e., hypoxanthine, xanthine, and uric acid). Oxidative stress was assessed using urinary allantoin. Mixed-models analysis was used to assess differences in purine/allantoin. RESULTS Mean allantoin levels over Days 3 and 4 were significantly lower in the KMC group than in the control group (p = .026). CONCLUSIONS Results provide preliminary evidence that KMC reduces neonatal oxidative stress processes and that urinary allantoin could serve as an effective noninvasive marker for future studies.
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Affiliation(s)
- Dorothy Forde
- Hahn School of Nursing, University of San Diego, CA, USA
- School of Nursing, University of California, San Francisco, CA, USA
| | - Douglas D Deming
- Department of Pediatrics, Division of Neonatology, School of Medicine, Loma Linda University, Loma, CA, USA
| | - John C Tan
- Department of Basic Sciences, Division of Biomedical Engineering Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Raylene M Phillips
- Department of Pediatrics, Division of Neonatology, School of Medicine, Loma Linda University, Loma, CA, USA
| | | | - Mary K Barger
- Hahn School of Nursing, University of San Diego, CA, USA
| | - Khaled Bahjri
- School of Pharmacy, Loma Linda University, Loma Linda, CA, USA
| | - Danilyn M Angeles
- Department of Pediatrics, Division of Neonatology, School of Medicine, Loma Linda University, Loma, CA, USA
- Department of Basic Sciences, Division of Physiology, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Danilo S Boskovic
- Department of Basic Sciences, Division of Biochemistry, School of Medicine, Loma Linda University, Loma Linda, CA, USA
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10
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Angeles DM, Boskovic DS, Tan JC, Shih W, Hoch E, Forde D, Phillips RM, Hopper A, Deming DD, Goldstein M, Truong G, Febre A, Pegis P, Lavery A, Kadri M, Banerji A, Mousselli I, Farha V, Fayard E. Oral dextrose reduced procedural pain without altering cellular ATP metabolism in preterm neonates: a prospective randomized trial. J Perinatol 2020; 40:888-895. [PMID: 32103160 PMCID: PMC7253349 DOI: 10.1038/s41372-020-0634-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/30/2020] [Accepted: 02/12/2020] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To examine the effects of 30% oral dextrose on biochemical markers of pain, adenosine triphosphate (ATP) degradation, and oxidative stress in preterm neonates experiencing a clinically required heel lance. STUDY DESIGN Utilizing a prospective study design, preterm neonates that met study criteria (n = 169) were randomized to receive either (1) 30% oral dextrose, (2) facilitated tucking, or (3) 30% oral dextrose and facilitated tucking 2 min before heel lance. Plasma markers of ATP degradation (hypoxanthine, uric acid) and oxidative stress (allantoin) were measured before and after the heel lance. Pain was measured using the premature infant pain profile-revised (PIPP-R). RESULTS Oral dextrose, administered alone or with facilitated tucking, did not alter plasma markers of ATP utilization and oxidative stress. CONCLUSION A single dose of 30% oral dextrose, given before a clinically required heel lance, decreased signs of pain without increasing ATP utilization and oxidative stress in premature neonates.
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Affiliation(s)
- Danilyn M. Angeles
- 0000 0000 9852 649Xgrid.43582.38Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA
| | - Danilo S. Boskovic
- 0000 0000 9852 649Xgrid.43582.38Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA USA
| | - John C. Tan
- 0000 0000 9852 649Xgrid.43582.38Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA USA
| | - Wendy Shih
- 0000 0000 9852 649Xgrid.43582.38School of Public Health, Loma Linda Univeristy, Loma Linda, CA USA
| | - Erin Hoch
- 0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Dorothy Forde
- 0000 0001 2297 6811grid.266102.1School of Nursing, University of California, San Francisco, CA USA
| | - Raylene M. Phillips
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Andrew Hopper
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Douglas D. Deming
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Mitchell Goldstein
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Giang Truong
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Aprille Febre
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Priscilla Pegis
- 0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Adrian Lavery
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Munaf Kadri
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Anamika Banerji
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Iman Mousselli
- 0000 0000 9852 649Xgrid.43582.38Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA USA
| | - Vora Farha
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
| | - Elba Fayard
- 0000 0000 9852 649Xgrid.43582.38Department of Pediatrics, School of Medicine, Loma Linda University, Loma Linda, CA USA ,0000 0004 0443 5757grid.411392.cLoma Linda University Children’s Hospital, Loma Linda, CA USA
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11
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Lo KC, Sullivan E, Bannen RM, Jin H, Rowe M, Li H, Pinapati RS, Cartwright AJ, Tan JC, Patel J, Keystone EC, Siminovitch KA. Comprehensive Profiling of the Rheumatoid Arthritis Antibody Repertoire. Arthritis Rheumatol 2019; 72:242-250. [DOI: 10.1002/art.41089] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/20/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Ken C. Lo
- Roche Sequencing Solutions Madison Wisconsin
| | | | | | - Huiyan Jin
- Roche Sequencing Solutions Madison Wisconsin
| | - Mark Rowe
- Roche Sequencing Solutions Madison Wisconsin
| | - Hanying Li
- Roche Sequencing Solutions Madison Wisconsin
| | | | | | - John C. Tan
- Roche Sequencing Solutions Madison Wisconsin
| | - Jigar Patel
- Roche Sequencing Solutions Madison Wisconsin
| | | | - Katherine A. Siminovitch
- University of Toronto, Mount Sinai Hospital, and Toronto General Hospital Toronto Ontario Canada
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12
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Dodean RA, Kancharla P, Li Y, Melendez V, Read L, Bane CE, Vesely B, Kreishman-Deitrick M, Black C, Li Q, Sciotti RJ, Olmeda R, Luong TL, Gaona H, Potter B, Sousa J, Marcsisin S, Caridha D, Xie L, Vuong C, Zeng Q, Zhang J, Zhang P, Lin H, Butler K, Roncal N, Gaynor-Ohnstad L, Leed SE, Nolan C, Huezo SJ, Rasmussen SA, Stephens MT, Tan JC, Cooper RA, Smilkstein MJ, Pou S, Winter RW, Riscoe MK, Kelly JX. Discovery and Structural Optimization of Acridones as Broad-Spectrum Antimalarials. J Med Chem 2019; 62:3475-3502. [PMID: 30852885 DOI: 10.1021/acs.jmedchem.8b01961] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Malaria remains one of the deadliest diseases in the world today. Novel chemoprophylactic and chemotherapeutic antimalarials are needed to support the renewed eradication agenda. We have discovered a novel antimalarial acridone chemotype with dual-stage activity against both liver-stage and blood-stage malaria. Several lead compounds generated from structural optimization of a large library of novel acridones exhibit efficacy in the following systems: (1) picomolar inhibition of in vitro Plasmodium falciparum blood-stage growth against multidrug-resistant parasites; (2) curative efficacy after oral administration in an erythrocytic Plasmodium yoelii murine malaria model; (3) prevention of in vitro Plasmodium berghei sporozoite-induced development in human hepatocytes; and (4) protection of in vivo P. berghei sporozoite-induced infection in mice. This study offers the first account of liver-stage antimalarial activity in an acridone chemotype. Details of the design, chemistry, structure-activity relationships, safety, metabolic/pharmacokinetic studies, and mechanistic investigation are presented herein.
