1
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Ashley SE, Bosco A, Tang MLK. Transcriptomic changes associated with oral immunotherapy for food allergy. Pediatr Allergy Immunol 2024; 35:e14106. [PMID: 38520061 DOI: 10.1111/pai.14106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/25/2024]
Abstract
This review summarizes recent advances in characterizing the transcriptional pathways associated with outcomes following Oral Immunotherapy. Recent technological advances including single-cell sequencing are transforming the ways in which the transcriptional landscape is understood. The application of these technologies is still in its infancy in food allergy but here we summarize current understanding of gene expression changes following oral immunotherapy for food allergy and specific signatures underpinning the different clinical outcomes of desensitization and remission (sustained unresponsiveness). T helper 2A cells have been identified as a cell type which correlates with disease activity and is modified by treatment. Molecular features at study entry may differentiate individuals who achieve more positive outcomes during OIT. Recent findings point to T cell anergy and Type 1 interferon pathways as potential mechanisms supporting redirection of the allergen-specific immune response away from allergy towards remission. Despite these developments in our understanding of immune mechanisms following OIT, there are still significant gaps. Additional studies examining immune signatures associated with long term and well-defined clinical outcomes are required to gain a more complete understanding of the pathways leading to remission of allergy, in order to optimize treatments and gain improved outcomes for patients.
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Affiliation(s)
- Sarah E Ashley
- Allergy Immunology, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Anthony Bosco
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona, USA
- Department of Immunobiology, The University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Mimi L K Tang
- Allergy Immunology, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
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2
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Zhang D, Zhang H, Lu J, Hu X. Multiomics Data Reveal the Important Role of ANXA2R in T Cell-mediated Rejection After Renal Transplantation. Transplantation 2024; 108:430-444. [PMID: 37677931 PMCID: PMC10798590 DOI: 10.1097/tp.0000000000004754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/14/2023] [Accepted: 06/29/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND T cell-mediated rejection (TCMR) is a severe issue after renal transplantation, but research on its T cell-receptor (TCR) repertoire is lacking. This study intended to elucidate the TCR repertoire landscape in TCMR and hence identify novel potential targets. METHODS A total of 12 multiomics data sets were collected. The TRUST4 algorithm was used to construct and analyze the TCR repertoire in renal allografts with TCMR and stable renal function. Then, novel TCR-related key genes were identified through various criteria and literature research. In bulk transcriptome, cell line, single-cell transcriptome data sets, multiple immune cell infiltration algorithms, and gene set enrichment analysis were used to analyze potential mechanisms of the identified key gene. Twenty-three pathological sections were collected for immunofluorescence staining in the clinical cohort. Finally, the diagnostic and prognostic values of ANXA2R were evaluated in multiple renal transplant data sets. RESULTS Allografts with TCMR showed significantly increased clonotype and specific clonal expansion. ANXA2R was found to be a novel key gene for TCMR and showed strong positive connections with the TCR complex and lymphocyte cells, especially CD8 + T cells. Immunofluorescence staining confirmed the existence of ANXA2R + CD8 + T cells, with their percentage significantly elevated in TCMR compared with stable renal function. Finally, both mRNA and protein levels of ANXA2R showed promising diagnostic and prognostic value for renal transplant recipients. CONCLUSIONS ANXA2R , identified as a novel TCR-related gene, had critical roles in clinicopathology, diagnosis, and prognosis in renal transplantation, which offered promising potential therapeutic targets.
