Single cell profiling of ?d hepatosplenic T-cell lymphoma unravels tumor cell heterogeneity associated with disease progression

Hepatosplenic T-cell lymphoma (HSTCL) is a rare but very aggressive lymphoma mostly derived from ?d T cells. The molecular pathogenesis driving HSTCL is largely unknown while only limited treatment options are available with poor outcomes. In this study, we performed paired single cell RNA-seq and T cell receptor (TCR) sequencing on biopsies collected from a HSTCL patient pre- and post- chemotherapy treatments. We characterized unique gene expressing signatures of malignant ?d T cells with a set of marker genes were newly identified in HSTCL (AREG, PLEKHA5, VCAM1 etc.). Although the malignant cells were expanded from a single TCR clonotype according to their TCR sequences, they evolved into two transcriptional distinct tumor subtypes during the disease progression. The Tumor_1 subtype was dominant in pre-treatment samples with highly aggressive phenotypes. The Tumor_2 had relative mild cancer hallmark signatures but expressed genes associated with survival and drug resistance (IL32, TOX2, AIF1, AKAP12 etc.), and finally became the major tumor subtype post-treatment. We further dissected the tumor microenvironment of the HSTCL and found CD8 memory T cells were clonal expanded post-treatment. In addition, we discovered dynamically rewiring cell-cell interaction networks during the treatment. The tumor cells had reduced interactions with the microenvironment post-treatment. Our study reveals heterogenous and dynamic tumor and microenvironment underlying pathogenesis of HSTCL and may contribute to identify novel targets for diagnosis and cure of HSTCL in the future. Overall design: Bone marrow and PBMC biopsies were collected from a HSTCL patient pre- and post- chemotherapies. Samples were proceed for single cell RNA-seq and T cell receptor sequencing