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Coombes BJ, Ovsyannikova IG, Schaid DJ, Warner ND, Poland GA, Kennedy RB. Polygenic Prediction of Cellular Immune Responses to Mumps Vaccine. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.23.24303277. [PMID: 38464113 PMCID: PMC10925362 DOI: 10.1101/2024.02.23.24303277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
In this report, we provide a follow-up analysis of a previously published genome-wide association study of host genetic variants associated with inter-individual variations in cellular immune responses to mumps vaccine. Here we report the results of a polygenic score (PGS) analysis showing how common variants can predict mumps vaccine response. We found higher PGS for IFNγ, IL-2, and TNFα were predictive of higher post-vaccine IFNγ (p-value = 2e-6), IL-2 (p = 2e-7), and TNFα (p = 0.004) levels, respectively. Control of immune responses after vaccination is complex and polygenic in nature. Our results suggest that the PGS-based approach enables better capture of the combined genetic effects that contribute to mumps vaccine-induced immunity, potentially offering a more comprehensive understanding than traditional single-variant GWAS. This approach will likely have broad utility in studying genetic control of immune responses to other vaccines and to infectious diseases.
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Haslund MM, Sørensen JK, Graff Stensballe L. Genetics and measles, mumps and rubella vaccine response in childhood and adolescence-A systematic review. Scand J Immunol 2023; 97:e13266. [PMID: 38157324 DOI: 10.1111/sji.13266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/20/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023]
Abstract
Measles, mumps and rubella (MMR) are contagious infectious diseases that can be prevented by immunization. However, MMR infections can occur in previously immunized individuals. The vaccine response is, among other factors, influenced by the combined effects of many genes. This systematic review investigates the genetic influence on measles, mumps and rubella antibody responses after childhood vaccination. In accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), systematic literature searches were conducted in the medical databases PubMed, EMBASE and PsycINFO. Search strings were adjusted for each database. Citations were included if they measured and compared the immune response with immunogenetics after vaccination with a vaccine containing one or more of the following components: measles, mumps and/or rubella, MMR. The measure of vaccine response studied was antibodies after vaccination. Forty-eight articles were included in the final analysis. The results suggest that genetic determinants, including host genes, and single nucleotide polymorphisms in immune-related genes influence the MMR antibody responses after vaccination. Specifically, replicated associations were found between HLA, CD46, RARB, IRF9, EIF2AK2, cytokine genes and MMR vaccine-induced humoral immune responses. This knowledge can be useful in understanding and predicting immune responses and may have implications for future vaccine strategies.
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Affiliation(s)
- Marie Mykløy Haslund
- The Child and Adolescent Clinic, The Juliane Marie Center, The Danish National University Hospital "Rigshospitalet", 9-Blegdamsvej, DK-2100, Copenhagen East, Denmark
| | - Jesper Kiehn Sørensen
- The Child and Adolescent Clinic, The Juliane Marie Center, The Danish National University Hospital "Rigshospitalet", 9-Blegdamsvej, DK-2100, Copenhagen East, Denmark
| | - Lone Graff Stensballe
- The Child and Adolescent Clinic, The Juliane Marie Center, The Danish National University Hospital "Rigshospitalet", 9-Blegdamsvej, DK-2100, Copenhagen East, Denmark
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Dudley MZ, Gerber JE, Budigan Ni H, Blunt M, Holroyd TA, Carleton BC, Poland GA, Salmon DA. Vaccinomics: A scoping review. Vaccine 2023; 41:2357-2367. [PMID: 36803903 PMCID: PMC10065969 DOI: 10.1016/j.vaccine.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 12/24/2022] [Accepted: 02/03/2023] [Indexed: 02/21/2023]
Abstract
BACKGROUND This scoping review summarizes a key aspect of vaccinomics by collating known associations between heterogeneity in human genetics and vaccine immunogenicity and safety. METHODS We searched PubMed for articles in English using terms covering vaccines routinely recommended to the general US population, their effects, and genetics/genomics. Included studies were controlled and demonstrated statistically significant associations with vaccine immunogenicity or safety. Studies of Pandemrix®, an influenza vaccine previously used in Europe, were also included, due to its widely publicized genetically mediated association with narcolepsy. FINDINGS Of the 2,300 articles manually screened, 214 were included for data extraction. Six included articles examined genetic influences on vaccine safety; the rest examined vaccine immunogenicity. Hepatitis B vaccine immunogenicity was reported in 92 articles and associated with 277 genetic determinants across 117 genes. Thirty-three articles identified 291 genetic determinants across 118 genes associated with measles vaccine immunogenicity, 22 articles identified 311 genetic determinants across 110 genes associated with rubella vaccine immunogenicity, and 25 articles identified 48 genetic determinants across 34 genes associated with influenza vaccine immunogenicity. Other vaccines had fewer than 10 studies each identifying genetic determinants of their immunogenicity. Genetic associations were reported with 4 adverse events following influenza vaccination (narcolepsy, GBS, GCA/PMR, high temperature) and 2 adverse events following measles vaccination (fever, febrile seizure). CONCLUSION This scoping review identified numerous genetic associations with vaccine immunogenicity and several genetic associations with vaccine safety. Most associations were only reported in one study. This illustrates both the potential of and need for investment in vaccinomics. Current research in this field is focused on systems and genetic-based studies designed to identify risk signatures for serious vaccine reactions or diminished vaccine immunogenicity. Such research could bolster our ability to develop safer and more effective vaccines.
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Affiliation(s)
- Matthew Z Dudley
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Institute for Vaccine Safety, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Jennifer E Gerber
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Survey Research Division, RTI International, Washington, DC, USA
| | - Haley Budigan Ni
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Office of Health Equity, California Department of Public Health, Richmond, CA, USA
| | - Madeleine Blunt
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Taylor A Holroyd
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; International Vaccine Access Center, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Bruce C Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada; Pharmaceutical Outcomes Programme, BC Children's Hospital, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Gregory A Poland
- Division of General Internal Medicine, Mayo Clinic, Rochester, MN, USA; Mayo Vaccine Research Group, Mayo Clinic, Rochester, MN, USA
| | - Daniel A Salmon
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Institute for Vaccine Safety, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA; Department of Health, Behavior & Society, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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Ishige T, Hara H, Hirano T, Kono T, Hanzawa K. Analysis of the Diversity of the AvBD Gene Region in Japanese Quail. J Hered 2021; 111:436-443. [PMID: 32852036 DOI: 10.1093/jhered/esaa035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/21/2020] [Indexed: 12/31/2022] Open
Abstract
The avian β-defensin (AvBD) gene region is an important component of the innate immune system, encoding a variety of antimicrobial peptides. The AvBD region forms a multigene cluster in a specific chromosomal region. Comparison of the AvBD region among various birds suggests the presence of defects, duplications, and pseudogenization at many loci. The AvBD region in certain galliform birds, namely chicken, turkey, and bobwhite quail, includes AvBD3, -6, and -7, with the latter exhibiting copy number variants (CNVs) in chickens. DNA for genomic analysis was extracted from the peripheral blood of 99 randomly selected quail (Coturnix japonica) from 6 inbred lines. Nine CjAvBD1 and 8 CjAvBD12 alleles were detected. Ten haplotypes, including three that were strain specific, were found in alleles from the quail AvBD1 (CjAvBD1) and -12 (CjAvBD12) loci. Next-generation sequencing was used to determine the nucleotide sequences of the CjAvBD gene region (56-70 kb) for 7 homozygous diplotypes of these 10 haplotypes. These 7 haplotypes contained between 12 and 16 CjAvBD genes and were composed of 11 common loci: CjAvBD1, -2, -4, -5, -8, -9, -10, -11, -12, -13, and -14, but lacked CjAvBD3 and -7. Furthermore, up to 5 CjAvBD101 (AvBD6 ortholog) CNVs were observed among the 7 haplotypes. In addition, we detected amino acid substitutions causing net charge mutations that could affect antimicrobial activity in CjAvBD4, -13, -14, and -101. These results suggest that the CjAvBD region is unique among the Galliformes and that its diversity results in potential functional variation in innate immunity.
