Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

Abstract

Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. We detected thousands of transcriptional elements differentially expressed between the CLL and normal B cells, including protein-coding genes, noncoding RNAs, and pseudogenes. Transposable elements are globally derepressed in CLL cells. In addition, two thousand genes-most of which are not differentially expressed-exhibit CLL-specific splicing patterns. Genes involved in metabolic pathways showed higher expression in CLL, while genes related to spliceosome, proteasome, and ribosome were among the most down-regulated in CLL. Clustering of the CLL samples according to RNA-seq derived gene expression levels unveiled two robust molecular subgroups, C1 and C2. C1/C2 subgroups and the mutational status of the immunoglobulin heavy variable (IGHV ) region were the only independent variables in predicting time to treatment in a multivariate analysis with main clinico-biological features. This subdivision was validated in an independent cohort of patients monitored through DNA microarrays. Further analysis shows that B-cell receptor (BCR) activation in the microenvironment of the lymph node may be at the origin of the C1/C2 differences.

The SF3B1 inhibitor spliceostatin A (SSA) elicits apoptosis in chronic lymphocytic leukaemia cells through downregulation of Mcl-1

“…8 They elicit changes in the RNA splicing profile in CLL cells and can affect important genes such as FOXP1, ATM and TNIP1 amongst others. 9,12 Therefore targeting the spliceosome may be a novel therapeutic approach for the treatment of CLL. Several compounds are available for this purpose, [13][14][15][16] including meayamycin B 17,18 and the structurally related spliceostatin A (SSA).…”

Cytokinesis arrest and multiple centrosomes in B cell chronic lymphocytic leukaemia

“…(A) Subset of genes differently expressed in CLL cells as reported by Ferreira et al 9. Shown are genes involved in centrosome assembly, duplication and regulation as well as genes regulated by TP53.…”

“…To identify genes that possibly contribute to the observed cytokinesis arrest, we searched a list of 3578 differentially expressed genes based on a publically available RNAseq data set obtained from 98 CLL patients and healthy donor control samples 9. We identified several genes encoding proteins known to be involved in cell cycle regulation to be dysregulated.…”

“…Candidate genes involved in the described cytokinesis defect were identified based on a list of differentially expressed genes from a previously analysed, publically available RNAseq data set based on a cohort of 98 CLL patients and healthy donor controls9 (European Genome‐Phenome Archive, under accession number EGAS00001000374). In Ferreira et al , 9 genes were considered differentially expressed when showing absolute fold change (Tumour/Normal) ≥ 2 with false discovery rate (FDR) < 0.01.…”

“…In Ferreira et al , 9 genes were considered differentially expressed when showing absolute fold change (Tumour/Normal) ≥ 2 with false discovery rate (FDR) < 0.01.…”