1. Wang DY, Salem J-EE, Cohen J V., et al. Fatal Toxic Effects Associated With Immune Checkpoint Inhibitors: A Systematic Review and Meta-analysis. JAMA Oncol. 2018;4(12):1721-1728. http://www.embase.com/search/results?subaction=viewrecord&from=export&id=L624011231. Accessed October 15, 2019.
2. Wei SC, Meijers WC, Axelrod ML, et al. A Genetic Mouse Model Recapitulates Immune Checkpoint Inhibitor–Associated Myocarditis and Supports a Mechanism-Based Therapeutic Intervention. Cancer Discov. 2020;11(3):614-639. doi:10.1158/2159-8290.cd-20-0856
3. Lv H, Havari E, Pinto S, et al. Impaired thymic tolerance to α-myosin directs autoimmunity to the heart in mice and humans. J Clin Invest. 2011;121(4):1561-1573. doi:10.1172/JCI44583
4. Gabrielsen ISM, Helgeland H, Akselsen H, et al. Transcriptomes of antigen presenting cells in human thymus. PLoS One. 2019;14(7):e0218858. doi:10.1371/JOURNAL.PONE.0218858
5. Johnson DB, Balko JM, Compton ML, et al. Fulminant myocarditis with combination immune checkpoint blockade. N Engl J Med. 2016;375(18):1749-1755. doi:10.1056/NEJMoa1609214
6. Hu J-RR, Florido R, Lipson EJ, et al. Cardiovascular toxicities associated with immune checkpoint inhibitors. Cardiovasc Res. 2019;115(5):854. https://academic.oup.com/cardiovascres/advance-article/doi/10.1093/cvr/cvz026/5304411. Accessed March 4, 2019.
7. Salem JE, Manouchehri A, Moey M, et al. Spectrum of cardiovascular toxicities of immune checkpoint inhibitors: A pharmacovigilance study. Lancet Oncol. 2018;19(12):1579. doi:10.1016/S1470-2045(18)30608-9
8. Moslehi J, Lichtman AH, Sharpe AH, Galluzzi L, Kitsis RN. Immune checkpoint inhibitor–associated myocarditis: manifestations and mechanisms. J Clin Invest. 2021;131(5). doi:10.1172/JCI145186
9. Zamami Y, Niimura T, Okada N, et al. Factors Associated With Immune Checkpoint Inhibitor–Related Myocarditis. JAMA Oncol. 2019;5(11):1635-1637. doi:10.1001/JAMAONCOL.2019.3113
10. Salem J-E, Allenbach Y, Vozy A, et al. Abatacept for Severe Immune Checkpoint Inhibitor–Associated Myocarditis. N Engl J Med. 2019;380(24):2377-2379. doi:10.1056/NEJMc1901677
11. Aran D, Looney AP, Liu L, et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. 2019;20(2):163-172. doi:10.1038/s41590-018-0276-y
12. Yang X, Bam M, Becker W, Nagarkatti PS, Nagarkatti M. Long Noncoding RNA AW112010 Promotes the Differentiation of Inflammatory T Cells by Suppressing IL-10 Expression through Histone Demethylation. J Immunol. 2020;205(4):987-993. doi:10.4049/jimmunol.2000330
13. Jackson R, Kroehling L, Khitun A, et al. The Translation of Non-Canonical Open Reading Frames Controls Mucosal Immunity. Vol 564. Nature Publishing Group; 2018:434-438. doi:10.1038/s41586-018-0794-7
14. Adamo L, Rocha-Resende C, Lin CY, et al. Myocardial B cells are a subset of circulating lymphocytes with delayed transit through the heart. JCI insight. 2020;5(3). doi:10.1172/JCI.INSIGHT.134700
15. Bönner F, Borg N, Burghoff S, Schrader J. Resident cardiac immune cells and expression of the ectonucleotidase enzymes CD39 and CD73 after ischemic injury. PLoS One. 2012;7(4). doi:10.1371/JOURNAL.PONE.0034730
16. Martini E, Kunderfranco P, Peano C, et al. Single-Cell Sequencing of Mouse Heart Immune Infiltrate in Pressure Overload-Driven Heart Failure Reveals Extent of Immune Activation. Circulation. 2019;140(25):2089-2107. doi:10.1161/CIRCULATIONAHA.119.041694