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Affiliation(s)
- Taichiro Ishige
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Hiromi Hara
- Department of Animal Science, Tokyo University of Agriculture, Atsugi, Japan
| | - Takashi Hirano
- Department of Animal Science, Tokyo University of Agriculture, Atsugi, Japan
| | - Tomohiro Kono
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Kei Hanzawa
- Department of Animal Science, Tokyo University of Agriculture, Atsugi, Japan
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Quin J, Sedmík J, Vukić D, Khan A, Keegan LP, O'Connell MA. ADAR RNA Modifications, the Epitranscriptome and Innate Immunity. Trends Biochem Sci 2021; 46:758-771. [PMID: 33736931 DOI: 10.1016/j.tibs.2021.02.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/28/2021] [Accepted: 02/18/2021] [Indexed: 12/22/2022]
Abstract
Modified bases act as marks on cellular RNAs so that they can be distinguished from foreign RNAs, reducing innate immune responses to endogenous RNA. In humans, mutations giving reduced levels of one base modification, adenosine-to-inosine deamination, cause a viral infection mimic syndrome, a congenital encephalitis with aberrant interferon induction. These Aicardi-Goutières syndrome 6 mutations affect adenosine deaminase acting on RNA 1 (ADAR1), which generates inosines in endogenous double-stranded (ds)RNA. The inosine base alters dsRNA structure to prevent aberrant activation of antiviral cytosolic helicase RIG-I-like receptors. We review how effects of inosines, ADARs, and other modified bases have been shown to be important in innate immunity and cancer.
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Affiliation(s)
- Jaclyn Quin
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Jiří Sedmík
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Dragana Vukić
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Anzer Khan
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Liam P Keegan
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic.
| | - Mary A O'Connell
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic.
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Genetic diversity of Japanese quail cathelicidins. Poult Sci 2021; 100:101046. [PMID: 33780752 PMCID: PMC8039728 DOI: 10.1016/j.psj.2021.101046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 12/29/2020] [Accepted: 02/04/2021] [Indexed: 11/24/2022] Open
Abstract
Japanese quail is a low-fat, meat-bird species exhibiting high disease resistance. Cathelicidins (CATHs) are host defense peptides conserved across numerous vertebrate species that play an important role in innate immunity. The activity of host defense peptides can be affected by amino acid substitutions. However, no polymorphisms in avian CATH genes have been reported to date. The aim of this study was to clarify the polymorphisms in CATHs in Japanese quail. DNA for genomic analyses was extracted from the peripheral blood of 99 randomly selected quail from 6 inbred lines. A total of 6, 4, 6, and 4 CjCATH1, -2, -3, and -B1 alleles were identified, respectively. Nine haplotypes, including 4 strain-specific haplotypes, were identified by combining alleles at the CjCATH1, -2, -3, and -B1 loci. In addition, 2 and 1 amino acid substitutions (I145F, Q148H, and P245H) predicted by PROVEAN and PolyPhen-2 to have deleterious effects were detected in CjCATH2 and -B1, respectively. Synthetic CjCATH2 and -B1 peptides exhibited greater antibacterial activity against Escherichia coli than chicken CATH2 and -B1, respectively. Furthermore, the CjCATHB1∗04 peptide exhibited less potent antimicrobial activity than other CjCATHB1 peptides examined. This is the first report of amino acid substitutions accompanied by changes in antibacterial activity in avian CATHs. These findings could be employed as indicators of improvements in innate immune response in poultry.
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Kennedy RB, Ovsyannikova IG, Palese P, Poland GA. Current Challenges in Vaccinology. Front Immunol 2020; 11:1181. [PMID: 32670279 PMCID: PMC7329983 DOI: 10.3389/fimmu.2020.01181] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022] Open
Abstract
The development of vaccines, which prime the immune system to respond to future infections, has led to global declines in morbidity and mortality from dreadful infectious communicable diseases. However, many pathogens of public health importance are highly complex and/or rapidly evolving, posing unique challenges to vaccine development. Several of these challenges include an incomplete understanding of how immunity develops, host and pathogen genetic variability, and an increased societal skepticism regarding vaccine safety. In particular, new high-dimensional omics technologies, aided by bioinformatics, are driving new vaccine development (vaccinomics). Informed by recent insights into pathogen biology, host genetic diversity, and immunology, the increasing use of genomic approaches is leading to new models and understanding of host immune system responses that may provide solutions in the rapid development of novel vaccine candidates.