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Affiliation(s)
- Di Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - He Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Jun Lu
- Department of Pathology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
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3
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Wang K, Hu X, Zhang J. Fast clonal family inference from large-scale B cell repertoire sequencing data. CELL REPORTS METHODS 2023; 3:100601. [PMID: 37788671 PMCID: PMC10626204 DOI: 10.1016/j.crmeth.2023.100601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/31/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023]
Abstract
Advances in high-throughput sequencing technologies have facilitated the large-scale characterization of B cell receptor (BCR) repertoires. However, the vast amount and high diversity of the BCR sequences pose challenges for efficient and biologically meaningful analysis. Here, we introduce fastBCR, an efficient computational approach for inferring B cell clonal families from massive BCR heavy chain sequences. We demonstrate that fastBCR substantially reduces the running time while ensuring high accuracy on simulated datasets with diverse numbers of B cell lineages and varying mutation rates. We apply fastBCR to real BCR sequencing data from peripheral blood samples of COVID-19 patients, showing that the inferred clonal families display disease-associated features, as well as corresponding antigen-binding specificity and affinity. Overall, our results demonstrate the advantages of fastBCR for analyzing BCR repertoire data, which will facilitate the identification of disease-associated antibodies and improve our understanding of the B cell immune response.
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Affiliation(s)
- Kaixuan Wang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Xihao Hu
- GV20 Therapeutics, Cambridge, MA, USA
| | - Jian Zhang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China.
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4
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Zong F, Long C, Hu W, Chen S, Dai W, Xiao ZX, Cao Y. Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires. Nucleic Acids Res 2023:7173809. [PMID: 37207341 DOI: 10.1093/nar/gkad400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/23/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
The utilization of high-throughput sequencing (HTS) for B-cell receptor (BCR) immune repertoire analysis has become widespread in the fields of adaptive immunity and antibody drug development. However, the sheer volume of sequences generated by these experiments presents a challenge in data processing. Specifically, multiple sequence alignment (MSA), a critical aspect of BCR analysis, remains inadequate for handling massive BCR sequencing data and lacks the ability to provide immunoglobulin-specific information. To address this gap, we introduce Abalign, a standalone program specifically designed for ultrafast MSA of BCR/antibody sequences. Benchmark tests demonstrate that Abalign achieves comparable or even better accuracy than state-of-the-art MSA tools, and shows remarkable advantages in terms of speed and memory consumption, reducing the time required for high-throughput analysis from weeks to hours. In addition to its alignment capabilities, Abalign offers a broad range of BCR analysis features, including extracting BCRs, constructing lineage trees, assigning VJ genes, analyzing clonotypes, profiling mutations, and comparing BCR immune repertoires. With its user-friendly graphic interface, Abalign can be easily run on personal computers instead of computing clusters. Overall, Abalign is an easy-to-use and effective tool that enables researchers to analyze massive BCR/antibody sequences, leading to new discoveries in the field of immunoinformatics. The software is freely available at http://cao.labshare.cn/abalign/.
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Affiliation(s)
- Fanjie Zong
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Chenyu Long
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Wanxin Hu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Shuang Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Wentao Dai
- NHC Key Laboratory of Reproduction Regulation & Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
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5
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Sindher SB, Chin AR, Aghaeepour N, Prince L, Maecker H, Shaw GM, Stevenson DK, Nadeau KC, Snyder M, Khatri P, Boyd SD, Winn VD, Angst MS, Chinthrajah RS. Advances and potential of omics studies for understanding the development of food allergy. FRONTIERS IN ALLERGY 2023; 4:1149008. [PMID: 37034151 PMCID: PMC10080041 DOI: 10.3389/falgy.2023.1149008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
The prevalence of food allergy continues to rise globally, carrying with it substantial safety, economic, and emotional burdens. Although preventative strategies do exist, the heterogeneity of allergy trajectories and clinical phenotypes has made it difficult to identify patients who would benefit from these strategies. Therefore, further studies investigating the molecular mechanisms that differentiate these trajectories are needed. Large-scale omics studies have identified key insights into the molecular mechanisms for many different diseases, however the application of these technologies to uncover the drivers of food allergy development is in its infancy. Here we review the use of omics approaches in food allergy and highlight key gaps in knowledge for applying these technologies for the characterization of food allergy development.
