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Aydin I.T.,Mount Sinai School of Medicine | Melamed R.D.,Columbia University | Adams S.J.,Mount Sinai School of Medicine | Castillo-Martin M.,Mount Sinai School of Medicine | And 8 more authors.
Journal of the National Cancer Institute

Background Melanoma is a heterogeneous tumor with subgroups requiring distinct therapeutic strategies. Genetic dissection of melanoma subgroups and identification of therapeutic agents are of great interest in the field. These efforts will ultimately lead to treatment strategies, likely combinatorial, based on genetic information. Methods To identify driver genes that can be targeted therapeutically, we screened metastatic melanomas for somatic mutations by exome sequencing followed by selecting those with available targeted therapies directed to the gene product or its functional partner. The FBXW7 gene and its substrate NOTCH1 were identified and further examined. Mutation profiling of FBXW7, biological relevance of these mutations and its inactivation, and pharmacological inhibition of NOTCH1 were examined using in vitro and in vivo assays. Results We found FBXW7 to be mutated in eight (8.1%) melanoma patients in our cohort (n = 103). Protein expression analysis in human tissue samples (n = 96) and melanoma cell lines (n = 20) showed FBXW7 inactivation as a common event in melanoma (40.0% of cell lines). As a result of FBXW7 loss, we observed an accumulation of its substrates, such as NOTCH1. Ectopic expression of mutant forms of FBXW7 (by 2.4-fold), as well as silencing of FBXW7 in immortalized melanocytes, accelerated tumor formation in vivo (by 3.9-fold). Its inactivation led to NOTCH1 activation, upregulation of NOTCH1 target genes (by 2.6-fold), and promotion of tumor angiogenesis and resulted in tumor shrinkage upon NOTCH1 inhibition (by fivefold). Conclusions Our data provides evidence on FBXW7 as a critical tumor suppressor mutated and inactivated in melanoma that results in sustained NOTCH1 activation and renders NOTCH signaling inhibition as a promising therapeutic strategy in this setting. © 2014 The Author. Source

Sathirapongsasuti J.F.,Harvard University | Sathirapongsasuti J.F.,Dana-Farber Cancer Institute | Sathirapongsasuti J.F.,University of California at Los Angeles | Lee H.,University of California at Los Angeles | And 8 more authors.

Motivation: The ability to detect copy-number variation (CNV) and loss of heterozygosity (LOH) from exome sequencing data extends the utility of this powerful approach that has mainly been used for point or small insertion/deletion detection.Results: We present ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads, and we assess both the method's power and the effects of confounding variables. We apply our method to a cancer exome resequencing dataset. As expected, accuracy and resolution are dependent on depth-of-coverage and capture probe design. © The Author 2011. Published by Oxford University Press. All rights reserved. Source

Schipmann S.,Skin Cancer Center Hornheide | Wermker K.,Skin Cancer Center Hornheide | Schulze H.-J.,Skin Cancer Center Hornheide | Kleinheinz J.,University Hospital Muenster | Brunner G.,Skin Cancer Center Hornheide
Journal of Cranio-Maxillofacial Surgery

Regulatory T cells (Tregs) are an essential component of the immune system, but are also involved in the suppression of anti-tumour immune responses. The study examines their immunoregulatory role including their transcription factor, FOXP3, in oral and cutaneous SCC. Tregs were detected by double-immunohistochemistry. FOXP3-mRNA-expression was examined in tumour tissue, as well as in skin-derived primary cells and cell lines of different malignancy. Tregs were found in the tumour microenvironment, and FOXP3-mRNA-expression was significantly higher than in normal skin. Intriguingly, single FOXP3+ cells exhibited morphologic characteristics of SCC cells. Consistent with this, endogenous FOXP3-mRNA-expression was indeed detected in the epidermal cell lineage and dramatically increased with increasing malignancy of the cells. SCCs recruit Tregs into their microenvironment, presumably in order to suppress immunosurveillance, thus avoiding destruction by the immune system. Endogenous FOXP3-expression in malignant epidermoid cells might present a novel mechanism of immune escape. © 2014 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rightsreserved. Source

Kuhlmann J.D.,TU Dresden | Kuhlmann J.D.,German Cancer Research Center | Wimberger P.,TU Dresden | Wimberger P.,German Cancer Research Center | And 5 more authors.
Clinical Chemistry and Laboratory Medicine

Background: Melanoma is the most aggressive skin cancer and, despite recent advances in therapy, about 20% of the patients die of their disease. Early relapse detection and monitoring of therapy response are crucial for efficient treatment of advanced melanoma. Thus, there is a need for blood-based biomarkers in melanoma management. Serum-derived U2 small nuclear RNA fragments (RNU2-1f) were previously shown to be blood-based biomarkers for gastrointestinal and gynecologic malignancies. Here we examined whether RNU2-1f may also serve as diagnostic biomarker in advanced melanoma. Methods: Circulating RNU2-1f levels were quantified by comparative reverse transcription PCR in a training cohort of patients with metastatic melanoma (n=33, thereof regionally metastasized to skin and lymph nodes, n=23, and distantly metastasized, n=10) vs. patients with benign naevi (n=16) vs. healthy controls (n=39). Results were validated in an independent patient cohort with distant metastasis (n=16) vs. controls (n=18). Results: Circulating RNU2-1f levels in the training cohort were significantly increased in serum of regionally and distantly metastatic patients, compared with patients with benign naevi or healthy controls (p<0.0001) and allowed accurate detection of regional (AUC 0.80) as well as distant (AUC 0.84) metastasis. In the validation cohort, increased RNU2-1f levels were confirmed and enabled highly specific detection of distant metastasis (sensitivity 81%, specificity 100%, AUC 0.94). Conclusions: This is the first report to suggest a blood-based snRNA serving as a diagnostic biomarker for melanoma metastasis. Our data provide a rationale for further defining clinical utility of circulating RNU2-1f in metastasis detection in the management of melanoma patients at risk of relapse and/or with advanced disease. © 2015 by De Gruyter. Source

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