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

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

Abstract:Background: Abdominal aortic aneurysm (AAA) is a life-threatening cardiovascular disease.32Although its pathogenesis is still poorly understood, recent evidence suggests that AAA displays33characteristics of an autoimmune disease. Particularly T cells responding to AAA-related antigens in34the aortic wall may contribute to the initial immune response. Single-cell RNA (scRNA) T- and B- cell35receptor (TCR and BCR) sequencing is a powerful tool to investigate clonality. However, difficulties36such as limited numbers of isolated cells must be considered during implementation and data analysis,37making biological interpretation challenging. Here, we perform a representative single cell immune38repertoire analysis in experimental murine AAA and show a reliable bioinformatic processing pipeline39highlighting opportunities and limitations of this approach.40Methods: We performed scRNA TCR and BCR sequencing of isolated lymphocytes from the41infrarenal aorta of male C57BL/6J mice 3, 7, 15, and 28 days after AAA induction via elastase42perfusion of the aorta. Sham-operated mice at day 3 and 28 as well as non-operated mice served as43controls.44Results: Comparison of complementarity-determining region (CDR3) length distribution of 179 B45cells and 796 T cells revealed neither differences between AAA and control nor between the disease46stages. We found no clonal expansion of B cells in AAA. For T cells, we identified expanded clones47in 11 of 16 AAA samples and in 1 of 8 control samples. Immune receptor repertoire comparison48indicated that only few clones were shared between the individual AAA samples. The most frequently49used V-genes in the TCR beta chain in AAA were TRBV3, TRBV19, and the splicing variant50TRBV12-2+TRBV13-2.51Conclusion: We found no clonal expansion of TCRs or BCRs in elastase-induced AAA in mice at52different disease stages. Our findings imply that a more precise characterization of TCR and BCR53distribution requires a more extensive number of lymphocytes to prevent undersampling and to54potentially detect rare clones. In summary, this paper examines TCR and BCR sequencing results,55identifies limitations and pitfalls, and offers guidance for future studies.

The Raw Data can be found here: https://zenodo.org/doi/10.5281/zenodo.10725979