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Affiliation(s)
- Sayantani B Sindher
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Palo Alto, CA, United States
| | - Andrew R Chin
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Palo Alto, CA, United States
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, United States
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Lawrence Prince
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Holden Maecker
- Department of Medicine, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, United States
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Palo Alto, CA, United States
| | - Michael Snyder
- Department of Genetics, Stanford University, Palo Alto, CA, United States
| | - Purvesh Khatri
- Department of Medicine, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Palo Alto, CA, United States
- Department of Pathology, Stanford University, Palo Alto, CA, United States
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - R Sharon Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Palo Alto, CA, United States
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6
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Zhu H, Tang K, Chen G, Liu Z. Biomarkers in oral immunotherapy. J Zhejiang Univ Sci B 2022; 23:705-731. [PMID: 36111569 PMCID: PMC9483607 DOI: 10.1631/jzus.b2200047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Food allergy (FA) is a global health problem that affects a large population, and thus effective treatment is highly desirable. Oral immunotherapy (OIT) has been showing reasonable efficacy and favorable safety in most FA subjects. Dependable biomarkers are needed for treatment assessment and outcome prediction during OIT. Several immunological indicators have been used as biomarkers in OIT, such as skin prick tests, basophil and mast cell reactivity, T cell and B cell responses, allergen-specific antibody levels, and cytokines. Other novel indicators also could be potential biomarkers. In this review, we discuss and assess the application of various immunological indicators as biomarkers for OIT.
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Affiliation(s)
- Haitao Zhu
- Department of Pediatrics (No. 3 Ward), Northwest Women's and Children's Hospital, Xi'an 710061, China
| | - Kaifa Tang
- Department of Urology, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Guoqiang Chen
- Department of Pediatrics (No. 3 Ward), Northwest Women's and Children's Hospital, Xi'an 710061, China
| | - Zhongwei Liu
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an 710068, China.
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7
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Zheng B, Yang Y, Chen L, Wu M, Zhou S. B-Cell Receptor Repertoire Sequencing: Deeper Digging into the Mechanisms and Clinical Aspects of Immune-mediated Diseases. iScience 2022; 25:105002. [PMID: 36157582 PMCID: PMC9494237 DOI: 10.1016/j.isci.2022.105002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
B cells play an essential role in adaptive immunity and are intimately correlated with pleiotropic immune-mediated diseases. Each B cell occupies a unique B cell receptor (BCR), and all BCRs throughout our body form “BCR repertoire.” With the development of sequencing technology and coupled bioinformatics, accumulating evidence indicates that BCR repertoire largely varies under physiological and pathological conditions. Therefore, comprehensive grasp of BCR repertoire will provide new insights into the pathogenesis of immune-mediated diseases and help exploit efficient diagnostic and treatment strategies. In this review, we start with an overview of BCR repertoire and related sequencing technologies and summarize their current applications in immune-mediated diseases. We also underscore the challenges of this emerging field and propose promising future directions in advancing BCR repertoire exploration.
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Affiliation(s)
- Bohao Zheng
- Wuxi School of Medicine, Jiangnan University, Wuxi, P. R. China
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Yuqing Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Lin Chen
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Mengrui Wu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
- Corresponding author
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8
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Song L, Ouyang Z, Cohen D, Cao Y, Altreuter J, Bai G, Hu X, Livak KJ, Li H, Tang M, Li B, Shirley Liu X. Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies. Cancer Immunol Res 2022; 10:788-799. [PMID: 35605261 PMCID: PMC9299271 DOI: 10.1158/2326-6066.cir-21-0965] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/17/2022] [Accepted: 05/20/2022] [Indexed: 01/03/2023]
Abstract
We applied our computational algorithm TRUST4 to assemble immune receptor (T-cell receptor/B-cell receptor) repertoires from approximately 12,000 RNA sequencing samples from The Cancer Genome Atlas and seven immunotherapy studies. From over 35 million assembled complete complementary-determining region 3 sequences, we observed that the expression of CCL5 and MZB1 is the most positively correlated genes with T-cell clonal expansion and B-cell clonal expansion, respectively. We analyzed amino acid evolution during B-cell receptor somatic hypermutation and identified tyrosine as the preferred residue. We found that IgG1+IgG3 antibodies together with FcRn were associated with complement-dependent cytotoxicity and antibody-dependent cellular cytotoxicity or phagocytosis. In addition to B-cell infiltration, we discovered that B-cell clonal expansion and IgG1+IgG3 antibodies are also correlated with better patient outcomes. Finally, we created a website, VisualizIRR, for users to interactively explore and visualize the immune repertoires in this study. See related Spotlight by Liu and Han, p. 786.
