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Bromberg Y, Capriotti E, Carter H. VarI-COSI 2018: a forum for research advances in variant interpretation and diagnostics. BMC Genomics 2019; 20:550. [PMID: 31307380 PMCID: PMC6631439 DOI: 10.1186/s12864-019-5862-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Yana Bromberg
- Department of Biochemistry and Microbiology, Lipman Hall 218, Rutgers University, New Brunswick, NJ, 08901, USA.
- Department of Genetics, Lipman Hall 218, Rutgers University, New Brunswick, NJ, 08901, USA.
| | - Emidio Capriotti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126, Bologna, Italy.
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, CA, 92093, USA.
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Reuterswärd P, Bergström S, Orikiiriza J, Lindquist E, Bergström S, Andersson Svahn H, Ayoglu B, Uhlén M, Wahlgren M, Normark J, Ribacke U, Nilsson P. Levels of human proteins in plasma associated with acute paediatric malaria. Malar J 2018; 17:426. [PMID: 30442134 PMCID: PMC6238294 DOI: 10.1186/s12936-018-2576-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023] Open
Abstract
Background The intimate interaction between the pathophysiology of the human host and the biology of the Plasmodium falciparum parasite results in a wide spectrum of disease outcomes in malaria. Development of severe disease is associated with a progressively augmented imbalance in pro- and anti-inflammatory responses to high parasite loads and sequestration of parasitized erythrocytes. Although these phenomena collectively constitute common denominators for the wide variety of discrete severe malaria manifestations, the mechanistic rationales behind discrepancies in outcome are poorly understood. Exploration of the human pathophysiological response by variations in protein profiles in plasma presents an excellent opportunity to increase the understanding. This is ultimately required for better prediction, prevention and treatment of malaria, which is essential for ongoing elimination and eradication efforts. Results An affinity proteomics approach was used to analyse 541 paediatric plasma samples collected from community controls and patients with mild or severe malaria in Rwanda. Protein profiles were generated with an antibody-based suspension bead array containing 255 antibodies targetting 115 human proteins. Here, 57 proteins were identified with significantly altered levels (adjusted p-values < 0.001) in patients with malaria compared to controls. From these, the 27 most significant proteins (adjusted p-values < 10−14) were selected for a stringent analysis approach. Here, 24 proteins showed elevated levels in malaria patients and included proteins involved in acute inflammatory response as well as cell adhesion. The remaining three proteins, also implicated in immune regulation and cellular adhesivity, displayed lower abundance in malaria patients. In addition, 37 proteins (adjusted p-values < 0.05) were identified with increased levels in patients with severe compared to mild malaria. This set includes, proteins involved in tissue remodelling and erythrocyte membrane proteins. Collectively, this approach has been successfully used to identify proteins both with known and unknown association with different stages of malaria. Conclusion In this study, a high-throughput affinity proteomics approach was used to find protein profiles in plasma linked to P. falciparum infection and malaria disease progression. The proteins presented herein are mainly involved in inflammatory response, cellular adhesion and as constituents of erythrocyte membrane. These findings have a great potential to provide increased conceptual understanding of host-parasite interaction and malaria pathogenesis. Electronic supplementary material The online version of this article (10.1186/s12936-018-2576-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Philippa Reuterswärd
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Sofia Bergström
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Judy Orikiiriza
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Sven Bergström
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Helene Andersson Svahn
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Burcu Ayoglu
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Medicine, Division of Immunology and Rheumatology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Mathias Uhlén
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Normark
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Ulf Ribacke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Peter Nilsson
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
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Ochsenkühn MA, Schmitt-Kopplin P, Harir M, Amin SA. Coral metabolite gradients affect microbial community structures and act as a disease cue. Commun Biol 2018; 1:184. [PMID: 30417121 PMCID: PMC6218554 DOI: 10.1038/s42003-018-0189-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
Abstract
Corals are threatened worldwide due to prevalence of disease and bleaching. Recent studies suggest the ability of corals to resist disease is dependent on maintaining healthy microbiomes that span coral tissues and surfaces, the holobiont. Although our understanding of the role endosymbiotic microbes play in coral health has advanced, the role surface-associated microbes and their chemical signatures play in coral health is limited. Using minimally invasive water sampling, we show that the corals Acropora and Platygyra harbor unique bacteria and metabolites at their surface, distinctly different from surrounding seawater. The surface metabolites released by the holobiont create concentration gradients at 0–5 cm away from the coral surface. These molecules are identified as chemo-attractants, antibacterials, and infochemicals, suggesting they may structure coral surface-associated microbes. Further, we detect surface-associated metabolites characteristic of healthy or white syndrome disease infected corals, a finding which may aid in describing effects of diseases. Michael Ochsenkühn et al. look at the microbial and metabolic composition of coral surfaces and the surrounding seawater. They find that the metabolites found on the surface of the coral create a concentration gradient that influences the surrounding microbiome.
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Affiliation(s)
- Michael A Ochsenkühn
- Biology Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, United Arab Emirates
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Centre Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.,Lehrstuhl für Analytische Lebensmittelchemie, Technische Universität München, Alte Akademie 10, 85354, Freising, Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Centre Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Shady A Amin
- Biology Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, United Arab Emirates. .,Chemistry Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, United Arab Emirates.
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Bromberg Y, Capriotti E, Carter H. VarI-SIG 2015: methods for personalized medicine - the role of variant interpretation in research and diagnostics. BMC Genomics 2016; 17 Suppl 2:425. [PMID: 27357578 PMCID: PMC4928159 DOI: 10.1186/s12864-016-2721-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, Lipman Hall 218, 08901, New Brunswick, NJ, USA. .,Department of Genetics, Rutgers University, Lipman Hall 218, 08901, New Brunswick, NJ, USA.
| | - Emidio Capriotti
- Institute for Mathematical Modeling of Biological Systems, Department of Biology, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, 40225, Düsseldorf, Germany.
