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Alfaro S, Acuña V, Ceriani R, Cavieres MF, Weinstein-Oppenheimer CR, Campos-Estrada C. Involvement of Inflammation and Its Resolution in Disease and Therapeutics. Int J Mol Sci 2022; 23:ijms231810719. [PMID: 36142625 PMCID: PMC9505300 DOI: 10.3390/ijms231810719] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/22/2022] Open
Abstract
Inflammation plays a critical role in the response to and survival from injuries and/or infections. It occurs in two phases: initiation and resolution; however, when these events do not resolve and persist over time, the inflammatory response becomes chronic, prompting diseases that affect several systems and organs, such as the vasculature and the skin. Here, we reviewed inflammation that occurs in selected infectious and sterile pathologies. Thus, the immune processes induced by bacterial sepsis as well as T. cruzi and SARS-CoV-2 infections are shown. In addition, vaccine adjuvants as well as atherosclerosis are revised as examples of sterile-mediated inflammation. An example of the consequences of a lack of inflammation resolution is given through the revision of wound healing and chronic wounds. Then, we revised the resolution of the latter through advanced therapies represented by cell therapy and tissue engineering approaches, showing how they contribute to control chronic inflammation and therefore wound healing. Finally, new pharmacological insights into the management of chronic inflammation addressing the resolution of inflammation based on pro-resolving mediators, such as lipoxin, maresin, and resolvins, examining their biosynthesis, biological properties, and pharmacokinetic and pharmaceuticals limitations, are given. We conclude that resolution pharmacology and advanced therapies are promising tools to restore the inflammation homeostasis.
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Affiliation(s)
- Sebastián Alfaro
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Avenida Gran Bretaña, Valparaíso 1093, Chile
| | - Vania Acuña
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Avenida Gran Bretaña, Valparaíso 1093, Chile
| | - Ricardo Ceriani
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Avenida Gran Bretaña, Valparaíso 1093, Chile
| | - María Fernanda Cavieres
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Avenida Gran Bretaña, Valparaíso 1093, Chile
| | - Caroline Ruth Weinstein-Oppenheimer
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Avenida Gran Bretaña, Valparaíso 1093, Chile
- Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Santa Marta 183, Valparaíso 1093, Chile
- Correspondence: (C.R.W.-O.); (C.C.-E.); Tel.: +56-32-2508419 (C.R.W.-O.); +56-32-2508140 (C.C.-E.)
| | - Carolina Campos-Estrada
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Avenida Gran Bretaña, Valparaíso 1093, Chile
- Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Santa Marta 183, Valparaíso 1093, Chile
- Correspondence: (C.R.W.-O.); (C.C.-E.); Tel.: +56-32-2508419 (C.R.W.-O.); +56-32-2508140 (C.C.-E.)
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Seki Y, Yoshihara Y, Nojima K, Momose H, Fukushi S, Moriyama S, Wagatsuma A, Numata N, Sasaki K, Kuzuoka T, Yato Y, Takahashi Y, Maeda K, Suzuki T, Mizukami T, Hamaguchi I. Safety and immunogenicity of the Pfizer/BioNTech SARS-CoV-2 mRNA third booster vaccine dose against the SARS-CoV-2 BA.1 and BA.2 Omicron variants. MED 2022; 3:406-421.e4. [PMID: 35815933 PMCID: PMC9040508 DOI: 10.1016/j.medj.2022.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/03/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022]
Abstract
Background The Omicron variant of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) was identified in Japan in November 2021. This variant contains up to 36 mutations in the spike protein, the target of neutralizing antibodies, and can escape vaccine-induced immunity. A booster vaccination campaign began with healthcare workers and high-risk groups. The safety and immunogenicity of the three-dose vaccination against Omicron remain unknown. Methods A total of 272 healthcare workers were initially evaluated for long-term vaccine safety and immunogenicity. We further established a vaccinee panel to evaluate the safety and immunogenicity against variants of concern (VOCs), including the Omicron variants, using a live virus microneutralization assay. Findings Two-dose vaccination induced robust anti-spike antibodies and neutralization titers (NTs) against the ancestral strain WK-521, whereas NTs against VOCs were significantly lower. Within 93–247 days of the second vaccine dose, NTs against Omicron were completely abolished in up to 80% of individuals in the vaccinee panel. Booster dose induced a robust increase in anti-spike antibodies and NTs against the WK-521, Delta, and Omicron variants. There were no significant differences in the neutralization ability of sera from boosted individuals among the Omicron subvariants BA.1, BA.1.1, and BA.2. Boosting increased the breadth of humoral immunity and cross-reactivity with Omicron without changes in cytokine signatures and adverse event rate. Conclusions The third vaccination dose is safe and increases neutralization against Omicron variants. Funding This study was supported by grants from AMED (grants JP21fk0108104 and JP21mk0102146). The SARS-CoV-2 Omicron variant, later named BA.1, has emerged as a highly transmissible variant due to the 36 mutations in its spike protein, which is the target of neutralizing antibodies; it can therefore escape vaccine-induced immunity. The Omicron subvariant, BA.2, was recently identified and has rapidly become a major variant of concern in many countries, including Japan. This study found that anti-spike antibody levels and neutralization ability decreased gradually 6–9 months after the second vaccination. A third dose dramatically increased the response against multiple Omicron variants. These results show that a booster shot increases neutralization antibodies against SARS-CoV-2 variants.
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Affiliation(s)
- Yohei Seki
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Yasuo Yoshihara
- National Hospital Organization Murayama Medical Center, Tokyo 208-0011, Japan
| | - Kiyoko Nojima
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Haruka Momose
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Shuetsu Fukushi
- Department of Virology 1, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Saya Moriyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Ayumi Wagatsuma
- National Hospital Organization Murayama Medical Center, Tokyo 208-0011, Japan
| | - Narumi Numata
- National Hospital Organization Murayama Medical Center, Tokyo 208-0011, Japan
| | - Kyohei Sasaki
- National Hospital Organization Murayama Medical Center, Tokyo 208-0011, Japan
| | - Tomoyo Kuzuoka
- National Hospital Organization Murayama Medical Center, Tokyo 208-0011, Japan
| | - Yoshiyuki Yato
- National Hospital Organization Murayama Medical Center, Tokyo 208-0011, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Ken Maeda
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Takuo Mizukami
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo 208-0011, Japan.