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Affiliation(s)
- Li Song
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zhangyi Ouyang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Experimental Hematology and Biochemistry, Beijing Institute of Radiation Medicine, Beijing, China
| | - David Cohen
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yang Cao
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gali Bai
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xihao Hu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Current affiliation: GV20 Therapeutics, Cambridge, MA, USA
| | - Kenneth J. Livak
- Department of Medical, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bo Li
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - X. Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Current affiliation: GV20 Therapeutics, Cambridge, MA, USA
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9
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Song L, Cohen D, Ouyang Z, Cao Y, Hu X, Liu XS. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nat Methods 2021; 18:627-630. [PMID: 33986545 PMCID: PMC9328942 DOI: 10.1038/s41592-021-01142-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/02/2021] [Indexed: 02/02/2023]
Abstract
We introduce the TRUST4 open-source algorithm for reconstruction of immune receptor repertoires in αβ/γδ T cells and B cells from RNA-sequencing (RNA-seq) data. Compared with competing methods, TRUST4 supports both FASTQ and BAM format and is faster and more sensitive in assembling longer-even full-length-receptor repertoires. TRUST4 can also call repertoire sequences from single-cell RNA-seq (scRNA-seq) data without V(D)J enrichment, and is compatible with both SMART-seq and 5' 10x Genomics platforms.
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Affiliation(s)
- Li Song
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David Cohen
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zhangyi Ouyang
- Department of Biotechnology, Beijing Institue of Radiation Medicine, Beijing, China
| | - Yang Cao
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xihao Hu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - X. Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard T.H. Chan School of Public Health, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA,: Corresponding author.
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10
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Barshow SM, Kulis MD, Burks AW, Kim EH. Mechanisms of oral immunotherapy. Clin Exp Allergy 2021; 51:527-535. [PMID: 33417257 PMCID: PMC9362513 DOI: 10.1111/cea.13824] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/14/2020] [Accepted: 12/30/2020] [Indexed: 10/19/2023]
Abstract
Food allergy presents a significant global health concern with up to 10% of the population affected in developed nations and a steadily increasing prevalence. In many cases, particularly with peanut, tree nut and shellfish, food allergy is a lifelong and potentially life-threatening diagnosis. While no 'cure' for IgE-mediated food allergy exists, oral immunotherapy (OIT) is a promising treatment modality with the peanut OIT drug Palforzia (Aimmune Therapeutics) the only treatment for food allergy that is currently approved by the United States Food and Drug Administration. OIT primarily induces a state of desensitization with only a minority of subjects achieving sustained unresponsiveness, a state of limited clinical remission that appears to be immunologically distinct from natural tolerance. Early humoural changes during OIT include an initial increase in allergen-specific IgE, which eventually decreases to below baseline levels as OIT progresses, and a gradual increase in allergen-specific IgA and IgG4 that continues throughout the course of OIT. Basophil hyporesponsiveness and decreased skin prick test wheal size are observed within the first year of OIT, and persistence after completion of therapy has been associated with sustained unresponsiveness. In the T-cell compartment, there is an initial expansion followed by a decline in the number and activity of T helper 2 (TH 2) cells, the latter of which may be dependent on an expansion of IL-10-producing cells, including regulatory T-cells. Our understanding of the immunomodulatory effects of OIT continues to evolve, with new technologies such as single-cell transcriptional profiling and antibody epitope analysis allowing for more detailed study of T-cell and B-cell responses to OIT. In this review, we present evidence to illustrate what is currently known about the immunologic changes induced by OIT, explore potential mechanisms and emphasize knowledge gaps where future research is needed.
