T-Cell Repertoire Characterization

This volume provides a comprehensive compilation of protocols in T cell repertoire analysis, from the leading experts in the field, representing both well-established methods and cutting-edge advances. Chapters broadly cover the emerging new T cell subsets, sequencing technologies for capturing TCR repertoire, and computational tools for analyzing an ever-growing TCR repertoire, with a particular focus on how to link the sequence with TCR antigen specificity. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, T-Cell Repertoire Characterization aims to be a useful practical guide to researches to help further their study in this field. 

Part I: A growing heterogeneity of T cell subsets

1. Ligand identification for Orphan MHC-agnostic T-cell receptors by whole genome CRISPR-Cas9 screening

Michael D Crowther, Mateusz Legut, Andrew K. Sewell

2. Discovery of HLA-E-presented epitopes: MHC-E/peptide binding and T cell recognition

Paula Ruibal, Kees L M C Franken, Krista E van Meijgaarden, Lucy C Walters, Andrew J McMichael, Geraldine M Gillespie, Simone A Joosten, Tom H M Ottenhoff

3. Identification of human antigen-specific T cells using class II MHC tetramer staining and enrichment

4. Characterization of KIR+CD8+ regulatory T cells in humans by scRNA- and TCR-seq

Jing Li, Julie Wilhelmy, Mark M. Davis

5. Detection of a-synuclein-specific T cells in Parkinson’s disease

Rekha Dhanwani, Alessandro Sette, Cecilia S. Lindestam Arlehamn

Part II: TCR repertoire sequencing and antigen analysis

6. The intra-tumoural T cell receptor repertoire – steps towards a useful clinical biomarker

7. Enriching and Characterizing T-Cell Repertoires from 3’ Barcoded Single-Cell Whole Transcriptome Amplification Products

Tasneem Jivanjee, Samira Ibrahim, Sarah K. Nyquist, G. James Gatter, Joshua D. Bromley, Swati Jaiswal, Bonnie Berger, Samuel M. Behar, J. Christopher Love, Alex K. Shalek

8. Tetramer associated T cell receptor sequencing

Michael Malone, Ke-yue Ma, Shu-qi Zhang, Ning Jiang You

9. T-cell Repertoire Characterization

Anna Pasetto and Marcus Buggert

10. Characterization of mouse CD4 TCR and its targeting antigen

Wenhua Liang and Feng Wang

11. Rapid identification of MHCII-binding peptides through microsphere-assisted peptide screening (MAPS)

Luke F. Bugada, Mason R. Smith, and Fei Wen

12. A high throughput strategy for T-Cell Receptor cloning and expression

Qiong Xia, Huang Huang, and Mark M. Davis

Part III: Computational Tools for TCR repertoire analysis

13. Epitope-specific T-cell receptor data and tools in the Immune Epitope Database

William Chronister, Alessandro Sette, and Bjoern Peters

14. A Bioinformatic Framework for Dissecting the Dynamics of T cells from Single-Cell Transcriptome

Lei Zhang and Jiesheng Li

15. Grouping T-Cell Antigen Receptors by Specificity

Chunlin Wang, Huang Huang, and Mark Davis

16. Flexible Distance-Based TCR Analysis in Python with tcrdist3

Koshlan Mayer-Blackwell, Andrew Fiore-Gartland, and Paul G. Thomas

17. Multimodal T cell analysis with CoNGA

Stefan A. Schattgen, William D. Hazelton, Paul G. Thomas, and Philip Bradley