| | - Isao Hamaguchi
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
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3
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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: 36] [Impact Index Per Article: 9.0] [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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4
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Bellavite P. Causality assessment of adverse events following immunization: the problem of multifactorial pathology. F1000Res 2020; 9:170. [PMID: 32269767 PMCID: PMC7111503 DOI: 10.12688/f1000research.22600.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/04/2020] [Indexed: 07/22/2023] Open
Abstract
The analysis of Adverse Events Following Immunization (AEFI) is important in a balanced epidemiological evaluation of vaccines and in the issues related to national vaccine injury compensation programs. If manufacturing defects or vaccine storage and delivering errors are excluded, the majority of adverse reactions to vaccines occur as excessive or biased inflammatory and immune responses. These unwanted phenomena, occasionally severe, are associated with many different endogenous and exogenous factors, which often interact in complex ways. The confirmation or denial of the causal link between an AEFI and vaccination is determined pursuant to WHO guidelines, which propose a four-step analysis and algorithmic diagramming. The evaluation process from the onset considers all possible "other causes" that can explain the AEFI and thus exclude the role of the vaccine. Subsequently, even if there was biological plausibility and temporal compatibility for a causal association between the vaccine and the AEFI, the guidelines ask to look for any possible evidence that the vaccine could not have caused that event. Such an algorithmic method presents some concerns that are discussed here, in the light of the multifactorial nature of the inflammatory and immune pathologies induced by vaccines, including emerging knowledge of genetic susceptibility to adverse effects. It is proposed that the causality assessment could exclude a consistent association of the adverse event with the vaccine only when the presumed "other cause" is independent of an interaction with the vaccine. Furthermore, the scientific literature should be viewed not as an exclusion criterion but as a comprehensive analysis of all the evidence for or against the role of the vaccine in causing an adverse reaction. These issues are discussed in relation to the laws that, in some countries, regulate the mandatory vaccinations and the compensation for those who have suffered serious adverse effects.
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Affiliation(s)
- Paolo Bellavite
- Department of Medicine, Section of General Pathology, University of Verona Medical School, Verona, 37134, Italy
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5
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Abstract
The analysis of Adverse Events Following Immunization (AEFI) is important in a balanced epidemiological evaluation of vaccines and in the issues related to vaccine injury compensation programs. The majority of adverse reactions to vaccines occur as excessive or biased inflammatory and immune responses. These unwanted phenomena, occasionally severe, are associated with many different endogenous and exogenous factors, which often interact in complex ways. The confirmation or denial of the causal link between an AEFI and vaccination is determined pursuant to WHO guidelines, which propose a four-step analysis and algorithmic diagramming. The evaluation process from the onset considers all possible "other causes" that might explain the AEFI and thus exclude the role of the vaccine. Subsequently, even if there was biological plausibility and temporal compatibility for a causal association between the vaccine and the AEFI, the guidelines ask to look for any possible evidence that the vaccine could not have caused that event. Such an algorithmic method presents several concerns that are discussed here, in the light of the multifactorial nature of the inflammatory and immune pathologies induced by vaccines, including emerging knowledge of genetic susceptibility to adverse effects. It is proposed that the causality assessment could exclude a consistent association of the adverse event with the vaccine only when the presumed "other cause" is independent of an interaction with the vaccine. Furthermore, the scientific literature should be viewed not as an exclusion criterion but as a comprehensive analysis of all the evidence for or against the role of the vaccine in causing an adverse reaction. Given these inadequacies in the evaluation of multifactorial diseases, the WHO guidelines need to be reevaluated and revised. These issues are discussed in relation to the laws that, in some countries, regulate the mandatory vaccinations and the compensation for those who have suffered serious adverse effects.
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Affiliation(s)
- Paolo Bellavite
- Department of Medicine, Section of General Pathology, University of Verona Medical School, Verona, 37134, Italy
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6
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Yang L, Gao H, Liu Z, Tang L. Identification of Phage Virion Proteins by Using the g-gap Tripeptide Composition. LETT ORG CHEM 2019. [DOI: 10.2174/1570178615666180910112813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phages are widely distributed in locations populated by bacterial hosts. Phage proteins can be divided into two main categories, that is, virion and non-virion proteins with different functions. In practice, people mainly use phage virion proteins to clarify the lysis mechanism of bacterial cells and develop new antibacterial drugs. Accurate identification of phage virion proteins is therefore essential to understanding the phage lysis mechanism. Although some computational methods have been focused on identifying virion proteins, the result is not satisfying which gives more room for improvement. In this study, a new sequence-based method was proposed to identify phage virion proteins using g-gap tripeptide composition. In this approach, the protein features were firstly extracted from the ggap tripeptide composition. Subsequently, we obtained an optimal feature subset by performing incremental feature selection (IFS) with information gain. Finally, the support vector machine (SVM) was used as the classifier to discriminate virion proteins from non-virion proteins. In 10-fold crossvalidation test, our proposed method achieved an accuracy of 97.40% with AUC of 0.9958, which outperforms state-of-the-art methods. The result reveals that our proposed method could be a promising method in the work of phage virion proteins identification.
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Affiliation(s)
- Liangwei Yang
- School of Computer Science and Engineering, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Gao
- School of Computer Science and Engineering, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zhen Liu
- School of Computer Science and Engineering, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Lixia Tang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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7
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Poland GA, Ovsyannikova IG, Kennedy RB. Personalized vaccinology: A review. Vaccine 2017; 36:5350-5357. [PMID: 28774561 PMCID: PMC5792371 DOI: 10.1016/j.vaccine.2017.07.062] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/19/2017] [Accepted: 07/12/2017] [Indexed: 12/18/2022]
Abstract
At the current time, the field of vaccinology remains empirical in many respects. Vaccine development, vaccine immunogenicity, and vaccine efficacy have, for the most part, historically been driven by an empiric “isolate-inactivate-inject” paradigm. In turn, a population-level public health paradigm of “the same dose for everyone for every disease” model has been the normative thinking in regard to prevention of vaccine-preventable infectious diseases. In addition, up until recently, no vaccines had been designed specifically to overcome the immunosenescence of aging, consistent with a post-WWII mentality of developing vaccines and vaccine programs for children. It is now recognized that the current lack of knowledge concerning how immune responses to vaccines are generated is a critical barrier to understanding poor vaccine responses in the elderly and in immunoimmaturity, discovery of new correlates of vaccine immunogenicity (vaccine response biomarkers), and a directed approach to new vaccine development. The new fields of vaccinomics and adversomics provide models that permit global profiling of the innate, humoral, and cellular immune responses integrated at a systems biology level. This has advanced the science beyond that of reductionist scientific approaches by revealing novel interactions between and within the immune system and other biological systems (beyond transcriptional level), which are critical to developing “downstream” adaptive humoral and cellular responses to infectious pathogens and vaccines. Others have applied systems level approaches to the study of antibody responses (a.k.a. “systems serology”), [1] high-dimensional cell subset immunophenotyping through CyTOF, [2,3] and vaccine induced metabolic changes [4]. In turn, this knowledge is being utilized to better understand the following: identifying who is at risk for which infections; the level of risk that exists regarding poor immunogenicity and/or serious adverse events; and the type or dose of vaccine needed to fully protect an individual. In toto, such approaches allow for a personalized approach to the practice of vaccinology, analogous to the substantial inroads that individualized medicine is playing in other fields of human health and medicine. Herein we briefly review the field of vaccinomics, adversomics, and personalized vaccinology.
