Genomic profiling reveals molecular heterogeneity in patients with Richter transformation (RT) and chronic lymphocytic leukemia (CLL)

Richter transformation (RT) represents the development of an aggressive lymphoma in chronic lymphocytic leukemia (CLL). Patients with RT and relapsed CLL have poor outcomes. Yet, the extent of molecular differences between the two entities has not been fully explored. In this pilot study, we conducted RNA-seq and targeted panel sequencing of nodal tissues from 12 patients, including seven with RT and five with CLL. Analysis of RNA-seq data revealed two major clusters, with five RT in cluster C1 and the remaining two RT and all five CLL in C2. Within C2, one of the CLL ultimately developed RT; it showed more similarity to the two RT than to the other CLL in expression profile, suggesting the presence of expression signature for RT prior to the clinical diagnosis. In addition, differentially expressed genes, the majority of which showed higher expression in C1 relative to C2, were enriched in pathways known to be important for CLL pathogenesis or transformation. Deconvolution of the bulk RNA-seq data revealed major differences in cellular composition between the two clusters, notably tumor B cells, macrophages M1, and CD8+ T cells. Furthermore, by targeted sequencing, we identified 51 genes that carried recurrent copy number alterations (CNAs) preferentially occurring in either cluster. Over 80% of these CNAs occurred in C2, mainly gains of 17q12q25 in CLL. Patients in C1 had shorter overall survival (median 11 months) compared to those in C2 (median 36 months). Together, our findings highlight noticeable differences in transcriptomic and genomic alterations between CLL versus RT. Simple SummaryChronic lymphocytic leukemia (CLL) is a type of blood cancer, representing the most common leukemia in the Western countries. A small percent of patients with CLL develop into an aggressive lymphoma, most commonly diffuse large B-cell lymphoma (DLBCL), a process known as Richter transformation (RT). In RT, previous studies have identified specific somatic events and molecular subtypes. A deep understanding of the molecular events driving CLL to RT will accelerate the development of therapeutic strategies. Using RNA-seq and targeted sequencing, this study revealed heterogeneity of gene expression, copy number alterations, and dysregulated pathways in a cohort of 12 RT/CLL.