TCR repertoire sequencing analysis using RNA on fibrotic livers

Fibrosis is the final path of nearly every form of chronic disease and accounts for up to 45% of all deaths in the developed world. However, antifibrotic therapies that target fibrogenic cells are lacking. We tested whether specific immunization against ADAM12 can elicit an antigen-specific cytotoxic T cell response to ameliorate liver fibrosis. In this study, we performed T cell receptor (TCR) alpha- and beta-chain repertoire sequencing on fibrotic livers to further characterize the T cell response and to detect potential TCR clonotypes. We observed TCR clonality of liver-infiltrating T cells from v-A12- and control-vaccinated mice with minimal overlap to v-CTRL mice in two α-chain sequences. However, the vast majority of expanded clones from v-A12-vaccinated animals showed a unique sequence pattern. Moreover, there was no overlap in the β-chain sequences between v-A12-vaccinated and control mice, suggesting a vaccination-induced expansion of antigen-specific TCR clonotypes. Livers were collected and used for total RNA extraction. Then total RNA was used for TCR alpha- and beta-chain sequencing. Comparative gene expression analysis of TCR alpha- and beta-chain seq data for livers from these four groups (sham_ v-CTRL, sham_v-A12, CCl4_v-CTRL and CCl4_v-A12) were performed.