Chronic lymphocytic leukaemia (CLL) is a frequent disease in which the genetic alterations determining the clinicobiological behaviour are not fully understood. Here we describe a comprehensive evaluation of the genomic landscape of 452 CLL cases and 54 patients with monoclonal B-lymphocytosis, a precursor disorder. We extend the number of CLL driver alterations, including changes in ZNF292, ZMYM3, ARID1A and PTPN11. We also identify novel recurrent mutations in non-coding regions, including the 3' region of NOTCH1, which cause aberrant splicing events, increase NOTCH1 activity and result in a more aggressive disease. In addition, mutations in an enhancer located on chromosome 9p13 result in reduced expression of the B-cell-specific transcription factor PAX5. The accumulative number of driver alterations (0 to ≥4) discriminated between patients with differences in clinical behaviour. This study provides an integrated portrait of the CLL genomic landscape, identifies new recurrent driver mutations of the disease, and suggests clinical interventions that may improve the management of this neoplasia.

Genome studies of chronic lymphocytic leukemia (CLL) have revealed the remarkable subclonal heterogeneity of the tumors, but the clinical implications of this phenomenon are not well known. We assessed the mutational status of 28 CLL driver genes by deep-targeted next-generation sequencing and copy number alterations (CNA) in 406 previously untreated patients and 48 sequential samples. We detected small subclonal mutations (0.6–25% of cells) in nearly all genes (26/28), and they were the sole alteration in 22% of the mutated cases. CNA tended to be acquired early in the evolution of the disease and remained stable, whereas the mutational heterogeneity increased in a subset of tumors. The prognostic impact of different genes was related to the size of the mutated clone. Combining mutations and CNA, we observed that the accumulation of driver alterations (mutational complexity) gradually shortened the time to first treatment independently of the clonal architecture, IGHV status and Binet stage. Conversely, the overall survival was associated with the increasing subclonal diversity of the tumors but it was related to the age of patients, IGHV and TP53 status of the tumors. In conclusion, our study reveals that both the mutational complexity and subclonal diversity influence the evolution of CLL.

NOTCH1 has been found recurrently mutated in a subset of patients with chronic lymphocytic leukemia (CLL). To analyze biological features and clinical impact of NOTCH1 mutations in CLL, we sequenced this gene in 565 patients. NOTCH1 mutations, found in 63 patients (11%), were associated with unmutated IGHV, high expression of CD38 and ZAP-70, trisomy 12, advanced stage and elevated lactate dehydrogenase. Sequential analysis in 200 patients demonstrated acquisition of mutation in one case (0.5%) and disappearance after treatment in two. Binet A and B patients with NOTCH1-mutated had a shorter time to treatment. NOTCH1-mutated patients were more frequently refractory to therapy and showed shorter progression-free and overall survival after complete remission. Overall survival was shorter in NOTCH1-mutated patients, although not independently from IGHV. NOTCH1 mutation increased the risk of transformation to diffuse large B-cell lymphoma independently from IGHV, with this being validated in resampling tests of replicability. In summary, NOTCH1 mutational status, that was rarely acquired during the course of the disease, identify a genetic subgroup with high risk of transformation and poor outcome. This recently identified genetic subgroup of CLL patients deserves prospective studies to define their best management.

Key Points• Mutations in the TLR/MYD88 pathway occur in 4% of patients with CLL, and they are the most frequent in young patients.• TLR/MYD88 mutations in CLL patients confer a good outcome, which is similar to that of the age-and gendermatched healthy population.Mutations in Toll-like receptor (TLR) and myeloid differentiation primary response 88 (MYD88) genes have been found in chronic lymphocytic leukemia (CLL) at low frequency. We analyzed the incidence, clinicobiological characteristics, and outcome of patients with TLR/MYD88 mutations in 587 CLL patients. Twenty-three patients (3.9%) had mutations, 19 in MYD88 (one with concurrent IRAK1 mutation), 2 TLR2 (one with concomitant TLR6 mutation), 1 IRAK1, and 1 TLR5. No mutations were found in IRAK2 and IRAK4. TLR/MYD88-mutated CLL overexpressed genes of the nuclear factor kB pathway. Patients with TLR/MYD88 mutations were significantly younger (83% age £50 years) than those with no mutations. TLR/MYD88 mutations were the most frequent in young patients. Patients with mutated TLR/MYD88 CLL had a higher frequency of mutated IGHV and low expression of CD38 and ZAP-70. Overall survival (OS) was better in TLR/MYD88-mutated than unmutated patients in the whole series (10-year OS, 100% vs 62%; P 5 .002), and in the subset of patients age £50 years (100% vs 70%; P 5 .02). In addition, relative OS of TLR/MYD88-mutated patients was similar to that in the age-and gender-matched population. In summary, TLR/MYD88 mutations identify a population of young CLL patients with favorable outcome. (Blood. 2014;123(24):3790-3796)

Several grading systems have been developed in the bone marrow transplantation setting in attempts to predict survival in patients with chronic graft-versus-host disease (cGVHD). In this study, we evaluated the prognostic value of the National Institutes of Health (NIH) scoring system and investigated for any additional prognostic factors in a series of 171 patients undergoing peripheral blood stem cell transplantation (PBSCT) from matched related donors. The cumulative incidence of cGVHD was 70%; cumulative incidences of mild, moderate, and severe cGVHD were 29%, 42% and 28%, respectively. Overall, 68% of patients were free from immunosuppression 5 years after transplantation. Absence of previous acute GVHD (aGVHD; hazard ratio [HR] = 2; P = .004) and mild cGVHD (HR = 4.2; P = .007) increased the probability of being off immunosuppressive treatment by the last follow-up. Overall survival (OS) at 5 years was 52%. Severe cGVHD, according to the NIH scoring system (HR = 13.27; P = .001) adversely influenced outcome, whereas de novo onset (HR = 0.094; P = .003) had a more favorable impact on survival. The combination of both variables allowed us to identify 4 different subgroups of patients with OS of 82%, 70%, 50%, and 25%. Our findings indicate that the NIH scoring system has some prognostic value in patients undergoing PBSCT and, together with the type of onset, must be considered to predict the possible outcome of patients who develop cGVHD.