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Abtahi H, Gholamzadeh M, Shahmoradi L, Shariat M. An information-based framework for development national twin registry: Scoping review and focus group discussion. Int J Health Plann Manage 2021; 36:1423-1444. [PMID: 34519094 DOI: 10.1002/hpm.3256] [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: 11/18/2020] [Revised: 04/26/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Registries in various clinical domains have been established in the last decades. The specific genetic structure of twins has enabled researchers to find answers to the role of genetics and the environment in medical sciences. Thus, twin registries were developed across the world to support twin studies. Our main objective was to devise a conceptual model for developing the national twin registry to ensure the success of this registry. METHODS In this descriptive and qualitative study, the combination of literature review and focus group discussions was applied to achieve suitable models for developing a national twin registry based on lessons learned from founded registries. The qualitative synthesis and reporting results were conducted based on the COREQ checklist. RESULTS According to a systematic literature review, the characteristics and employed strategies employed by established twin registries were recognized. Moreover, based on our objectives, suitable models for registry development were defined. The source of information, the different levels of data, and the information flow were determined based on this model. CONCLUSION Suggesting a conceptual framework for twin registry development at the national level based on the experiences of other countries could contribute to a greater understanding of twin registry implementation efficiently.
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Affiliation(s)
- Hamidreza Abtahi
- Associate Professor of Pulmonary and Critical Care Department, Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Marsa Gholamzadeh
- Ph.D. Student in Medical Informatics, Health Information Management Department, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Shahmoradi
- Associate Professor of Health Information Management, Health Information Management Department, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Mamak Shariat
- Family Health Research Institute, Maternal-Fetal and Neonatal Research Center, Tehran University of Medical Science, Tehran, Iran
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2
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Tanno H, Gould TM, McDaniel JR, Cao W, Tanno Y, Durrett RE, Park D, Cate SJ, Hildebrand WH, Dekker CL, Tian L, Weyand CM, Georgiou G, Goronzy JJ. Determinants governing T cell receptor α/β-chain pairing in repertoire formation of identical twins. Proc Natl Acad Sci U S A 2020; 117:532-540. [PMID: 31879353 PMCID: PMC6955297 DOI: 10.1073/pnas.1915008117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The T cell repertoire in each individual includes T cell receptors (TCRs) of enormous sequence diversity through the pairing of diverse TCR α- and β-chains, each generated by somatic recombination of paralogous gene segments. Whether the TCR repertoire contributes to susceptibility to infectious or autoimmune diseases in concert with disease-associated major histocompatibility complex (MHC) polymorphisms is unknown. Due to a lack in high-throughput technologies to sequence TCR α-β pairs, current studies on whether the TCR repertoire is shaped by host genetics have so far relied only on single-chain analysis. Using a high-throughput single T cell sequencing technology, we obtained the largest paired TCRαβ dataset so far, comprising 965,523 clonotypes from 15 healthy individuals including 6 monozygotic twin pairs. Public TCR α- and, to a lesser extent, TCR β-chain sequences were common in all individuals. In contrast, sharing of entirely identical TCRαβ amino acid sequences was very infrequent in unrelated individuals, but highly increased in twins, in particular in CD4 memory T cells. Based on nucleotide sequence identity, a subset of these shared clonotypes appeared to be the progeny of T cells that had been generated during fetal development and had persisted for more than 50 y. Additional shared TCRαβ in twins were encoded by different nucleotide sequences, implying that genetic determinants impose structural constraints on thymic selection that favor the selection of TCR α-β pairs with entire sequence identities.