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Affiliation(s)
- G A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA.
| | - I G Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA
| | - R B Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA
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8
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Simon WL, Salk HM, Ovsyannikova IG, Kennedy RB, Poland GA. Cytokine production associated with smallpox vaccine responses. Immunotherapy 2015; 6:1097-112. [PMID: 25428648 DOI: 10.2217/imt.14.72] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Smallpox was eradicated 34 years ago due to the success of the smallpox vaccine; yet, the vaccine continues to be studied because of its importance in responding to potential biological warfare and the adverse events associated with current smallpox vaccines. Interindividual variations in vaccine response are observed and are, in part, due to genetic variation. In some cases, these varying responses lead to adverse events, which occur at a relatively high rate for the smallpox vaccine compared with other vaccines. Here, we aim to summarize the cytokine responses associated with smallpox vaccine response to date. Along with a description of each of these cytokines, we describe the genetic and adverse event data associated with cytokine responses to smallpox vaccination.
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Affiliation(s)
- Whitney L Simon
- Mayo Vaccine Research Group, Mayo Clinic, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, USA
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9
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Abstract
Here we introduce the ReliefF machine learning algorithm and some of its extensions for detecting and characterizing epistasis in genetic association studies. We provide a general overview of the method and then highlight some of the modifications that have greatly improved its power for genetic analysis. We end with a few examples of published studies of complex human diseases that have used ReliefF.
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10
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Oberg AL, McKinney BA, Schaid DJ, Pankratz VS, Kennedy RB, Poland GA. Lessons learned in the analysis of high-dimensional data in vaccinomics. Vaccine 2015; 33:5262-70. [PMID: 25957070 DOI: 10.1016/j.vaccine.2015.04.088] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 04/16/2015] [Accepted: 04/23/2015] [Indexed: 12/17/2022]
Abstract
The field of vaccinology is increasingly moving toward the generation, analysis, and modeling of extremely large and complex high-dimensional datasets. We have used data such as these in the development and advancement of the field of vaccinomics to enable prediction of vaccine responses and to develop new vaccine candidates. However, the application of systems biology to what has been termed "big data," or "high-dimensional data," is not without significant challenges-chief among them a paucity of gold standard analysis and modeling paradigms with which to interpret the data. In this article, we relate some of the lessons we have learned over the last decade of working with high-dimensional, high-throughput data as applied to the field of vaccinomics. The value of such efforts, however, is ultimately to better understand the immune mechanisms by which protective and non-protective responses to vaccines are generated, and to use this information to support a personalized vaccinology approach in creating better, and safer, vaccines for the public health.
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Affiliation(s)
- Ann L Oberg
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA; Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, USA
| | - Brett A McKinney
- Tandy School of Computer Science, Department of Mathematics, University of Tulsa, Tulsa, OK, USA
| | - Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA; Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, USA
| | - V Shane Pankratz
- UNM Health Sciences Library & Informatics Center, Division of Nephrology, University of New Mexico, Albuquerque, NM, USA
| | | | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, USA.
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11
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Pellegrino P, Falvella FS, Perrone V, Carnovale C, Brusadelli T, Pozzi M, Antoniazzi S, Cheli S, Perrotta C, Clementi E, Radice S. The first steps towards the era of personalised vaccinology: predicting adverse reactions. THE PHARMACOGENOMICS JOURNAL 2014; 15:284-7. [PMID: 25287071 DOI: 10.1038/tpj.2014.57] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/01/2014] [Accepted: 08/21/2014] [Indexed: 01/11/2023]
Abstract
Until now, the occurrence of adverse reactions among individuals inoculated with identical vaccines has been ascribed to unpredictable stochastic processes. Recent advances in pharmacogenomics indicate that some features of host response to immunisation are influenced by genetic traits, henceforth predictable. The ability to predict the adverse reaction to vaccination would represent an important step towards the development of personalised vaccinology and could enhance public confidence in the safety of vaccines. Herein, we have reviewed all the available information on the association between genetic variants and the risk for healthy subjects to develop adverse reactions.