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Affiliation(s)
- Suzanne M Barshow
- University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
- Duke University School of Medicine, Durham, NC, USA
| | - Michael D Kulis
- University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - A Wesley Burks
- University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Edwin H Kim
- University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
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11
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KAMATANI Y, NAKAMURA Y. Genetic variations in medical research in the past, at present and in the future. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:324-335. [PMID: 34121043 PMCID: PMC8403528 DOI: 10.2183/pjab.97.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
Abstract
As we look so different, our genomic sequences vary enormously. The differences in our genome, genetic variations, have played very significant roles in medical research and have contributed to improvement of medical managements in the last 2-3 decades. Genetic variations include germline variations, somatic mutations, and diversities in receptor genes of rearranged immune cells, T cells and B cells. Germline variants are in some cases causative of genetic diseases, are associated with the risk of various diseases, and also affect drug efficacies or adverse events. Some somatic mutations are causative of tumor development. Recent DNA sequencing technologies allow us to perform single-cell analysis or detailed repertoire analysis of B and T cells. It is critically important to investigate temporal changes in immune environment in various anatomical regions in the next one to two decades. In this review article, we would like to introduce the roles of genetic variations in medical fields in the past, at present and in the future.
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Affiliation(s)
- Yoichiro KAMATANI
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusuke NAKAMURA
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
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12
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Hoh RA, Joshi SA, Lee JY, Martin BA, Varma S, Kwok S, Nielsen SCA, Nejad P, Haraguchi E, Dixit PS, Shutthanandan SV, Roskin KM, Zhang W, Tupa D, Bunning BJ, Manohar M, Tibshirani R, Fernandez-Becker NQ, Kambham N, West RB, Hamilton RG, Tsai M, Galli SJ, Chinthrajah RS, Nadeau KC, Boyd SD. Origins and clonal convergence of gastrointestinal IgE + B cells in human peanut allergy. Sci Immunol 2020; 5:5/45/eaay4209. [PMID: 32139586 DOI: 10.1126/sciimmunol.aay4209] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 02/07/2020] [Indexed: 12/18/2022]
Abstract
B cells in human food allergy have been studied predominantly in the blood. Little is known about IgE+ B cells or plasma cells in tissues exposed to dietary antigens. We characterized IgE+ clones in blood, stomach, duodenum, and esophagus of 19 peanut-allergic patients, using high-throughput DNA sequencing. IgE+ cells in allergic patients are enriched in stomach and duodenum, and have a plasma cell phenotype. Clonally related IgE+ and non-IgE-expressing cell frequencies in tissues suggest local isotype switching, including transitions between IgA and IgE isotypes. Highly similar antibody sequences specific for peanut allergen Ara h 2 are shared between patients, indicating that common immunoglobulin genetic rearrangements may contribute to pathogenesis. These data define the gastrointestinal tract as a reservoir of IgE+ B lineage cells in food allergy.