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Affiliation(s)
- Hidetaka Tanno
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Timothy M Gould
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94304
| | - Jonathan R McDaniel
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Wenqiang Cao
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94304
| | - Yuri Tanno
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Russell E Durrett
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Daechan Park
- Department of Life Sciences, Ajou University, Suwon 16499, South Korea
| | - Steven J Cate
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - William H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Cornelia L Dekker
- Department of Pediatrics (Infectious Diseases), Stanford University School of Medicine, Stanford, CA 94305
| | - Lu Tian
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305
| | - Cornelia M Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94304
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712;
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Jörg J Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305;
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94304
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3
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Wu PW, Mason KE, Durbin-Johnson BP, Salemi M, Phinney BS, Rocke DM, Parker GJ, Rice RH. Proteomic analysis of hair shafts from monozygotic twins: Expression profiles and genetically variant peptides. Proteomics 2017; 17. [PMID: 28544375 DOI: 10.1002/pmic.201600462] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/03/2017] [Accepted: 05/16/2017] [Indexed: 11/10/2022]
Abstract
Forensic association of hair shaft evidence with individuals is currently assessed by comparing mitochondrial DNA haplotypes of reference and casework samples, primarily for exclusionary purposes. Present work tests and validates more recent proteomic approaches to extract quantitative transcriptional and genetic information from hair samples of monozygotic twin pairs, which would be predicted to partition away from unrelated individuals if the datasets contain identifying information. Protein expression profiles and polymorphic, genetically variant hair peptides were generated from ten pairs of monozygotic twins. Profiling using the protein tryptic digests revealed that samples from identical twins had typically an order of magnitude fewer protein expression differences than unrelated individuals. The data did not indicate that the degree of difference within twin pairs increased with age. In parallel, data from the digests were used to detect genetically variant peptides that result from common nonsynonymous single nucleotide polymorphisms in genes expressed in the hair follicle. Compilation of the variants permitted sorting of the samples by hierarchical clustering, permitting accurate matching of twin pairs. The results demonstrate that genetic differences are detectable by proteomic methods and provide a framework for developing quantitative statistical estimates of personal identification that increase the value of hair shaft evidence.
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Affiliation(s)
- Pei-Wen Wu
- Forensic Science Graduate Program and Department of Environmental Toxicology, University of California, Davis, CA, USA
| | - Katelyn E Mason
- Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Blythe P Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California, Davis, CA, USA
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, CA, USA
| | - Brett S Phinney
- Proteomics Core Facility, University of California, Davis, CA, USA
| | - David M Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California, Davis, CA, USA
| | - Glendon J Parker
- Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, CA, USA.,Protein-Based Identification Technologies, Orem, UT, USA
| | - Robert H Rice
- Forensic Science Graduate Program and Department of Environmental Toxicology, University of California, Davis, CA, USA
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4
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Qi Q, Cavanagh MM, Le Saux S, NamKoong H, Kim C, Turgano E, Liu Y, Wang C, Mackey S, Swan GE, Dekker CL, Olshen RA, Boyd SD, Weyand CM, Tian L, Goronzy JJ. Diversification of the antigen-specific T cell receptor repertoire after varicella zoster vaccination. Sci Transl Med 2016; 8:332ra46. [PMID: 27030598 DOI: 10.1126/scitranslmed.aaf1725] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/18/2016] [Indexed: 12/29/2022]
Abstract
Diversity and size of the antigen-specific T cell receptor (TCR) repertoire are two critical determinants for successful control of chronic infection. Varicella zoster virus (VZV) that establishes latency during childhood can escape control mechanisms, in particular with increasing age. We examined the TCR diversity of VZV-reactive CD4 T cells in individuals older than 50 years by studying three identical twin pairs and three unrelated individuals before and after vaccination with live attenuated VZV. Although all individuals had a small number of dominant T cell clones, the breadth of the VZV-specific repertoire differed markedly. A genetic influence was seen for the sharing of individual TCR sequences from antigen-reactive cells but not for repertoire richness or the selection of dominant clones. VZV vaccination favored the expansion of infrequent VZV antigen-reactive TCRs, including those from naïve T cells with lesser boosting of dominant T cell clones. Thus, vaccination does not reinforce the in vivo selection that occurred during chronic infection but leads to a diversification of the VZV-reactive T cell repertoire. However, a single-booster immunization seems insufficient to establish new clonal dominance. Our results suggest that repertoire analysis of antigen-specific TCRs can be an important readout to assess whether a vaccination was able to generate memory cells in clonal sizes that are necessary for immune protection.