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Affiliation(s)
- Rozalia A Dodean
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States.,Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Papireddy Kancharla
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States
| | - Yuexin Li
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States.,Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Victor Melendez
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Lisa Read
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Charles E Bane
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Brian Vesely
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Mara Kreishman-Deitrick
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Chad Black
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Qigui Li
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Richard J Sciotti
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Raul Olmeda
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Thu-Lan Luong
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Heather Gaona
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Brittney Potter
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Jason Sousa
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Sean Marcsisin
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Diana Caridha
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Lisa Xie
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Chau Vuong
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Qiang Zeng
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Jing Zhang
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Ping Zhang
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Hsiuling Lin
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Kirk Butler
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Norma Roncal
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Lacy Gaynor-Ohnstad
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Susan E Leed
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Christina Nolan
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Stephanie J Huezo
- Department of Natural Sciences and Mathematics , Dominican University of California , San Rafael , California 94901 , United States
| | - Stephanie A Rasmussen
- Department of Natural Sciences and Mathematics , Dominican University of California , San Rafael , California 94901 , United States
| | | | | | - Roland A Cooper
- Department of Natural Sciences and Mathematics , Dominican University of California , San Rafael , California 94901 , United States
| | - Martin J Smilkstein
- Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Sovitj Pou
- Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Rolf W Winter
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States.,Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Michael K Riscoe
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States.,Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Jane X Kelly
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States.,Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
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13
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Itakura T, Webster A, Chintala SK, Wang Y, Gonzalez JM, Tan JC, Vranka JA, Acott T, Craft CM, Sibug Saber ME, Jeong S, Stamer WD, Martemyanov KA, Fini ME. GPR158 in the Visual System: Homeostatic Role in Regulation of Intraocular Pressure. J Ocul Pharmacol Ther 2019; 35:203-215. [PMID: 30855200 DOI: 10.1089/jop.2018.0135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Purpose: GPR158 is a newly characterized family C G-protein-coupled receptor, previously identified in functional screens linked with biological stress, including one for susceptibility to ocular hypertension/glaucoma induced by glucocorticoid stress hormones. In this study, we investigated GPR158 function in the visual system. Methods: Gene expression and protein immunolocalization analyses were performed in mouse and human brain and eye to identify tissues where GPR158 might function. Gene expression was perturbed in mice, and in cultures of human trabecular meshwork cells of the aqueous outflow pathway, to investigate function and mechanism. Results: GPR158 is highly expressed in the brain, and in this study, we show prominent expression specifically in the visual center of the cerebral cortex. Expression was also observed in the eye, including photoreceptors, ganglion cells, and trabecular meshwork. Protein was also localized to the outer plexiform layer of the neural retina. Gpr158 deficiency in knockout (KO) mice conferred short-term protection against the intraocular pressure increase that occurred with aging, but this was reversed over time. Most strikingly, the pressure lowering effect of the acute stress hormone, epinephrine, was negated in KO mice. In contrast, no disruption of the electroretinogram was observed. Gene overexpression in cell cultures enhanced cAMP production in response to epinephrine, suggesting a mechanism for intraocular pressure regulation. Overexpression also increased survival of cells subjected to oxidative stress linked to ocular hypertension, associated with TP53 pathway activation. Conclusions: These findings implicate GPR158 as a homeostatic regulator of intraocular pressure and suggest GPR158 could be a pharmacological target for managing ocular hypertension.
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Affiliation(s)
- Tatsuo Itakura
- 1 USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California
| | - Andrew Webster
- 1 USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California
| | - Shravan K Chintala
- 1 USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California
| | - Yuchen Wang
- 2 Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida
| | - Jose M Gonzalez
- 3 Doheny Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California
| | - J C Tan
- 3 Doheny Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California
| | - Janice A Vranka
- 4 Casey Eye Institute, Oregon Health and Science University, Portland, Oregon
| | - Ted Acott
- 4 Casey Eye Institute, Oregon Health and Science University, Portland, Oregon
| | - Cheryl Mae Craft
- 5 USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of USC, University of Southern California, Los Angeles, California.,6 Department of Integrative Anatomical Sciences, Keck School of Medicine of USC, University of Southern California, Los Angeles, California
| | - Maria E Sibug Saber
- 7 Department of Pathology, Keck School of Medicine of USC, University of Southern California, Los Angeles, California
| | - Shinwu Jeong
- 8 USC Institute for Genetic Medicine, Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California
| | - W Daniel Stamer
- 9 Department of Ophthalmology, Duke University, Durham, North Carolina
| | | | - M Elizabeth Fini
- 1 USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, California
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14
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Reindl-Schwaighofer R, Heinzel A, Kainz A, van Setten J, Jelencsics K, Hu K, Loza BL, Kammer M, Heinze G, Hruba P, Koňaříková A, Viklicky O, Boehmig GA, Eskandary F, Fischer G, Claas F, Tan JC, Albert TJ, Patel J, Keating B, Oberbauer R. Contribution of non-HLA incompatibility between donor and recipient to kidney allograft survival: genome-wide analysis in a prospective cohort. Lancet 2019; 393:910-917. [PMID: 30773281 DOI: 10.1016/s0140-6736(18)32473-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/18/2018] [Accepted: 09/27/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND The introduction of HLA matching of donors and recipients was a breakthrough in kidney transplantation. However, half of all transplanted kidneys still fail within 15 years after transplantation. Epidemiological data suggest a fundamental role of non-HLA alloimmunity. METHODS We genotyped 477 pairs of deceased donors and first kidney transplant recipients with stable graft function at three months that were transplanted between Dec 1, 2005, and April 30, 2015. Genome-wide genetic mismatches in non-synonymous single nucleotide polymorphisms (nsSNPs) were calculated to identify incompatibilities in transmembrane and secreted proteins. We estimated the association between nsSNP mismatch and graft loss in a Cox proportional hazard model, adjusting for HLA mismatch and clinical covariates. Customised peptide arrays were generated to screen for antibodies against genotype-derived mismatched epitopes in 25 patients with biopsy-confirmed chronic antibody-mediated rejection. FINDINGS 59 268 nsSNPs affecting a transmembrane or secreted protein were analysed. The median number of nsSNP mismatches in immune-accessible transmembrane and secreted proteins between donors and recipients was 1892 (IQR 1850-1936). The degree of nsSNP mismatch was independently associated with graft loss in a multivariable model adjusted for HLA eplet mismatch (HLA-A, HLA-B, HLA-C, HLA-DP, HLA-DQ, and HLA-DR). Each increase by a unit of one IQR had an HR of 1·68 (95% CI 1·17-2·41, p=0·005). 5-year death censored graft survival was 98% in the quartile with the lowest mismatch, 91% in the second quartile, 89% in the third quartile, and 82% in the highest quartile (p=0·003, log-rank test). Customised peptide arrays verified a donor-specific alloimmune response to genetically predicted mismatched epitopes. INTERPRETATION Genetic mismatch of non-HLA haplotypes coding for transmembrane or secreted proteins is associated with an increased risk of functional graft loss independently of HLA incompatibility. As in HLA alloimmunity, donor-specific alloantibodies can be identified against genotype derived non-HLA epitopes. FUNDING Austrian Science Fund, WWTF (Vienna Science and Technology Fund), and Ministry of Health of the Czech Republic.
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Affiliation(s)
| | - Andreas Heinzel
- Department of Nephrology, Medical University of Vienna, Vienna, Austria
| | - Alexander Kainz
- Department of Nephrology, Medical University of Vienna, Vienna, Austria
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Kira Jelencsics
- Department of Nephrology, Medical University of Vienna, Vienna, Austria
| | - Karin Hu
- Department of Nephrology, Medical University of Vienna, Vienna, Austria
| | - Bao-Li Loza
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Kammer
- Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Georg Heinze
- Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Petra Hruba
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Alena Koňaříková
- Department of Nephrology, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Ondrej Viklicky
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czech Republic; Department of Nephrology, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Georg A Boehmig
- Department of Nephrology, Medical University of Vienna, Vienna, Austria
| | - Farsad Eskandary
- Department of Nephrology, Medical University of Vienna, Vienna, Austria
| | - Gottfried Fischer
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Frans Claas
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, Netherlands
| | | | | | | | - Brendan Keating
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Rainer Oberbauer
- Department of Nephrology, Medical University of Vienna, Vienna, Austria.
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15
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Heffron AS, Mohr EL, Baker D, Haj AK, Buechler CR, Bailey A, Dudley DM, Newman CM, Mohns MS, Koenig M, Breitbach ME, Rasheed M, Stewart LM, Eickhoff J, Pinapati RS, Beckman E, Li H, Patel J, Tan JC, O’Connor DH. Antibody responses to Zika virus proteins in pregnant and non-pregnant macaques. PLoS Negl Trop Dis 2018; 12:e0006903. [PMID: 30481182 PMCID: PMC6286021 DOI: 10.1371/journal.pntd.0006903] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/07/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022] Open
Abstract
The specificity of the antibody response against Zika virus (ZIKV) is not well-characterized. This is due, in part, to the antigenic similarity between ZIKV and closely related dengue virus (DENV) serotypes. Since these and other similar viruses co-circulate, are spread by the same mosquito species, and can cause similar acute clinical syndromes, it is difficult to disentangle ZIKV-specific antibody responses from responses to closely-related arboviruses in humans. Here we use high-density peptide microarrays to profile anti-ZIKV antibody reactivity in pregnant and non-pregnant macaque monkeys with known exposure histories and compare these results to reactivity following DENV infection. We also compare cross-reactive binding of ZIKV-immune sera to the full proteomes of 28 arboviruses. We independently confirm a purported ZIKV-specific IgG antibody response targeting ZIKV nonstructural protein 2B (NS2B) that was recently reported in ZIKV-infected people and we show that antibody reactivity in pregnant animals can be detected as late as 127 days post-infection (dpi). However, we also show that these responses wane over time, sometimes rapidly, and in one case the response was elicited following DENV infection in a previously ZIKV-exposed animal. These results suggest epidemiologic studies assessing seroprevalence of ZIKV immunity using linear epitope-based strategies will remain challenging to interpret due to susceptibility to false positive results. However, the method used here demonstrates the potential for rapid profiling of proteome-wide antibody responses to a myriad of neglected diseases simultaneously and may be especially useful for distinguishing antibody reactivity among closely related pathogens.