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Affiliation(s)
- P Pellegrino
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, University Hospital 'Luigi Sacco', Universitá di Milano, Milan, Italy
| | - F S Falvella
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, University Hospital 'Luigi Sacco', Universitá di Milano, Milan, Italy
| | - V Perrone
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, University Hospital 'Luigi Sacco', Universitá di Milano, Milan, Italy
| | - C Carnovale
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, University Hospital 'Luigi Sacco', Universitá di Milano, Milan, Italy
| | - T Brusadelli
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, University Hospital 'Luigi Sacco', Universitá di Milano, Milan, Italy
| | - M Pozzi
- Scientific Institute, IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - S Antoniazzi
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - S Cheli
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, University Hospital 'Luigi Sacco', Universitá di Milano, Milan, Italy
| | - C Perrotta
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, University Hospital 'Luigi Sacco', Universitá di Milano, Milan, Italy
| | - E Clementi
- 1] Scientific Institute, IRCCS E. Medea, Bosisio Parini, Lecco, Italy [2] Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, Consiglio Nazionale delle Ricerche Institute of Neuroscience, University Hospital 'Luigi Sacco', Universitá di Milano, Milan, Italy
| | - S Radice
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences, University Hospital 'Luigi Sacco', Universitá di Milano, Milan, Italy
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12
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Xiong F, Janko M, Walker M, Makropoulos D, Weinstock D, Kam M, Hrebien L. Analysis of cytokine release assay data using machine learning approaches. Int Immunopharmacol 2014; 22:465-79. [DOI: 10.1016/j.intimp.2014.07.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 07/01/2014] [Accepted: 07/21/2014] [Indexed: 12/18/2022]
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13
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Batista-Duharte A, Portuondo D, Pérez O, Carlos IZ. Systemic immunotoxicity reactions induced by adjuvanted vaccines. Int Immunopharmacol 2014; 20:170-80. [DOI: 10.1016/j.intimp.2014.02.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/04/2014] [Accepted: 02/21/2014] [Indexed: 02/08/2023]
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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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Haralambieva IH, Oberg AL, Dhiman N, Ovsyannikova IG, Kennedy RB, Grill DE, Jacobson RM, Poland GA. High-dimensional gene expression profiling studies in high and low responders to primary smallpox vaccination. J Infect Dis 2012; 206:1512-20. [PMID: 22949304 DOI: 10.1093/infdis/jis546] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The mechanisms underlying smallpox vaccine-induced variations in immune responses are not well understood, but are of considerable interest to a deeper understanding of poxvirus immunity and correlates of protection. METHODS We assessed transcriptional messenger RNA expression changes in 197 recipients of primary smallpox vaccination representing the extremes of humoral and cellular immune responses. RESULTS The 20 most significant differentially expressed genes include a tumor necrosis factor-receptor superfamily member, an interferon (IFN) gene, a chemokine gene, zinc finger protein genes, nuclear factors, and histones (P ≤ 1.06E(-20), q ≤ 2.64E(-17)). A pathway analysis identified 4 enriched pathways with cytokine production by the T-helper 17 subset of CD4+ T cells being the most significant pathway (P = 3.42E(-05)). Two pathways (antiviral actions of IFNs, P = 8.95E(-05); and IFN-α/β signaling pathway, P = 2.92E(-04)), integral to innate immunity, were enriched when comparing high with low antibody responders (false discovery rate, < 0.05). Genes related to immune function and transcription (TLR8, P = .0002; DAPP1, P = .0003; LAMP3, P = 9.96E(-05); NR4A2, P ≤ .0002; EGR3, P = 4.52E(-05)), and other genes with a possible impact on immunity (LNPEP, P = 3.72E(-05); CAPRIN1, P = .0001; XRN1, P = .0001), were found to be expressed differentially in high versus low antibody responders. CONCLUSION We identified novel and known immunity-related genes and pathways that may account for differences in immune response to smallpox vaccination.
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Affiliation(s)
- Iana H Haralambieva
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota 55905, USA
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16
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Ovsyannikova IG, Haralambieva IH, Kennedy RB, Pankratz VS, Vierkant RA, Jacobson RM, Poland GA. Impact of cytokine and cytokine receptor gene polymorphisms on cellular immunity after smallpox vaccination. Gene 2012; 510:59-65. [PMID: 23009887 DOI: 10.1016/j.gene.2012.08.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 08/08/2012] [Accepted: 08/16/2012] [Indexed: 11/17/2022]
Abstract
We explored associations between SNPs in cytokine/cytokine receptor genes and cellular immunity in subjects following primary smallpox vaccination. We also analyzed the genotype-phenotype associations discovered in the Caucasian subjects among a cohort of African-Americans. In Caucasians we found 277 associations (p<0.05) between gene SNPs and inter-individual variations in IFN-α, IL-12p40, IL-1β, IL-2, and TNF-α secretion levels. A collection of SNPs in the IL1RN, IL2RB, IL4R, IL6, IL10RB, IL12A, and IL12RB2 genes had consistent associations among both Caucasians and African-Americans. A regulatory SNP (rs452204) in the IL1RN gene was significantly associated with higher levels of IL-2 secretion in an allele dose-dependent manner in both race groups (p=0.05 for Caucasians and p=0.002 for African-Americans). IL12RB2 polymorphism rs3790567 was associated with a dose-related decrease in IL-1β secretion (p=0.009 for Caucasians and p=0.01 for African-Americans). Our results demonstrate that variations in smallpox vaccine-induced cytokine responses are modulated by genetic polymorphisms in cytokine and cytokine receptor genes.
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17
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Lousberg EL, Diener KR, Brown MP, Hayball JD. Innate immune recognition of poxviral vaccine vectors. Expert Rev Vaccines 2012; 10:1435-49. [PMID: 21988308 DOI: 10.1586/erv.11.121] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The study of poxviruses pioneered the field of vaccinology after Jenner's remarkable discovery that 'vaccination' with the phylogenetically related cowpox virus conferred immunity to the devastating disease of smallpox. The study of poxviruses continues to enrich the field of virology because the global eradication of smallpox provides a unique example of the potency of effective immunization. Other poxviruses have since been developed as vaccine vectors for clinical and veterinary applications and include modified vaccinia virus strains such as modified vaccinia Ankara and NYVAC as well as the avipox viruses, fowlpox virus and canarypox virus. Despite the empirical development of poxvirus-based vectored vaccines, it is only now becoming apparent that we need to better understand how the innate arm of the immune system drives adaptive immunity to poxviruses, and how this information is relevant to vaccine design strategies, which are the topics addressed in this article.
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Affiliation(s)
- Erin L Lousberg
- Experimental Therapeutics Laboratory, Hanson Institute, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
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18
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Tokuda Y, Yagi T, Yoshii K, Ikeda Y, Fuwa M, Ueno M, Nakano M, Omi N, Tanaka M, Mori K, Kageyama M, Nagasaki I, Yagi K, Kinoshita S, Tashiro K. An approach to predict the risk of glaucoma development by integrating different attribute data. SPRINGERPLUS 2012; 1:41. [PMID: 23961367 PMCID: PMC3725912 DOI: 10.1186/2193-1801-1-41] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 10/15/2012] [Indexed: 11/10/2022]
Abstract
Primary open-angle glaucoma (POAG) is one of the major causes of blindness worldwide and considered to be influenced by inherited and environmental factors. Recently, we demonstrated a genome-wide association study for the susceptibility to POAG by comparing patients and controls. In addition, the serum cytokine levels, which are affected by environmental and postnatal factors, could be also obtained in patients as well as in controls, simultaneously. Here, in order to predict the effective diagnosis of POAG, we developed an “integration approach” using different attribute data which were integrated simply with several machine learning methods and random sampling. Two data sets were prepared for this study. The one is the “training data set”, which consisted of 42 POAG and 42 controls. The other is the “test data set” consisted of 73 POAG and 52 controls. We first examined for genotype and cytokine data using the training data set with general machine learning methods. After the integration approach was applied, we obtained the stable accuracy, using the support vector machine method with the radial basis function. Although our approach was based on well-known machine learning methods and a simple process, we demonstrated that the integration with two kinds of attributes, genotype and cytokines, was effective and helpful in diagnostic prediction of POAG.