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Affiliation(s)
- Qian Qi
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA. Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Mary M Cavanagh
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA. Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Sabine Le Saux
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA. Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Hong NamKoong
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA. Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Chulwoo Kim
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA. Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Emerson Turgano
- Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yi Liu
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Chen Wang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Sally Mackey
- Division of Infectious Diseases, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Gary E Swan
- Department of Medicine, Stanford Prevention Research Center, Stanford University, Stanford, CA 94305, USA
| | - Cornelia L Dekker
- Division of Infectious Diseases, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Richard A Olshen
- Department of Statistics, Stanford University, Stanford, CA 94305, USA. Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Cornelia M Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA. Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Lu Tian
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Jörg J Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA. Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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5
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Qi Q, Cavanagh MM, Le Saux S, Wagar LE, Mackey S, Hu J, Maecker H, Swan GE, Davis MM, Dekker CL, Tian L, Weyand CM, Goronzy JJ. Defective T Memory Cell Differentiation after Varicella Zoster Vaccination in Older Individuals. PLoS Pathog 2016; 12:e1005892. [PMID: 27764254 PMCID: PMC5072604 DOI: 10.1371/journal.ppat.1005892] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/23/2016] [Indexed: 12/12/2022] Open
Abstract
Vaccination with attenuated live varicella zoster virus (VZV) can prevent zoster reactivation, but protection is incomplete especially in an older population. To decipher the molecular mechanisms underlying variable vaccine responses, T- and B-cell responses to VZV vaccination were examined in individuals of different ages including identical twin pairs. Contrary to the induction of VZV-specific antibodies, antigen-specific T cell responses were significantly influenced by inherited factors. Diminished generation of long-lived memory T cells in older individuals was mainly caused by increased T cell loss after the peak response while the expansion of antigen-specific T cells was not affected by age. Gene expression in activated CD4 T cells at the time of the peak response identified gene modules related to cell cycle regulation and DNA repair that correlated with the contraction phase of the T cell response and consequently the generation of long-lived memory cells. These data identify cell cycle regulatory mechanisms as targets to reduce T cell attrition in a vaccine response and to improve the generation of antigen-specific T cell memory, in particular in an older population.
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Affiliation(s)
- Qian Qi
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California, United States of America
- Department of Medicine, VAPAHCS, Palo Alto, California, United States of America
| | - Mary M. Cavanagh
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California, United States of America
- Department of Medicine, VAPAHCS, Palo Alto, California, United States of America
| | - Sabine Le Saux
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California, United States of America
- Department of Medicine, VAPAHCS, Palo Alto, California, United States of America
| | - Lisa E. Wagar
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, United States of America
| | - Sally Mackey
- Department of Pediatrics-Infectious Diseases, Stanford University, Stanford, California, United States of America
| | - Jinyu Hu
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California, United States of America
- Department of Medicine, VAPAHCS, Palo Alto, California, United States of America
| | - Holden Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, United States of America
| | - Gary E. Swan
- Department of Medicine, Stanford Prevention Research Center, Stanford University, Stanford, California, United States of America
| | - Mark M. Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, United States of America
| | - Cornelia L. Dekker
- Department of Pediatrics-Infectious Diseases, Stanford University, Stanford, California, United States of America
| | - Lu Tian
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Cornelia M. Weyand
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California, United States of America
- Department of Medicine, VAPAHCS, Palo Alto, California, United States of America
| | - Jörg J. Goronzy
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California, United States of America
- Department of Medicine, VAPAHCS, Palo Alto, California, United States of America
- * E-mail:
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6
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Rubelt F, Bolen CR, McGuire HM, Vander Heiden JA, Gadala-Maria D, Levin M, Euskirchen GM, Mamedov MR, Swan GE, Dekker CL, Cowell LG, Kleinstein SH, Davis MM. Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells. Nat Commun 2016; 7:11112. [PMID: 27005435 PMCID: PMC5191574 DOI: 10.1038/ncomms11112] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/20/2016] [Indexed: 01/10/2023] Open
Abstract
The adaptive immune system's capability to protect the body requires a highly diverse lymphocyte antigen receptor repertoire. However, the influence of individual genetic and epigenetic differences on these repertoires is not typically measured. By leveraging the unique characteristics of B, CD4+ T and CD8+ T-lymphocyte subsets from monozygotic twins, we quantify the impact of heritable factors on both the V(D)J recombination process and on thymic selection. We show that the resulting biases in both V(D)J usage and N/P addition lengths, which are found in naïve and antigen experienced cells, contribute to significant variation in the CDR3 region. Moreover, we show that the relative usage of V and J gene segments is chromosomally biased, with ∼1.5 times as many rearrangements originating from a single chromosome. These data refine our understanding of the heritable mechanisms affecting the repertoire, and show that biases are evident on a chromosome-wide level. The diversity of antigen receptor specificities is largely generated by random recombination of its segments. Here the authors show, by genetic comparison of monozygotic twin lymphocyte subsets, that individual genetic and epigenetic biases also contribute to the shape of the B and T cell repertoires.