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Affiliation(s)
- Richard B Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, United States
| | - Inna G Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, United States
| | - Peter Palese
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, United States
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Keindl M, Fedotkina O, du Plessis E, Jain R, Bergum B, Mygind Jensen T, Laustrup Møller C, Falhammar H, Nyström T, Catrina SB, Jörneskog G, Groop L, Eliasson M, Eliasson B, Brismar K, Nilsson PM, Berg TJ, Appel S, Lyssenko V. Increased Plasma Soluble Interleukin-2 Receptor Alpha Levels in Patients With Long-Term Type 1 Diabetes With Vascular Complications Associated With IL2RA and PTPN2 Gene Polymorphisms. Front Endocrinol (Lausanne) 2020; 11:575469. [PMID: 33193091 PMCID: PMC7664831 DOI: 10.3389/fendo.2020.575469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/06/2020] [Indexed: 12/27/2022] Open
Abstract
Type 1 diabetes (T1D) is largely considered an autoimmune disease leading to the destruction of insulin-producing pancreatic β cells. Further, patients with T1D have 3-4-fold increased risk of developing micro- and macrovascular complications. However, the contribution of immune-related factors contributing to these diabetes complications are poorly understood. Individuals with long-term T1D who do not progress to vascular complications offer a great potential to evaluate end-organ protection. The aim of the present study was to investigate the association of inflammatory protein levels with vascular complications (retinopathy, nephropathy, cardiovascular disease) in individuals with long-term T1D compared to individuals who rapidly progressed to complications. We studied a panel of inflammatory markers in plasma of patients with long-term T1D with (n = 81 and 26) and without (n = 313 and 25) vascular complications from two cross-sectional Scandinavian cohorts (PROLONG and DIALONG) using Luminex technology. A subset of PROLONG individuals (n = 61) was screened for circulating immune cells using multicolor flow cytometry. We found that elevated plasma levels of soluble interleukin-2 receptor alpha (sIL-2R) were positively associated with the complication phenotype. Risk carriers of polymorphisms in the IL2RA and PTPN2 gene region had elevated plasma levels of sIL-2R. In addition, cell surface marker analysis revealed a shift from naïve to effector T cells in T1D individuals with vascular complications as compared to those without. In contrast, no difference between the groups was observed either in IL-2R cell surface expression or in regulatory T cell population size. In conclusion, our data indicates that IL2RA and PTPN2 gene variants might increase the risk of developing vascular complications in people with T1D, by affecting sIL-2R plasma levels and potentially lowering T cell responsiveness. Thus, elevated sIL-2R plasma levels may serve as a biomarker in monitoring the risk for developing diabetic complications and thereby improve patient care.
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Affiliation(s)
- Magdalena Keindl
- Center for Diabetes Research, Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
- Broegelmann Research Laboratory, Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
- *Correspondence: Valeriya Lyssenko, ; Magdalena Keindl,
| | - Olena Fedotkina
- Center for Diabetes Research, Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Elsa du Plessis
- Center for Diabetes Research, Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Ruchi Jain
- Department of Clinical Science, Lund University Diabetes Centre, Malmö, Sweden
| | - Brith Bergum
- Broegelmann Research Laboratory, Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
- Flow Cytometry Core Facility, Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Troels Mygind Jensen
- Research Unit for General Practice & Danish Ageing Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Clinical Epidemiology, Steno Diabetes Center Copenhagen (SDCC), Gentofte, Denmark
| | | | - Henrik Falhammar
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Department of Endocrinology, Metabolism and Diabetes, Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Nyström
- Department of Clinical Science and Education, Division of Internal Medicine, Unit for Diabetes Research, Karolinska Institute, South Hospital, Stockholm, Sweden
| | - Sergiu-Bogdan Catrina
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Department of Endocrinology, Metabolism and Diabetes, Karolinska University Hospital, Stockholm, Sweden
- Center for Diabetes, Academica Specialist Centrum, Stockholm, Sweden
| | - Gun Jörneskog
- Karolinska Institute, Department of Clinical Sciences, Danderyd University Hospital, Division of Internal Medicine, Stockholm, Sweden
| | - Leif Groop
- Department of Clinical Science, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mats Eliasson
- Department of Public Health and Clinical Medicine, Sunderby Research Unit, Umeå University, Umeå, Sweden
| | - Björn Eliasson
- Department of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Kerstin Brismar
- Department of Endocrinology, Metabolism and Diabetes, Karolinska University Hospital, Stockholm, Sweden
| | - Peter M. Nilsson
- Department of Clinical Science, Lund University Diabetes Centre, Malmö, Sweden
| | - Tore Julsrud Berg
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Silke Appel
- Broegelmann Research Laboratory, Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
- Flow Cytometry Core Facility, Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Valeriya Lyssenko
- Center for Diabetes Research, Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
- Department of Clinical Science, Lund University Diabetes Centre, Malmö, Sweden
- *Correspondence: Valeriya Lyssenko, ; Magdalena Keindl,
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Abstract
There is substantial variation between individuals in the immune response to vaccination. In this review, we provide an overview of the plethora of studies that have investigated factors that influence humoral and cellular vaccine responses in humans. These include intrinsic host factors (such as age, sex, genetics, and comorbidities), perinatal factors (such as gestational age, birth weight, feeding method, and maternal factors), and extrinsic factors (such as preexisting immunity, microbiota, infections, and antibiotics). Further, environmental factors (such as geographic location, season, family size, and toxins), behavioral factors (such as smoking, alcohol consumption, exercise, and sleep), and nutritional factors (such as body mass index, micronutrients, and enteropathy) also influence how individuals respond to vaccines. Moreover, vaccine factors (such as vaccine type, product, adjuvant, and dose) and administration factors (schedule, site, route, time of vaccination, and coadministered vaccines and other drugs) are also important. An understanding of all these factors and their impacts in the design of vaccine studies and decisions on vaccination schedules offers ways to improve vaccine immunogenicity and efficacy.
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McLean HQ, Fiebelkorn AP, Ogee-Nwankwo A, Hao L, Coleman LA, Adebayo A, Icenogle JP. Rubella virus neutralizing antibody response after a third dose of measles-mumps-rubella vaccine in young adults. Vaccine 2018; 36:5732-5737. [DOI: 10.1016/j.vaccine.2018.08.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 06/21/2018] [Accepted: 08/03/2018] [Indexed: 11/25/2022]
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Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar). Mar Genomics 2018; 39:26-38. [DOI: 10.1016/j.margen.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 12/16/2017] [Accepted: 01/08/2018] [Indexed: 02/06/2023]
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Haralambieva IH, Gibson MJ, Kennedy RB, Ovsyannikova IG, Warner ND, Grill DE, Poland GA. Characterization of rubella-specific humoral immunity following two doses of MMR vaccine using proteome microarray technology. PLoS One 2017; 12:e0188149. [PMID: 29145521 PMCID: PMC5690594 DOI: 10.1371/journal.pone.0188149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/01/2017] [Indexed: 11/18/2022] Open
Abstract
Introduction//Background The lack of standardization of the currently used commercial anti-rubella IgG antibody assays leads to frequent misinterpretation of results for samples with low/equivocal antibody concentration. The use of alternative approaches in rubella serology could add new information leading to a fuller understanding of rubella protective immunity and neutralizing antibody response after vaccination. Methods We applied microarray technology to measure antibodies to all rubella virus proteins in 75 high and 75 low rubella virus-specific antibody responders after two MMR vaccine doses. These data were used in multivariate penalized logistic regression modeling of rubella-specific neutralizing antibody response after vaccination. Results We measured antibodies to all rubella virus structural proteins (i.e., the glycoproteins E1 and E2 and the capsid C protein) and to the non-structural protein P150. Antibody levels to each of these proteins were: correlated with the neutralizing antibody titer (p<0.006); demonstrated differences between the high and the low antibody responder groups (p<0.008); and were components of the model associated with/predictive of vaccine-induced rubella virus-specific neutralizing antibody titers (misclassification error = 0.2). Conclusion Our study supports the use of this new technology, as well as the use of antibody profiles/patterns (rather than single antibody measures) as biomarkers of neutralizing antibody response and correlates of protective immunity in rubella virus serology.