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Affiliation(s)
- Anna S. Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Emma L. Mohr
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States of America
| | - David Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Amelia K. Haj
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Connor R. Buechler
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Adam Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mariel S. Mohns
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Michelle Koenig
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Meghan E. Breitbach
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mustafa Rasheed
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Laurel M. Stewart
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Jens Eickhoff
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Richard S. Pinapati
- Technology Innovation, Roche Sequencing Solutions, Madison, WI, United States of America
| | - Erica Beckman
- Technology Innovation, Roche Sequencing Solutions, Madison, WI, United States of America
| | - Hanying Li
- Technology Innovation, Roche Sequencing Solutions, Madison, WI, United States of America
| | - Jigar Patel
- Technology Innovation, Roche Sequencing Solutions, Madison, WI, United States of America
| | - John C. Tan
- Technology Innovation, Roche Sequencing Solutions, Madison, WI, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
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16
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Abstract
Inversion polymorphisms in the African malaria vector Anopheles gambiae segregate along climatic gradients of aridity. Despite indirect evidence of their adaptive significance, little is known of the phenotypic targets of selection or the underlying genetic mechanisms. Here we adopt a systems genetics approach to explore the interaction of two inversions on opposite arms of chromosome 2 with gender, climatic conditions, and one another. We measure organismal traits and transcriptional profiles in 8-d-old adults of both sexes and four alternative homokaryotypic classes reared under two alternative climatic regimes. We show that karyotype strongly influences both organismal traits and transcriptional profiles but that the strength and direction of the effects depend upon complex interactions with gender and environmental conditions and between inversions on independent arms. Our data support the suppressed recombination model for the role of inversions in local adaptation, and-supported by transcriptional and physiological measurements following perturbation with the drug rapamycin-suggest that one mechanism underlying their adaptive role may be the maintenance of energy homeostasis.
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Affiliation(s)
- Changde Cheng
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - John C Tan
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Computer Science, Indiana University, Bloomington, IN 47405
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556;
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
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17
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Nair SC, Xu R, Pattaradilokrat S, Wu J, Qi Y, Zilversmit M, Ganesan S, Nagarajan V, Eastman RT, Orandle MS, Tan JC, Myers TG, Liu S, Long CA, Li J, Su XZ. A Plasmodium yoelii HECT-like E3 ubiquitin ligase regulates parasite growth and virulence. Nat Commun 2017; 8:223. [PMID: 28790316 PMCID: PMC5548792 DOI: 10.1038/s41467-017-00267-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/12/2017] [Indexed: 01/18/2023] Open
Abstract
Infection of mice with strains of Plasmodium yoelii parasites can result in different pathology, but molecular mechanisms to explain this variation are unclear. Here we show that a P. yoelii gene encoding a HECT-like E3 ubiquitin ligase (Pyheul) influences parasitemia and host mortality. We genetically cross two lethal parasites with distinct disease phenotypes, and identify 43 genetically diverse progeny by typing with microsatellites and 9230 single-nucleotide polymorphisms. A genome-wide quantitative trait loci scan links parasite growth and host mortality to two major loci on chromosomes 1 and 7 with LOD (logarithm of the odds) scores = 6.1 and 8.1, respectively. Allelic exchange of partial sequences of Pyheul in the chromosome 7 locus and modification of the gene expression alter parasite growth and host mortality. This study identifies a gene that may have a function in parasite growth, virulence, and host–parasite interaction, and therefore could be a target for drug or vaccine development. Many strains of Plasmodium differ in virulence, but factors that control these distinctions are not known. Here the authors comparatively map virulence loci using the offspring from a P. yoelii YM and N67 genetic cross, and identify a putative HECT E3 ubiquitin ligase that may explain the variance.
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Affiliation(s)
- Sethu C Nair
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ruixue Xu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Sittiporn Pattaradilokrat
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jian Wu
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yanwei Qi
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Martine Zilversmit
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vijayaraj Nagarajan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard T Eastman
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marlene S Orandle
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John C Tan
- The Eck Institute of Global Health, Department of Biological Sciences, University of Notre Dame, Indiana, 46556, USA
| | - Timothy G Myers
- Genomic Technologies Section, Research Technologies Branch, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shengfa Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China
| | - Carole A Long
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China.
| | - Xin-Zhuan Su
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA. .,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, China.
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18
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Abstract
Sequencing-based whole-transcriptome analysis (i.e., RNA-Seq) can be a powerful tool when used to measure gene expression, detect novel transcripts, characterize transcript isoforms, and identify sequence polymorphisms. However, this method can be inefficient when the goal is to study only one component of the transcriptome, such as long noncoding RNAs (lncRNAs), which constitute only a small fraction of transcripts in a total RNA sample. Here, we describe a target enrichment method where a total RNA sample is converted to a sequencing-ready cDNA library and hybridized to a complex pool of lncRNA-specific biotinylated long oligonucleotide capture probes prior to sequencing. The resulting sequence data are highly enriched for the targets of interest, dramatically increasing the efficiency of next-generation sequencing approaches for the analysis of lncRNAs.
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Affiliation(s)
- John C Tan
- Roche NimbleGen, Inc, 500 S. Rosa Road, Madison, WI, USA.
| | | | - Liang Feng
- Roche NimbleGen, Inc, 500 S. Rosa Road, Madison, WI, USA
| | | | - Daniel Burgess
- Roche NimbleGen, Inc, 500 S. Rosa Road, Madison, WI, USA.
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19
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Lo KC, Tan JC, Sullivan E, Bannen R, Richmond T, Grupp F, Weiser S, Heindl D, Stengele KP, Thomas A. Abstract A156: Anti-p53 auto-antibody serum profiling using high-density peptide arrays. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6074.cricimteatiaacr15-a156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer is a result of a number of genetic alterations that disturb normal, controlled cell growth and differentiation. Mutational events leading to the activation of oncogenes or the inactivation of tumor-suppressor genes have been linked causally to the formation of tumors. p53 is one of the most important regulators of transcription, cellular cycle, DNA repair and apoptosis detected to date. Anti-p53 antibodies have been detected in the serum of cancer patients. This immune response is probably due to a self-immunization process linked to the strong immunogenicity of the p53 protein, and is associated predominantly with p53 missense mutation and p53 accumulation in the tumor. Auto-antibodies have also been proposed as potential diagnostic biomarkers for early stage diagnosis of cancers, since an increase in serum levels of certain auto-antibodies has been shown to precede the development of disease symptoms and correlate with cancer incidence for various cancers including breast and lung cancer.
Here we systematically evaluate reactivity of antibodies in p53 positive serum samples and identify reactive epitopes to normal and mutant peptides using a high-density (2.9 Million) peptide microarray. We assess the effect of linker length, peptide length, and flanking serines on antibody detection. We propose peptide array design parameters that can be applied to a whole proteome level to enable biomarker discovery and validation of novel auto-antibody epitopes associated with cancer.
Citation Format: Ken C. Lo, John C. Tan, Eric Sullivan, Ryan Bannen, Todd Richmond, Florian Grupp, Stefan Weiser, Dieter Heindl, Klaus-Peter Stengele, Albert Thomas. Anti-p53 auto-antibody serum profiling using high-density peptide arrays. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A156.
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20
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Cheeseman IH, Miller B, Tan JC, Tan A, Nair S, Nkhoma SC, De Donato M, Rodulfo H, Dondorp A, Branch OH, Mesia LR, Newton P, Mayxay M, Amambua-Ngwa A, Conway DJ, Nosten F, Ferdig MT, Anderson TJC. Population Structure Shapes Copy Number Variation in Malaria Parasites. Mol Biol Evol 2015; 33:603-20. [PMID: 26613787 PMCID: PMC4760083 DOI: 10.1093/molbev/msv282] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.
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Affiliation(s)
- Ian H Cheeseman
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Becky Miller
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - John C Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Asako Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Marcos De Donato
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Hectorina Rodulfo
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Oralee H Branch
- Division of Parasitology, Department of Microbiology, New York University School of Medicine
| | - Lastenia Ruiz Mesia
- Laboratorio De Investigaciones De Productos Naturales Y Antiparasitarios, Universidad Nacional De La Amazonia Peruana, Iquitos, Peru
| | - Paul Newton
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
| | | | - David J Conway
- Medical Research Council Unit, Fajara, Banjul, The Gambia Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Michael T Ferdig
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Tim J C Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
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21
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Geraci NS, Tan JC, McDowell MA. Characterization of microRNA expression profiles in Leishmania-infected human phagocytes. Parasite Immunol 2015; 37:43-51. [PMID: 25376316 DOI: 10.1111/pim.12156] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/29/2014] [Indexed: 12/14/2022]
Abstract
Leishmania are intracellular protozoa that influence host immune responses eliciting parasite species-specific pathologies. MicroRNAs (miRNAs) are short single-stranded ribonucleic acids that complement gene transcripts to block protein translation and have been shown to regulate immune system molecular mechanisms. Human monocyte-derived dendritic cells (DC) and macrophages (MP) were infected in vitro with Leishmania major or Leishmania donovani parasites. Small RNAs were isolated from total RNA and sequenced to identify mature miRNAs associated with leishmanial infections. Normalized sequence read count profiles revealed a global downregulation in miRNA expression among host cells following infection. Most identified miRNAs were expressed at higher levels in L. donovani-infected cells relative to L. major-infected cells. Pathway enrichments using in silico-predicted gene targets of differentially expressed miRNAs showed evidence of potentially universal MAP kinase signalling pathway effects. Whereas JAK-STAT and TGF-β signalling pathways were more highly enriched using targets of miRNAs upregulated in L. donovani-infected cells, these data provide evidence in support of a selective influence on host cell miRNA expression and regulation in response to differential Leishmania infections.