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Affiliation(s)
- Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Helen M McGuire
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Deaptment of Computational Biology &Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Daniel Gadala-Maria
- Interdepartmental Program in Computational Biology and Bioinformatics, Deaptment of Computational Biology &Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Mikhail Levin
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ghia M Euskirchen
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California 94304, USA
| | - Murad R Mamedov
- Program in Immunology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Gary E Swan
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, California 94304, USA
| | - Cornelia L Dekker
- Department of Pediatrics (Infectious Diseases), Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Deaptment of Computational Biology &Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, 06520, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Institute of Immunity, Department of Microbiology and Immunology, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA
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7
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The CODATwins Project: The Cohort Description of Collaborative Project of Development of Anthropometrical Measures in Twins to Study Macro-Environmental Variation in Genetic and Environmental Effects on Anthropometric Traits. Twin Res Hum Genet 2015; 18:348-60. [PMID: 26014041 DOI: 10.1017/thg.2015.29] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
For over 100 years, the genetics of human anthropometric traits has attracted scientific interest. In particular, height and body mass index (BMI, calculated as kg/m2) have been under intensive genetic research. However, it is still largely unknown whether and how heritability estimates vary between human populations. Opportunities to address this question have increased recently because of the establishment of many new twin cohorts and the increasing accumulation of data in established twin cohorts. We started a new research project to analyze systematically (1) the variation of heritability estimates of height, BMI and their trajectories over the life course between birth cohorts, ethnicities and countries, and (2) to study the effects of birth-related factors, education and smoking on these anthropometric traits and whether these effects vary between twin cohorts. We identified 67 twin projects, including both monozygotic (MZ) and dizygotic (DZ) twins, using various sources. We asked for individual level data on height and weight including repeated measurements, birth related traits, background variables, education and smoking. By the end of 2014, 48 projects participated. Together, we have 893,458 height and weight measures (52% females) from 434,723 twin individuals, including 201,192 complete twin pairs (40% monozygotic, 40% same-sex dizygotic and 20% opposite-sex dizygotic) representing 22 countries. This project demonstrates that large-scale international twin studies are feasible and can promote the use of existing data for novel research purposes.
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8
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Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJL, Furman D, Shen-Orr S, Dekker CL, Swan GE, Butte AJ, Maecker HT, Davis MM. Variation in the human immune system is largely driven by non-heritable influences. Cell 2015; 160:37-47. [PMID: 25594173 DOI: 10.1016/j.cell.2014.12.020] [Citation(s) in RCA: 702] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/20/2014] [Accepted: 11/14/2014] [Indexed: 12/31/2022]
Abstract
There is considerable heterogeneity in immunological parameters between individuals, but its sources are largely unknown. To assess the relative contribution of heritable versus non-heritable factors, we have performed a systems-level analysis of 210 healthy twins between 8 and 82 years of age. We measured 204 different parameters, including cell population frequencies, cytokine responses, and serum proteins, and found that 77% of these are dominated (>50% of variance) and 58% almost completely determined (>80% of variance) by non-heritable influences. In addition, some of these parameters become more variable with age, suggesting the cumulative influence of environmental exposure. Similarly, the serological responses to seasonal influenza vaccination are also determined largely by non-heritable factors, likely due to repeated exposure to different strains. Lastly, in MZ twins discordant for cytomegalovirus infection, more than half of all parameters are affected. These results highlight the largely reactive and adaptive nature of the immune system in healthy individuals.
