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Elster C, Ommer-Bläsius M, Lang A, Vajen T, Pfeiler S, Feige M, Yau Pang T, Böttenberg M, Verheyen S, Lê Quý K, Chernigovskaya M, Kelm M, Winkels H, Schmidt SV, Greiff V, Gerdes N. Application and challenges of TCR and BCR sequencing to investigate T- and B-cell clonality in elastase-induced experimental murine abdominal aortic aneurysm. Front Cardiovasc Med 2023; 10:1221620. [PMID: 38034381 PMCID: PMC10686233 DOI: 10.3389/fcvm.2023.1221620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Background An abdominal aortic aneurysm (AAA) is a life-threatening cardiovascular disease. Although its pathogenesis is still poorly understood, recent evidence suggests that AAA displays autoimmune disease characteristics. Particularly, T cells responding to AAA-related antigens in the aortic wall may contribute to an initial immune response. Single-cell RNA (scRNA) T cell receptor (TCR) and B cell receptor (BCR) sequencing is a powerful tool for investigating clonality. However, difficulties such as limited numbers of isolated cells must be considered during implementation and data analysis, making biological interpretation challenging. Here, we perform a representative single-cell immune repertoire analysis in experimental murine AAA and show a reliable bioinformatic processing pipeline highlighting opportunities and limitations of this approach. Methods We performed scRNA TCR and BCR sequencing of isolated lymphocytes from the infrarenal aorta of male C57BL/6J mice 3, 7, 14, and 28 days after AAA induction via elastase perfusion of the aorta. Sham-operated mice at days 3 and 28 and non-operated mice served as controls. Results Comparison of complementarity-determining region (CDR3) length distribution of 179 B cells and 796 T cells revealed neither differences between AAA and control nor between the disease stages. We found no clonal expansion of B cells in AAA. For T cells, we identified several clones in 11 of 16 AAA samples and one of eight control samples. Immune receptor repertoire comparison indicated that only a few clones were shared between the individual AAA samples. The most frequently used V-genes in the TCR beta chain in AAA were TRBV3, TRBV19, and the splicing variant TRBV12-2 + TRBV13-2. Conclusion We found no clonal expansion of B cells but evidence for clonal expansion of T cells in elastase-induced AAA in mice. Our findings imply that a more precise characterization of TCR and BCR distribution requires a more extensive number of lymphocytes to prevent undersampling and potentially detect rare clones. Thus, further experiments are necessary to confirm our findings. In summary, this paper examines TCR and BCR sequencing results, identifies limitations and pitfalls, and offers guidance for future studies.
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Affiliation(s)
- Christin Elster
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Miriam Ommer-Bläsius
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Alexander Lang
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Tanja Vajen
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Susanne Pfeiler
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Milena Feige
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Tin Yau Pang
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
- Department of Biology, Institute for Computer Science, Heinrich Heine University, Düsseldorf, Germany
| | - Marius Böttenberg
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Sarah Verheyen
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Khang Lê Quý
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Malte Kelm
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
- Cardiovascular Research Institute Düsseldorf (CARID), Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Holger Winkels
- Department of Cardiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Susanne V. Schmidt
- Institute of Innate Immunity, Medical Faculty and University Hospital, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Norbert Gerdes
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
- Cardiovascular Research Institute Düsseldorf (CARID), Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
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Narang S, Kaduk M, Chernyshev M, Karlsson Hedestam GB, Corcoran MM. Adaptive immune receptor genotyping using the corecount program. Front Immunol 2023; 14:1125884. [PMID: 37114042 PMCID: PMC10126697 DOI: 10.3389/fimmu.2023.1125884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/27/2023] [Indexed: 04/29/2023] Open
Abstract
We present a new Rep-Seq analysis tool called corecount, for analyzing genotypic variation in immunoglobulin (IG) and T cell receptor (TCR) genes. corecount is highly efficient at identifying V alleles, including those that are infrequently used in expressed repertoires and those that contain 3' end variation that are otherwise refractory to reliable identification during germline inference from expressed libraries. Furthermore, corecount facilitates accurate D and J gene genotyping. The output is highly reproducible and facilitates the comparison of genotypes from multiple individuals, such as those from clinical cohorts. Here, we applied corecount to the genotypic analysis of IgM libraries from 16 individuals. To demonstrate the accuracy of corecount, we Sanger sequenced all the heavy chain IG alleles (65 IGHV, 27 IGHD and 7 IGHJ) from one individual from whom we also produced two independent IgM Rep-seq datasets. Genomic analysis revealed that 5 known IGHV and 2 IGHJ sequences are truncated in current reference databases. This dataset of genomically validated alleles and IgM libraries from the same individual provides a useful resource for benchmarking other bioinformatic programs that involve V, D and J assignments and germline inference, and may facilitate the development of AIRR-Seq analysis tools that can take benefit from the availability of more comprehensive reference databases.
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