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Affiliation(s)
- Ramona A Hoh
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shilpa A Joshi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brock A Martin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Kwok
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sandra C A Nielsen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Parastu Nejad
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emily Haraguchi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Priya S Dixit
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Swetha V Shutthanandan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Krishna M Roskin
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45267, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Wenming Zhang
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dana Tupa
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bryan J Bunning
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Monali Manohar
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert Tibshirani
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA 94305, USA.,Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Nielsen Q Fernandez-Becker
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Neeraja Kambham
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert G Hamilton
- Division of Allergy and Clinical Immunology, Department of Medicine, and Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mindy Tsai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephen J Galli
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rebecca S Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA.,Division of Pulmonary, Allergy and Critical Care Medicine and Division of Allergy, Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA.,Division of Pulmonary, Allergy and Critical Care Medicine and Division of Allergy, Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA
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13
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Dissecting efficiency of a 5' rapid amplification of cDNA ends (5'-RACE) approach for profiling T-cell receptor beta repertoire. PLoS One 2020; 15:e0236366. [PMID: 32702062 PMCID: PMC7377388 DOI: 10.1371/journal.pone.0236366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/02/2020] [Indexed: 01/21/2023] Open
Abstract
Deep sequencing of T-cell receptor (TCR) genes is powerful at profiling immune repertoire. To prepare a TCR sequencing library, multiplex polymerase chain reaction (mPCR) is widely applied and is highly efficient. That is, most mPCR products contain the region critical for antigen recognition, which also indicates regular V(D)J recombination. Multiplex PCR, however, may suffer from primer bias. A promising alternative is 5'-RACE, which avoids primer bias by applying only one primer pair. In 5'-RACE data, however, non-regular V(D)J recombination (e.g., TCR sequences without a V gene segment) has been observed and the frequency varies (30-80%) between studies. This suggests that the cause of or how to reduce non-regular TCR sequences is not yet well known by the science community. Although it is possible to speculate the cause by comparing the 5'-RACE protocols, careful experimental confirmation is needed and such a systematic study is still not available. Here, we examined the 5'-RACE protocol of a commercial kit and demonstrated how a modification increased the fraction of regular TCR-β sequences to >85%. We also found a strong linear correlation between the fraction of short DNA fragments and the percentage of non-regular TCR-β sequences, indicating that the presence of short DNA fragments in the library was the main cause of non-regular TCR-β sequences. Therefore, thorough removal of short DNA fragments from a 5'-RACE library is the key to high data efficiency. We highly recommend conducting a fragment length analysis before sequencing, and the fraction of short DNA fragments can be used to estimate the percentage of non-regular TCR sequences. As deep sequencing of TCR genes is still relatively expensive, good quality control should be valuable.
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14
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Abstract
Details about IgE-producing B cells in the gut in the context of food allergy are scarce, despite the frequent exposure of the gut and its associated lymphoid tissues to dietary antigens. A new study finds that IgE-producing B cells are enriched in gut tissues and are probably generated from local antibody isotype switching.
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Affiliation(s)
- Onyinye I. Iweala
- Department of Medicine, Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology, University of North Carolina at Chapel Hill, USA,Department of Pediatrics, University of North Carolina Food Allergy Initiative, Division of Allergy, Immunology and Rheumatology, University of North Carolina at Chapel Hill, USA.,
| | - A. Wesley Burks
- Department of Pediatrics, University of North Carolina Food Allergy Initiative, Division of Allergy, Immunology and Rheumatology, University of North Carolina at Chapel Hill, USA
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15
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Ko TM, Kiyotani K, Chang JS, Park JH, Yin Yew P, Chen YT, Wu JY, Nakamura Y. Immunoglobulin profiling identifies unique signatures in patients with Kawasaki disease during intravenous immunoglobulin treatment. Hum Mol Genet 2019; 27:2671-2677. [PMID: 29771320 PMCID: PMC6048982 DOI: 10.1093/hmg/ddy176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/01/2018] [Accepted: 05/01/2018] [Indexed: 12/18/2022] Open
Abstract
Identifying the causes of high fever syndromes such as Kawasaki disease (KD) remains challenging. To investigate pathogen exposure signatures in suspected pathogen-mediated diseases such as KD, we performed immunoglobulin (Ig) profiling using a next-generation sequencing method. After intravenous Ig (IVIG) treatment, we observed disappearance of clonally expanded IgM clonotypes, which were dominantly observed in acute-phase patients. The complementary-determining region 3 (CDR3) sequences of dominant IgM clonotypes in acute-phase patients were commonly observed in other Ig isotypes. In acute-phase KD patients, we identified 32 unique IgM CDR3 clonotypes shared in three or more cases. Furthermore, before the IVIG treatment, the sums of dominant IgM clonotypes in IVIG-resistant KD patients were significantly higher than those of IVIG-sensitive KD patients. Collectively, we demonstrate a novel approach for identifying certain Ig clonotypes for potentially interacting with pathogens involved in KD; this approach could be applied for a wide variety of fever-causing diseases of unknown origin.