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Affiliation(s)
- Yuichi Tokuda
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kajiicho 465, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, 602-8566 Japan
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19
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Umlauf BJ, Ovsyannikova IG, Haralambieva IH, Kennedy RB, Vierkant RA, Pankratz VS, Jacobson RM, Poland GA. Correlations between vaccinia-specific immune responses within a cohort of armed forces members. Viral Immunol 2011; 24:415-20. [PMID: 21958369 DOI: 10.1089/vim.2011.0029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Widespread vaccination with vaccinia virus (VACV) resulted in the eradication of smallpox; however, the licensed VACV-containing vaccines are associated with adverse events (AEs), making them unsuitable for certain high-risk populations. A better understanding of the host immune response following smallpox vaccination could result in vaccines with similar immunogenicity profiles to pre-eradication vaccines with a lower incidence of AEs. To study the immune response to VACV, we recruited 1,076 armed forces members who had been vaccinated with one dose of Dryvax(®). We measured multiple VACV-specific immune responses: neutralizing antibody titer, the level of 12 secreted cytokines in peripheral blood mononuclear cell (PBMC) cultures (IL-1β, IL-2, IL-4, IL-6, IL-10, IL-12p40, IL-12p70, TNF-α, IFN-γ, IFN-α, IFN-β, and IL-18), and the number of IFN-γ- and CD8(+) IFN-γ-secreting cells. We analyzed these data to determine correlations between immune response measures. We detected a strong proinflammatory response in concert with a Th-1-like cytokine response pattern at a median time point of 15.3 mo following primary vaccination. We also detected correlations between neutralizing antibody titer and secreted IL-2, as well as secreted IFN-γ (p=0.009 and p=0.0007, respectively). We also detected strong correlations between the proinflammatory cytokines IL-1β, TNF-α, IL-6, and IL-12p40 (p<0.0001). These results further advance our knowledge of vaccinia-specific cellular immune responses. Notably, vaccine-induced proinflammatory responses were not correlated with neutralizing antibody titers, suggesting that further attenuation to reduce inflammatory immune responses may result in decreased AEs without sacrificing VACV immunogenicity and population seropositivity.
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Affiliation(s)
- Benjamin J Umlauf
- Vaccine Research Group, Mayo Clinic, Rochester, Minnesota 55905, USA
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20
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Judkowski V, Bunying A, Ge F, Appel JR, Law K, Sharma A, Raja- Gabaglia C, Norori P, Santos RG, Giulianotti MA, Slifka MK, Douek DC, Graham BS, Pinilla C. GM-CSF production allows the identification of immunoprevalent antigens recognized by human CD4+ T cells following smallpox vaccination. PLoS One 2011; 6:e24091. [PMID: 21931646 PMCID: PMC3170313 DOI: 10.1371/journal.pone.0024091] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 07/29/2011] [Indexed: 12/25/2022] Open
Abstract
The threat of bioterrorism with smallpox and the broad use of vaccinia vectors for other vaccines have led to the resurgence in the study of vaccinia immunological memory. The importance of the role of CD4+ T cells in the control of vaccinia infection is well known. However, more CD8+ than CD4+ T cell epitopes recognized by human subjects immunized with vaccinia virus have been reported. This could be, in part, due to the fact that most of the studies that have identified human CD4+ specific protein-derived fragments or peptides have used IFN-γ production to evaluate vaccinia specific T cell responses. Based on these findings, we reasoned that analyzing a large panel of cytokines would permit us to generate a more complete analysis of the CD4 T cell responses. The results presented provide clear evidence that TNF-α is an excellent readout of vaccinia specificity and that other cytokines such as GM-CSF can be used to evaluate the reactivity of CD4+ T cells in response to vaccinia antigens. Furthermore, using these cytokines as readout of vaccinia specificity, we present the identification of novel peptides from immunoprevalent vaccinia proteins recognized by CD4+ T cells derived from smallpox vaccinated human subjects. In conclusion, we describe a “T cell–driven” methodology that can be implemented to determine the specificity of the T cell response upon vaccination or infection. Together, the single pathogen in vitro stimulation, the selection of CD4+ T cells specific to the pathogen by limiting dilution, the evaluation of pathogen specificity by detecting multiple cytokines, and the screening of the clones with synthetic combinatorial libraries, constitutes a novel and valuable approach for the elucidation of human CD4+ T cell specificity in response to large pathogens.
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Affiliation(s)
- Valeria Judkowski
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Alcinette Bunying
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Feng Ge
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Jon R. Appel
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Kingyee Law
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Atima Sharma
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Claudia Raja- Gabaglia
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Patricia Norori
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Radleigh G. Santos
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida, United States of America
| | - Marc A. Giulianotti
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida, United States of America
| | - Mark K. Slifka
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Clemencia Pinilla
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
- * E-mail:
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Abstract
Vaccine informatics is an emerging research area that focuses on development and applications of bioinformatics methods that can be used to facilitate every aspect of the preclinical, clinical, and postlicensure vaccine enterprises. Many immunoinformatics algorithms and resources have been developed to predict T- and B-cell immune epitopes for epitope vaccine development and protective immunity analysis. Vaccine protein candidates are predictable in silico from genome sequences using reverse vaccinology. Systematic transcriptomics and proteomics gene expression analyses facilitate rational vaccine design and identification of gene responses that are correlates of protection in vivo. Mathematical simulations have been used to model host-pathogen interactions and improve vaccine production and vaccination protocols. Computational methods have also been used for development of immunization registries or immunization information systems, assessment of vaccine safety and efficacy, and immunization modeling. Computational literature mining and databases effectively process, mine, and store large amounts of vaccine literature and data. Vaccine Ontology (VO) has been initiated to integrate various vaccine data and support automated reasoning.