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Affiliation(s)
- Petter Brodin
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institutet, 17121 Solna, Sweden; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tianxiang Gao
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sanchita Bhattacharya
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Cesar J Lopez Angel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - David Furman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Shai Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Gary E Swan
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Atul J Butte
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA; Center for Pediatric Bioinformatics, Lucille Packard Children's Hospital, Stanford University, Stanford, CA 94304, USA
| | - Holden T Maecker
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA; Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94304, USA.
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9
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B-cell repertoire responses to varicella-zoster vaccination in human identical twins. Proc Natl Acad Sci U S A 2014; 112:500-5. [PMID: 25535378 DOI: 10.1073/pnas.1415875112] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Adaptive immune responses in humans rely on somatic genetic rearrangements of Ig and T-cell receptor loci to generate diverse antigen receptors. It is unclear to what extent an individual's genetic background affects the characteristics of the antibody repertoire used in responding to vaccination or infection. We studied the B-cell repertoires and clonal expansions in response to attenuated varicella-zoster vaccination in four pairs of adult identical twins and found that the global antibody repertoires of twin pair members showed high similarity in antibody heavy chain V, D, and J gene segment use, and in the length and features of the complementarity-determining region 3, a major determinant of antigen binding. These twin similarities were most pronounced in the IgM-expressing B-cell pools, but were seen to a lesser extent in IgG-expressing B cells. In addition, the degree of antibody somatic mutation accumulated in the B-cell repertoire was highly correlated within twin pair members. Twin pair members had greater numbers of shared convergent antibody sequences, including mutated sequences, suggesting similarity among memory B-cell clonal lineages. Despite these similarities in the memory repertoire, the B-cell clones used in acute responses to ZOSTAVAX vaccination were largely unique to each individual. Taken together, these results suggest that the overall B-cell repertoire is significantly shaped by the underlying germ-line genome, but that stochastic or individual-specific effects dominate the selection of clones in response to an acute antigenic stimulus.
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10
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Dominguez-Salas P, Moore SE, Baker MS, Bergen AW, Cox SE, Dyer RA, Fulford AJ, Guan Y, Laritsky E, Silver MJ, Swan GE, Zeisel SH, Innis SM, Waterland RA, Prentice AM, Hennig BJ. Maternal nutrition at conception modulates DNA methylation of human metastable epialleles. Nat Commun 2014; 5:3746. [PMID: 24781383 PMCID: PMC4015319 DOI: 10.1038/ncomms4746] [Citation(s) in RCA: 332] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/26/2014] [Indexed: 01/23/2023] Open
Abstract
In experimental animals, maternal diet during the periconceptional period influences the establishment of DNA methylation at metastable epialleles in the offspring, with permanent phenotypic consequences. Pronounced naturally occurring seasonal differences in the diet of rural Gambian women allowed us to test this in humans. We show that significant seasonal variations in methyl-donor nutrient intake of mothers around the time of conception influence 13 relevant plasma biomarkers. The level of several of these maternal biomarkers predicts increased/decreased methylation at metastable epialleles in DNA extracted from lymphocytes and hair follicles in infants postnatally. Our results demonstrate that maternal nutritional status during early pregnancy causes persistent and systemic epigenetic changes at human metastable epialleles.
