Tumor microenvironmental genomic alterations in juvenile nasopharyngeal angiofibroma

Background To better characterize the pathophysiology of juvenile nasopharyngeal angiofibroma (JNA), endothelial and stromal cells were evaluated by genomic imbalances in association with transcript expression levels of genes mapped on these altered regions. Methods. High-resolution comparative genomic hybridization (HR-CGH) was used in laser-captured endothelial and stromal cells from 9 JNAs. Ten genes were evaluated by quantitative real-timereverse transcription polymerase chain reaction (qRT-PCR) in 15 cases. Results. Although gains were more frequently detected in endothelial cells, 57% of chromosomal alterations were common by both components. Gene expression analyses revealed a positive correlation between endothelial and stromal components for ASPM, CDH1, CTNNB1, FGF18, and SUPT16H. A significant difference was found for FGF18 and AURKB overexpression in stromal cells and AR down-expression in endothelial cells. Conclusions. A similar pattern of gene expression and chromosomal imbalances in both exponents would suggest a common mechanism of functional regulation. AURKB, FGF18, and SUPT16H were identified as potential molecular markers in JNA. (C) 2011 Wiley Periodicals, Inc. Head Neck 34: 485-492, 2012Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), BrazilConselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), Brazi

Genomic screening of testicular germ cell tumors from monozygotic twins

Background: Testicular germ cell tumors (TGCTs) account for 1-2% of all tumors in young and middle aged men. A 75-fold increase in TCGT development has been reported for monozygotic (MZ) twins. Therefore, the occurrence of simultaneous tumors in MZ twins emphasizes the importance of genetic factors that influence the risk of developing these tumors. Genomic screening was performed for one family containing MZ twins with testicular germ cell tumors, in order to define alterations associated with risk of tumor development.Methods: Copy number alterations were evaluated using array-CGH (4x44K, Agilent Technologies) in one seminoma and one embryonal carcinoma (EC) from MZ twins. In addition, genomic alterations from the tumors and peripheral blood cells of the twins were compared to the parental genomes via their peripheral blood cells.Results: Embryonal carcinoma (Twin-1 t) presented a lower frequency of genomic alterations compared to the seminoma (Twin-2 t). One minimal common region of loss was observed in 9p13.1-p12 in the comparison between DNA from blood samples for Twin-1 and Twin-2. In this region is mapped the CNTNAP3 gene which was confirmed as involved in losses by qPCR. Comparative analysis of novel CNVs between the Twin-1 t and Twin-2 t showed five minimal common regions involving gain at chromosomes 12 (12p12.3-p11.1 and 12p13.33-p12.3), while losses were observed at 10p15.3-p15.2, 13q21.1-q21.2 and 15q11.1-q11.2. In addition, one exclusive rare copy number alteration was detected in Twin-1 t and Twin-2 t, and 19 novel alterations were identified in the Twin-2 t.Conclusion: Distinct genomic profiles for MZ twins with phenotypically different TGCT were described. Of particular interest, 12p gains were detected exclusively in tumor samples. In peripheral blood samples, loss of 9p13.1-p12 was the unique novel CNV shared by the twins, confirming the involvement of CNTNAP3 gene in TGCTs development. Although similar CNV profiles were shared by both the peripheral blood and tumor samples of the twins, tumor-specific CNV loci were identified for seminoma and non-seminomatous tumors. These findings suggest the presence of de novo germline structural alterations and TGCT predisposition.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Genomic Signatures Predict Poor Outcome in Undifferentiated Pleomorphic Sarcomas and Leiomyosarcomas