17. Heather JM, Spindler MJ, Alonso MH, et al. Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information. bioRxiv. December 2021:2021.12.20.473544. doi:10.1101/2021.12.20.473544
18. Rosskopf S, Leitner J, Paster W, et al. A Jurkat 76 based triple parameter reporter system to evaluate TCR functions and adoptive T cell strategies. Oncotarget. 2018;9(25):17608-17619. doi:10.18632/oncotarget.24807
19. Jutz S, Leitner J, Schmetterer K, et al. Assessment of costimulation and coinhibition in a triple parameter T cell reporter line: Simultaneous measurement of NF-κB, NFAT and AP-1. J Immunol Methods. 2016;430:10-20. doi:10.1016/j.jim.2016.01.007
20. Gil-Cruz C, Perez-Shibayama C, de Martin A, et al. Microbiota-derived peptide mimics drive lethal inflammatory cardiomyopathy. Science (80- ). 2019;366(6467):881-886. doi:10.1126/science.aav3487
21. Massilamany C, Gangaplara A, Steffen D, Reddy J. Identification of novel mimicry epitopes for cardiac myosin heavy chain-α that induce autoimmune myocarditis in A/J mice. Cell Immunol. 2011;271(2):438-449. doi:10.1016/J.CELLIMM.2011.08.013
22. Paul S, Sidney J, Sette A, Peters B. TepiTool: A pipeline for computational prediction of T cell epitope candidates. Curr Protoc Immunol. 2016;2016:18.19.1-18.19.24. doi:10.1002/cpim.12
23. Falk K, Rotzschke O, Stevanovic S, Jung G, Rammenseet H-G. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. 1991.
24. Mombaerts P, Iacomini J, Johnson RS, Herrup K, Tonegawa S, Papaioannou VE. RAG-1-deficient mice have no mature B and T lymphocytes. Cell. 1992;68(5):869-877. doi:10.1016/0092-8674(92)90030-G
25. Satija R, Farrell JA, Gennert D, Schier AF, Regev A. Spatial reconstruction of single-cell gene expression data. 2015;33(5):495-502. doi:10.1038/nbt.3192
26. Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36(5):411-420. doi:10.1038/nbt.4096
27. Stuart T, Butler A, Hoffman P, et al. Comprehensive Integration of Single-Cell Data. Cell. 2019;177(7):1888-1902.e21. doi:10.1016/j.cell.2019.05.031
28. Wu Y, Borde M, Heissmeyer V, et al. FOXP3 controls regulatory T cell function through cooperation with NFAT. Cell. 2006;126(2):375-387. doi:10.1016/J.CELL.2006.05.042
29. Oh HM, Oh JM, Choi SC, et al. An efficient method for the rapid establishment of Epstein-Barr virus immortalization of human B lymphocytes. Cell Prolif. 2003;36(4):191-197. doi:10.1046/J.1365-2184.2003.00276.X
30. Granato M, Santarelli R, Farina A, et al. Epstein-Barr Virus Blocks the Autophagic Flux and Appropriates the Autophagic Machinery To Enhance Viral Replication. J Virol. 2014;88(21):12715. doi:10.1128/JVI.02199-14
31. Wölfl M, Greenberg PD. Antigen-specific activation and cytokine-facilitated expansion of naive, human CD8+ T cells. Nat Protoc 2014 94. 2014;9(4):950-966. doi:10.1038/nprot.2014.064
32. Eberhardt CS, Kissick HT, Patel MR, et al. Functional HPV-specific PD-1+ stem-like CD8 T cells in head and neck cancer. Nat 2021 5977875. 2021;597(7875):279-284. doi:10.1038/s41586-021-03862-z
33. Oksanen J, Blanchet FG, Friendly M, et al. Package “vegan” Title Community Ecology Package Version 2.5-7. 2020.
34. Nazarov V, immunarch.bot, Rumynskiy E. immunarch: An R Package for Painless Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires. June 2020. doi:10.5281/ZENODO.3893991