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Affiliation(s)
- Paula Dominguez-Salas
- MRC International Nutrition Group at MRC Keneba, The Gambia and London School of Hygiene & Tropical Medicine, EPH, LSHTM, Keppel Street, London WC1E 7HT, UK
| | - Sophie E Moore
- MRC International Nutrition Group at MRC Keneba, The Gambia and London School of Hygiene & Tropical Medicine, EPH, LSHTM, Keppel Street, London WC1E 7HT, UK
| | - Maria S Baker
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates Street, Houston, Texas 77030, USA
| | - Andrew W Bergen
- Center for Health Sciences, SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025-3493, USA
| | - Sharon E Cox
- MRC International Nutrition Group at MRC Keneba, The Gambia and London School of Hygiene & Tropical Medicine, EPH, LSHTM, Keppel Street, London WC1E 7HT, UK
| | - Roger A Dyer
- Department of Pediatrics, University of British Columbia, Room 179, Child and Family Institute, 950 West 28th Avenue Vancouver, British Columbia, Canada V5Z 4H4
| | - Anthony J Fulford
- MRC International Nutrition Group at MRC Keneba, The Gambia and London School of Hygiene & Tropical Medicine, EPH, LSHTM, Keppel Street, London WC1E 7HT, UK
| | - Yongtao Guan
- 1] Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates Street, Houston, Texas 77030, USA [2] Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Eleonora Laritsky
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates Street, Houston, Texas 77030, USA
| | - Matt J Silver
- MRC International Nutrition Group at MRC Keneba, The Gambia and London School of Hygiene & Tropical Medicine, EPH, LSHTM, Keppel Street, London WC1E 7HT, UK
| | - Gary E Swan
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, California 94305-5411, USA
| | - Steven H Zeisel
- Nutrition Research Institute, Department of Nutrition, Gillings School of Global Public Health and School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, 500 Laureate Way, Kannapolis, North Carolina 28081, USA
| | - Sheila M Innis
- Department of Pediatrics, University of British Columbia, Room 179, Child and Family Institute, 950 West 28th Avenue Vancouver, British Columbia, Canada V5Z 4H4
| | - Robert A Waterland
- 1] Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates Street, Houston, Texas 77030, USA [2] Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Andrew M Prentice
- MRC International Nutrition Group at MRC Keneba, The Gambia and London School of Hygiene & Tropical Medicine, EPH, LSHTM, Keppel Street, London WC1E 7HT, UK
| | - Branwen J Hennig
- MRC International Nutrition Group at MRC Keneba, The Gambia and London School of Hygiene & Tropical Medicine, EPH, LSHTM, Keppel Street, London WC1E 7HT, UK
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11
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Horowitz A, Strauss-Albee DM, Leipold M, Kubo J, Nemat-Gorgani N, Dogan OC, Dekker CL, Mackey S, Maecker H, Swan GE, Davis MM, Norman PJ, Guethlein LA, Desai M, Parham P, Blish CA. Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry. Sci Transl Med 2013; 5:208ra145. [PMID: 24154599 PMCID: PMC3918221 DOI: 10.1126/scitranslmed.3006702] [Citation(s) in RCA: 421] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Natural killer (NK) cells play critical roles in immune defense and reproduction, yet remain the most poorly understood major lymphocyte population. Because their activation is controlled by a variety of combinatorially expressed activating and inhibitory receptors, NK cell diversity and function are closely linked. To provide an unprecedented understanding of NK cell repertoire diversity, we used mass cytometry to simultaneously analyze 37 parameters, including 28 NK cell receptors, on peripheral blood NK cells from 5 sets of monozygotic twins and 12 unrelated donors of defined human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) genotype. This analysis revealed a remarkable degree of NK cell diversity, with an estimated 6000 to 30,000 phenotypic populations within an individual and >100,000 phenotypes in the donor panel. Genetics largely determined inhibitory receptor expression, whereas activation receptor expression was heavily environmentally influenced. Therefore, NK cells may maintain self-tolerance through strictly regulated expression of inhibitory receptors while using adaptable expression patterns of activating and costimulatory receptors to respond to pathogens and tumors. These findings further suggest the possibility that discrete NK cell subpopulations could be harnessed for immunotherapeutic strategies in the settings of infection, reproduction, and transplantation.
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Affiliation(s)
- Amir Horowitz
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dara M. Strauss-Albee
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Michael Leipold
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jessica Kubo
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ozge C. Dogan
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Cornelia L. Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sally Mackey
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Holden Maecker
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gary E. Swan
- Center for Health Sciences, SRI International, Menlo Park, CA, 94025, USA
| | - Mark M. Davis
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Paul J. Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lisbeth A. Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Manisha Desai
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Catherine A. Blish
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
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