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Affiliation(s)
- Iana H. Haralambieva
- Mayo Vaccine Research Group, Mayo Clinic and Foundation, Rochester, MN, United States of America
| | - Michael J. Gibson
- Mayo Vaccine Research Group, Mayo Clinic and Foundation, Rochester, MN, United States of America
| | - Richard B. Kennedy
- Mayo Vaccine Research Group, Mayo Clinic and Foundation, Rochester, MN, United States of America
| | - Inna G. Ovsyannikova
- Mayo Vaccine Research Group, Mayo Clinic and Foundation, Rochester, MN, United States of America
| | - Nathaniel D. Warner
- Division of Biomedical Statistics and Informatics- Department of Health Science Research, Mayo Clinic and Foundation, Rochester, MN, United States of America
| | - Diane E. Grill
- Division of Biomedical Statistics and Informatics- Department of Health Science Research, Mayo Clinic and Foundation, Rochester, MN, United States of America
| | - Gregory A. Poland
- Mayo Vaccine Research Group, Mayo Clinic and Foundation, Rochester, MN, United States of America
- * E-mail:
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Yacoub HA, Al-Maghrabi OA, Ahmed ES, Uversky VN. Abundance and functional roles of intrinsic disorder in the antimicrobial peptides of the NK-lysin family. J Biomol Struct Dyn 2016; 35:836-856. [DOI: 10.1080/07391102.2016.1164077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Haitham A. Yacoub
- Faculty of Science, Department of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia
- Department of Cell Biology, Genetic Engineering and Biotechnology Division, National Research Centre, P.O. Box 12622, Gizza, Egypt
| | - Omar A. Al-Maghrabi
- Faculty of Science, Department of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia
| | - Ekram S. Ahmed
- Department of Cell Biology, Genetic Engineering and Biotechnology Division, National Research Centre, P.O. Box 12622, Gizza, Egypt
| | - Vladimir N. Uversky
- Faculty of Sciences, Department of Biological Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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Ovsyannikova IG, Salk HM, Larrabee BR, Pankratz VS, Poland GA. Single nucleotide polymorphisms/haplotypes associated with multiple rubella-specific immune response outcomes post-MMR immunization in healthy children. Immunogenetics 2015; 67:547-61. [PMID: 26329766 DOI: 10.1007/s00251-015-0864-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/03/2015] [Indexed: 12/11/2022]
Abstract
The observed heterogeneity in rubella-specific immune response phenotypes post-MMR vaccination is thought to be explained, in part, by inter-individual genetic variation. In this study, single nucleotide polymorphisms (SNPs) and multiple haplotypes in several candidate genes were analyzed for associations with more than one rubella-specific immune response outcome, including secreted IFN-γ, secreted IL-6, and neutralizing antibody titers. Overall, we identified 23 SNPs in 10 different genes that were significantly associated with at least two rubella-specific immune responses. Of these SNPs, we detected eight in the PVRL3 gene, five in the PVRL1 gene, one in the TRIM22 gene, two in the IL10RB gene, two in the TLR4 gene, and five in other genes (PVR, ADAR, ZFP57, MX1, and BTN2A1/BTN3A3). The PVRL3 gene haplotype GACGGGGGCAGCAAAAAGAAGAGGAAAGAACAA was significantly associated with both higher IFN-γ secretion (t-statistic 4.43, p < 0.0001) and higher neutralizing antibody titers (t-statistic 3.14, p = 0.002). Our results suggest that there is evidence of multigenic associations among identified gene SNPs and that polymorphisms in these candidate genes contribute to the overall observed differences between individuals in response to live rubella virus vaccine. These results will aid our understanding of mechanisms behind rubella-specific immune response to MMR vaccine and influence the development of vaccines in the future.
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Affiliation(s)
- Inna G Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Guggenheim 611C, 200 1st Street S.W., Rochester, Minnesota, 55905, USA
| | - Hannah M Salk
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Guggenheim 611C, 200 1st Street S.W., Rochester, Minnesota, 55905, USA
| | - Beth R Larrabee
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - V Shane Pankratz
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Guggenheim 611C, 200 1st Street S.W., Rochester, Minnesota, 55905, USA.
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15
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Ovsyannikova IG, Salk HM, Larrabee BR, Pankratz VS, Poland GA. Single-nucleotide polymorphism associations in common with immune responses to measles and rubella vaccines. Immunogenetics 2014; 66:663-9. [PMID: 25139337 DOI: 10.1007/s00251-014-0796-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/11/2014] [Indexed: 02/08/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) in candidate immune response genes were evaluated for associations with measles- and rubella-specific neutralizing antibodies, interferon (IFN)-γ, and interleukin (IL)-6 secretion in two separate association analyses in a cohort of healthy immunized subjects. We identified six SNP associations shared between the measles-specific and rubella-specific immune responses, specifically neutralizing antibody titers (DDX58), secreted IL-6 (IL10RB, IL12B), and secreted IFN-γ (IFNAR2, TLR4). An intronic SNP (rs669260) in the antiviral innate immune receptor gene, DDX58, was significantly associated with increased neutralizing antibody titers for both measles and rubella viral antigens post-MMR vaccination (p values 0.02 and 0.0002, respectively). Significant associations were also found between IL10RB (rs2284552; measles study p value 0.006, rubella study p value 0.00008) and IL12B (rs2546893; measles study p value 0.005, rubella study p value 0.03) gene polymorphisms and variations in both measles- and rubella virus-specific IL-6 responses. We also identified associations between individual SNPs in the IFNAR2 and TLR4 genes that were associated with IFN-γ secretion for both measles and rubella vaccine-specific immune responses. These results are the first to indicate that there are SNP associations in common across measles and rubella vaccine immune responses and that SNPs from multiple genes involved in innate and adaptive immune response regulation may contribute to the overall human antiviral response.
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Affiliation(s)
- Inna G Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Guggenheim 611C, 200 1st Street S.W., Rochester, MN, 55905, USA
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16
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Kennedy RB, Ovsyannikova IG, Haralambieva IH, Lambert ND, Pankratz VS, Poland GA. Genetic polymorphisms associated with rubella virus-specific cellular immunity following MMR vaccination. Hum Genet 2014; 133:1407-17. [PMID: 25098560 DOI: 10.1007/s00439-014-1471-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 07/18/2014] [Indexed: 12/11/2022]
Abstract
Rubella virus causes a relatively benign disease in most cases, although infection during pregnancy can result in serious birth defects. An effective vaccine has been available since the early 1970s and outbreaks typically do not occur among highly vaccinated (≥2 doses) populations. Nevertheless, considerable inter-individual variation in immune response to rubella immunization does exist, with single-dose seroconversion rates ~95 %. Understanding the mechanisms behind this variability may provide important insights into rubella immunity. In the current study, we examined associations between single nucleotide polymorphisms (SNPs) in selected cytokine, cytokine receptor, and innate/antiviral genes and immune responses following rubella vaccination in order to understand genetic influences on vaccine response. Our approach consisted of a discovery cohort of 887 subjects aged 11-22 at the time of enrollment and a replication cohort of 542 older adolescents and young adults (age 18-40). Our data indicate that SNPs near the butyrophilin genes (BTN3A3/BTN2A1) and cytokine receptors (IL10RB/IFNAR1) are associated with variations in IFNγ secretion and that multiple SNPs in the PVR gene, as well as SNPs located in the ADAR gene, exhibit significant associations with rubella virus-specific IL-6 secretion. This information may be useful, not only in furthering our understanding immune responses to rubella vaccine, but also in identifying key pathways for targeted adjuvant use to boost immunity in those with weak or absent immunity following vaccination.
