Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes

Area of Science:

• Immunology
• Bioinformatics
• Computational Biology

Background:

• High-throughput single-cell sequencing (scSeq) enables simultaneous profiling of adaptive immune receptor repertoires (VDJ repertoires) and transcriptomes in B and T lymphocytes.
• Existing tools primarily focus on gene expression, lacking dedicated software for single-cell immune repertoire analysis.
• Integrated analysis of immune repertoire parameters (germline gene usage, clonal expansion, somatic hypermutation) and transcriptional states is crucial for high-resolution lymphocyte analysis and antigen-specificity inference.

Purpose of the Study:

• To introduce Platypus, an open-source software platform designed for user-friendly investigation of B-cell receptor (BCR) and T-cell receptor (TCR) repertoires from scSeq experiments.
• To provide a framework for automating and simplifying single-cell immune repertoire analysis, incorporating transcriptional data.
• To demonstrate Platypus's capabilities in analyzing and visualizing single-cell immune repertoire and transcriptome data.

Main Methods:

• Development of Platypus, an open-source software platform with a user-friendly interface.
• Integration of BCR and TCR repertoire analysis with transcriptional information, including unsupervised clustering, gene expression, and gene ontology.
• Application of Platypus to analyze scSeq data from B and T cells of convalescent COVID-19 patients.

Main Results:

• Platypus facilitates the automated and integrated analysis of single-cell immune repertoires and transcriptomes.
• Analysis of COVID-19 patient data using Platypus revealed unique insights into repertoire features and transcriptional profiles of clonally expanded lymphocytes.
• The software enables visualization of complex single-cell immune repertoire and transcriptome data.

Conclusions:

• Platypus addresses the need for dedicated software in single-cell immune repertoire analysis.
• The platform expedites progress in understanding lymphocyte populations by integrating repertoire and transcriptional data.
• Platypus enhances the high-resolution analysis of lymphocytes and the inference of antigen-specificity from scSeq data.