Genetic and transcriptional heterogeneity of Chronic lymphocytic leukaemia (CLL) limits prevention of disease progression. Longitudinal single-cell transcriptomics represents the state-of-the-art method to profile the disease heterogeneity at diagnosis and to inform about disease evolution. Here, we apply single-cell RNA-seq to a CLL case, sampled at diagnosis and relapse, that was treated with FCR (Fludarabine, Cyclophosphamide, Rituximab) and underwent a dramatic decrease in CD19 expression during disease progression. Computational analyses revealed a major switch in clones' dominance during treatment. The clone that expanded at relapse showed 17p and 3p chromosomal deletions, and up-regulation of pathways related to motility, cytokine signaling and antigen presentation. Single-cell RNA-seq uniquely revealed that this clone was already present at low frequency at diagnosis, and it displays feature of plasma cell differentiation, consistent with a more aggressive phenotype. This study shows the benefit of single-cell profiling of CLL heterogeneity at diagnosis, to identify clones that might otherwise not be recognized and to determine the best treatment options.

Centre for Haematology Department of Immunology and Inflammation Imperial College London London United Kingdom

Department of Haematology and Oncology University Hospital Pilsen Pilsen Czechia

Department of Surgery and Cancer Imperial College London London United Kingdom

Faculty of Medicine in Pilsen Institute of Medical Genetics Charles University Prague and Faculty Hospital Pilsen Czechia

Hugh and Josseline Langmuir Centre for Myeloma Research Centre for Haematology Department of Immunology and Inflammation Imperial College London London United Kingdom

Imperial BRC Genomics Facility Imperial College London London United Kingdom

Laboratory of Tumor Biology and Immunotherapy Biomedical Center Faculty of Medicine in Pilsen Charles University Pilsen Czechia

NTIS Faculty of Applied Science University of West Bohemia Pilsen Czechia

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