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Affiliation(s)
- Richard B Kennedy
- Mayo Vaccine Research Group, Mayo Clinic, Guggenheim 611C, 200 First Street SW, Rochester, MN, 55905, USA
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17
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Dheilly NM, Adema C, Raftos DA, Gourbal B, Grunau C, Du Pasquier L. No more non-model species: the promise of next generation sequencing for comparative immunology. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 45:56-66. [PMID: 24508980 PMCID: PMC4096995 DOI: 10.1016/j.dci.2014.01.022] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 05/21/2023]
Abstract
Next generation sequencing (NGS) allows for the rapid, comprehensive and cost effective analysis of entire genomes and transcriptomes. NGS provides approaches for immune response gene discovery, profiling gene expression over the course of parasitosis, studying mechanisms of diversification of immune receptors and investigating the role of epigenetic mechanisms in regulating immune gene expression and/or diversification. NGS will allow meaningful comparisons to be made between organisms from different taxa in an effort to understand the selection of diverse strategies for host defence under different environmental pathogen pressures. At the same time, it will reveal the shared and unique components of the immunological toolkit and basic functional aspects that are essential for immune defence throughout the living world. In this review, we argue that NGS will revolutionize our understanding of immune responses throughout the animal kingdom because the depth of information it provides will circumvent the need to concentrate on a few "model" species.
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Affiliation(s)
- Nolwenn M Dheilly
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France.
| | - Coen Adema
- Center for Evolutionary and Theoretical Immunology, Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
| | - David A Raftos
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Benjamin Gourbal
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France
| | - Christoph Grunau
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France
| | - Louis Du Pasquier
- University of Basel, Institute of Zoology and Evolutionary Biology, Basel, Switzerland
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Haralambieva IH, Lambert ND, Ovsyannikova IG, Kennedy RB, Larrabee BR, Pankratz VS, Poland GA. Associations between single nucleotide polymorphisms in cellular viral receptors and attachment factor-related genes and humoral immunity to rubella vaccination. PLoS One 2014; 9:e99997. [PMID: 24945853 PMCID: PMC4063777 DOI: 10.1371/journal.pone.0099997] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/21/2014] [Indexed: 12/30/2022] Open
Abstract
Background Viral attachment and cell entry host factors are important for viral replication, pathogenesis, and the generation and sustenance of immune responses after infection and/or vaccination, and are plausible genetic regulators of vaccine-induced immunity. Methods Using a tag-SNP approach in candidate gene study, we assessed the role of selected cell surface receptor genes, attachment factor-related genes, along with other immune genes in the genetic control of immune response variations after live rubella vaccination in two independent study cohorts. Results Our analysis revealed evidence for multiple associations between genetic variants in the PVR, PVRL2, CD209/DC-SIGN, RARB, MOG, IL6 and other immune function-related genes and rubella-specific neutralizing antibodies after vaccination (meta p-value <0.05). Conclusion Our results indicate that multiple SNPs from genes involved in cell adhesion, viral attachment, and viral entry, as well as others in genes involved in signaling and/or immune response regulation, play a role in modulating humoral immune responses following live rubella vaccination.
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MESH Headings
- Adolescent
- Adult
- Antibodies, Neutralizing/biosynthesis
- Antibodies, Viral/biosynthesis
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/immunology
- Child
- Cohort Studies
- Female
- Gene Expression
- Host-Pathogen Interactions
- Humans
- Immunity, Humoral
- Interleukin-6/genetics
- Interleukin-6/immunology
- Lectins, C-Type/genetics
- Lectins, C-Type/immunology
- Male
- Measles-Mumps-Rubella Vaccine/administration & dosage
- Measles-Mumps-Rubella Vaccine/immunology
- Myelin-Oligodendrocyte Glycoprotein/genetics
- Myelin-Oligodendrocyte Glycoprotein/immunology
- Polymorphism, Single Nucleotide
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/immunology
- Receptors, Retinoic Acid/genetics
- Receptors, Retinoic Acid/immunology
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- Rubella/immunology
- Rubella/prevention & control
- Rubella/virology
- Rubella virus/immunology
- Vaccination
- Virus Attachment/drug effects
- Virus Internalization/drug effects
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Affiliation(s)
- Iana H. Haralambieva
- Mayo Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
- Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Nathaniel D. Lambert
- Mayo Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
- Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Inna G. Ovsyannikova
- Mayo Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
- Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Richard B. Kennedy
- Mayo Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
- Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Beth R. Larrabee
- Division of Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - V. Shane Pankratz
- Mayo Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
- Division of Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Gregory A. Poland
- Mayo Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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19
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Ovsyannikova IG, Pankratz VS, Larrabee BR, Jacobson RM, Poland GA. HLA genotypes and rubella vaccine immune response: additional evidence. Vaccine 2014; 32:4206-13. [PMID: 24837503 DOI: 10.1016/j.vaccine.2014.04.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 03/26/2014] [Accepted: 04/28/2014] [Indexed: 10/25/2022]
Abstract
Recent population-based studies have demonstrated the genetic heritability of rubella vaccine response and assessed that the HLA system may explain about 20% of the inter-individual variance in humoral immune response to this vaccine. Our earlier studies compared HLA allelic associations with rubella vaccine-specific antibodies between two smaller cohorts of healthy Rochester, MN, children (346 and 396 subjects) after two doses of rubella-containing vaccine. This study found that specific HLA alleles were consistently associated with rubella-specific antibody titers (B*27:05, DPA1*02:01, and DPB1*04:01 alleles). The current study examined HLA associations in an independent larger cohort of 1012 healthy San Diego, CA, subjects (age 19-40 years) after rubella vaccine in order to replicate our previous findings in the Rochester subjects. Two HLA associations of comparable magnitudes were consistently observed between B*27:05 (median NT50 Rochester cohort 48.9, p=0.067; San Diego cohort 54.8, p=0.047) and DPB1*04:01 (median NT50 Rochester cohort 61.6, p<0.001; San Diego cohort 70.8, p=0.084) alleles and rubella virus-neutralizing antibody titers. Additional HLA alleles resulted in consistent effects on IL-6 production in both cohorts, but did not meet criteria for statistical significance. Our data suggest these HLA alleles play a role in rubella vaccine-induced immunity and provide the basis for future studies that may explain the mechanism(s) by which these HLA polymorphisms affect immune responses to rubella vaccine.