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Affiliation(s)
- Tai-Ming Ko
- Department of Medicine, University of Chicago, Chicago, Illinois, USA.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Kazuma Kiyotani
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Jeng-Sheng Chang
- Department of Pediatrics, China Medical University Hospital, Taichung, Taiwan.,College of Medicine, China Medical University, Taichung, Taiwan
| | - Jae-Hyun Park
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Poh Yin Yew
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Yusuke Nakamura
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
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16
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Zelm MC, McKenzie CI, Varese N, Rolland JM, O'Hehir RE. Recent developments and highlights in immune monitoring of allergen immunotherapy. Allergy 2019; 74:2342-2354. [PMID: 31587309 DOI: 10.1111/all.14078] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/15/2022]
Abstract
Allergic diseases are the most common chronic immune-mediated disorders and can manifest with an enormous diversity in clinical severity and symptoms. Underlying mechanisms for the adverse immune response to allergens and its downregulation by treatment are still being revealed. As a result, there have been, and still are, major challenges in diagnosis, prediction of disease progression/evolution and treatment. Currently, the only corrective treatment available is allergen immunotherapy (AIT). AIT modifies the immune response through long-term repeated exposure to defined doses of allergen. However, as the treatment usually needs to be continued for several years to be effective, and can be accompanied by adverse reactions, many patients face difficulties completing their schedule. Long-term therapy also potentially incurs high costs. Therefore, there is a great need for objective markers to predict or to monitor individual patient's beneficial changes in immune response during therapy so that efficacy can be identified as early as possible. In this review, we specifically address recent technical developments that have generated new insights into allergic disease pathogenesis, and how these could potentially be translated into routine laboratory assays for disease monitoring during AIT that are relatively inexpensive, robust and scalable.
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Affiliation(s)
- Menno C. Zelm
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia
- Department of Respiratory Medicine Allergy and Clinical Immunology (Research) Central Clinical School Monash University, and Alfred Hospital Melbourne VIC Australia
| | - Craig I. McKenzie
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia
| | - Nirupama Varese
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia
- Department of Respiratory Medicine Allergy and Clinical Immunology (Research) Central Clinical School Monash University, and Alfred Hospital Melbourne VIC Australia
| | - Jennifer M. Rolland
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia
- Department of Respiratory Medicine Allergy and Clinical Immunology (Research) Central Clinical School Monash University, and Alfred Hospital Melbourne VIC Australia
| | - Robyn E. O'Hehir
- Department of Immunology and Pathology Central Clinical School Monash University Melbourne VIC Australia
- Department of Respiratory Medicine Allergy and Clinical Immunology (Research) Central Clinical School Monash University, and Alfred Hospital Melbourne VIC Australia
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17
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Miller JM, Davis CM, Anvari S. The clinical and immune outcomes after food allergen immunotherapy emphasizing the development of tolerance. Curr Opin Pediatr 2019; 31:821-827. [PMID: 31693593 DOI: 10.1097/mop.0000000000000831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW The present review serves to outline the direction of food allergy immunotherapy research with an emphasis on clinical and immunologic outcomes. It helps to delineate sustained unresponsiveness achieved from food immunotherapy as the clinical outcome most similar to immune tolerance. RECENT FINDINGS We will discuss the difference between immune tolerance, desensitization, and sustained unresponsiveness in relation to food immunotherapy by discussing the clinical and immunologic changes which have been recently discovered. SUMMARY Research has recently shown that oral immunotherapy is most efficacious clinically at achieving desensitization to a food and sustained unresponsiveness.