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Affiliation(s)
- N S Geraci
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
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22
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Hickner PV, Mori A, Zeng E, Tan JC, Severson DW. Whole transcriptome responses among females of the filariasis and arbovirus vector mosquito Culex pipiens implicate TGF-β signaling and chromatin modification as key drivers of diapause induction. Funct Integr Genomics 2015; 15:439-47. [PMID: 25634120 DOI: 10.1007/s10142-015-0432-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 01/05/2015] [Accepted: 01/16/2015] [Indexed: 11/30/2022]
Abstract
Culex pipiens mosquitoes are important disease vectors inhabiting temperate zones, worldwide. The seasonal reduction in temperature and photoperiod accompanying late summer and early fall prompts female mosquitoes to enter diapause, a stage of developmental arrest and physiological conditioning that enhances survival during the winter months. To investigate the molecular mechanisms underlying diapause induction, we used custom whole transcriptome microarrays to identify differences in gene expression following exposure to nondiapause (long days, 25 °C) and diapause-inducing (short days, 18 °C) environmental conditions. Using a two-way ANOVA, we identified 1130 genes that were differentially expressed. We used the expression of these genes across three time points to construct a gene co-expression network comprising five modules. Genes in modules 1, 2, and 3 were largely up-regulated, while genes in modules 4 and 5 were down-regulated when compared to nondiapause conditions. Pathway enrichment analysis of the network modules revealed some potential regulatory mechanisms driving diapause induction. Module 1 was enriched for genes in the TGF-ß and Wnt signaling pathways; module 2 was enriched for genes involved in insect hormone biosynthesis, specifically, ecdysone synthesis; module 3 was enriched for genes involved in chromatin modification; and module 5 was enriched for genes in the circadian rhythm pathway. Our results suggest that TGF-β signaling and chromatin modification are key drivers for the integration of environmental signals into the diapause induction phase in C. pipiens mosquitoes.
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Affiliation(s)
- Paul V Hickner
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 107C Galvin Life Sciences, Notre Dame, IN, 46556, USA,
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Takala-Harrison S, Jacob CG, Arze C, Cummings MP, Silva JC, Dondorp AM, Fukuda MM, Hien TT, Mayxay M, Noedl H, Nosten F, Kyaw MP, Nhien NTT, Imwong M, Bethell D, Se Y, Lon C, Tyner SD, Saunders DL, Ariey F, Mercereau-Puijalon O, Menard D, Newton PN, Khanthavong M, Hongvanthong B, Starzengruber P, Fuehrer HP, Swoboda P, Khan WA, Phyo AP, Nyunt MM, Nyunt MH, Brown TS, Adams M, Pepin CS, Bailey J, Tan JC, Ferdig MT, Clark TG, Miotto O, MacInnis B, Kwiatkowski DP, White NJ, Ringwald P, Plowe CV. Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia. J Infect Dis 2014; 211:670-9. [PMID: 25180241 DOI: 10.1093/infdis/jiu491] [Citation(s) in RCA: 325] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The emergence of artemisinin-resistant Plasmodium falciparum in Southeast Asia threatens malaria treatment efficacy. Mutations in a kelch protein encoded on P. falciparum chromosome 13 (K13) have been associated with resistance in vitro and in field samples from Cambodia. METHODS P. falciparum infections from artesunate efficacy trials in Bangladesh, Cambodia, Laos, Myanmar, and Vietnam were genotyped at 33 716 genome-wide single-nucleotide polymorphisms (SNPs). Linear mixed models were used to test associations between parasite genotypes and parasite clearance half-lives following artesunate treatment. K13 mutations were tested for association with artemisinin resistance, and extended haplotypes on chromosome 13 were examined to determine whether mutations arose focally and spread or whether they emerged independently. RESULTS The presence of nonreference K13 alleles was associated with prolonged parasite clearance half-life (P = 1.97 × 10(-12)). Parasites with a mutation in any of the K13 kelch domains displayed longer parasite clearance half-lives than parasites with wild-type alleles. Haplotype analysis revealed both population-specific emergence of mutations and independent emergence of the same mutation in different geographic areas. CONCLUSIONS K13 appears to be a major determinant of artemisinin resistance throughout Southeast Asia. While we found some evidence of spreading resistance, there was no evidence of resistance moving westward from Cambodia into Myanmar.
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Affiliation(s)
| | | | - Cesar Arze
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore
| | - Michael P Cummings
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore
| | | | - Mark M Fukuda
- Armed Forces Research Institute of Medical Sciences, Bangkok
| | - Tran Tinh Hien
- Center for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital Faculty of Postgraduate Studies, University of Health Sciences Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford
| | - Harald Noedl
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Austria
| | - Francois Nosten
- Mahidol-Oxford Tropical Medicine Research Unit Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford
| | - Myat P Kyaw
- Department of Medical Research (Lower Myanmar), Yangon
| | - Nguyen Thanh Thuy Nhien
- Center for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University
| | - Delia Bethell
- Armed Forces Research Institute of Medical Sciences, Bangkok
| | - Youry Se
- Armed Forces Research Institute of Medical Sciences
| | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences
| | - Stuart D Tyner
- Armed Forces Research Institute of Medical Sciences, Bangkok
| | | | | | | | - Didier Menard
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford
| | | | | | - Peter Starzengruber
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Austria
| | - Hans-Peter Fuehrer
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Austria
| | - Paul Swoboda
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Austria
| | - Wasif A Khan
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Aung Pyae Phyo
- Mahidol-Oxford Tropical Medicine Research Unit Shoklo Malaria Research Unit Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Myaing M Nyunt
- Howard Hughes Medical Institute/Center for Vaccine Development
| | - Myat H Nyunt
- Department of Medical Research (Lower Myanmar), Yangon
| | - Tyler S Brown
- Howard Hughes Medical Institute/Center for Vaccine Development
| | - Matthew Adams
- Howard Hughes Medical Institute/Center for Vaccine Development
| | | | - Jason Bailey
- Howard Hughes Medical Institute/Center for Vaccine Development
| | - John C Tan
- Research and Development, Roche NimbleGen, Madison, Wisconsin
| | - Michael T Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Indiana
| | - Taane G Clark
- Faculty of Epidemiology and Population Health Faculty Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Olivo Miotto
- Mahidol-Oxford Tropical Medicine Research Unit MRC Centre for Genomics and Global Health, Oxford University and Wellcome Trust Sanger Institute Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Bronwyn MacInnis
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Dominic P Kwiatkowski
- MRC Centre for Genomics and Global Health, Oxford University and Wellcome Trust Sanger Institute Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Pascal Ringwald
- Drug Resistance and Containment Unit, Global Malaria Programme, World Health Organization, Geneva, Switzerland
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Jacob CG, Tan JC, Miller BA, Tan A, Takala-Harrison S, Ferdig MT, Plowe CV. A microarray platform and novel SNP calling algorithm to evaluate Plasmodium falciparum field samples of low DNA quantity. BMC Genomics 2014; 15:719. [PMID: 25159520 PMCID: PMC4153902 DOI: 10.1186/1471-2164-15-719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 08/11/2014] [Indexed: 01/07/2023] Open
Abstract
Background Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In areas with adequate cold chain facilities, large volumes of leukocyte-depleted patient blood can be frozen for use in parasite genomic analyses. In more remote endemic areas smaller volumes of infected blood are taken by finger prick, and dried and stored on filter paper. These dried blood spots do not generally yield enough concentrated parasite DNA for whole-genome sequencing. Results A DNA microarray was designed for use on field samples to type a genome-wide set of SNPs which prior sequencing had shown to be variable in Africa, Southeast Asia, and Papua New Guinea. An algorithm was designed to call SNPs in samples with low parasite DNA. With this new algorithm SNP-calling accuracy of 98% was measured by hybridizing purified DNA from malaria lab strains and comparing calls with SNPs called from full genome sequences. An average accuracy of >98% was likewise obtained for DNA extracted from malaria field samples collected in studies in Southeast Asia, with an average call rate of > 82%. Conclusion This new high-density microarray provided high quality SNP calls from a wide range of parasite DNA quantities, and represents a robust tool for genome-wide analysis of malaria parasites in diverse settings.
