Identification of B cell epitopes of Per a 5 allergen using bioinformatic approach

DeepLBCEPred: A Bi-LSTM and multi-scale CNN-based deep learning method for predicting linear B-cell epitopes

The epitope is the site where antigens and antibodies interact and is vital to understanding the immune system. Experimental identification of linear B-cell epitopes (BCEs) is expensive, is labor-consuming, and has a low throughput. Although a few computational methods have been proposed to address this challenge, there is still a long way to go for practical applications. We proposed a deep learning method called DeepLBCEPred for predicting linear BCEs, which consists of bi-directional long short-term memory (Bi-LSTM), feed-forward attention, and multi-scale convolutional neural networks (CNNs). We extensively tested the performance of DeepLBCEPred through cross-validation and independent tests on training and two testing datasets. The empirical results showed that the DeepLBCEPred obtained state-of-the-art performance. We also investigated the contribution of different deep learning elements to recognize linear BCEs. In addition, we have developed a user-friendly web application for linear BCEs prediction, which is freely available for all scientific researchers at: http://www.biolscience.cn/DeepLBCEPred/.

Per a 5-derived T-cell peptides modulate NF-kB signalling to ameliorate allergic inflammation systemically in murine model of cockroach allergic hyper-reactivity

Peptide immunotherapy (PIT) represents a safe and efficacious therapeutic regimen with in-consequential side-effects. The present study aims to identify T-cell epitopes of Per a 5 allergen, a delta class GST from Periplaneta americana and investigate effect of peptide treatment in murine model of cockroach allergen-mediated hyper-reactivity. The epitopes (TC-P1, TC-P2, and TC-P3) were identified as promiscuous MHC-II binders by MHC-Pred, ProPred, and IEDB analysis tool. Murine model of cockroach allergic hyper-reactivity was generated in Balb/c mice. A marked reduction in cellular infiltration in lungs (3-fold compared with Non-IT) was observed in T3-IT group as evidenced by total leucocyte count in BALF and histology. Specific IgE levels were reduced 3-fold in T2-IT and T3-IT compared with Non-IT with increase in IgG2a levels. IL-4 and IL-13 were reduced upto 2.5-fold in treatment groups compared with Non-IT group. Splenocytes revealed significant increase in levels of CD4+FoxP3+ T cells in TC-P1 and TC-P2 mice demonstrating a systemic shift towards Tregs. Peptide treatment downregulated NF-kB signalling in lung and enhanced the levels of immune-regulatory molecules α1-antitrypsin and elafin. Our results indicate that TC-P1 and TC-P3 alter Th2 cytokine milieu and antibody isotype ratio to suppress allergic inflammation. PIT modulates local and systemic mechanisms to resolve inflammation and possess potential for treatment in cockroach allergy.