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Affiliation(s)
- Jennifer M Miller
- Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Baylor College of Medicine
- Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Texas Children's Hospital, Houston, Texas, USA
| | - Carla M Davis
- Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Baylor College of Medicine
- Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Texas Children's Hospital, Houston, Texas, USA
| | - Sara Anvari
- Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Baylor College of Medicine
- Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Texas Children's Hospital, Houston, Texas, USA
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18
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Abstract
IgE antibodies are essential mediators of allergies. In a recent study in Science, Croote et al. (2018) characterize IgE cells isolated from individuals allergic to peanuts. Their findings provide insight into the differentiation of IgE cells in humans and have implications for our understanding of allergic disease.
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Affiliation(s)
- Carlos J Aranda
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Maria A Curotto de Lafaille
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA; Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.
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19
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Vickery BP, Ebisawa M, Shreffler WG, Wood RA. Current and Future Treatment of Peanut Allergy. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2019; 7:357-365. [DOI: 10.1016/j.jaip.2018.11.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 12/14/2022]
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20
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Croote D, Darmanis S, Nadeau KC, Quake SR. High-affinity allergen-specific human antibodies cloned from single IgE B cell transcriptomes. Science 2019; 362:1306-1309. [PMID: 30545888 DOI: 10.1126/science.aau2599] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022]
Abstract
Immunoglobulin E (IgE) antibodies protect against helminth infections but can also cause life-threatening allergic reactions. Despite their role in human health, the cells that produce these antibodies are rarely observed and remain enigmatic. We isolated single IgE B cells from individuals with food allergies and used single-cell RNA sequencing to elucidate the gene expression and splicing patterns unique to these cells. We identified a surprising example of convergent evolution in which IgE antibodies underwent identical gene rearrangements in unrelated individuals. Through the acquisition of variable region mutations, these IgE antibodies gained high affinity and unexpected cross-reactivity to the clinically important peanut allergens Ara h 2 and Ara h 3. These findings provide insight into IgE B cell transcriptomics and enable biochemical dissection of this antibody class.
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Affiliation(s)
- Derek Croote
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA 94305, USA.,Department of Medicine, Stanford University, Stanford, CA 94305, USA.,Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. .,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.,Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
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21
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Zewde M, Kiyotani K, Park JH, Fang H, Yap KL, Yew PY, Alachkar H, Kato T, Mai TH, Ikeda Y, Matsuda T, Liu X, Ren L, Deng B, Harada M, Nakamura Y. The era of immunogenomics/immunopharmacogenomics. J Hum Genet 2018; 63:865-875. [PMID: 29785006 DOI: 10.1038/s10038-018-0468-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 11/09/2022]
Abstract
Although germline alterations and somatic mutations in disease cells have been extensively analyzed, molecular changes in immune cells associated with disease conditions have not been characterized in depth. It is clear that our immune system has a critical role in various biological and pathological conditions, such as infectious diseases, autoimmune diseases, drug-induced skin and liver toxicity, food allergy, and rejection of transplanted organs. The recent development of cancer immunotherapies, particularly drugs modulating the immune checkpoint molecules, has clearly demonstrated the importance of host immune cells in cancer treatments. However, the molecular mechanisms by which these new therapies kill tumor cells are still not fully understood. In this regard, we have begun to explore the role of newly developed tools such as next-generation sequencing in the genetic characterization of both cancer cells and host immune cells, a field that is called immunogenomics/ immunopharmacogenomics. This new field has enormous potential to help us better understand changes in our immune system during the course of various disease conditions. Here we report the potential of deep sequencing of T-cell and B-cell receptors in capturing the molecular contribution of the immune system, which we believe plays critical roles in the pathogenesis of various human diseases.
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Affiliation(s)
- Makda Zewde
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Kazuma Kiyotani
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.,Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Jae-Hyun Park
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Hua Fang
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Kai Lee Yap
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Poh Yin Yew
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Houda Alachkar
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Taigo Kato
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Tu H Mai
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Yuji Ikeda
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Tatsuo Matsuda
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiao Liu
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Lili Ren
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Boya Deng
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Makiko Harada
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Yusuke Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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