Transcriptional changes in peanut-specific CD4+ T cells over the course of oral immunotherapy

Weiqi Wang, Shu-Chen Lyu, Xuhuai Ji, Sheena Gupta, Monali Manohar, Gopal K R Dhondalay, Sharon Chinthrajah, Sandra Andorf, Scott D Boyd, Robert Tibshirani, Stephen J Galli, Kari C Nadeau, Holden T Maecker, Weiqi Wang, Shu-Chen Lyu, Xuhuai Ji, Sheena Gupta, Monali Manohar, Gopal K R Dhondalay, Sharon Chinthrajah, Sandra Andorf, Scott D Boyd, Robert Tibshirani, Stephen J Galli, Kari C Nadeau, Holden T Maecker

Abstract

Oral immunotherapy (OIT) can successfully desensitize allergic individuals to offending foods such as peanut. Our recent clinical trial (NCT02103270) of peanut OIT allowed us to monitor peanut-specific CD4+ T cells, using MHC-peptide Dextramers, over the course of OIT. We used a single-cell targeted RNAseq assay to analyze these cells at 0, 12, 24, 52, and 104 weeks of OIT. We found a transient increase in TGFβ-producing cells at 52 weeks in those with successful desensitization, which lasted until 117 weeks. We also performed clustering and identified 5 major clusters of Dextramer+ cells, which we tracked over time. One of these clusters appeared to be anergic, while another was consistent with recently described TFH13 cells. The other 3 clusters appeared to be Th2 cells by their coordinated production of IL-4 and IL-13, but they varied in their expression of STAT signaling proteins and other markers. A cluster with high expression of STAT family members also showed a possible transient increase at week 24 in those with successful desensitization. Single cell TCRαβ repertoire sequences were too diverse to track clones over time. Together with increased TGFβ production, these changes may be mechanistic predictors of successful OIT that should be further investigated.

Keywords: CD4+ T cell; Food allergy; OIT; Peanut allergy; RNAseq; Single cell.

Copyright © 2020 Elsevier Inc. All rights reserved.

Figures

Figure 1.
Figure 1.
Longitudinal trend of Dex+ cells per marker, grouped by OFC results. Data (mean values with standard errors) were obtained from single cell RNAseq assay of 30 patients (11 females and 19 males), over five time points (week 0 to week 104).
Figure 2.
Figure 2.
Starplots showing the segregation of cells along the OIT process, based on the primary endpoint (OFC results at week 117). Group 1 (red): failure, Group 2 (green): success, Group 3 (blue): placebo. Starplots were generated using single cell RNAseq assay of 30 patients (11 females and 19 males).
Figure 3.
Figure 3.
Clustering (with Ward’s minimum variance method, Euclidean distance) on longitudinal cellular phenotypes of Dex+ cells only. Clusters 1 – 5 are color highlighted from top to bottom. Data were obtained from single cell RNAseq assay of 30 patients (11 females and 19 males).
Figure 4.
Figure 4.
Cluster signatures (week 0, 12, 24, 52, 104 combined). The bar length represents positive call rate (percentage of cells expressing the marker). Data were obtained from single cell RNAseq assay of 30 patients (11 females and 19 males).
Figure 5.
Figure 5.
Proportions of Clusters over time in all patients (top left), or in the outcome groups as listed. Note the transient expansion in the “success” group of cluster 3 at week 24, relative to the “failure” group. Data were obtained from single cell RNAseq assay of 30 patients (11 females and 19 males).
Figure 6.
Figure 6.
Positive marker call rates exhibiting distinguishing features of 5 clusters, with change over time (mean values with standard errors). Data were obtained from single cell RNAseq assay of 30 patients (11 females and 19 males).

Source: PubMed

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