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Affiliation(s)
- Inna G Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA; Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, MN 55905, USA
| | - V Shane Pankratz
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Beth R Larrabee
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Robert M Jacobson
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA; Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA; Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA; Program in Translational Immunovirology and Biodefense, Mayo Clinic, Rochester, MN 55905, USA.
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20
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Kennedy RB, Ovsyannikova IG, Haralambieva IH, Lambert ND, Pankratz VS, Poland GA. Genome-wide SNP associations with rubella-specific cytokine responses in measles-mumps-rubella vaccine recipients. Immunogenetics 2014; 66:493-9. [PMID: 24811271 DOI: 10.1007/s00251-014-0776-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/23/2014] [Indexed: 11/30/2022]
Abstract
Genetic polymorphisms are known to affect responses to both viral infection and vaccination. Our previous work has described genetic polymorphisms significantly associated with variations in immune response to rubella vaccine from multiple gene families with known immune function, including HLA, cytokine and cytokine receptor genes, and in genes controlling innate and adaptive immunity. In this study, we assessed cellular immune responses (IFNγ and IL-6) in a cohort of healthy younger individuals and performed genome-wide SNP analysis on these same individuals. Here, we report the first genome-wide association study focused on immune responses following rubella vaccination. Our results indicate that rs16928280 in protein tyrosine phosphatase delta (PTPRD) and a collection of SNPs in ACO1 (encoding an iron regulatory protein) are associated with interindividual variations in IFNγ response to rubella virus stimulation. In contrast, we did not identify any significant genetic associations with rubella-specific IL-6 response. These genetic regions may influence rubella vaccine-induced IFNγ responses and warrant further studies in additional cohorts in order to confirm these findings.
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Affiliation(s)
- Richard B Kennedy
- Mayo Vaccine Research Group, Mayo Clinic, Guggenheim 611C, 200 First Street SW, Rochester, MN, 55905, USA
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21
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Kennedy RB, Ovsyannikova IG, Lambert ND, Haralambieva IH, Poland GA. The personal touch: strategies toward personalized vaccines and predicting immune responses to them. Expert Rev Vaccines 2014; 13:657-69. [PMID: 24702429 DOI: 10.1586/14760584.2014.905744] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The impact of vaccines on public health and wellbeing has been profound. Smallpox has been eradicated, polio is nearing eradication, and multiple diseases have been eliminated from certain areas of the world. Unfortunately, we now face diseases such as hepatitis C, malaria or tuberculosis, as well as new and re-emerging pathogens for which we lack effective vaccines. Empirical approaches to vaccine development have been successful in the past, but may not be up to the current infectious disease challenges facing us. New, directed approaches to vaccine design, development, and testing need to be developed. Ideally these approaches will capitalize on cutting-edge technologies, advanced analytical and modeling strategies, and up-to-date knowledge of both pathogen and host. These approaches will pay particular attention to the causes of inter-individual variation in vaccine response in order to develop new vaccines tailored to the unique needs of individuals and communities within the population.
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22
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Lambert ND, Haralambieva IH, Ovsyannikova IG, Larrabee BR, Pankratz VS, Poland GA. Characterization of humoral and cellular immunity to rubella vaccine in four distinct cohorts. Immunol Res 2014; 58:1-8. [PMID: 24375276 PMCID: PMC4212652 DOI: 10.1007/s12026-013-8475-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Although vaccination campaigns have significantly reduced the global burden of rubella disease, there are still regional outbreaks and cases of congenital rubella syndrome. Rubella vaccination elicits a strong humoral as well as cellular response. The relationship between these two measures in response to rubella vaccine is poorly understood. We have previously reported no correlation between rubella-virus-specific cytokine secretion and IgG antibody levels after rubella vaccination. In the current study, we extend our previous work to report correlations between secreted cytokines and functional neutralizing antibodies after rubella vaccination in four distinct cohorts. There was evidence of significant differences (p < 0.05) in rubella-virus-specific humoral and cellular responses between cohorts. When investigating relationships between rubella-vaccine-specific humoral and cellular immunity, we observed a significant correlation between neutralizing antibodies and IFN-γ (r(s) = 0.21, p = 0.0004). We also observed correlations in subjects with extreme humoral immune phenotypes and IFN-γ levels in two of the four cohorts (r(s) = 0.32, p = 0.01; r(s) = 0.36, p = 0.01, respectively). These findings indicate that there is a high level of heterogeneity in rubella-specific immune responses between study populations. We believe that the novel correlation discovered between IFN-γ and neutralizing antibody titers will give future insight into the functional mechanisms of immunity induced by rubella virus and other live viral vaccines.
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Affiliation(s)
- Nathaniel D Lambert
- Mayo Vaccine Research Group, Mayo Clinic, Guggenheim 611C, 200 First Street SW, Rochester, MN, 55905, USA
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23
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Haralambieva IH, Ovsyannikova IG, Pankratz VS, Kennedy RB, Jacobson RM, Poland GA. The genetic basis for interindividual immune response variation to measles vaccine: new understanding and new vaccine approaches. Expert Rev Vaccines 2013; 12:57-70. [PMID: 23256739 DOI: 10.1586/erv.12.134] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The live-attenuated measles vaccine is effective, but measles outbreaks still occur in vaccinated populations. This warrants elucidation of the determinants of measles vaccine-induced protective immunity. Interindividual variability in markers of measles vaccine-induced immunity, including neutralizing antibody levels, is regulated in part by host genetic factor variations. This review summarizes recent advances in our understanding of measles vaccine immunogenetics relative to the perspective of developing better measles vaccines. Important genetic regulators of measles vaccine-induced immunity, such as HLA class I and HLA class II genotypes, single nucleotide polymorphisms in cytokine/cytokine receptor genes (IL12B, IL12RB1, IL2, IL10) and the cell surface measles virus receptor CD46 gene, have been identified and independently replicated. New technologies present many opportunities for identification of novel genetic signatures and genetic architectures. These findings help explain a variety of immune response-related phenotypes and promote a new paradigm of 'vaccinomics' for novel vaccine development.