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22
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Ovsyannikova IG, Vierkant RA, Pankratz VS, Jacobson RM, Poland GA. Human leukocyte antigen genotypes in the genetic control of adaptive immune responses to smallpox vaccine. J Infect Dis 2011; 203:1546-55. [PMID: 21592983 PMCID: PMC3096794 DOI: 10.1093/infdis/jir167] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 01/24/2011] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The role of human leukocyte antigen (HLA) genes in mediating adaptive immune responses to smallpox vaccine remains unknown. METHODS We determined genotypes for a group of individuals (n = 1071) who received a single dose of smallpox vaccine (Dryvax, Wyeth Laboratories) and examined associations between HLA alleles and 15 immune outcomes to smallpox vaccine on a per-locus and a per-allele level. RESULTS We found significant associations between the HLA-B and HLA - DQB1 loci and vaccinia-induced antibodies (P = .04 for each locus), with the HLA-B*1302 (P = .036), B*3802 (P = .011), DQB1*0302 (P = .015), and DQB1*0604 (P = .017) alleles being associated with higher levels. Significant global associations were identified between vaccinia-specific interferon (IFN)-γ and DQA1 (P = .003), interleukin (IL)-1β and HLA-B (P = .004), tumor necrosis factor (TNF)-α and HLA-B (P = .006), and IL-6 and HLA-B locus (P = .016) for secreted cytokines, as well as between CD8α(+) IFN-γ Elispot responses and DQB1 (P = .027). Subjects carrying B*3906 (P = .006) and B*5701 (P < .001) secreted higher levels of IL-1β than did subjects who did not carry these alleles. Subjects carrying the B*5301 (P = .047) and B*5601 (P = .008) alleles secreted less IL-1β, compared with subjects who did not carry these alleles. The B*3502 (P = .009), B*5601 (P = .004), and B*5701 (P < .001) alleles were significantly associated with variations in TNF-α secretion. CONCLUSIONS These data suggest that variations in antibody and cellular IFN-γ, IL-1β, TNF-α, and IL-6 immune responses after receipt of smallpox vaccine are genetically controlled by HLA genes or genes in close linkage disequilibrium to these alleles.
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Affiliation(s)
- Inna G. Ovsyannikova
- Mayo Clinic Vaccine Research Group
- Program in Translational Immunovirology and Biodefense
| | | | | | - Robert M. Jacobson
- Mayo Clinic Vaccine Research Group
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group
- Program in Translational Immunovirology and Biodefense
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
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23
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Oberg AL, Kennedy RB, Li P, Ovsyannikova IG, Poland GA. Systems biology approaches to new vaccine development. Curr Opin Immunol 2011; 23:436-43. [PMID: 21570272 DOI: 10.1016/j.coi.2011.04.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 12/11/2022]
Abstract
The current 'isolate, inactivate, inject' vaccine development strategy has served the field of vaccinology well, and such empirical vaccine candidate development has even led to the eradication of smallpox. However, such an approach suffers from limitations, and as an empirical approach, does not fully utilize our knowledge of immunology and genetics. A more complete understanding of the biological processes culminating in disease resistance is needed. The advent of high-dimensional assay technology and 'systems biology' along with a vaccinomics approach [1,2•] is spawning a new era in the science of vaccine development. Here we review recent developments in systems biology and strategies for applying this approach and its resulting data to expand our knowledge base and drive directed development of new vaccines. We also provide applied examples and point out new directions for the field in order to illustrate the power of systems biology.
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Affiliation(s)
- Ann L Oberg
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
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24
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Abstract
Measuring cytokine production is an integral part of measuring immune response during immunotherapy. Current technologies allow the simultaneous quantification of multiple cytokines in a variety of tissues. Patterns of cytokine response can be referred to as cytokine profiles. This article discusses the experimental design and data analysis of a number of studies that examined cytokine profiles in humans. We highlight potential sources of variability, both due to assay nuances and the diversity of human populations. We present strategies for analyzing data, emphasizing both multidimensional analysis and the value of treating each donor as his or her own control.
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Affiliation(s)
- Janet C Siebert
- Robert W Franz Cancer Research Center, Earle A Chiles Research Institute, Providence Cancer Center, Portland, OR 97213, USA.
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25
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Abstract
Multiplex technologies at both the mRNA and protein level have given researchers the ability to determine the co-ordinated cellular response to any given stimuli, in both biological and laboratory-derived fluids. This article examines some of the different mRNA and protein multiplex platforms available and how they may be used in assessing vaccine immunity.
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Affiliation(s)
- Gendie E Lash
- Reproductive and Vascular Biology Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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26
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Abstract
The eradication of smallpox, one of the great triumphs of medicine, was accomplished through the prophylactic administration of live vaccinia virus, a comparatively benign relative of variola virus, the causative agent of smallpox. Nevertheless, recent fears that variola virus may be used as a biological weapon together with the present susceptibility of unimmunized populations have spurred the development of new-generation vaccines that are safer than the original and can be produced by modern methods. Predicting the efficacy of such vaccines in the absence of human smallpox, however, depends on understanding the correlates of protection. This review outlines the biology of poxviruses with particular relevance to vaccine development, describes protein targets of humoral and cellular immunity, compares animal models of orthopoxvirus disease with human smallpox, and considers the status of second- and third-generation smallpox vaccines.
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Affiliation(s)
- Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-3210, USA.
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27
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Cohen JI, Hohman P, Fulton R, Turk SP, Qin J, Thatcher K, Hornung RL. Kinetics of serum cytokines after primary or repeat vaccination with the smallpox vaccine. J Infect Dis 2010; 201:1183-91. [PMID: 20214479 DOI: 10.1086/651453] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The smallpox vaccine is associated with more serious adverse events than any other live attenuated vaccine in use today. Although studies have examined serum cytokine levels in primary vaccine recipients at 1 and 3-5 weeks after vaccination with the smallpox vaccine, serial measurements have not been performed, and studies in revaccinated subjects have not been conducted. METHODS We analyzed cytokine responses in both primary vaccine recipients and revaccinated subjects every other day for 2 weeks after vaccination. RESULTS Primary vaccine recipients had maximal levels of granulocyte-colony-stimulating factor on days 6-7 after vaccination; peak levels of tumor necrosis factor (TNF)-alpha, soluble TNF receptor 1, interferon (IFN)-gamma, IFN-inducible protein-10 (IP-10), interleukin (IL)-6, and tissue inhibitor of metalloproteinases-1 on days 8-9 after vaccination; peak levels of soluble TNF receptor 2 and monokine induced by IFN-gamma (MIG) on days 10-11 after vaccination; and peak levels of granulocyte-macrophage-colony-stimulating factor on days 12-13 after vaccination. Primary vaccine recipients were significantly more likely to have higher peak levels of IFN-gamma, IP-10, and MIG after vaccination than were revaccinated subjects. Primary vaccine recipients were significantly more likely to have fatigue, lymphadenopathy, and headache, as well as a longer duration of these symptoms and more hours missed from work, compared with revaccinated subjects. CONCLUSIONS The increased frequency and duration of symptoms observed in primary vaccine recipients, compared with revaccinated subjects, paralleled the increases in serum cytokine levels in these individuals. TRIAL REGISTRATION Clinicaltrials.gov identifier NCT00325975.
