Abstract
High-throughput single-cell sequencing (scSeq) technologies are revolutionizing the ability to molecularly profile B and T lymphocytes by offering the opportunity to simultaneously obtain information on adaptive immune receptor repertoires (VDJ repertoires) and transcriptomes. An integrated quantification of immune repertoire parameters, such as germline gene usage, clonal expansion, somatic hypermutation and transcriptional states opens up new possibilities for the high-resolution analysis of lymphocytes and the inference of antigen-specificity. While multiple tools now exist to investigate gene expression profiles from scSeq of transcriptomes, there is a lack of software dedicated to single-cell immune repertoires. Here, we present Platypus, an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. Platypus provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. To showcase the capabilities of Platypus, we use it to analyze and visualize single-cell immune repertoires and transcriptomes from B and T cells from convalescent COVID-19 patients, revealing unique insight into the repertoire features and transcriptional profiles of clonally expanded lymphocytes. Platypus will expedite progress by facilitating the analysis of single-cell immune repertoire and transcriptome sequencing.
Highlights
Immune repertoires are comprised of a diverse collection of B-cell receptors (BCRs) and T-cell receptors (TCRs), which enable molecular recognition to a vast number of pathogen and disease antigens
While Platypus is optimized for data generated by the 10× Genomics System, it is adaptable to other cell-barcode based single-cell sequencing (scSeq) data (e.g. RAGE-seq, Split-Seq [10,23])
We have demonstrated here that Platypus enables rapid extraction, integration and analysis of scSeq of lymphocyte repertoires and transcriptomes to uncover meaningful insight on lymphocyte immunobiology and function
Summary
Immune repertoires are comprised of a diverse collection of B-cell receptors (BCRs) and T-cell receptors (TCRs), which enable molecular recognition to a vast number of pathogen and disease antigens. One major challenge in immune repertoire sequencing is acquiring information on correct receptor chain pairing [variable light (VL) and variable heavy (VH) for BCR and variable alpha (V␣) and variable beta (V) for TCR], which greatly complicates identification of clonal groups and antigen-specificity [5,6]. Recent developments in microfluidic and scSeq technologies have made it possible to obtain information on immune repertoires or transcriptional profiles at highthroughput [7,8,9]. Several of these methods have been tailored for lymphocytes, making it possible to perform parallel sequencing of immune repertoires and whole transcriptomes [10,11].
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