Clonal Evolution Analysis of Paediatric Lymphoma Reveals a Highly Diversified Cellular Status and Potential Targets for Precision Medicine

Tracer Yong – Dept of Microbiology Tumor and Cell biology – Karolinska Institutet; Roberta Daulerio – Dept of Microbiology Tumor and Cell biology – Karolinska Institutet; Fredrik Baecklund – Dept of Microbiology Tumor and Cell biology – Karolinska Institutet

Abstract Text: Lymphoma is the third most common paediatric cancer. To reveal mechanisms underlying lymphomagenesis, we combined single cell RNA sequencing (scRNAseq) and immune receptor sequencing (VDJseq) of paediatric samples from non-cancerous reactive lymph nodes (n=7) and the three major types of paediatric lymphoma; Burkitt (BL, n=3), Hodgkin (HL, n=4), and T lymphoblastic lymphoma (TLL, n=5). VDJ clonal expansion was used for cancer cell annotation for BL and TLL. To investigate the tumour microenvironment in HL, we integrated scRNAseq with spatial transcriptomics. We identified a cycling cluster that consisted of dark-zone germinal centre B cells (DZGCBs) in reactive lymph nodes but harbours cancer cells from the BL and TLL samples, suggesting that the highly proliferative programme normally used by DZGCB cells is important for lymphomagenesis. Based on VDJseq, we identified hyperexpanded lymphoma clones in each BL and TLL. These lymphoma clones had a diverse transcriptomics profile, with BL sharing programme with germinal centre B cells, memory B cells, and plasma cells. TLL underwent a unique transcriptomic shift bridging the T helper cell cluster and cycling cluster, suggesting lymphomagenesis is continuous. Trajectory analysis showed a diverse transcription profile towards the cycling cluster, indicating the mechanism of this transition. Using a predictive treatment score, we observed heterogeneity in gene expression of the hyperexpanded clones highlighting the efficacy and short-coming of current treatment. Finally, spatial resolved transcriptomics revealed exhausted T cells proximal to Reed-Sternberg cells in HL. Our data reveals that paediatric lymphomagenesis is characterized by its diversified transcriptome and identifies novel targets for therapy.