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24
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Poland GA, Kennedy RB, McKinney BA, Ovsyannikova IG, Lambert ND, Jacobson RM, Oberg AL. Vaccinomics, adversomics, and the immune response network theory: individualized vaccinology in the 21st century. Semin Immunol 2013; 25:89-103. [PMID: 23755893 DOI: 10.1016/j.smim.2013.04.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 03/23/2013] [Accepted: 04/18/2013] [Indexed: 02/08/2023]
Abstract
Vaccines, like drugs and medical procedures, are increasingly amenable to individualization or personalization, often based on novel data resulting from high throughput "omics" technologies. As a result of these technologies, 21st century vaccinology will increasingly see the abandonment of a "one size fits all" approach to vaccine dosing and delivery, as well as the abandonment of the empiric "isolate-inactivate-inject" paradigm for vaccine development. In this review, we discuss the immune response network theory and its application to the new field of vaccinomics and adversomics, and illustrate how vaccinomics can lead to new vaccine candidates, new understandings of how vaccines stimulate immune responses, new biomarkers for vaccine response, and facilitate the understanding of what genetic and other factors might be responsible for rare side effects due to vaccines. Perhaps most exciting will be the ability, at a systems biology level, to integrate increasingly complex high throughput data into descriptive and predictive equations for immune responses to vaccines. Herein, we discuss the above with a view toward the future of vaccinology.
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25
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Genome-wide characterization of transcriptional patterns in high and low antibody responders to rubella vaccination. PLoS One 2013; 8:e62149. [PMID: 23658707 PMCID: PMC3641062 DOI: 10.1371/journal.pone.0062149] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/18/2013] [Indexed: 12/16/2022] Open
Abstract
Immune responses to current rubella vaccines demonstrate significant inter-individual variability. We performed mRNA-Seq profiling on PBMCs from high and low antibody responders to rubella vaccination to delineate transcriptional differences upon viral stimulation. Generalized linear models were used to assess the per gene fold change (FC) for stimulated versus unstimulated samples or the interaction between outcome and stimulation. Model results were evaluated by both FC and p-value. Pathway analysis and self-contained gene set tests were performed for assessment of gene group effects. Of 17,566 detected genes, we identified 1,080 highly significant differentially expressed genes upon viral stimulation (p<1.00E−15, FDR<1.00E−14), including various immune function and inflammation-related genes, genes involved in cell signaling, cell regulation and transcription, and genes with unknown function. Analysis by immune outcome and stimulation status identified 27 genes (p≤0.0006 and FDR≤0.30) that responded differently to viral stimulation in high vs. low antibody responders, including major histocompatibility complex (MHC) class I genes (HLA-A, HLA-B and B2M with p = 0.0001, p = 0.0005 and p = 0.0002, respectively), and two genes related to innate immunity and inflammation (EMR3 and MEFV with p = 1.46E−08 and p = 0.0004, respectively). Pathway and gene set analysis also revealed transcriptional differences in antigen presentation and innate/inflammatory gene sets and pathways between high and low responders. Using mRNA-Seq genome-wide transcriptional profiling, we identified antigen presentation and innate/inflammatory genes that may assist in explaining rubella vaccine-induced immune response variations. Such information may provide new scientific insights into vaccine-induced immunity useful in rational vaccine development and immune response monitoring.
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Effects of a single nucleotide polymorphism in the chicken NK-lysin gene on antimicrobial activity and cytotoxicity of cancer cells. Proc Natl Acad Sci U S A 2012; 109:12087-92. [PMID: 22783018 DOI: 10.1073/pnas.1209161109] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
NK-lysin is an effector protein of the innate immune system and an important component of host protection. We isolated a SNP in the NK-lysin coding sequence among different chicken breeds. This A to G substitution at the position 271 nucleotide in the ORF results in an Asn (N) to Asp (D) amino acid alteration. We synthesized two 30-aa peptides (N29N and N29D) to compare the biological activity of the helix 2-loop-helix 3 region of NK-lysin resulting from the polymorphic gene. Both peptides were found to be cytotoxic in bacteria and tumor cell cultures at micromolar concentrations. The N29N peptide, however, exhibited greater antibacterial and anticancer activity than the N29D peptide. Circular dichroism spectroscopy of the two peptides in negatively charged single unilamellar vesicles showed spectra typical of α-helical peptides. The helical profile of N29D was reduced substantially compared with that of N29N. However, no structural change was observed in neutral vesicles. ζ-Potential measurements of liposomes incubated with increasing peptide concentrations allowed surface charge neutralization with a negatively charged lipid, but not with a zwitterionic lipid. This result suggests that a difference in electrostatic interaction between lipid membranes and the helical peptides results from the polymorphic gene and is subsequently an important factor in cell lytic activity of variant NK-lysin peptides.
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27
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Arav-Boger R, Wojcik GL, Duggal P, Ingersoll RG, Beaty T, Pass RF, Yolken RH. Polymorphisms in Toll-like receptor genes influence antibody responses to cytomegalovirus glycoprotein B vaccine. BMC Res Notes 2012; 5:140. [PMID: 22414065 PMCID: PMC3317442 DOI: 10.1186/1756-0500-5-140] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/13/2012] [Indexed: 01/27/2023] Open
Abstract
Background Congenital Cytomegalovirus (CMV) infection is an important medical problem that has yet no current solution. A clinical trial of CMV glycoprotein B (gB) vaccine in young women showed promising efficacy. Improved understanding of the basis for prevention of CMV infection is essential for developing improved vaccines. Results We genotyped 142 women previously vaccinated with three doses of CMV gB for single nucleotide polymorphisms (SNPs) in TLR 1-4, 6, 7, 9, and 10, and their associated intracellular signaling genes. SNPs in the platelet-derived growth factor receptor (PDGFRA) and integrins were also selected based on their role in binding gB. Specific SNPs in TLR7 and IKBKE (inhibitor of nuclear factor kappa-B kinase subunit epsilon) were associated with antibody responses to gB vaccine. Homozygous carriers of the minor allele at four SNPs in TLR7 showed higher vaccination-induced antibody responses to gB compared to heterozygotes or homozygotes for the common allele. SNP rs1953090 in IKBKE was associated with changes in antibody level from second to third dose of vaccine; homozygotes for the minor allele exhibited lower antibody responses while homozygotes for the major allele showed increased responses over time. Conclusions These data contribute to our understanding of the immunogenetic mechanisms underlying variations in the immune response to CMV vaccine.
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Affiliation(s)
- Ravit Arav-Boger
- Department of Pediatrics, Division of Infectious Diseases, Johns Hopkins Hospital, Baltimore, Maryland 21287-4933, USA.
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Kennedy RB, Ovsyannikova IG, Haralambieva IH, O'Byrne MM, Jacobson RM, Pankratz VS, Poland GA. Multigenic control of measles vaccine immunity mediated by polymorphisms in measles receptor, innate pathway, and cytokine genes. Vaccine 2012; 30:2159-67. [PMID: 22265947 DOI: 10.1016/j.vaccine.2012.01.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 11/30/2011] [Accepted: 01/08/2012] [Indexed: 11/28/2022]
Abstract
Measles infection and vaccine response are complex biological processes that involve both viral and host genetic factors. We have previously investigated the influence of genetic polymorphisms on vaccine immune response, including measles vaccines, and have shown that polymorphisms in HLA, cytokine, cytokine receptor, and innate immune response genes are associated with variation in vaccine response but do not account for all of the inter-individual variance seen in vaccinated populations. In the current study we report the findings of a multigenic analysis of measles vaccine immunity, indicating a role for the measles virus receptor CD46, innate pattern-recognition receptors (DDX58, TLR2, 4, 5, 7 and 8) and intracellular signaling intermediates (MAP3K7, NFKBIA), and key antiviral molecules (VISA, OAS2, MX1, PKR) as well as cytokines (IFNA1, IL4, IL6, IL8, IL12B) and cytokine receptor genes (IL2RB, IL6R, IL8RA) in the genetic control of both humoral and cellular immune responses. This multivariate approach provided additional insights into the genetic control of measles vaccine responses over and above the information gained by our previous univariate SNP association analyses.