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Affiliation(s)
| | | | | | | | | | | | - Christopher V Plowe
- Malaria Group, Howard Hughes Medical Institute / Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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O'Neil ST, Dzurisin JDK, Williams CM, Lobo NF, Higgins JK, Deines JM, Carmichael RD, Zeng E, Tan JC, Wu GC, Emrich SJ, Hellmann JJ. Gene expression in closely related species mirrors local adaptation: consequences for responses to a warming world. Mol Ecol 2014; 23:2686-98. [PMID: 24766086 DOI: 10.1111/mec.12773] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 04/18/2014] [Accepted: 04/23/2014] [Indexed: 11/27/2022]
Abstract
Local adaptation of populations could preclude or slow range expansions in response to changing climate, particularly when dispersal is limited. To investigate the differential responses of populations to changing climatic conditions, we exposed poleward peripheral and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared their whole-transcriptome expression. We found evidence of simple population differentiation in both species, and in the species with previously identified population structure and phenotypic local adaptation, we found several hundred genes that responded in a synchronized and localized fashion. These genes were primarily involved in energy metabolism and oxidative stress, and expression levels were most divergent between populations in the same environment in which we previously detected divergence for metabolism. We found no localized genes in the species with less population structure and for which no local adaptation was previously detected. These results challenge the assumption that species are functionally similar across their ranges and poleward peripheral populations are preadapted to warmer conditions. Rather, some taxa deserve population-level consideration when predicting the effects of climate change because they respond in genetically based, distinctive ways to changing conditions.
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Affiliation(s)
- Shawn T O'Neil
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
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Cassone BJ, Kamdem C, Cheng C, Tan JC, Hahn MW, Costantini C, Besansky NJ. Gene expression divergence between malaria vector sibling species Anopheles gambiae and An. coluzzii from rural and urban Yaoundé Cameroon. Mol Ecol 2014; 23:2242-59. [PMID: 24673723 DOI: 10.1111/mec.12733] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 03/05/2014] [Accepted: 03/05/2014] [Indexed: 01/07/2023]
Abstract
Divergent selection based on aquatic larval ecology is a likely factor in the recent isolation of two broadly sympatric and morphologically identical African mosquito species, the malaria vectors Anopheles gambiae and An. coluzzii. Population-based genome scans have revealed numerous candidate regions of recent positive selection, but have provided few clues as to the genetic mechanisms underlying behavioural and physiological divergence between the two species, phenotypes which themselves remain obscure. To uncover possible genetic mechanisms, we compared global transcriptional profiles of natural and experimental populations using gene-based microarrays. Larvae were sampled as second and fourth instars from natural populations in and around the city of Yaoundé, capital of Cameroon, where the two species segregate along a gradient of urbanization. Functional enrichment analysis of differentially expressed genes revealed that An. coluzzii--the species that breeds in more stable, biotically complex and potentially polluted urban water bodies--overexpresses genes implicated in detoxification and immunity relative to An. gambiae, which breeds in more ephemeral and relatively depauperate pools and puddles in suburbs and rural areas. Moreover, our data suggest that such overexpression by An. coluzzii is not a transient result of induction by xenobiotics in the larval habitat, but an inherent and presumably adaptive response to repeatedly encountered environmental stressors. Finally, we find no significant overlap between the differentially expressed loci and previously identified genomic regions of recent positive selection, suggesting that transcriptome divergence is regulated by trans-acting factors rather than cis-acting elements.
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Affiliation(s)
- Bryan J Cassone
- Eck Institute for Global Health & Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556-0369, USA
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Nair SC, Pattaradilokrat S, Zilversmit MM, Dommer J, Nagarajan V, Stephens MT, Xiao W, Tan JC, Su XZ. Genome-wide polymorphisms and development of a microarray platform to detect genetic variations in Plasmodium yoelii. Mol Biochem Parasitol 2014; 194:9-15. [PMID: 24685548 DOI: 10.1016/j.molbiopara.2014.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/14/2014] [Accepted: 03/20/2014] [Indexed: 11/18/2022]
Abstract
The rodent malaria parasite Plasmodium yoelii is an important model for studying malaria immunity and pathogenesis. One approach for studying malaria disease phenotypes is genetic mapping, which requires typing a large number of genetic markers from multiple parasite strains and/or progeny from genetic crosses. Hundreds of microsatellite (MS) markers have been developed to genotype the P. yoelii genome; however, typing a large number of MS markers can be labor intensive, time consuming, and expensive. Thus, development of high-throughput genotyping tools such as DNA microarrays that enable rapid and accurate large-scale genotyping of the malaria parasite will be highly desirable. In this study, we sequenced the genomes of two P. yoelii strains (33X and N67) and obtained a large number of single nucleotide polymorphisms (SNPs). Based on the SNPs obtained, we designed sets of oligonucleotide probes to develop a microarray that could interrogate ∼11,000 SNPs across the 14 chromosomes of the parasite in a single hybridization. Results from hybridizations of DNA samples of five P. yoelii strains or cloned lines (17XNL, YM, 33X, N67 and N67C) and two progeny from a genetic cross (N67×17XNL) to the microarray showed that the array had a high call rate (∼97%) and accuracy (99.9%) in calling SNPs, providing a simple and reliable tool for typing the P. yoelii genome. Our data show that the P. yoelii genome is highly polymorphic, although isogenic pairs of parasites were also detected. Additionally, our results indicate that the 33X parasite is a progeny of 17XNL (or YM) and an unknown parasite. The highly accurate and reliable microarray developed in this study will greatly facilitate our ability to study the genetic basis of important traits and the disease it causes.
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Affiliation(s)
- Sethu C Nair
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sittiporn Pattaradilokrat
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Martine M Zilversmit
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Dommer
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vijayaraj Nagarajan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melissa T Stephens
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Wenming Xiao
- Metabolism Branch, National Cancer Institutes, National Institutes of Health, Bethesda, MD 20892, USA
| | - John C Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Affiliation(s)
- E L Lum
- Department of Medicine, Division of Nephrology, Kidney Transplantation, UCLA David Geffen School of Medicine, Los Angeles, CA
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Sarro J, Andrews E, Sun L, Behura SK, Tan JC, Zeng E, Severson DW, Duman-Scheel M. Requirement for commissureless2 function during dipteran insect nerve cord development. Dev Dyn 2013; 242:1466-77. [PMID: 24026811 DOI: 10.1002/dvdy.24059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/08/2013] [Accepted: 09/03/2013] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND In Drosophila melanogaster, commissureless (comm) function is required for proper nerve cord development. Although comm orthologs have not been identified outside of Drosophila species, some insects possess orthologs of Drosophila comm2, which may also regulate embryonic nerve cord development. Here, this hypothesis is explored through characterization of comm2 genes in two disease vector mosquitoes. RESULTS Culex quinquefasciatus (West Nile and lymphatic filiariasis vector) has three comm2 genes that are expressed in the developing nerve cord. Aedes aegypti (dengue and yellow fever vector) has a single comm2 gene that is expressed in commissural neurons projecting axons toward the midline. Loss of comm2 function in both A. aegypti and D. melanogaster was found to result in loss of commissure defects that phenocopy the frazzled (fra) loss of function phenotypes observed in both species. Loss of fra function in either insect was found to result in decreased comm2 transcript levels during nerve cord development. CONCLUSIONS The results of this investigation suggest that Fra down-regulates repulsion in precrossing commissural axons by regulating comm2 levels in both A. aegypti and D. melanogaster, both of which require Comm2 function for proper nerve cord development.
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Affiliation(s)
- Joseph Sarro
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
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Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O'Brien J, Djimde A, Doumbo O, Zongo I, Ouedraogo JB, Michon P, Mueller I, Siba P, Nzila A, Borrmann S, Kiara SM, Marsh K, Jiang H, Su XZ, Amaratunga C, Fairhurst R, Socheat D, Nosten F, Imwong M, White NJ, Sanders M, Anastasi E, Alcock D, Drury E, Oyola S, Quail MA, Turner DJ, Ruano-Rubio V, Jyothi D, Amenga-Etego L, Hubbart C, Jeffreys A, Rowlands K, Sutherland C, Roper C, Mangano V, Modiano D, Tan JC, Ferdig MT, Amambua-Ngwa A, Conway DJ, Takala-Harrison S, Plowe CV, Rayner JC, Rockett KA, Clark TG, Newbold CI, Berriman M, MacInnis B, Kwiatkowski DP. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature 2012; 487:375-9. [PMID: 22722859 PMCID: PMC3738909 DOI: 10.1038/nature11174] [Citation(s) in RCA: 384] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 04/30/2012] [Indexed: 02/02/2023]
Abstract
Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance. Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome.
