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