Gene amplification as double minutes or homogeneously staining regions in solid tumors:Origin and structure

Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model). In the present paper we investigated 10 cell lines from solid tumors showing MYCN amplification as dmin or hsr. Particularly revealing results were provided by the two subclones of the neuroblastoma cell line STA-NB-10, one showing dmin-only and the second hsr-only amplification. Both subclones showed a deletion, at 2p24.3, whose extension matched the amplicon extension. Additionally, the amplicon structure of the dmin and hsr forms was identical. This strongly argues that the episome model, already demonstrated in leukemias, applies to solid tumors as well, and that dmin and hsr are two faces of the same coin. The organization of the duplicated segments varied from very simple (no apparent changes from the normal sequence) to very complex. MYCN was always overexpressed (significantly overexpressed in three cases). The fusion junctions, always mediated by nonhomologous end joining, occasionally juxtaposed truncated genes in the same transcriptional orientation. Fusion transcripts involving NBAS (also known as NAG), FAM49A, BC035112 (also known as NCRNA00276), and SMC6 genes were indeed detected, although their role in the context of the tumor is not clear

Rare recurrent t(15;21) translocations disrupting RUNX1 in myeloid leukemia.

status: publishe

The transcriptome plasticity of genomic amplification in cancer

Genomic amplification, in the form of homogeneously staining regions, double minutes, and ring/giant rod-shaped markers, is a pivotal event in many tumors. It was recently shown that amplifications as extra-chromosomal DNA are present in nearly half of all tumors, representing a driving force towards their accelerated evolution. To achieve a better understanding of the implications of genomic amplifications we focused on their structure and impact upon transcription. Amplified cancer-associated genes are often overexpressed as a direct consequence of the copy number gain. We analyzed the whole genome (WGS) and transcriptome (RNA-seq) sequencing data of nine small lung carcinoma (SCLC), seven neuroblastoma (NB) and three well- differentiated liposarcoma (WDLPS) cell lines, all carrying genomic amplifications. A widespread heterogeneity was detected in the amplicon arrangement of many cell lines, disclosing the progressive evolution of their structure through cell division. By integrating the WGS (structural variation calling) and RNA-seq (chimeras detection) data we detected a burst of chimeric transcripts partially derived from post- transcriptional events (i.e cis- or trans-splicing) in most of the analyzed cell lines. Notably, we found PVT1 and RLF as hotspots for cis- or trans-splicing events in SCLC and NB cell lines with MYC and MYCL1 amplifications, respectively. In WDLPS cell lines we found fusion genes originated by extremely complex genomic rearrangements, such as those involving three partner genes or assembled by multiple interposed non-contiguous, non-collinear genomic fragments (spliced out in the mature transcript). Our results strongly indicate that the “amplification/overexpression” paradigm does not cover all aspects of the genomic amplification impact upon transcription. The extraordinary transcriptome plasticity herein described, enriching the genetic repertoire of cancer cells with genomic amplifications, likely provides a selective advantage and might have a crucial role in cancer establishment and progression

Comparative study of morphological ECG features classificators: An application on athletes undergone to acute physical stress

Several methods for automatic heartbeat classification have been developed, but few efforts have been devoted to the recognition of the small ECG changes occurring in healthy people as a response to stimuli. Herein, we describe a procedure for the extraction, selection and classification of features summarizing morphological ECG changes. The proposed procedure is composed by the following stages: 1) extraction of a set of heartbeat morphological features; 2) selection of a subset of features; 3) subject normalization 4) classification. The selection of a subset of features enabled us to summarize ECG changes with only three non redundant features. In addition we performed a comparison between four classificators: k-nearest-neighbors (k-NN), artificial neural networks (ANN), support vector machines (SVM) and naive Bayes classifiers (nB). In order to cope with the possible non linear separation problem, we evaluated two strategies: a subject factor normalization on feature space and the usage of kernel functions for classifiers. The results of the comparison recommended the usage of subject normalization, irrespectively from the classificator: with or without normalization we had the best performance of classification for the linear-SVM and AN

Clinical management of drug-induced cardiotoxicity in patients with HER-2+ breast cancer: current recommendations and future outlook

Introduction: Human epidermal growth factor receptor two (HER2) target therapies have drastically revolutionized the treatment of HER2-positive breast cancer. Starting with trastuzumab, early phase III trials have already highlighted its significant cardiotoxicity, which is also present, albeit to a lesser extent, in the new generation drugs. Also given the growing population of patients with cardiovascular diseases, it is vital to set up proper long-term follow-up to prevent morbidity related to the development of cardiotoxicity. Areas covered: This review discusses the mechanisms of action underlying the cardiotoxicity of HER2 targeted therapies and the main clinical evidence on the toxicity of these drugs. In addition, the patterns of patient assessment prior to the initiation of therapy with HER2 targeted therapies are discussed, as well as the main evidence concerning the follow-up and management of cardiotoxicity. Expert opinion: The mechanisms of cardiotoxicity of new HER2 drugs need further study and, likewise, methods to prevent, monitor and identify HER-2-induced cardiotoxicity need to be implemented. Although some studies highlight the validity of cardiac biomarkers as predictive factors for cardiotoxicity, their actual usefulness and timing is still debated. Further studies are needed to assess the effectiveness of possible pharmacological primary prevention