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Affiliation(s)
- Magnus Manske
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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Cheeseman IH, Miller BA, Nair S, Nkhoma S, Tan A, Tan JC, Al Saai S, Phyo AP, Moo CL, Lwin KM, McGready R, Ashley E, Imwong M, Stepniewska K, Yi P, Dondorp AM, Mayxay M, Newton PN, White NJ, Nosten F, Ferdig MT, Anderson TJC. A major genome region underlying artemisinin resistance in malaria. Science 2012; 336:79-82. [PMID: 22491853 DOI: 10.1126/science.1215966] [Citation(s) in RCA: 314] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Evolving resistance to artemisinin-based compounds threatens to derail attempts to control malaria. Resistance has been confirmed in western Cambodia and has recently emerged in western Thailand, but is absent from neighboring Laos. Artemisinin resistance results in reduced parasite clearance rates (CRs) after treatment. We used a two-phase strategy to identify genome region(s) underlying this ongoing selective event. Geographical differentiation and haplotype structure at 6969 polymorphic single-nucleotide polymorphisms (SNPs) in 91 parasites from Cambodia, Thailand, and Laos identified 33 genome regions under strong selection. We screened SNPs and microsatellites within these regions in 715 parasites from Thailand, identifying a selective sweep on chromosome 13 that shows strong association (P = 10(-6) to 10(-12)) with slow CRs, illustrating the efficacy of targeted association for identifying the genetic basis of adaptive traits.
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Affiliation(s)
- Ian H Cheeseman
- Texas Biomedical Research Institute, San Antonio, TX 78245, USA
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Galvan MD, Foreman DB, Zeng E, Tan JC, Bohlson SS. Complement component C1q regulates macrophage expression of Mer tyrosine kinase to promote clearance of apoptotic cells. J Immunol 2012; 188:3716-23. [PMID: 22422887 DOI: 10.4049/jimmunol.1102920] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Failure to efficiently clear apoptotic cells is linked to defects in development and the onset of autoimmunity. Complement component C1q is required for efficient engulfment of apoptotic cells in mice and humans; however, the molecular mechanisms leading to C1q-dependent engulfment are not fully understood. In this study, we used primary mouse macrophages to identify and characterize a novel molecular mechanism for macrophage-mediated C1q-dependent engulfment of apoptotic cells. We found that macrophage activation with C1q resulted in cycloheximide-sensitive enhanced engulfment, indicating a requirement for de novo protein synthesis. To investigate the cycloheximide-sensitive pathway, C1q-elicited macrophage transcripts were identified by microarray. C1q triggered the expression of Mer tyrosine kinase (Mer) and the Mer ligand growth arrest-specific 6: a receptor-ligand pair that mediates clearance of apoptotic cells. Full-length native C1q, and not the collagen-like tail or heat-denatured protein, stimulated Mer expression. This novel pathway is specific to C1q because mannose-binding lectin, a related collectin, failed to upregulate Mer expression and function. Soluble Mer-Fc fusion protein inhibited C1q-dependent engulfment of apoptotic cells, indicating a requirement for Mer. Moreover, Mer-deficient macrophages failed to respond to C1q with enhanced engulfment. Our results suggest that C1q elicits a macrophage phenotype specifically tailored for apoptotic cell clearance, and these data are consistent with the established requirement for C1q in prevention of autoimmunity.
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Affiliation(s)
- Manuel D Galvan
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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Carrasco MA, Tan JC, Duman JG. A cross-species compendium of proteins/gene products related to cold stress identified by bioinformatic approaches. J Insect Physiol 2011; 57:1127-1135. [PMID: 21565197 DOI: 10.1016/j.jinsphys.2011.04.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 04/26/2011] [Accepted: 04/27/2011] [Indexed: 05/30/2023]
Abstract
The purpose of this investigation was to construct a compendium of low temperature responsive proteins/gene products across species as identified by bioinformatics based approaches, thus allowing low temperature researchers a searchable database. Another purpose was to identify specific low temperature responsive proteins/gene products across at least two different species. We generated a database containing 2030 low temperature responsive protein/gene product entries, of which 1353 were up-regulated and 549 were down-regulated in response to various cold exposures across 34 different species; including bacteria (9 species), yeast (1 species), animals (including nematodes (1 species), collembola (2 species), insects (5 species), fish (1 species), amphibians (1 species), reptiles (1 species), mammals (2 species)), and plants (moss (1 species), gymnosperms (1 species) and angiosperms (9 species)). There were 39 studies using 12 different cold treatments; 20 used proteomics and 18 used transcriptomics. Concerning our purpose of identifying specific temperature responsive proteins/gene products across species, we found 113 shared proteins/gene products groups, each of which was found in at least two species. Of these shared proteins/gene products groups, 58 proteins/gene products (including protein/gene product families) that were consistently regulated, meaning always either up- or down-regulated, across species. Another 23 proteins/gene products were inconsistently regulated, meaning that the proteins/gene products were up-regulated in some species and treatments while being down-regulated in other species and treatments. An additional 32 proteins/gene products that are part of larger family headings and are difficult to separate from related member proteins (such the ribosomal proteins, 30S, 50S, and others) were inconsistently regulated. This work is an attempt to create a centralized database and repository for low temperature responsive proteins/gene products in all species.
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Affiliation(s)
- Martin A Carrasco
- University of Notre Dame, Galvin Life Sciences, Notre Dame, IN 46556, USA.
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Cassone BJ, Molloy MJ, Cheng C, Tan JC, Hahn MW, Besansky NJ. Divergent transcriptional response to thermal stress by Anopheles gambiae larvae carrying alternative arrangements of inversion 2La. Mol Ecol 2011; 20:2567-80. [PMID: 21535279 DOI: 10.1111/j.1365-294x.2011.05114.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The African malaria mosquito Anopheles gambiae is polymorphic for chromosomal inversion 2La, whose frequency strongly correlates with degree of aridity across environmental gradients. Recent physiological studies have associated 2La with resistance to desiccation in adults and thermal stress in larvae, consistent with its proposed role in aridity tolerance. However, the genetic basis of these traits remains unknown. To identify genes that could be involved in the differential response to thermal stress, we compared global gene expression profiles of heat-hardened 2La or 2L+(a) larvae at three time points, for up to eight hours following exposure to the heat stress. Treatment and control time series, replicated four times, revealed a common and massive induction of a core set of heat-shock genes regardless of 2La orientation. However, clear differences between the 2La and 2L+(a) arrangements emerged at the earliest (0.25 h) time point, in the intensity and nature of the stress response. Overall, 2La was associated with the more aggressive response: larger numbers of genes were heat responsive and up-regulated. Transcriptionally induced genes were enriched for functions related to ubiquitin-proteasomal degradation, chaperoning and energy metabolism. The more muted transcriptional response of 2L+(a) was largely repressive, including genes involved in proteolysis and energy metabolism. These results may help explain the maintenance of the 2La inversion polymorphism in An. gambiae, as the survival benefits offered by high thermal sensitivity in harsh climates could be offset by the metabolic costs of such a drastic response in more equable climates.
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Affiliation(s)
- Bryan J Cassone
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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Singh PP, LeMaire C, Tan JC, Zeng E, Schorey JS. Exosomes released from M. tuberculosis infected cells can suppress IFN-γ mediated activation of naïve macrophages. PLoS One 2011; 6:e18564. [PMID: 21533172 PMCID: PMC3077381 DOI: 10.1371/journal.pone.0018564] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/12/2011] [Indexed: 01/18/2023] Open
Abstract
Background Macrophages infected with Mycobacterium tuberculosis (M.tb) are known to be refractory to IFN-γ stimulation. Previous studies have shown that M.tb express components such as the 19-kDa lipoprotein and peptidoglycan that can bind to macrophage receptors including the Toll-like receptor 2 resulting in the loss in IFN-γresponsiveness. However, it is unclear whether this effect is limited to infected macrophages. We have previously shown that M.tb-infected macrophages release exosomes which are 30–100 nm membrane bound vesicles of endosomal origin that function in intercellular communication. These exosomes contain mycobacterial components including the 19-kDa lipoprotein and therefore we hypothesized that macrophages exposed to exosomes may show limited response to IFN-γ stimulation. Methodology/Principal Findings Exosomes were isolated from resting as well as M.tb-infected RAW264.7 macrophages. Mouse bone marrow-derived macrophages (BMMØ) were treated with exosomes +/− IFN-γ. Cells were harvested and analyzed for suppression of IFN-γ responsive genes by flow cytometry and real time PCR. We found that exosomes derived from M.tb H37Rv-infected but not from uninfected macrophages inhibited IFN-γ induced MHC class II and CD64 expression on BMMØ. This inhibition was only partially dependent on the presence of lipoproteins but completely dependent on TLR2 and MyD88. The exosomes isolated from infected cells did not inhibit STAT1 Tyrosine phosphorylation but down-regulated IFN-γ induced expression of the class II major histocompatibity complex transactivator; a key regulator of class II MHC expression. Microarray studies showed that subsets of genes induced by IFN-γ were inhibited by exosomes from H37Rv-infeced cells including genes involved in antigen presentation. Moreover, this set of genes partially overlapped with the IFN-γ-induced genes inhibited by H37Rv infection. Conclusions Our study suggests that exosomes, as carriers of M.tb pathogen associated molecular patterns (PAMPs), may provide a mechanism by which M.tb may exert its suppression of a host immune response beyond the infected cell.
