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Genes, Chromosomes & Cancer

Anna Palau, Mar Mallo, Laura Palomo, Ines Rodríguez-Hernández, Jeannine Diesch, Diana Campos, Isabel Granada, Jordi Juncà, Hans G Drexler, Francesc Solé, Marcus Buschbeck
Leukemia cell lines have been widely used in the hematology field to unravel mechanistic insights and to test new therapeutic strategies. Myelodysplastic syndromes (MDS) comprise a heterogeneous group of diseases that are characterized by ineffective hematopoiesis and frequent progress to acute myeloid leukemia (AML). A few cell lines have been established from MDS patients after progression to AML but their characterization is incomplete. Here we provide a detailed description of the immunophenotypic profile of the MDS-derived cell lines SKK-1, SKM-1, F-36P; and MOLM-13...
October 17, 2016: Genes, Chromosomes & Cancer
Irsan E Kooi, Saskia E van Mil, David MacPherson, Berber M Mol, Annette C Moll, Hanne Meijers-Heijboer, Gertjan J L Kaspers, Jacqueline Cloos, Hein Te Riele, Josephine C Dorsman
Several murine retinoblastoma models have been generated by deleting the genes encoding for retinoblastoma susceptibility protein pRb and one of its family members p107 or p130. In Rb(-/-) p107(-/-) retinoblastomas, somatic copy number alterations (SCNAs) like Mdm2 amplification or Cdkn2a deletion targeting the p53-pathway occur, which is uncommon for human retinoblastoma. In our study, we determined SCNAs in retinoblastomas developing in Rb(-/-) p130(-/-) mice and compared this to murine Rb(-/-) p107(-/-) tumors and human tumors...
October 17, 2016: Genes, Chromosomes & Cancer
Clémentine Sarkozy, Sophie Kaltenbach, Pierre Faurie, Danielle Canioni, Françoise Berger, Alexandra Traverse-Glehen, Hervé Ghesquieres, Gilles Salles, Emmanuel Bachy, Marie-Alexandra Alyanakian, Olivier Hermine, Bénédicte Neven, Elizabeth Macintyre, Serge Romana, Thierry Jo Molina, Felipe Suarez, Vahid Asnafi, Julie Bruneau
Plasma-cell post-transplantation lymphoproliferative disorder (PC-PTLD) is a rare monomorphic PTLD entity divided into plasma cell myeloma (PCM) and plasmacytoma-like lesion (PLL) PTLD. To date, there are no exhaustive published cytogenetic data on PC-PTLD. We report array-based comparative genomic hybridization (aCGH) of 10 cases of PCM and PLL-PTLD. Patients had received kidney (n=6), heart (n=2), lung (n=1) or bone marrow (n=1) transplantation. There were six men and median age at time of PTLD was 56.5 years (3-74)...
October 17, 2016: Genes, Chromosomes & Cancer
Jonas Leichsenring, Anna-Lena Volckmar, Nikolaus Magios, Cristiano Manuel Morais de Oliveira, Roland Penzel, Regine Brandt, Martina Kirchner, Farastuk Bozorgmehr, Michael Thomas, Peter Schirmacher, Arne Warth, Volker Endris, Albrecht Stenzinger
Patients with NSCLC harboring activating mutations in the EGFR benefit from targeted therapies. A synonymous polymorphism (rs1050171, p.Q787Q) was shown to be associated with improved overall survival (OS) in colorectal cancer patients. As data in NSCLC are limited, we retrospectively analyzed associations of p.Q787Q with clinicopathological parameters including clinical response and outcome in patients with lung adenocarcinoma (ADC) who received tyrosine kinase inhibitor (TKI) therapy. Of 642 ADC patients whose tumors were profiled by next generation sequencing, 102 (15...
October 17, 2016: Genes, Chromosomes & Cancer
Samuel B Pattle, Natasa Utjesanovic, Athena Togo, Lucy Wells, Brendan Conn, Hannah Monaghan, Elizabeth Junor, Ingolfur Johannessen, Kate Cuschieri, Simon Talbot
Squamous cell carcinomas of the hypopharynx (HPSCC) and oropharynx (OPSCC) have markedly different patient outcomes. Differences in HPV prevalence between these two patient groups may account for some of this difference, but other molecular markers of prognosis or pathological phenotype have not been established. Copy number gain of oncogenes is a well-established molecular change contributing to HNSCC development. Quantitative PCR was used to explore copy number gains of specific genes (3q - PIK3CA, TP63; 11q13...
October 17, 2016: Genes, Chromosomes & Cancer
Nicole E McNeil, Hesed M Padilla-Nash, Floryne O Buishand, Yue Hue, Thomas Ried
Human colorectal carcinomas are defined by a non-random distribution of genomic imbalances that are characteristic for this disease. Often, these imbalances affect entire chromosomes. Understanding the role of these aneuploidies for carcinogenesis is of utmost importance. Currently, established transgenic mice do not recapitulate the pathognonomic genome aberration profile of human colorectal carcinomas. We have developed a novel model based on the spontaneous transformation of murine colon epithelial cells...