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Affiliation(s)
- Jeffrey I Cohen
- Medical Virology Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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28
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Wright PF, Durbin AP, Whitehead SS, Ikizler MR, Henderson S, Blaney JE, Thumar B, Ankrah S, Rock MT, McKinney BA, Murphy BR, Schmidt AC. Phase 1 trial of the dengue virus type 4 vaccine candidate rDEN4{Delta}30-4995 in healthy adult volunteers. Am J Trop Med Hyg 2009; 81:834-41. [PMID: 19861619 DOI: 10.4269/ajtmh.2009.09-0131] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
rDEN4Delta30-4995 is a live attenuated dengue virus type 4 (DENV4) vaccine candidate specifically designed as a further attenuated derivative of the rDEN4Delta30 parent virus. In a previous study, 5 of 20 vaccinees who received 10(5) plaque-forming units (PFU) of rDEN4Delta30 developed a transient elevation of the serum alanine aminotransferase (ALT) level and an asymptomatic maculopapular rash developed in 10 of 20. In the current study, 28 healthy adult volunteers were randomized to receive 10(5) PFU of rDEN4Delta30-4995 (20) or placebo (8) as a single subcutaneous injection. The vaccine was safe, well-tolerated, and immunogenic. An asymptomatic generalized maculopapular rash and elevations in ALT levels were observed in 10% of the rDEN4Delta30-4995 vaccinees. None of the rDEN4Delta30-4995 vaccinees became viremic, yet 95% developed a four-fold or greater increase in neutralizing antibody titers. Thus, rDEN4Delta30-4995 was demonstrated to be safe, highly attenuated, and immunogenic. However, an asymptomatic localized erythematous rash at the injection site was seen in 17/20 rDEN4Delta30-4995 vaccinees. Therefore, alternative DENV4 vaccine strains were selected for further clinical development.
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Affiliation(s)
- Peter F Wright
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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29
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Kennedy RB, Ovsyannikova IG, Jacobson RM, Poland GA. The immunology of smallpox vaccines. Curr Opin Immunol 2009; 21:314-20. [PMID: 19524427 PMCID: PMC2826713 DOI: 10.1016/j.coi.2009.04.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 04/21/2009] [Indexed: 02/01/2023]
Abstract
In spite of the eradication of smallpox over 30 years ago; orthopox viruses such as smallpox and monkeypox remain serious public health threats both through the possibility of bioterrorism and the intentional release of smallpox and through natural outbreaks of emerging infectious diseases such as monkeypox. The eradication effort was largely made possible by the availability of an effective vaccine based on the immunologically cross-protective vaccinia virus. Although the concept of vaccination dates back to the late 1800s with Edward Jenner, it is only in the past decade that modern immunologic tools have been applied toward deciphering poxvirus immunity. Smallpox vaccines containing vaccinia virus elicit strong humoral and cellular immune responses that confer cross-protective immunity against variola virus for decades after immunization. Recent studies have focused on: establishing the longevity of poxvirus-specific immunity, defining key immune epitopes targeted by T and B cells, developing subunit-based vaccines, and developing genotypic and phenotypic immune response profiles that predict either vaccine response or adverse events following immunization.
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Affiliation(s)
- Richard B Kennedy
- Mayo Clinic Vaccine Research Group, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, United States,Department of Internal Medicine, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, United States
| | - Inna G Ovsyannikova
- Mayo Clinic Vaccine Research Group, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, United States,Department of Internal Medicine, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, United States,Program in Translational Immunovirology and Biodefense, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, United States
| | - Robert M Jacobson
- Mayo Clinic Vaccine Research Group, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, United States,Department of Pediatric and Adolescent Medicine, Mayo Clinic, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905 United States
| | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, United States,Department of Internal Medicine, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, United States,Program in Translational Immunovirology and Biodefense, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, United States
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30
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Reif DM, Motsinger-Reif AA, McKinney BA, Rock MT, Crowe JE, Moore JH. Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination. Genes Immun 2009; 10:112-9. [PMID: 18923431 PMCID: PMC2692715 DOI: 10.1038/gene.2008.80] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 08/27/2008] [Indexed: 11/09/2022]
Abstract
Complex clinical outcomes, such as adverse reaction to vaccination, arise from the concerted interactions among the myriad components of a biological system. Therefore, comprehensive etiological models can be developed only through the integrated study of multiple types of experimental data. In this study, we apply this paradigm to high-dimensional genetic and proteomic data collected to elucidate the mechanisms underlying the development of adverse events (AEs) in patients after smallpox vaccination. As vaccination was successful in all of the patients under study, the AE outcomes reported likely represent the result of interactions among immune system components that result in excessive or prolonged immune stimulation. In this study, we examined 1442 genetic variables (single nucleotide polymorphisms) and 108 proteomic variables (serum cytokine concentrations) to model AE risk. To accomplish this daunting analytical task, we employed the Random Forests (RF) method to filter the most important attributes, then we used the selected attributes to build a final decision tree model. This strategy is well suited to integrated analysis, as relevant attributes may be selected from categorical or continuous data. Importantly, RF is a natural approach for studying the type of gene-gene, gene-protein and protein-protein interactions we hypothesize to be involved in the development of clinical AEs. RF importance scores for particular attributes take interactions into account, and there may be interactions across data types. Combining information from previous studies on AEs related to smallpox vaccination with the genetic and proteomic attributes identified by RF, we built a comprehensive model of AE development that includes the cytokines intercellular adhesion molecule-1 (ICAM-1 or CD54), interleukin-10 (IL-10), and colony stimulating factor-3 (CSF-3 or G-CSF) and a genetic polymorphism in the cytokine gene interleukin-4 (IL4). The biological factors included in the model support our hypothesized mechanism for the development of AEs involving prolonged stimulation of inflammatory pathways and an imbalance of normal tissue damage repair pathways. This study shows the utility of RF for such analytical tasks, while both enhancing and reinforcing our working model of AE development after smallpox vaccination.
