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Huang J, Zhang W, Xiang R, Tan L, Liu P, Tao Z, Deng Y, Tong H, Xu Y. The early-phase transcriptome and the clinical efficacy analysis in three modes of subcutaneous immunotherapy for allergic rhinitis. World Allergy Organ J 2023; 16:100811. [PMID: 37701629 PMCID: PMC10493265 DOI: 10.1016/j.waojou.2023.100811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 07/24/2023] [Accepted: 08/12/2023] [Indexed: 09/14/2023] Open
Abstract
Background Allergen immunotherapy is the only etiological treatment for allergic rhinitis. Objective To analyze the efficacy, safety, and mechanism of subcutaneous immunotherapy (SCIT). Methods The efficacy, safety, and serum immunological changes of 3 modes of subcutaneous immunotherapy were compared. Peripheral blood mononuclear cells (PBMC) transcriptome changes were obtained on the Illumina sequencing platforms. We confirmed differentially expressed genes (DEGs) by quantitative real-time polymerase chain reaction (PCR). The DEGs were analyzed by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction (PPI) networks. The correlation between the common DEGs and clinical indicators was analyzed by Origin 2022. Results The 3 SCITs were all effective after 1 year. The Combined Symptom and Medication Score (CSMS) and Visual Analog Score (VAS) in rush immunotherapy (RIT) are lowest after 24 and 48 weeks of treatment among the 3 groups. After treatment, the levels of sIgE, sIgE/tIgE, Th2 cytokines, Th17 cytokines, and percentage of peripheral eosinophils (EOS%) decreased significantly (P<0.05), while the levels of Th1 type cytokines did not change significantly. Transcriptome analysis identified 24, 24, and 91 DEGs at W3 and 42, 52, 175 DEGs at W7 in conventional immunotherapy (CIT), cluster immunotherapy (CLIT), and RIT groups, respectively. The pathways and functions involved in SCIT include secretion of Th1/2 cytokines, immune cell differentiation. Unlike CIT and CLIT, DEGs are also involved in T cell tolerance induction, T cell anergy, and lymphocyte anergy in RIT. CXCR1, CXCR2, and IER3 had a specific effect on reflecting the improvement of symptoms in allergic rhinitis patients with SCIT. Conclusion The clinical efficacy of RIT appeared earlier than CIT and CLIT. Clinicians can use the highly conserved gene expression profile to evaluate responses to immunotherapy.
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Affiliation(s)
- Jingyu Huang
- Department of Rhinology and Allergy, Otolaryngology-Head and Neck Surgery Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wei Zhang
- Department of Rhinology and Allergy, Otolaryngology-Head and Neck Surgery Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Rong Xiang
- Department of Rhinology and Allergy, Otolaryngology-Head and Neck Surgery Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lu Tan
- Department of Rhinology and Allergy, Otolaryngology-Head and Neck Surgery Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Peiqiang Liu
- Department of Rhinology and Allergy, Otolaryngology-Head and Neck Surgery Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zezhang Tao
- Department of Rhinology and Allergy, Otolaryngology-Head and Neck Surgery Center, Renmin Hospital of Wuhan University, Wuhan, China
- Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuqin Deng
- Department of Rhinology and Allergy, Otolaryngology-Head and Neck Surgery Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Huan Tong
- Wound Repair&Rehabilitation Center Department, Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, China
| | - Yu Xu
- Department of Rhinology and Allergy, Otolaryngology-Head and Neck Surgery Center, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, China
- Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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Forsberg A, Huoman J, Söderholm S, Bhai Mehta R, Nilsson L, Abrahamsson TR, Ernerudh J, Gustafsson M, Jenmalm MC. Pre- and postnatal Lactobacillus reuteri treatment alters DNA methylation of infant T helper cells. Pediatr Allergy Immunol 2020; 31:544-553. [PMID: 32150651 DOI: 10.1111/pai.13240] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/20/2019] [Accepted: 01/27/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Perinatal childhood exposures, including probiotic supplementation, may affect epigenetic modifications and impact on immune maturation and allergy development. The aim of this study was to assess the effects of pre- and postnatal Lactobacillus reuteri supplementation on DNA methylation in relation to immune maturation and allergy development. METHODS DNA methylation patterns were investigated for allergy-related T helper subsets using a locus-specific method and at a genome-wide scale using the Illumina 450K array. From a randomised, double-blind, placebo-controlled allergy prevention trial with pre- and postnatal probiotic supplementation, CD4+ T helper cells were obtained at birth (from cord blood), and 12 and 24 months of age (total (placebo/probiotics); locus-specific method: CB = 32 (17/15), 12 months = 24 (9/15), 24 months = 35 (15/20); Illumina: CB = 19 (10/9), 12 months = 10 (6/4), 24 months = 19(11/8)). RESULTS Comparing probiotics to placebo, the greatest genome-wide differential DNA methylation was observed at birth, where the majority of sites were hypomethylated, indicating transcriptional accessibility in the probiotic group. Bioinformatic analyses, including network analyses, revealed a module containing 91 genes, enriched for immune-related pathways such as chemotaxis, PI3K-Akt, MAPK and TGF-β signalling. A majority of the module genes were associated with atopic manifestations (OR = 1.43, P = 2.4 × 10-6 ), and a classifier built on this model could predict allergy development (AUC = 0.78, P = 3.0 × 10e-3 ). Pathways such as IFN-γ signalling and T-cell activation were more hypermethylated at birth compared with later in life in both intervention groups over time, in line with DNA methylation patterns in the IFNG locus obtained by the locus-specific methodology. CONCLUSION Maternal L. reuteri supplementation during pregnancy alters DNA methylation patterns in CD4+ T cells towards enhanced immune activation at birth, which may affect immune maturation and allergy development.
