TEPITOPEpan: Extending TEPITOPE for Peptide Binding Prediction Covering over 700 HLA-DR Molecules

<div><h3>Motivation</h3><p>Accurate identification of peptides binding to specific Major Histocompatibility Complex Class II (MHC-II) molecules is of great importance for elucidating the underlying mechanism of immune recognition, as well as for developing effective epitope-based vaccines and promising immunotherapies for many severe diseases. Due to extreme polymorphism of MHC-II alleles and the high cost of biochemical experiments, the development of computational methods for accurate prediction of binding peptides of MHC-II molecules, particularly for the ones with few or no experimental data, has become a topic of increasing interest. TEPITOPE is a well-used computational approach because of its good interpretability and relatively high performance. However, TEPITOPE can be applied to only 51 out of over 700 known HLA DR molecules.</p> <h3>Method</h3><p>We have developed a new method, called TEPITOPEpan, by extrapolating from the binding specificities of HLA DR molecules characterized by TEPITOPE to those uncharacterized. First, each HLA-DR binding pocket is represented by amino acid residues that have close contact with the corresponding peptide binding core residues. Then the pocket similarity between two HLA-DR molecules is calculated as the sequence similarity of the residues. Finally, for an uncharacterized HLA-DR molecule, the binding specificity of each pocket is computed as a weighted average in pocket binding specificities over HLA-DR molecules characterized by TEPITOPE.</p> <h3>Result</h3><p>The performance of TEPITOPEpan has been extensively evaluated using various data sets from different viewpoints: predicting MHC binding peptides, identifying HLA ligands and T-cell epitopes and recognizing binding cores. Among the four state-of-the-art competing pan-specific methods, for predicting binding specificities of unknown HLA-DR molecules, TEPITOPEpan was roughly the second best method next to NETMHCIIpan-2.0. Additionally, TEPITOPEpan achieved the best performance in recognizing binding cores. We further analyzed the motifs detected by TEPITOPEpan, examining the corresponding literature of immunology. Its online server and PSSMs therein are available at <a href="http://www.biokdd.fudan.edu.cn/Service/TEPITOPEpan/">http://www.biokdd.fudan.edu.cn/Service/TEPITOPEpan/</a>.</p> </div

Low-Cost Fabrication of Paper-Based Microfluidic Devices by One-Step Plotting

In this technical note, we describe a facile method for one-step fabrication of paper-based microfluidic devices, by simply using commercially available permanent markers and metal templates with specific patterns. The fabrication process involves only a single step of plotting pattern in paper; it can be typically finished within 1 min. The ink marks formed in the patterned paper will act as the hydrophobic barriers to define the hydrophilic flow paths or separate test zones. Various paper devices can be created by using different templates with corresponding patterns. Transparent adhesive tape-sandwiched devices could protect their assay surfaces from potential contamination. In the proof-of-concept experiments, circular paper test zones (∼3 mm diameter) were fabricated for colorimetric and quantification detection of prostate-specific antigen (PSA) as a model target, based on dot-immunogold staining assays coupled with gold enhancement amplification. Several serum specimens were additionally evaluated with this new approach and the results were compared with the commercial chemiluminescence immunoassay, validating its feasibility of practical applications. Such a one-step plotting method for paper patterning does not require any specialized equipments and skills, is quite inexpensive and rapid, and thus holds great potential to find wide applications especially in remote regions and resource-limited environments such as small laboratories and private clinics

AUC on Epan-Set4.

<p>Highest values for each allele are highlighted in bold.</p

The number of errors on predicting binding cores of 20 complexes in EpanCore-Set8.

<p>The binding cores of 2 complexes cannot be predicted by TEPITOPE, since it doesn't cover DRB3*01:01 and DRB3*02:01.</p

Performance of TEPITOPEpan with different alphas in terms of AUC.

<p>The highest value in each row of columns for is highlighted in bold. 1-KNN means the result of using only specificity vector(s) in the library with highest similarity to derive PSSM.</p

The HLA-DR amino acid residue positions of each pockets in TEPITOPEpan profile.

<p>The first column gives nine pockets (P1 to P9). The second column shows corresponding residue positions in contact with each pocket.</p

Available X-ray structures of MHC class II HLA-peptide complexe.

<p>The table shows complex structures retrieved from PDB. The columns in the table give PDB ID, HLA-DR restriction and bound peptide (binding core highlighted in bold).</p

Comparing of different pan-specific methods by the sequence logos of peptides restricted to HLA-DRB1*04:02, DRB1*11:01, DRB1*12:01, DRB1*13:01.

<p>Comparing of different pan-specific methods by the sequence logos of peptides restricted to HLA-DRB1*04:02, DRB1*11:01, DRB1*12:01, DRB1*13:01.</p