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Babron MC, Perdry H, Handel AE, Ramagopalan SV, Damotte V, Fontaine B, Müller-Myhsok B, Ebers GC, Clerget-Darpoux F. Determination of the real effect of genes identified in GWAS: the example of IL2RA in multiple sclerosis. Eur J Hum Genet 2011; 20:321-5. [PMID: 22085902 DOI: 10.1038/ejhg.2011.197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Genome-wide association studies (GWAS), although efficient to detect genes involved in complex diseases, are not designed to measure the real effect of the genes. This is illustrated here by the example of IL2RA in multiple sclerosis (MS). Association between IL2RA and MS is clearly established, although the functional variation is still unknown: the effect of IL2RA might be better described by several SNPs than by a single one. This study investigates whether a pair of SNPs better explains the observed linkage and association data than a single SNP. In total, 522 trio families and 244 affected sib-pairs were typed for 26 IL2RA SNPs. For each SNP and pairs of SNPs, the phased genotypes of patients and controls were compared to determine the SNP set offering the best risk discrimination. Consistency between the genotype risks provided by the retained set and the identical by descent allele sharing in affected sib-pairs was assessed. After controlling for multiple testing, the set of SNPs rs2256774 and rs3118470, provides the best discrimination between the case and control genotype distributions (P-corrected=0.009). The relative risk between the least and most at-risk genotypes is 3.54 with a 95% confidence interval of [2.14-5.94]. Furthermore, the linkage information provided by the allele sharing between affected sibs is consistent with the retained set (P=0.80) but rejects the SNP reported in the literature (P=0.006). Establishing a valid modeling of a disease gene is essential to test its potential interaction with other genes and to reconstruct the pathophysiological pathways.
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Ovsyannikova IG, Haralambieva IH, Vierkant RA, O'Byrne MM, Jacobson RM, Poland GA. The association of CD46, SLAM and CD209 cellular receptor gene SNPs with variations in measles vaccine-induced immune responses: a replication study and examination of novel polymorphisms. Hum Hered 2011; 72:206-23. [PMID: 22086389 DOI: 10.1159/000331585] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Accepted: 08/09/2011] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The measles virus (MV) interacts with two known cellular receptors: CD46 and SLAM. The transmembrane receptor CD209 interacts with MV and augments dendritic cell infection. METHODS 764 subjects previously immunized with measles-mumps-rubella vaccine were genotyped for 66 candidate SNPs in the CD46, SLAM and CD209 genes as part of a larger study. RESULTS A previously detected association of the CD46 SNP rs2724384 with measles-specific antibodies was successfully replicated in this study. Increased representation of the minor allele G for an intronic CD46 SNP was associated with an allele dose-related decrease (978 vs. 522 mIU/ml, p = 0.0007) in antibody levels. This polymorphism rs2724384 also demonstrated associations with IL-6 (p = 0.02), IFN-α (p = 0.007) and TNF-α (p = 0.0007) responses. Two polymorphisms (coding rs164288 and intronic rs11265452) in the SLAM gene that were associated with measles antibody levels in our previous study were associated with IFN-γ Elispot (p = 0.04) and IL-10 responses (p = 0.0008), respectively, in this study. We found associations between haplotypes, AACGGAATGGAAAG (p = 0.009) and GGCCGAGAGGAGAG (p < 0.001), in the CD46 gene and TNF-α secretion. CONCLUSION Understanding the functional and mechanistic consequences of these genetic polymorphisms on immune response variations could assist in directing new measles and potentially other viral vaccine design, and in better understanding measles immunogenetics.
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Poland GA, Ovsyannikova IG, Kennedy RB, Haralambieva IH, Jacobson RM. Vaccinomics and a new paradigm for the development of preventive vaccines against viral infections. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:625-36. [PMID: 21732819 PMCID: PMC3166201 DOI: 10.1089/omi.2011.0032] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this article we define vaccinomics as the integration of immunogenetics and immunogenomics with systems biology and immune profiling. Vaccinomics is based on the use of cutting edge, high-dimensional (so called "omics") assays and novel bioinformatics approaches to the development of next-generation vaccines and the expansion of our capabilities in individualized medicine. Vaccinomics will allow us to move beyond the empiric "isolate, inactivate, and inject" approach characterizing past vaccine development efforts, and toward a more detailed molecular and systemic understanding of the carefully choreographed series of biological processes involved in developing viral vaccine-induced "immunity." This enhanced understanding will then be applied to overcome the obstacles to the creation of effective vaccines to protect against pathogens, particularly hypervariable viruses, with the greatest current impact on public health. Here we provide an overview of how vaccinomics will inform vaccine science, the development of new vaccines and/or clinically relevant biomarkers or surrogates of protection, vaccine response heterogeneity, and our understanding of immunosenescence.
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Affiliation(s)
- Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota 55905, USA.
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O'Meara MM, Disis ML. Therapeutic cancer vaccines and translating vaccinomics science to the global health clinic: emerging applications toward proof of concept. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:579-88. [PMID: 21732821 DOI: 10.1089/omi.2010.0149] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As vaccines evolve to be a more common treatment for some cancers, further research is needed to improve the process of developing vaccines and assessing response to treatment. Vaccinomics involves a wide-ranging integration of multiple high throughput technologies including transcriptional, translational, and posttranslational population-based assessments of the human genome, transcriptome, proteome, and immunome. Vaccinomics combines the fields of immunogenetics, immunogenomics, immunoproteomics, and basic immunology to create vaccines that are tailor made to an individual or groups of individuals. This broad range of omics applications to tumor immunology includes antigen discovery, diagnostic biomarkers, cancer vaccine development, predictors of immune response, and clinical response biomarkers. These technologies have aided in the advancement of cancer vaccine development, as illustrated in examples including NY-ESO-1 originally defined by SEREX, and HER2/neu peptides analyzed via high-throughput epitope prediction methods. As technology improves, it presents an opportunity to improve cancer immunotherapy on a global scale, and attention must also be given to utilize these high-throughput methods for the understanding of cancer and immune signatures across populations.
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Affiliation(s)
- Megan M O'Meara
- Tumor Vaccine Group, Center for Translational Medicine in Women's Health, University of Washington, Seattle, Washington 98195-8050, USA
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