Regulatory and Effector T cells in Oral Immunotherapy for Food Allergy

This study consisted of a clinical trial for peanut oral immunotherapy (OIT) and a follow-up project (see below). Patients were included from 2013-2015, and samples from the last timepoints were collected in 2017. The study focused on peanut-specific CD4+ T cell responses before, during, and after OIT with peanut protein. We analyzed T cell gene expression, cytokine production, and T cell receptor β (TCRβ) and TCRα clonotypes, both in bulk T cell populations and single cells, and sought to correlate these data with differences in clinical sensitivity between peanut-allergic patients before OIT, and with differences in clinical outcome after OIT. The goal was to better understand the role of peanut-specific effector and regulatory T cells in peanut allergy and tolerance, which may inform more effective therapies (e.g., OIT combined with biologicals, probiotics, or adjuvants) in the future. Tolerance Following Peanut Oral Immunotherapy (PNOIT2, NCT01750879): The unifying objective of this project is to determine whether peanut oral immunotherapy (PNOIT)-induced clinical tolerance in the context of food allergy is significantly associated with the expansion of a specific regulatory T cell subset (CD45RA-, CD25++, FoxP3+ +) that is thought to be inducible in the gut-associated lymphoid compartment and associated with immunological tolerance. The hypothesis of the study is that the induction of Treg cells will be associated with clinical tolerance. The investigators will measure the change from baseline of induced Treg cells as a frequency of total CD4+ T cells during active treatment and compare that between participants who achieve significant clinical tolerance and those who do not. High Threshold Peanut Challenge Study (PAID-UP, NCT02698033): This protocol was designed to better characterize a sub-population of peanut-sensitized individuals who may be non-allergic, despite significant sensitization, or who may be allergic, but at high threshold doses. By specifically targeting participants who met the initial screening criteria of an earlier study, NCT01750879, but failed to react during the pre-treatment 443 mg challenge to peanut, the investigators anticipate that they will identify individuals who have become spontaneously tolerant, despite persistent sensitization. The investigators might also find that clinical sensitivity persists but only with higher thresholds, or that sensitivity has increased (or is variable) since the previous allergen exposure. By repeating food challenges through to a full serving dose (7.4 gram), the investigators will distinguish participants who react only at higher doses from those who were not truly peanut-allergic, address whether their sensitivity has changed, and have the opportunity to further investigate their immune response to peanut allergen. Methods: Peripheral blood mononuclear cells were isolated from patient blood samples, and stimulated with peanut protein. Peanut-activated CD4+ T cells were sorted based on the activation marker CD154. For a more recent study, the activation marker CD137 was used as well. Total RNA from peanut-activated CD154+ and resting CD154- CD69- T cells was used for cDNA synthesis and amplification (SMARTer ultra low input RNA kit for sequencing - v3; Clontech Laboratories). Libraries were prepared and sequenced on the Illumina HiSeq platform, at a read depth of approximately 30 million reads per sample. Genomic DNA from CD154+ and CD154- CD69- T cells was used to amplify and sequence the TCRβ CDR3 regions (immunoSEQ assay; Adaptive Biotechnologies). The immunoSEQ approach generates an 87 base-pair fragment capable of identifying the VDJ region spanning each unique CDR3. Amplicons were sequenced using the Illumina NextSeq platform. Using a baseline developed from a suite of synthetic templates, primer concentrations and computational corrections were used to correct for the primer bias common to multiplex PCR reactions. Raw sequence data were filtered on the basis of TCRβ V, D, and J gene definitions provided by the IMGT database (www.imgt.org) and binned using a modified nearest-neighbor algorithm to merge closely related sequences and remove both PCR and sequencing errors. For single-cell analysis, we aimed to recover TCR variable sequences from high-throughput single-cell libraries generated by popular platforms such as SeqWell and DropSeq. We paired TCR information with T cell single-cell RNA sequencing results from patients undergoing peanut OIT to show clonal expansion-related T cell phenotypes. ]]>
Inclusion Criteria: Diagnosis of peanut allergy by medical history. Evidence of peanut-specific IgE by either: A positive skin prick test to peanut (reaction wheal at least 5 mm larger than saline control) or Serum peanut-specific IgE >5 kU/L at screening visit. Ara h 2-specific IgE >0.35 kU/L at screening visit. Ability to provide informed consent. Males and females of all ethnic/racial groups aged 7-55 years old who are otherwise healthy. React to less than 443 mg of peanut protein during double-blind placebo-controlled food challenge. Exclusion Criteria: History of severe anaphylaxis as defined by hypoxia (cyanosis or SpO2 <92% during reaction), documented hypotension (documented systolic BP >30% below predicted normal for sex, height, weight or from known baseline), neurological compromise (confusion, loss of consciousness), or incontinence. Severe or Moderate asthma as defined using the severity criteria of the current NHBLI Guidelines for the Diagnosis and Management of Asthma (http://www.nhlbi.nih.gov/guidelines/asthma/). Poorly-controlled asthma as defined by FEV1 <80% or any of the following symptoms: nighttime awakening >2 days/week or rescue medication use >2 days/week. Diagnosis of other severe or complicating medical problems, including autoimmune or chronic immune inflammatory conditions or gastrointestinal inflammatory conditions, including Celiac Disease, Inflammatory Bowel Disease and Eosinophilic Gastrointestinal Disorders. Inability to cooperate with and/or perform oral food challenge procedures. Primary Immune Deficiency Allergy to oat confirmed by skin prick testing and history. Current use of beta blockers, angiotensin converting enzyme inhibitors, or monoamine oxidase inhibitors. Women of childbearing potential who are pregnant, planning to become pregnant, or breastfeeding. Hemoglobin level less than 12.5 gm/dL at screening. Weight <23 kg. Use within the past 6 months of other systemic immunomodulatory treatments including allergen immunotherapy, or use of biologics with an immune target, including omalizumab. Past or current medical problems or findings from physical examination or laboratory testing that are not listed above, which, in the opinion of the investigator, may pose additional risks from participation in the study, may interfere with the participant's ability to comply with study requirements or that may impact the quality or interpretation of the data obtained from the study may also exclude a participant from the study. ]]>