Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets.

Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a large number of somatic mutations and structural alterations. However, the clinical significance of these alterations is still not well defined. In this study, we have integrated the analysis of targeted next-generation sequencing of 106 genes and genomic copy number alterations (CNA) in 150 DLBCL. The clinically significant findings were validated in an independent cohort of 111 patients. Germinal center B-cell and activated B-cell DLBCL had a differential profile of mutations, altered pathogenic pathways and CNA. Mutations in genes of the NOTCH pathway and tumor suppressor genes (TP53/CDKN2A), but not individual genes, conferred an unfavorable prognosis, confirmed in the independent validation cohort. A gene expression profiling analysis showed that tumors with NOTCH pathway mutations had a significant modulation of downstream target genes, emphasizing the relevance of this pathway in DLBCL. An in silico drug discovery analysis recognized 69 (46%) cases carrying at least one genomic alteration considered a potential target of drug response according to early clinical trials or preclinical assays in DLBCL or other lymphomas. In conclusion, this study identifies relevant pathways and mutated genes in DLBCL and recognizes potential targets for new intervention strategies.

Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia.

In our individualized systems medicine program, personalized treatment options are identified and administered to chemorefractory acute myeloid leukemia (AML) patients based on exome sequencing and ex vivo drug sensitivity and resistance testing data. Here, we analyzed how clonal heterogeneity affects the responses of 13 AML patients to chemotherapy or targeted treatments using ultra-deep (average 68 000 × coverage) amplicon resequencing. Using amplicon resequencing, we identified 16 variants from 4 patients (frequency 0.54-2%) that were not detected previously by exome sequencing. A correlation-based method was developed to detect mutation-specific responses in serial samples across multiple time points. Significant subclone-specific responses were observed for both chemotherapy and targeted therapy. We detected subclonal responses in patients where clinical European LeukemiaNet (ELN) criteria showed no response. Subclonal responses also helped to identify putative mechanisms underlying drug sensitivities, such as sensitivity to azacitidine in DNMT3A mutated cell clones and resistance to cytarabine in a subclone with loss of NF1 gene. In summary, ultra-deep amplicon resequencing method enables sensitive quantification of subclonal variants and their responses to therapies. This approach provides new opportunities for designing combinatorial therapies blocking multiple subclones as well as for real-time assessment of such treatments.

Usefulness of transoesophageal echocardiography before circumferential pulmonary vein ablation in patients with atrial fibrillation: is it really mandatory?

AIMS: Transoesophageal echocardiography (TEE) is recommended prior to circumferential pulmonary vein ablation (CPVA) in patients with atrial fibrillation (AF) to identify left atrial (LA) or left atrial appendage (LAA) wall thrombi. It is not clear whether all patients undergoing CPVA should receive pre-procedural TEE. We wanted to assess the incidence of LA thrombus in these patients and to identify factors associated with its presence. METHODS AND RESULTS: Consecutive patients referred for CPVA from 2004 to 2009 underwent TEE within 48 h prior to the procedure. Of 408 patients included in the study, 6 patients (1.47%) had LA thrombi, persistent AF, and LA dilation. Compared with patients without thrombus, these six patients had larger LA diameter (P = 0.0001) and more frequently were women (P = 0.002), had persistent AF (P = 0.04), and had underlying structural cardiac disease (P = 0.014). The likelihood of presenting LA thrombus increased with the number of these four risk factors present (P < 0.001). None of the patients with paroxysmal AF and without LA dilation had LA thrombus. A cut-off value of 48.5 mm LA diameter yielded 83% sensitivity, 92% specificity, and a 10.1 likelihood ratio to predict LA thrombus appearance. CONCLUSION: The incidence of LA thrombus prior to CPVA is low. Persistent AF, female sex, structural cardiopathy, and LA dilation were associated with the presence of LA thrombus. Our data suggest that the use of TEE prior to CPVA to detect LA thrombi might not be needed in patients with paroxysmal AF and no LA dilation or structural cardiopathy.

Quantification of left ventricular asynchrony throughout the whole cardiac cycle with a computed algorithm: application for optimizing resynchronization therapy.

INTRODUCTION: Measurement of left ventricular (LV) asynchrony is usually determined on single time points from spectral tissue Doppler imaging (TDI) scans that are frequently difficult to identify or not representative of the whole cardiac cycle. Our aim was to validate a new asynchrony index that evaluates the motion of the LV walls throughout the whole cardiac cycle. METHODS AND RESULTS: Ten healthy volunteers and 50 patients undergoing cardiac resynchronization therapy (CRT) were studied with TDI. Wall displacement tracings from the septal and lateral LV walls were analyzed. Cross-correlation was calculated and 2 indices were obtained to assess LV asynchrony: the time delay and the superposition index (SI) between wall displacements. These results were compared between healthy volunteers and CRT patients, and between responders and nonresponders to CRT. Also, the optimal interventricular (VV) interval was based upon the best matching level. Volunteers showed lower asynchrony indices (83 +/- 2% SI, 17 +/- 8 ms time delay) as compared with CRT patients (63 +/- 15% SI, 73 +/- 60 ms time delay, P < 0.05). Responders also had more LV dyssynchrony than nonresponders (58 +/- 15% SI and 92 +/- 66 ms vs 68 +/- 12% and 48 +/- 34 ms, P < 0.05). The optimum VV interval selected by the computed algorithm showed an excellent concordance (Kappa = 0.90, P < 0.05) with that determined by other validated methods for optimizing the programming of CRT devices. CONCLUSIONS: This approach allows measurement of LV intraventricular asynchrony throughout the cardiac cycle, being useful to determine the optimum VV interval and to select candidates for CRT.