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Affiliation(s)
- Anna Forsberg
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johanna Huoman
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Simon Söderholm
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Ratnesh Bhai Mehta
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lennart Nilsson
- Allergy Center, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Thomas R Abrahamsson
- Crown Princess Victoria's Child and Youth Hospital, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Jan Ernerudh
- Department of Clinical Immunology and Transfusion Medicine, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Mika Gustafsson
- Department of Physics, Chemistry and Biology, Bioinformatics, Linköping University, Linköping, Sweden
| | - Maria C Jenmalm
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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Salmani A, Mohammadi M, Farid Hosseini R, Tavakol Afshari J, Fouladvand A, Dehnavi S, Khoshkhooi M, Jabbari Azad F. A significant increase in expression of FOXP3 and IL-17 genes in patients with allergic rhinitis underwent accelerated rush immunotherapy. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2019; 22:989-996. [PMID: 31807241 PMCID: PMC6880522 DOI: 10.22038/ijbms.2019.32979.7878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Objective(s): Allergic rhinitis (AR) is a common hypersensitivity disease worldwide. Immunotherapy has been performed as the best treatment for years. This study aimed to study the gene expression pattern of immune system cells following an accelerated rush immunotherapy protocol (ARIT) in patients with AR. Materials and Methods: Fifteen patients with AR (15–55 years old) resident in Mashhad, Iran, with positive prick test to regional aeroallergens (weed mix, grass mix, tree mix, and Salsola) enrolled in this study. All patients were treated for three months with 3-day ARIT protocol between July 2015 and August 2016. Clinical symptoms and quality of life were recorded by two questioners. The expression levels of FOXP3, TGF-β, IL-10, IL-17, IL-4, and IFN-γ genes in patient’s peripheral blood mononuclear cells were evaluated by SYBR Green real-time RT-PCR technique. Results: The severity of disease and quality of life showed significant improvement following ARIT (P-value<0.05). Gene expression of IFN-γ and IL-10 was increased whereas TGF-β and IL-4 down-regulated, following ARIT, but these changes were not significant. However, gene expression of FOXP3 and IL-17 was significantly increased after intervention when compared with the baseline (P-value< 0.002). Conclusion: Significant up-regulation of FOXP3 and IL-17 genes, additionally, a significant improvement in the clinical signs following ARIT might be related to increases in HLA-DR- and FOXP3+ Treg population at the initiation phase of ARIT. Employing the flow cytometry technique to study the phenotype of these cells is suggested for future studies.
