Datasset to the publication: Application and challenges of TCR and BCR sequencing to investigate T and B cell clonality in abdominal aortic aneurysm

<p>Title: Application and challenges of TCR and BCR sequencing to investigate T and B cell clonality in abdominal aortic aneurysm</p> <p>Abstract:<br>Background: Abdominal aortic aneurysm (AAA) is a life-threatening cardiovascular disease.32<br>Although its pathogenesis is still poorly understood, recent evidence suggests that AAA displays33<br>characteristics of an autoimmune disease. Particularly T cells responding to AAA-related antigens in34<br>the aortic wall may contribute to the initial immune response. Single-cell RNA (scRNA) T- and B- cell35<br>receptor (TCR and BCR) sequencing is a powerful tool to investigate clonality. However, difficulties36<br>such as limited numbers of isolated cells must be considered during implementation and data analysis,37<br>making biological interpretation challenging. Here, we perform a representative single cell immune38<br>repertoire analysis in experimental murine AAA and show a reliable bioinformatic processing pipeline39<br>highlighting opportunities and limitations of this approach.40<br>Methods: We performed scRNA TCR and BCR sequencing of isolated lymphocytes from the41<br>infrarenal aorta of male C57BL/6J mice 3, 7, 15, and 28 days after AAA induction via elastase42<br>perfusion of the aorta. Sham-operated mice at day 3 and 28 as well as non-operated mice served as43<br>controls.44<br>Results: Comparison of complementarity-determining region (CDR3) length distribution of 179 B45<br>cells and 796 T cells revealed neither differences between AAA and control nor between the disease46<br>stages. We found no clonal expansion of B cells in AAA. For T cells, we identified expanded clones47<br>in 11 of 16 AAA samples and in 1 of 8 control samples. Immune receptor repertoire comparison48<br>indicated that only few clones were shared between the individual AAA samples. The most frequently49<br>used V-genes in the TCR beta chain in AAA were TRBV3, TRBV19, and the splicing variant50<br>TRBV12-2+TRBV13-2.51<br>Conclusion: We found no clonal expansion of TCRs or BCRs in elastase-induced AAA in mice at52<br>different disease stages. Our findings imply that a more precise characterization of TCR and BCR53<br>distribution requires a more extensive number of lymphocytes to prevent undersampling and to54<br>potentially detect rare clones. In summary, this paper examines TCR and BCR sequencing results,55<br>identifies limitations and pitfalls, and offers guidance for future studies.</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>The Raw Data can be found here: https://zenodo.org/doi/10.5281/zenodo.10725979</p> <p>&nbsp;</p>