Acquired Initiating Mutations in Early Hematopoietic Cells of CLL Patients

Abstract

Appropriate cancer care requires a thorough understanding of the natural history of the disease, including the cell of origin, the pattern of clonal evolution, and the functional consequences of the mutations. Using deep sequencing of flow-sorted cell populations from patients with chronic lymphocytic leukemia (CLL), we established the presence of acquired mutations in multipotent hematopoietic progenitors. Mutations affected known lymphoid oncogenes, including BRAF, NOTCH1, and SF3B1. NFKBIE and EGR2 mutations were observed at unexpectedly high frequencies, 10.7% and 8.3% of 168 advanced-stage patients, respectively. EGR2 mutations were associated with a shorter time to treatment and poor overall survival. Analyses of BRAF and EGR2 mutations suggest that they result in deregulation of B-cell receptor (BCR) intracellular signaling. Our data propose disruption of hematopoietic and early B-cell differentiation through the deregulation of pre-BCR signaling as a phenotypic outcome of CLL mutations and show that CLL develops from a pre-leukemic phase. SIGNIFICANCE:The origin and pathogenic mechanisms of CLL are not fully understood. The current work indicates that CLL develops from pre-leukemic multipotent hematopoietic progenitors carrying somatic mutations. It advocates for abnormalities in early B-cell differentiation as a phenotypic convergence of the diverse acquired mutations observed in CLL. Cancer Discov; 4(9); 1088-1101

EGR2 mutations define a new clinically aggressive subgroup of chronic lymphocytic leukemia

“…These domains are highly conserved between orthologues in different species (Supplemental Figure S1). The somatic nature of EGR2 mutations affecting codons E356, H384, D411, and E412 has been previously confirmed 13,14,19,29 . With the exception of R318Q, all identified amino acid substitutions were predicted damaging with a SIFT score <0.05 45 .…”

“…Missense mutations within the EGR2 gene were recently reported in progressive and/or relapsing CLL patients and hence indicated to be associated with a worse clinical outcome 29 . Here, by investigating large well-characterized cohorts, we not only confirm and significantly extend this observation, but also reveal that EGR2-mutated CLL patients display distinctive clinicobiological features and a rapidly progressive disease course.…”

“…Probes targeting all coding exons or hotspot regions of 27 known CLL driver genes and/or genes previously reported in EGR2-mutated CLL 19,29,[37][38][39][40][41][42][43][44] were designed using Agilent"s SureDesign service (https://earray.chem.agilent.com/suredesign/home.htm, Supplemental Table S4). …”

“…Recurrent missense mutations within the EGR2 (early growth response 2) gene, a versatile transcription factor involved in differentiation of hematopoietic cells 26-28 , were recently reported in approximately 8% of advanced-stage CLL patients and appeared to be associated with a worse outcome 29 . Notably, EGR2 mutations were predominantly observed within the three zinc-finger domains located in exon 2.…”

“…EGR2 is activated through ERK phosphorylation upon B-cell receptor (BcR) stimulation 26 and we have previously shown that EGR2-mutated CLL patients display altered expression of EGR2 down-stream target genes compared to patients wildtype for EGR2, thus pointing to a pathogenic role for EGR2 mutations through dysregulated BcR signaling 29 . In addition, global DNA methylation investigations linked abnormal EGR2 activity with aberrant hypomethylation of transcription factor binding sites in CLL 30 .…”