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Affiliation(s)
- Amirabbas Salmani
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojgan Mohammadi
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Farid Hosseini
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Ali Fouladvand
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sajad Dehnavi
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Khoshkhooi
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Ono C, Yu Z, Kasahara Y, Kikuchi Y, Ishii N, Tomita H. Fluorescently activated cell sorting followed by microarray profiling of helper T cell subtypes from human peripheral blood. PLoS One 2014; 9:e111405. [PMID: 25379667 PMCID: PMC4224392 DOI: 10.1371/journal.pone.0111405] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 10/02/2014] [Indexed: 12/31/2022] Open
Abstract
Background Peripheral blood samples have been subjected to comprehensive gene expression profiling to identify biomarkers for a wide range of diseases. However, blood samples include red blood cells, white blood cells, and platelets. White blood cells comprise polymorphonuclear leukocytes, monocytes, and various types of lymphocytes. Blood is not distinguishable, irrespective of whether the expression profiles reflect alterations in (a) gene expression patterns in each cell type or (b) the proportion of cell types in blood. CD4+ Th cells are classified into two functionally distinct subclasses, namely Th1 and Th2 cells, on the basis of the unique characteristics of their secreted cytokines and their roles in the immune system. Th1 and Th2 cells play an important role not only in the pathogenesis of human inflammatory, allergic, and autoimmune diseases, but also in diseases that are not considered to be immune or inflammatory disorders. However, analyses of minor cellular components such as CD4+ cell subpopulations have not been performed, partly because of the limited number of these cells in collected samples. Methodology/Principal Findings We describe fluorescently activated cell sorting followed by microarray (FACS–array) technology as a useful experimental strategy for characterizing the expression profiles of specific immune cells in the circulation. We performed reproducible gene expression profiling of Th1 and Th2, respectively. Our data suggest that this procedure provides reliable information on the gene expression profiles of certain small immune cell populations. Moreover, our data suggest that GZMK, GZMH, EOMES, IGFBP3, and STOM may be novel markers for distinguishing Th1 cells from Th2 cells, whereas IL17RB and CNTNAP1 can be Th2-specific markers. Conclusions/Significance Our approach may help in identifying aberrations and novel therapeutic or diagnostic targets for diseases that affect Th1 or Th2 responses and elucidating the involvement of a subpopulation of immune cells in some diseases.
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Affiliation(s)
- Chiaki Ono
- Department of Disaster Psychiatry, Internal Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Biological Psychiatry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Zhiqian Yu
- Department of Disaster Psychiatry, Internal Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Biological Psychiatry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshiyuki Kasahara
- Department of Disaster Psychiatry, Internal Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Biological Psychiatry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshie Kikuchi
- Department of Disaster Psychiatry, Internal Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Biological Psychiatry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naoto Ishii
- Department of Microbiology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroaki Tomita
- Department of Disaster Psychiatry, Internal Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Biological Psychiatry, Tohoku University Graduate School of Medicine, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- * E-mail:
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Davis LS, Bhutani S, Barnett SR, Khan DA. Early gene expression changes with rush immunotherapy. Clin Mol Allergy 2011; 9:12. [PMID: 21961521 PMCID: PMC3195724 DOI: 10.1186/1476-7961-9-12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Accepted: 09/30/2011] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND To examine whether whole genome expression profiling could reveal changes in mRNA expression of peripheral blood mononuclear cells (PBMC) from allergic patients undergoing rush immunotherapy (RIT) that might be manifest within the first few months of treatment. METHODS For this study, PBMC from three allergic patients undergoing RIT were assessed at four timepoints: prior to RIT, at 1 week and 7 week post-RIT, during build-up and at 4 months, after establishment of a maintenance dose. PBMC mRNA gene expression changes over time were determined by oligonucleotide microarrays using the Illumina Human-6 BeadChip Platform, which simultaneously interrogates expression profiles of > 47,000 transcripts. Differentially expressed genes were identified using well-established statistical analysis for microarrays. In addition, we analyzed peripheral blood basophil high-affinity IgE receptor (Fc epsilon RI) expression and T-regulatory cell frequency as detected by expression of CD3+CD4+CD25bright cells at each timepoint using flow cytometry. RESULTS In comparing the initial 2 timepoints with the final 2 timepoints and analyzing for genes with ≥1.5-fold expression change (p less than or equal to 0.05, BH-FDR), we identified 507 transcripts. At a 2-fold change (p less than or equal to 0.05, BH-FDR), we found 44 transcripts. Of these, 28 were up-regulated and 16 were down-regulated genes. From these datasets, we have identified changes in immunologically relevant genes from both the innate and adaptive response with upregulation of expressed genes for molecules including IL-1β, IL-8, CD40L, BTK and BCL6. At the 4 month timepoint, we noted a downward trend in Fc epsilon RI expression in each of the three patients and increased allergen-specific IgG4 levels. No change was seen in the frequency of peripheral T-regulatory cells expressed over the four timepoints. CONCLUSIONS We observed significant changes in gene expression early in peripheral blood samples from allergic patients undergoing RIT. Moreover, serum levels for allergen specific IgG4 also increased over the course of treatment. These studies suggest that RIT induces rapid and dynamic alterations in both innate and adaptive immunity which can be observed in the periphery of allergic patients. These alterations could be directly related to the therapeutic shift in the allergen-specific class of immunoglobulin.
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Affiliation(s)
- Laurie S Davis
- Department of Internal Medicine, Division of Rheumatic Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8884, USA.