<div><p>Undifferentiated high-grade pleomorphic sarcomas (UPSs) display aggressive clinical behavior and frequently develop local recurrence and distant metastasis. Because these sarcomas often share similar morphological patterns with other tumors, particularly leiomyosarcomas (LMSs), classification by exclusion is frequently used. In this study, array-based comparative genomic hybridization (array CGH) was used to analyze 20 UPS and 17 LMS samples from untreated patients. The LMS samples presented a lower frequency of genomic alterations compared with the UPS samples. The most frequently altered UPS regions involved gains at 20q13.33 and 7q22.1 and losses at 3p26.3. Gains at 8q24.3 and 19q13.12 and losses at 9p21.3 were frequently detected in the LMS samples. Of these regions, gains at 1q21.3, 11q12.2-q12.3, 16p11.2, and 19q13.12 were significantly associated with reduced overall survival times in LMS patients. A multivariate analysis revealed that gains at 1q21.3 were an independent prognostic marker of shorter survival times in LMS patients (HR = 13.76; <i>P</i> = 0.019). Although the copy number profiles of the UPS and LMS samples could not be distinguished using unsupervised hierarchical clustering analysis, one of the three clusters presented cases associated with poor prognostic outcome (<i>P = </i>0.022). A relative copy number analysis for the <i>ARNT</i>, <i>SLC27A3,</i> and <i>PBXIP1</i> genes was performed using quantitative real-time PCR in 11 LMS and 16 UPS samples. Gains at 1q21-q22 were observed in both tumor types, particularly in the UPS samples. These findings provide strong evidence for the existence of a genomic signature to predict poor outcome in a subset of UPS and LMS patients.</p></div

Unsupervised hierarchical clustering of 20 undifferentiated pleomorphic sarcomas (UPSs) and 17 leiomyosarcomas (LMSs).

<p>(A) In the dendrogram, cluster 1 is shown in green, cluster 2 is shown in blue, and cluster 3 is shown in red. Clusters related to the sites of anatomical origin were not observed for these tumors; origin sites include the following regions: upper extremity (pink), lower extremity (purple), trunk (orange), retroperitoneum (yellow), and head and neck (rose). (B) Genomic alterations were detected in clusters 1 (C1; 11 cases), 2 (C2; 16 cases), and 3 (C3; 10 cases). The top bars (blue) indicate genetic gains, whereas the lower bars (red) indicate genetic losses. The images shown were adapted from the output of the Nexus 6.0 software program.</p

Overall survival curves from LMS patients with specific genomic alterations.

<p>Gains at (A) 1q21.3, (B) 11q12.2-q12.3, (C) 16p11.2, and (D) 19q13.12 were associated with shorter survival times. P-values were determined using the Log-rank test.</p

Genomic imbalances more frequently detected in UPS and LMS.

<p>Legend: UPS - Undifferentiated Pleomorphic Sarcomas; LMS - Leiomyosarcomas.</p

Clinical and histopathological data from patients (20 UPS and 17 LMS).

<p>Abbreviations - F: Female, M: Male, DD: Death by disease, NED: No evidence of disease, AD: Alive with disease, LF: Loss of follow-up; MD: metastasis at diagnosis.</p><p>Treatment – QT: Chemotherapy; RT: Radiotherapy; 0: Surgery; 1: Neoadjuvant therapy; 2: Adjuvant therapy; 3: Chemotherapy without surgery.</p>*<p>Selected for qPCR validation.</p>a<p>Samples from the same patient.</p>b<p>Patients with Li-Fraumeni Syndrome.</p>c<p>Time to last follow-up from diagnosis.</p>d<p>Samples of different patients obtained from expansion of primary tumor surgical (remnant of primary tumor).</p

Quantification of DNA copy number alterations using qPCR for the <i>ARNT</i>, <i>PBXIP1, SLC27A3,</i> and <i>CCND1</i> genes.

<p>Eight primer pairs were designed, including (A) three for <i>ARNT</i> (ARNT-P1, ARNT-P2, and ARNT-P3); (B) two for <i>PBXIP1</i> (PBXIP1-P1 and PBXIP1-P2) and one for <i>SLC27A3</i> (SLC27A3-P1); and (C) two for <i>CCND1</i> (CCND1-P1 and CCND1-P2).</p