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huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level.

Lize Wu1,2, Ziwei Xue3, Siqian Jin3

  • 1Institute of Immunology and Department of Rheumatology at Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.

Nucleic Acids Research
|October 4, 2021
PubMed
Summary

A new database, huARdb, offers a comprehensive resource for human antigen receptors. It links single-cell immune profiling data, including T-cell receptor (TCR) and B-cell receptor (BCR) sequences and transcriptomes, to advance immunology research.

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Area of Science:

  • Immunology
  • Genomics
  • Bioinformatics

Background:

  • T-cell receptors (TCRs) and B-cell receptors (BCRs) are crucial for adaptive immunity, with diversity generated by V(D)J recombination.
  • Single-cell immune profiling enables high-throughput study of TCR/BCR clonotypes and functions.
  • A comprehensive database linking this data was previously unavailable.

Purpose of the Study:

  • To introduce the human Antigen Receptor database (huARdb), a large-scale resource for human single-cell immune profiling data.
  • To provide a centralized platform for accessing and analyzing TCR/BCR sequences and transcriptomes.
  • To facilitate research into adaptive immunity by offering a multi-perspective atlas of human antigen receptors.

Main Methods:

  • Compiled data from 215 datasets, including 444,794 high-confidence T and B cells (hcT/B cells).
  • Processed all datasets using a uniform workflow: sequence alignment, cell subtype prediction, unsupervised clustering, and clonotype definition.
  • Developed a user-friendly web interface with interactive visualization for single-cell transcriptome and TCR/BCR analysis.

Main Results:

  • Established huARdb, a database containing full-length TCR/BCR sequences and transcriptomes for a large cohort of human immune cells.
  • Implemented a standardized data processing pipeline ensuring data consistency and quality.
  • Created an accessible web platform for querying, browsing, downloading, and depositing data.

Conclusions:

  • huARdb serves as a comprehensive and multi-perspective atlas for human antigen receptors.
  • The database and its interface empower biologists to analyze immune cell data at the single-cell level.
  • This resource is expected to significantly advance the understanding of adaptive immunity in health and disease.