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Moneret-Vautrin DA. Immunothérapie sublinguale et orale de l’allergie alimentaire : effets cliniques et signification des modifications immunologiques. REVUE FRANCAISE D ALLERGOLOGIE 2011. [DOI: 10.1016/j.reval.2011.01.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Application of T cell-based transcriptomics to identify three candidate biomarkers for monitoring anti-TGFbetaR therapy. Pharmacogenet Genomics 2010; 20:147-56. [PMID: 20084050 DOI: 10.1097/fpc.0b013e328335731c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The development of targeted drugs would greatly benefit from the simultaneous identification of biomarkers to determine the aspects of bioactivity, drug safety and efficacy, particularly when affecting receptor-signaling pathways. However, the establishment of appropriate systems to monitor drug-induced events requires an accessible surrogate tissue for functional read out. METHODS Therefore we present a universal platform based upon T cell-based gene expression profiling for the identification of biomarkers using the antitransforming growth factor beta receptor inhibitor LY2109761 as an example. RESULTS Our initial screen revealed 12 candidate genes specifically regulated in T cells by the inhibitor. In subsequent in-vitro and in-vivo analyses, the combined monitoring of independent gene regulation of three genes was established in peripheral blood mononuclear cells as novel pharmacodynamic candidate biomarkers for antitransforming growth factor beta receptor based therapies. CONCLUSION Overall, the proposed concept of biomarker identification can be easily adapted towards other drug candidates for whom gene regulation can be established in cellular components of peripheral blood.
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Jones SM, Pons L, Roberts JL, Scurlock AM, Perry TT, Kulis M, Shreffler WG, Steele P, Henry KA, Adair M, Francis JM, Durham S, Vickery BP, Zhong X, Burks AW. Clinical efficacy and immune regulation with peanut oral immunotherapy. J Allergy Clin Immunol 2009; 124:292-300, 300.e1-97. [PMID: 19577283 DOI: 10.1016/j.jaci.2009.05.022] [Citation(s) in RCA: 498] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 04/28/2009] [Accepted: 05/12/2009] [Indexed: 01/22/2023]
Abstract
BACKGROUND Oral immunotherapy (OIT) has been thought to induce clinical desensitization to allergenic foods, but trials coupling the clinical response and immunologic effects of peanut OIT have not been reported. OBJECTIVE The study objective was to investigate the clinical efficacy and immunologic changes associated with OIT. METHODS Children with peanut allergy underwent an OIT protocol including initial day escalation, buildup, and maintenance phases, and then oral food challenge. Clinical response and immunologic changes were evaluated. RESULTS Of 29 subjects who completed the protocol, 27 ingested 3.9 g peanut protein during food challenge. Most symptoms noted during OIT resolved spontaneously or with antihistamines. By 6 months, titrated skin prick tests and activation of basophils significantly declined. Peanut-specific IgE decreased by 12 to 18 months, whereas IgG(4) increased significantly. Serum factors inhibited IgE-peanut complex formation in an IgE-facilitated allergen binding assay. Secretion of IL-10, IL-5, IFN-gamma, and TNF-alpha from PBMCs increased over a period of 6 to 12 months. Peanut-specific forkhead box protein 3 T cells increased until 12 months and decreased thereafter. In addition, T-cell microarrays showed downregulation of genes in apoptotic pathways. CONCLUSION Oral immunotherapy induces clinical desensitization to peanut, with significant longer-term humoral and cellular changes. Microarray data suggest a novel role for apoptosis in OIT.
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Affiliation(s)
- Stacie M Jones
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, Ark, USA
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Staratschek-Jox A, Classen S, Gaarz A, Debey-Pascher S, Schultze JL. Blood-based transcriptomics: leukemias and beyond. Expert Rev Mol Diagn 2009; 9:271-80. [PMID: 19379085 DOI: 10.1586/erm.09.9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In 1999, Golub et al. proposed for the first time microarray-based transcriptional profiling to be used as a new technology for the differential diagnosis of acute myeloid leukemias and acute lymphocytic leukemias. This very preliminary study sparked great enthusiasm beyond the leukemias. Over the last 10 years, numerous studies addressed the use of gene expression profiling of peripheral blood from patients with malignancies, infectious diseases, autoimmunity and even cardiovascular diseases. Despite this great effort, no single test has yet been established using microarray-based transcriptional profiling of peripheral blood. Here we highlight the advances in the field of blood transcriptomics during the last 10 years and also critically discuss the issues that need to be resolved before blood transcriptomics will become part of daily diagnostics in the leukemias, as well as in other diseases showing involvement of peripheral blood.
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Affiliation(s)
- Andrea Staratschek-Jox
- Group Leader Functional Genomics, Genomics and Immunoregulation, LIMES (Life and Medical Sciences Bonn), Program Unit Molecular Immune and Cell Biology, University of Bonn, Karlrobert-Kreitenstrasse 13, D-53115 Bonn, Germany.
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