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Affiliation(s)
- Prachi P. Singh
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Christopher LeMaire
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - John C. Tan
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Erliang Zeng
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Jeffery S. Schorey
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
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Tan JC, Miller BA, Tan A, Patel JJ, Cheeseman IH, Anderson TJC, Manske M, Maslen G, Kwiatkowski DP, Ferdig MT. An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations. Genome Biol 2011; 12:R35. [PMID: 21477297 PMCID: PMC3218861 DOI: 10.1186/gb-2011-12-4-r35] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/04/2011] [Accepted: 04/08/2011] [Indexed: 11/13/2022] Open
Abstract
We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples. The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination.
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Affiliation(s)
- John C Tan
- The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA
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Samarakoon U, Regier A, Tan A, Desany BA, Collins B, Tan JC, Emrich SJ, Ferdig MT. High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum. BMC Genomics 2011; 12:116. [PMID: 21324207 PMCID: PMC3055840 DOI: 10.1186/1471-2164-12-116] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 02/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Knowledge of the origins, distribution, and inheritance of variation in the malaria parasite (Plasmodium falciparum) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenges to high-throughput sequencing technologies. We explore the viability of the Roche 454 Genome Sequencer FLX (GS FLX) high throughput sequencing technology for both whole genome sequencing and fine-resolution characterization of genetic exchange in malaria parasites. RESULTS We present a scheme to survey recombination in the haploid stage genomes of two sibling parasite clones, using whole genome pyrosequencing that includes a sliding window approach to predict recombination breakpoints. Whole genome shotgun (WGS) sequencing generated approximately 2 million reads, with an average read length of approximately 300 bp. De novo assembly using a combination of WGS and 3 kb paired end libraries resulted in contigs ≤ 34 kb. More than 8,000 of the 24,599 SNP markers identified between parents were genotyped in the progeny, resulting in a marker density of approximately 1 marker/3.3 kb and allowing for the detection of previously unrecognized crossovers (COs) and many non crossover (NCO) gene conversions throughout the genome. CONCLUSIONS By sequencing the 23 Mb genomes of two haploid progeny clones derived from a genetic cross at more than 30× coverage, we captured high resolution information on COs, NCOs and genetic variation within the progeny genomes. This study is the first to resequence progeny clones to examine fine structure of COs and NCOs in malaria parasites.
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Affiliation(s)
- Upeka Samarakoon
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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Patel JJ, Thacker D, Tan JC, Pleeter P, Checkley L, Gonzales JM, Deng B, Roepe PD, Cooper RA, Ferdig MT. Chloroquine susceptibility and reversibility in a Plasmodium falciparum genetic cross. Mol Microbiol 2010; 78:770-87. [PMID: 20807203 DOI: 10.1111/j.1365-2958.2010.07366.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mutations in the Plasmodium falciparum chloroquine (CQ) resistance transporter (PfCRT) are major determinants of verapamil (VP)-reversible CQ resistance (CQR). In the presence of mutant PfCRT, additional genes contribute to the wide range of CQ susceptibilities observed. It is not known if these genes influence mechanisms of chemosensitization by CQR reversal agents. Using quantitative trait locus (QTL) mapping of progeny clones from the HB3 × Dd2 cross, we show that the P. falciparum multidrug resistance gene 1 (pfmdr1) interacts with the South-East Asia-derived mutant pfcrt haplotype to modulate CQR levels. A novel chromosome 7 locus is predicted to contribute with the pfcrt and pfmdr1 loci to influence CQR levels. Chemoreversal via a wide range of chemical structures operates through a direct pfcrt-based mechanism. Direct inhibition of parasite growth by these reversal agents is influenced by pfcrt mutations and additional loci. Direct labelling of purified recombinant PfMDR1 protein with a highly specific photoaffinity CQ analogue, and lack of competition for photolabelling by VP, supports our QTL predictions. We find no evidence that pfmdr1 copy number affects CQ response in the progeny; however, inheritance patterns indicate that an allele-specific interaction between pfmdr1 and pfcrt is part of the complex genetic background of CQR.
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Affiliation(s)
- Jigar J Patel
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, 205 Galvin Life Sciences, Notre Dame, IN 46556, USA
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Tan JC, Tan A, Checkley L, Honsa CM, Ferdig MT. Variable numbers of tandem repeats in Plasmodium falciparum genes. J Mol Evol 2010; 71:268-78. [PMID: 20730584 DOI: 10.1007/s00239-010-9381-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 08/09/2010] [Indexed: 11/29/2022]
Abstract
Genome variation studies in Plasmodium falciparum have focused on SNPs and, more recently, large-scale copy number polymorphisms and ectopic rearrangements. Here, we examine another source of variation: variable number tandem repeats (VNTRs). Interspersed low complexity features, including the well-studied P. falciparum microsatellite sequences, are commonly classified as VNTRs; however, this study is focused on longer coding VNTR polymorphisms, a small class of copy number variations. Selection against frameshift mutation is a main constraint on tandem repeats (TRs) in coding regions, while limited propagation of TRs longer than 975 nt total length is a minor restriction in coding regions. Comparative analysis of three P. falciparum genomes reveals that more than 9% of all P. falciparum ORFs harbor VNTRs, much more than has been reported for any other species. Moreover, genotyping of VNTR loci in a drug-selected line, progeny of a genetic cross, and 334 field isolates demonstrates broad variability in these sequences. Functional enrichment analysis of ORFs harboring VNTRs identifies stress and DNA damage responses along with chromatin modification activities, suggesting an influence on genome mutability and functional variation. Analysis of the repeat units and their flanking regions in both P. falciparum and Plasmodium reichenowi sequences implicates a replication slippage mechanism in the generation of TRs from an initially unrepeated sequence. VNTRs can contribute to rapid adaptation by localized sequence duplication. They also can confound SNP-typing microarrays or mapping short-sequence reads and therefore must be accounted for in such analyses.
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Affiliation(s)
- John C Tan
- The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
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Clyne TW, Golosnoy IO, Tan JC, Markaki AE. Porous materials for thermal management under extreme conditions. Philos Trans A Math Phys Eng Sci 2006; 364:125-146. [PMID: 18272456 DOI: 10.1098/rsta.2005.1682] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A brief analysis is presented of how heat transfer takes place in porous materials of various types. The emphasis is on materials able to withstand extremes of temperature, gas pressure, irradiation, etc. i.e. metals and ceramics, rather than polymers. A primary aim is commonly to maximize either the thermal resistance (i.e. provide insulation) or the rate of thermal equilibration between the material and a fluid passing through it (i.e. to facilitate heat exchange). The main structural characteristics concern porosity (void content), anisotropy, pore connectivity and scale. The effect of scale is complex, since the permeability decreases as the structure is refined, but the interfacial area for fluid-solid heat exchange is, thereby, raised. The durability of the pore structure may also be an issue, with a possible disadvantage of finer scale structures being poor microstructural stability under service conditions. Finally, good mechanical properties may be required, since the development of thermal gradients, high fluid fluxes, etc. can generate substantial levels of stress. There are, thus, some complex interplays between service conditions, pore architecture/scale, fluid permeation characteristics, convective heat flow, thermal conduction and radiative heat transfer. Such interplays are illustrated with reference to three examples: (i) a thermal barrier coating in a gas turbine engine; (ii) a Space Shuttle tile; and (iii) a Stirling engine heat exchanger. Highly porous, permeable materials are often made by bonding fibres together into a network structure and much of the analysis presented here is oriented towards such materials.
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Affiliation(s)
- T W Clyne
- Department of Materials Science & Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ, UK.
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Worst TJ, Tan JC, Robertson DJ, Freeman WM, Hyytia P, Kiianmaa K, Vrana KE. Transcriptome analysis of frontal cortex in alcohol-preferring and nonpreferring rats. J Neurosci Res 2005; 80:529-38. [PMID: 15846778 DOI: 10.1002/jnr.20496] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although it is widely accepted that alcohol abuse and alcoholism have a significant genetic component of risk, the identities of the genes themselves remain obscure. To illuminate such potential genetic contributions, DNA macroarrays were used to probe for differences in normative cortical gene expression between rat strains genetically selected for alcohol self-administration preference, AA (Alko, alcohol) and P (Indiana, preferring), or avoidance, ANA (Alko, nonalcohol) and NP (Indiana, nonpreferring). Among 1,176 genes studied, six demonstrated confirmable, differential expression following comparison of ethanol-naive AA and ANA rats. Specifically, the mRNA level for metabotropic glutamate receptor 3 (mGluR3) was down-regulated in the AA vs. ANA lines. In contrast, calcium channel subunit alpha2delta1 (cacna2d1), vesicle-associated membrane protein 2 (VAMP2), syntaxin 1 (both syntaxin 1a and 1b; STX1a and STX1b), and syntaxin binding protein (MUNC-18) mRNAs were found to be increased in frontal cortex following comparison of AA with ANA animals. Bioinformatic analysis of these molecular targets showed that mGluR3 and cacna2d1 fall within chromosomal locations reported to be alcohol-related by the Collaborative Study on the Genetics of Alcoholism (COGA) as well as quantitative trait loci (QTL) studies. To determine further whether these differences were strain specific, the above-mentioned genes were compared in ethanol-preferring (P) and -nonpreferring (NP) selected lines. VAMP2 was the only gene that displayed statistically different mRNA levels in a comparison of P and NP rats. In conclusion, the altered cortical gene expression illuminated here would have the effect of altering neurotransmitter release in AA rats (compared with ANA rats). Such alterations, however, might not be a universal characteristic of all animal models of alcohol abuse and will also require further investigation in post-mortem human samples.