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Affiliation(s)
- D M Reif
- National Center for Computational Toxicology, US Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
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Poland GA, Ovsyannikova IG, Jacobson RM. Personalized vaccines: the emerging field of vaccinomics. Expert Opin Biol Ther 2009; 8:1659-67. [PMID: 18847302 DOI: 10.1517/14712598.8.11.1659] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The next 'golden age' in vaccinology will be ushered in by the new science of vaccinomics. In turn, this will inform and allow the development of personalized vaccines, based on our increasing understanding of immune response phenotype: genotype information. Rapid advances in developing such data are already occurring for hepatitis B, influenza, measles, mumps, rubella, anthrax and smallpox vaccines. In addition, newly available data suggest that some vaccine-related adverse events may also be genetically determined and, therefore, predictable. This paper reviews the basis and logic of personalized vaccines, and describes recent advances in the field.
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Affiliation(s)
- Gregory A Poland
- Mayo Clinic College of Medicine, Mayo Vaccine Research Group, Program in TranslationalImmunovirology and Biodefense, Mayo Clinic, Rochester, Minnesota 55905, USA.
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Ryan JE, Dhiman N, Ovsyannikova IG, Vierkant RA, Pankratz VS, Poland GA. Response surface methodology to determine optimal cytokine responses in human peripheral blood mononuclear cells after smallpox vaccination. J Immunol Methods 2008; 341:97-105. [PMID: 19038260 DOI: 10.1016/j.jim.2008.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 11/03/2008] [Accepted: 11/04/2008] [Indexed: 10/21/2022]
Abstract
Feasibility, amount of sample aliquots, processing time and cost are critical considerations for optimizing and conducting assays for large-population based studies. Well designed statistical approaches that quickly identify optimal conditions for a given assay could assist efficient completion of the laboratory assays for such studies. For example, assessment of the profile of secreted cytokines is important in understanding the immune response after vaccination. To characterize the cytokine immune response following smallpox vaccination, PBMC obtained from recently vaccinated subjects were stimulated with varying doses of live or UV-inactivated vaccinia virus and cultured for up to 8 days. In this paper, we describe a novel statistical method to identify optimal operating conditions for length in culture and virus MOI in order to measure a panel of secreted Th1, Th2, and inflammatory cytokines. This statistical method is comprised of two components. It first identifies a subset of the possible time in culture by virus MOI combinations to be studied. It then utilizes response surface analysis techniques to predict the optimal operating conditions for the measurement of each secreted cytokine. This method was applied, and the predicted optimal combinations of length in culture and virus MOI for maximum vaccinia-specific cytokine secretion were identified. The use of the response surface methodology can be applied to the optimization of other laboratory assays; especially when the number of PBMC available limits the testing of all possible combinations of parameters.
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Affiliation(s)
- Jenna E Ryan
- Mayo Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, United States
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McKinney BA. Informatics approaches for identifying biologic relationships in time‐series data. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2008; 1:60-68. [DOI: 10.1002/wnan.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Brett A. McKinney
- Department of Genetics, University of Alabama School of Medicine, Birmingham, AL, 35294 USA
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Reif DM, McKinney BA, Motsinger AA, Chanock SJ, Edwards KM, Rock MT, Moore JH, Crowe JE. Genetic basis for adverse events after smallpox vaccination. J Infect Dis 2008; 198:16-22. [PMID: 18454680 DOI: 10.1086/588670] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Identifying genetic factors associated with the development of adverse events might allow screening before vaccinia virus administration. Two independent clinical trials of the smallpox vaccine (Aventis Pasteur) were conducted in healthy, vaccinia virus-naive adult volunteers. Volunteers were assessed repeatedly for local and systemic adverse events (AEs) associated with the receipt of vaccine and underwent genotyping for 1,442 singlenucleotide polymorphisms (SNPs). In the first study, 36 SNPs in 26 genes were associated with systemic AEs (P <or= .05); these 26 genes were tested in the second study. In the final analysis, 3 SNPs were consistently associated with AEs in both studies. The presence of a nonsynonymous SNP in the methylenetetrahydrofolate reductase (MTHFR)gene was associated with the risk ofAEin both trials (odds ratio [OR], 2.3 [95% confidence interval {CI}, 1.1-5.2] [P = .04] and OR, 4.1 [95% CI, 1.4 -11.4] [P<.01]). Two SNPs in the interferon regulatory factor-1 (IRF1) gene were associated with the risk of AE in both sample sets (OR, 3.2 [95% CI, 1.1-9.8] [P = .03] andOR, 3.0 [95% CI, 1.1- 8.3] [P = .03]). Genetic polymorphisms in genes expressing an enzyme previously associated with adverse reactions to a variety of pharmacologic agents (MTHFR) and an immunological transcription factor (IRF1) were associated with AEs after smallpox vaccination in 2 independent study samples.
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Affiliation(s)
- David M Reif
- Computational Genetics Laboratory, Dartmouth Medical School, Lebanon, New Hampshire, USA
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McKinney BA, Reif DM, White BC, Crowe JE, Moore JH. Evaporative cooling feature selection for genotypic data involving interactions. Bioinformatics 2007; 23:2113-20. [PMID: 17586549 PMCID: PMC3988427 DOI: 10.1093/bioinformatics/btm317] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The development of genome-wide capabilities for genotyping has led to the practical problem of identifying the minimum subset of genetic variants relevant to the classification of a phenotype. This challenge is especially difficult in the presence of attribute interactions, noise and small sample size. METHODS Analogous to the physical mechanism of evaporation, we introduce an evaporative cooling (EC) feature selection algorithm that seeks to obtain a subset of attributes with the optimum information temperature (i.e. the least noise). EC uses an attribute quality measure analogous to thermodynamic free energy that combines Relief-F and mutual information to evaporate (i.e. remove) noise features, leaving behind a subset of attributes that contain DNA sequence variations associated with a given phenotype. RESULTS EC is able to identify functional sequence variations that involve interactions (epistasis) between other sequence variations that influence their association with the phenotype. This ability is demonstrated on simulated genotypic data with attribute interactions and on real genotypic data from individuals who experienced adverse events following smallpox vaccination. The EC formalism allows us to combine information entropy, energy and temperature into a single information free energy attribute quality measure that balances interaction and main effects. AVAILABILITY Open source software, written in Java, is freely available upon request.
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Affiliation(s)
- B A McKinney
- Department of Genetics, University of Alabama School of Medicine, Birmingham, AL 35294, USA.
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