Whole-exome sequencing in relapsing chronic lymphocytic leukemia: clinical impact of recurrent RPS15 mutations

Abstract

Key Points• Whole-exome sequencing of CLL patients who relapsed after FCR treatment revealed frequent mutations in RPS15.• RPS15 mutations are likely to be early clonal events and confer poor prognosis.Fludarabine, cyclophosphamide, and rituximab (FCR) is first-line treatment of medically fit chronic lymphocytic leukemia (CLL) patients; however, despite good response rates, many patients eventually relapse. Although recent high-throughput studies have identified novel recurrent genetic lesions in adverse prognostic CLL, the mechanisms leading to relapse after FCR therapy are not completely understood. To gain insight into this issue, we performed whole-exome sequencing of sequential samples from 41 CLL patients who were uniformly treated with FCR but relapsed after a median of 2 years. In addition to mutations with known adverse-prognostic impact (TP53, NOTCH1, ATM, SF3B1, NFKBIE, and BIRC3), a large proportion of cases (19.5%) harbored mutations in RPS15, a gene encoding a component of the 40S ribosomal subunit. Extended screening, totaling 1119 patients, supported a role for RPS15 mutations in aggressive CLL, with one-third of RPS15-mutant cases also carrying TP53 aberrations. In most cases, selection of dominant, relapse-specific subclones was observed over time. However, RPS15 mutations were clonal before treatment and remained stable at relapse. Notably, all RPS15 mutations represented somatic missense variants and resided within a 7 amino-acid, evolutionarily conserved region. We confirmed the recently postulated direct interaction between RPS15 and MDM2/MDMX and transient expression of mutant RPS15 revealed defective regulation of endogenous p53 compared with wild-type RPS15. In summary, we provide novel insights into the heterogeneous genetic landscape of CLL relapsing after FCR treatment and highlight a novel mechanism underlying clinical aggressiveness involving a mutated ribosomal protein, potentially representing an early

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 .…”

“…In addition, for 41 patients in the screening cohort EGR2 mutation status was derived from WES data 19 .…”

“…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). …”

“…ATM, NOTCH1, SF3B1, TP53) 13,14 with a long tail of genes altered in <5% of cases (e.g. CHD2 15 , MED12 16 , NFKBIE 17 , POT1 18 , RPS15 19 , SETD2 20 , XPO1 21 ). Though integration of molecular information has been proposed to improve classical risk stratification models [22][23][24][25] , a substantial proportion of patients with a dismal clinical course will not be captured by these algorithms, hence indicating a need to identify additional molecular markers of disease aggressiveness.…”

U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden

“…The bulk of projects applied for between 2010 and 2016 were related to colorectal cancer (40%), hematological malignancies (28%), prostate cancer and brain tumors (10% each). The first study based on sample materials from U-CAN patients was recently published [12]. The many ongoing research initiatives include molecular subclassification of the material, discovery and validation of prognostic and predictive factors and validation of new biomarkers.…”