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Affiliation(s)
- Travis J Worst
- Center for the Neurobehavioral Study of Alcohol, Department of Physiology and Pharmacology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA
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Look M, Chew SP, Tan YC, Liew SE, Cheong DM, Tan JC, Wee SB, Teh CH, Low CH. Post-operative pain in needlescopic versus conventional laparoscopic cholecystectomy: a prospective randomised trial. J R Coll Surg Edinb 2001; 46:138-42. [PMID: 11478009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
BACKGROUND Needlescopic cholecystectomy (NC) utilises instruments and ports smaller than 3 mm in diameter compared with the 5 mm ones used in conventional laparoscopic cholecystectomy (LC). Post-operative pain control and recovery has been thought to be superior in NC, when compared with historical controls with LC, but has not been proven in a prospective fashion. PATIENTS AND METHODS A prospective randomised trial of NC versus LC for patients with symptomatic gallstone disease, with standardisation of post-operative analgesia and daily assessment of post-operative pain, using a 5-point visual analogue scale. RESULTS There were 64 eligible patients randomised into NC (28) and LC (36). Four patients who had NC were converted to LC due to technical problems. Another three and six patients from the NC and LC groups, respectively, had conversion to open surgery. Post-operative pain scores were low in both groups. Mean pain scores for those with successful NC and LC were: 1.24 versus 1.43 for the day of operation (P = 0.49), 0.86 versus 0.83 for the first day post-operatively (P = 0.92) and 0.75 versus 0.81 for the second post-operative day (P = 0.87). The mean number of intra-muscular analgesic injections required were 0.76 versus 0.83 after NC and LC, respectively (P = 0.93). There were no significant differences between the two groups in the time taken to return to feeding, eating a normal diet and discharge from hospital. CONCLUSION There is no advantage of NC over LC in terms of post-operative pain or recovery. Nevertheless, NC can be performed safely and expediently and has an excellent cosmetic outcome and high patient acceptability.
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Affiliation(s)
- M Look
- Department of Surgery, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433.
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Abstract
Research is continually seeking to better describe the relationship between pseudophakic capsular opacification and underlying cell biology, surgical technique, and intra-ocular lens biomaterial and design. Outcomes are reviewed from prospective, randomized studies that investigate the importance of capsulorhexis size, pharmacological treatment, and lens material in influencing capsular opacification and the need for capsulotomy. The results of several studies support the role of lens edge profile in inhibiting lens epithelial cell migration. A large post-mortem study also examines how lens type may affect anterior capsular opacification formation. Of particular interest is a histological report that sheds additional light on understanding cellular processes in posterior capsu-lar opacification.
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Affiliation(s)
- J C Tan
- Glaucoma Research Unit, Moorfields Eye Hospital, London, United Kingdom.
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Affiliation(s)
- J C Tan
- Glaucoma Research Unit, Moorfields Eye Hospital, London, UK
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Poinoosawmy D, Tan JC, Bunce C, Hitchings RA. The ability of the GDx Nerve Fibre Analyser neural network to diagnose glaucoma. Graefes Arch Clin Exp Ophthalmol 2001; 239:122-7. [PMID: 11372541 DOI: 10.1007/s004170100256] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
PURPOSE To evaluate the neural network used by the GDx in a group of normal subjects, patients with ocular hypertension (OHT) and patients with normal-pressure glaucoma (NPG). METHODS The GDx neural network produces a "number" that indicates the likelihood that glaucoma is present. This number was compared in three groups representing different stages of health and disease, namely, normal controls (n = 101), OHT (n = 102) and NPG (105). The GDx number's ability to differentiate between normal and glaucoma individuals was then investigated. We also studied the relationship between the GDx number and retinal nerve fibre layer (RNFL) average thickness and visual field status to examine how well the GDx number reflects disease severity. RESULTS The GDx number was significantly different among the groups (P < 0.01); it was highest in NPG and lowest in normal controls. The GDx number differentiated between glaucoma and normal with sensitivity of 92.3% and specificity of 96%. When combined with the parameter of RNFL average thickness, sensitivity and specificity were 88.5% and 100% respectively. In NPG a significant correlation was found between the GDx number and RNFL average thickness(rho = -0.88, P < 0.001) and visual field mean deviation (rho = -0.64, P < 0.001). CONCLUSION The GDx number is able to differentiate between groups of normal, OHT and NPG subjects. Its close relationship with RNFL average thickness and visual field status in glaucoma indicates that it is able to reflect disease severity. Furthermore, its measured ability to distinguish between normal individuals and those with glaucoma demonstrates potential for use in glaucoma diagnosis.
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Affiliation(s)
- D Poinoosawmy
- Glaucoma Research Unit, Moorfields Eye Hospital, City Road, London, EC1V 2PD, UK
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Affiliation(s)
- C C Lim
- Department of Diagnostic Imaging, Tan Tock Seng Hosptial, Singapore
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Poinoosawmy D, Tan JC, Bunce C, Membrey LW, Hitchings RA. Longitudinal nerve fibre layer thickness change in normal-pressure glaucoma. Graefes Arch Clin Exp Ophthalmol 2000; 238:965-9. [PMID: 11196359 DOI: 10.1007/s004170000203] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
PURPOSE To investigate longitudinal retinal nerve fibre layer (RNFL) thickness change in patients with normal-pressure glaucoma (NPG) and to assess how this may be related to visual fields. METHODS NPG patients and normal subjects who had had serial GDx nerve fibre layer Analyzer II imaging and Humphrey visual fields performed at least 18 months apart were selected for study. These measurements were compared between groups at baseline and at subsequent follow-up, for change over time. RESULTS Seventy-five NPG patients and 35 normal subjects were studied. Significant differences in RNFL thickness were found between NPG patients and normal controls at baseline (P < or = 0.001). Over the same time, there was greater RNFL thinning in NPG patients than in normal subjects (P < or = 0.0001). RNFL thinning in NPG was negatively correlated with visual field log MD at baseline (P < 0.001) and change in MD over time (P < 0.001). CONCLUSION Reduction of RNFL thickness over time was significantly greater in NPG patients than in normal subjects, indicating that NPG patients' RNFL had thinned at a faster rate. NPG patients with initially better visual fields had a greater reduction in RNFL thickness than did those with initially more advanced visual field defects, suggesting that more RNFL change may be observed when glaucoma is at an earlier stage. There was a direct relationship between RNFL thinning and visual field deterioration.
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Affiliation(s)
- D Poinoosawmy
- Glaucoma Research Unit, Moorfields Eye Hospital, City Road, London EC1V 2PD, UK
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Tan SY, Chen TP, Lee SH, Tan PS, Chua CT, Teo SM, Thiruventhiran T, Wo M, Loh CS, Hassan A, Tan JC, Koh SN. Cadaveric renal transplantation at University Hospital Kuala Lumpur: a preliminary report. Transplant Proc 2000; 32:1811-2. [PMID: 11119947 DOI: 10.1016/s0041-1345(00)01363-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- S Y Tan
- Department of Medicine, University Hospital, Kuala Lumpur, Malaysia
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Affiliation(s)
- T P Chen
- Renal Unit, University Hospital, Kuala Lumpur, Malaysia
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Yong PT, Teh CH, Look M, Wee SB, Tan JC, Chew SP, Low CH. Removal of a dinner fork from the stomach by double-snare endoscopic extraction. Hong Kong Med J 2000; 6:319-21. [PMID: 11025854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Long and pointed foreign objects in the stomach are difficult to remove by endoscopy, and they can cause complications such as perforation and impaction. The endoscopic removal of long and pointed objects involves the following principles: (1) presenting the blunt end cephalad to prevent perforation or impaction during extraction; (2) orienting the long axis of the object in the line of extraction; and (3) applying traction to the foreign body without losing grip. Currently practised methods of extraction, which use a protector hood or an overtube, do not address these three principles. We report on a case in which an ingested metal dinner fork was removed from the stomach by using a double wire-loop snare technique. This method uses two snares to hold the object and allows the endoscopist to change the presentation, orient the axis, and maintain traction to allow the safe removal of long and pointed objects.
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Affiliation(s)
- P T Yong
- Grace Polyclinic, 134 East Coast Road, Singapore 428819, Singapore
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