Abstract
BackgroundThe human leukocyte antigen (HLA) proteins play a fundamental role in the adaptive immune system as they present peptides to T cells. Mass-spectrometry-based immunopeptidomics is a promising and powerful tool for characterizing the immunopeptidomic landscape of HLA proteins, that is the peptides presented on HLA proteins. Despite the growing interest in the technology, and the recent rise of immunopeptidomics-specific identification pipelines, there is still a gap in data-analysis and software tools that are specialized in analyzing and visualizing immunopeptidomics data.ResultsWe present the IPTK library which is an open-source Python-based library for analyzing, visualizing, comparing, and integrating different omics layers with the identified peptides for an in-depth characterization of the immunopeptidome. Using different datasets, we illustrate the ability of the library to enrich the result of the identified peptidomes. Also, we demonstrate the utility of the library in developing other software and tools by developing an easy-to-use dashboard that can be used for the interactive analysis of the results.ConclusionIPTK provides a modular and extendable framework for analyzing and integrating immunopeptidomes with different omics layers. The library is deployed into PyPI at https://pypi.org/project/IPTKL/ and into Bioconda at https://anaconda.org/bioconda/iptkl, while the source code of the library and the dashboard, along with the online tutorials are available at https://github.com/ikmb/iptoolkit.
Highlights
The human leukocyte antigen (HLA) proteins play a fundamental role in the adaptive immune system as they present peptides to T cells
The HLA loci contain, among others, the loci that encode for the classical HLA class I proteins, HLA-A, HLA-B and HLA-C and the classical HLA class II proteins, HLA-DR, HLA-DP and HLA-DQ [2]
Different HLA alleles have been associated with a wide spectrum of autoimmune and inflammatory diseases, for example, inflammatory bowel disease [4, 5], multiple sclerosis [6] and systemic lupus erythematosus (SLE) [7], but have been implicated in pharmacogenomics and precision medicine. It has been recently shown by Sazonovs et al [8] that carriers of HLA-DQA1*05 alleles are more likely to develop anti-drug antibodies towards Infliximab and Adalimumab
Summary
The human leukocyte antigen (HLA) proteins play a fundamental role in the adaptive immune system as they present peptides to T cells. Different HLA alleles have been associated with a wide spectrum of autoimmune and inflammatory diseases, for example, inflammatory bowel disease [4, 5], multiple sclerosis [6] and systemic lupus erythematosus (SLE) [7], but have been implicated in pharmacogenomics and precision medicine. It has been recently shown by Sazonovs et al [8] that carriers of HLA-DQA1*05 alleles are more likely to develop anti-drug antibodies towards Infliximab and Adalimumab
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