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Dr., 92093, La Jolla, CA, USA.
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Handelman SK, Seweryn M, Smith RM, Hartmann K, Wang D, Pietrzak M, Johnson AD, Kloczkowski A, Sadee W. Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs). BMC Genomics 2015; 16 Suppl 8:S8. [PMID: 26111110 PMCID: PMC4480832 DOI: 10.1186/1471-2164-16-s8-s8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Over the past 50,000 years, shifts in human-environmental or human-human interactions shaped genetic differences within and among human populations, including variants under positive selection. Shaped by environmental factors, such variants influence the genetics of modern health, disease, and treatment outcome. Because evolutionary processes tend to act on gene regulation, we test whether regulatory variants are under positive selection. We introduce a new approach to enhance detection of genetic markers undergoing positive selection, using conditional entropy to capture recent local selection signals. RESULTS We use conditional logistic regression to compare our Adjusted Haplotype Conditional Entropy (H|H) measure of positive selection to existing positive selection measures. H|H and existing measures were applied to published regulatory variants acting in cis (cis-eQTLs), with conditional logistic regression testing whether regulatory variants undergo stronger positive selection than the surrounding gene. These cis-eQTLs were drawn from six independent studies of genotype and RNA expression. The conditional logistic regression shows that, overall, H|H is substantially more powerful than existing positive-selection methods in identifying cis-eQTLs against other Single Nucleotide Polymorphisms (SNPs) in the same genes. When broken down by Gene Ontology, H|H predictions are particularly strong in some biological process categories, where regulatory variants are under strong positive selection compared to the bulk of the gene, distinct from those GO categories under overall positive selection. . However, cis-eQTLs in a second group of genes lack positive selection signatures detectable by H|H, consistent with ancient short haplotypes compared to the surrounding gene (for example, in innate immunity GO:0042742); under such other modes of selection, H|H would not be expected to be a strong predictor.. These conditional logistic regression models are adjusted for Minor allele frequency(MAF); otherwise, ascertainment bias is a huge factor in all eQTL data sets. Relationships between Gene Ontology categories, positive selection and eQTL specificity were replicated with H|H in a single larger data set. Our measure, Adjusted Haplotype Conditional Entropy (H|H), was essential in generating all of the results above because it: 1) is a stronger overall predictor for eQTLs than comparable existing approaches, and 2) shows low sequential auto-correlation, overcoming problems with convergence of these conditional regression statistical models. CONCLUSIONS Our new method, H|H, provides a consistently more robust signal associated with cis-eQTLs compared to existing methods. We interpret this to indicate that some cis-eQTLs are under positive selection compared to their surrounding genes. Conditional entropy indicative of a selective sweep is an especially strong predictor of eQTLs for genes in several biological processes of medical interest. Where conditional entropy is a weak or negative predictor of eQTLs, such as innate immune genes, this would be consistent with balancing selection acting on such eQTLs over long time periods. Different measures of selection may be needed for variant prioritization under other modes of evolutionary selection.
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Affiliation(s)
- Samuel K Handelman
- Center for Pharmacogenomics, The Ohio State University College of Medicine, Graves Hall, 330 W. 10th Ave., Columbus, OH 43210, USA
| | - Michal Seweryn
- Mathematical Biosciences Institute, Jennings Hall 3rd Floor, 1735 Neil Ave., Columbus, OH 43210, USA
- Faculty of Mathematics and Computer Science, Łódź University, Narutowicza 65, 90-131 Łódź, Poland
- Division of Biostatistics, The Ohio State University College of Public Health, Cunz Hall, 1841 Neil Avenue, Columbus, OH 43210-1240, USA
| | - Ryan M Smith
- Center for Pharmacogenomics, The Ohio State University College of Medicine, Graves Hall, 330 W. 10th Ave., Columbus, OH 43210, USA
| | - Katherine Hartmann
- Center for Pharmacogenomics, The Ohio State University College of Medicine, Graves Hall, 330 W. 10th Ave., Columbus, OH 43210, USA
| | - Danxin Wang
- Center for Pharmacogenomics, The Ohio State University College of Medicine, Graves Hall, 330 W. 10th Ave., Columbus, OH 43210, USA
| | - Maciej Pietrzak
- Center for Pharmacogenomics, The Ohio State University College of Medicine, Graves Hall, 330 W. 10th Ave., Columbus, OH 43210, USA
- Division of Biostatistics, The Ohio State University College of Public Health, Cunz Hall, 1841 Neil Avenue, Columbus, OH 43210-1240, USA
| | - Andrew D Johnson
- Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, USA
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, 700 Children's Drive, Columbus OH 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, 700 Children's Drive, Columbus OH 43205, USA
- Kavli Institute for Theoretical Physics China, Chinese Academy of Sciences, Beijing 100190, China
| | - Wolfgang Sadee
- Center for Pharmacogenomics, The Ohio State University College of Medicine, Graves Hall, 330 W. 10th Ave., Columbus, OH 43210, USA
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Bromberg Y, Capriotti E. VarI-SIG 2014--From SNPs to variants: interpreting different types of genetic variants. BMC Genomics 2015; 16 Suppl 8:I1. [PMID: 26110281 PMCID: PMC4480323 DOI: 10.1186/1471-2164-16-s8-i1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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