October 17, 2016: Genes, Chromosomes & Cancer
Karan Rai, Robert Pilarski, Getachew Boru, Muneeb Rehman, Ahmad H Saqr, James B Massengill, Arun Singh, Meghan J Marino, Frederick H Davidorf, Colleen M Cebulla, Mohamed Abdel-Rahman
Uveal melanoma (UM) is the most commonly diagnosed primary intraocular tumor in adults. Familial UM (FUM), defined as two or more family members diagnosed with UM, is rare and estimated at less than 1% of all UM. Currently, BAP1 is the only gene known to contribute significant risk for UM. In this study we aimed to estimate the frequency of BAP1 mutation in FUM and to characterize the family and personal histories of other cancers in these families. We identified 32 families with FUM, including seven families previously reported by our group...
October 8, 2016: Genes, Chromosomes & Cancer
Mareike Doerrenberg, Andreas Kloetgen, Kebria Hezaveh, Wilhelm Wössmann, Kirsten Bleckmann, Martin Stanulla, Martin Schrappe, Alice C McHardy, Arndt Borkhardt, Jessica I Hoell
For reasons not yet understood, nearly all infants with acute lymphoblastic leukemia (ALL) are diagnosed with the B-cell type, with T-ALL in infancy representing a very rare exception. Clinical and molecular knowledge about infant T-ALL is still nearly completely lacking and it is also still unclear whether it represents a distinct disease compared to childhood T-ALL. To address this, we performed exome sequencing of three infant cases, which enabled the detection of mutations in NOTCH2, NOTCH3, PTEN, and KRAS...
September 26, 2016: Genes, Chromosomes & Cancer
Valentina Damiano, Giulia Brisotto, Silvia Borgna, Alessandra di Gennaro, Michela Armellin, Tiziana Perin, Michela Guardascione, Roberta Maestro, Manuela Santarosa
Loss of expression of miR-200 family members has been implicated in cellular plasticity, a phenomenon that accounts for epithelial-to-mesenchymal transition (EMT) and stem-like features of many carcinomas and is considered a major cause of tumor aggressiveness and drug resistance. Nevertheless, the mechanisms of miR-200 downregulation in breast cancer are still largely unknown. Here we show that miR-200c expression inversely correlates with miR-200c/miR-141 locus methylation in triple-negative breast tumors (TNBC)...
September 22, 2016: Genes, Chromosomes & Cancer
Hu Dou, Xi Chen, Yi Huang, Yongchun Su, Ling Lu, Jie Yu, Yibing Yin, Liming Bao
The cytokine receptor-like factor 2 (CRLF2) gene plays an important role in early B-cell development. Aberrations in CRLF2 activate the JAK-STAT signaling pathway that contributes to B-cell acute lymphoblastic leukemia (B-ALL). The prognostic significance of CRLF2 overexpression and P2RY8-CRLF2 fusion in various B-ALL risk subgroups has not been well established. Two hundred seventy-one patients with newly diagnosed childhood B-ALL were enrolled from a Chinese population. The prevalence of CRLF2 overexpression, CRLF2-P2RY8 fusion, CRLF2 F232C mutation, and JAK2 and IL7R mutational status were analyzed, and the prognostic impact of CRLF2 overexpression and P2RY8-CRLF2 on B-ALL was evaluated by assessing their influence on overall survival and event-free survival...
September 16, 2016: Genes, Chromosomes & Cancer
Noralane M Lindor, Melissa C Larson, Melissa S DeRycke, Shannon K McDonnell, Saurabh Baheti, Zachary C Fogarty, Aung Ko Win, John D Potter, Daniel D Buchanan, Mark Clendenning, Polly A Newcomb, Graham Casey, Steven Gallinger, Loïc Le Marchand, John L Hopper, Mark A Jenkins, Ellen L Goode, Stephen N Thibodeau
MicroRNAs (miRNAs) regulate up to one-third of all protein-coding genes including genes relevant to cancer. Variants within miRNAs have been reported to be associated with prognosis, survival, response to chemotherapy across cancer types, in vitro parameters of cell growth, and altered risks for development of cancer. Five miRNA variants have been reported to be associated with risk for development of colorectal cancer (CRC). In this study, we evaluated germline genetic variation in 1,123 miRNAs in 899 individuals with CRCs categorized by clinical subtypes and in 204 controls...
September 16, 2016: Genes, Chromosomes & Cancer
Abdelkader Heddar, Pierre Fermey, Sophie Coutant, Emilie Angot, Jean-Christophe Sabourin, Paul Michelin, Nathalie Parodi, Françoise Charbonnier, Myriam Vezain, Gaëlle Bougeard, Stéphanie Baert-Desurmont, Thierry Frébourg, Isabelle Tournier
Germline mutations of EXT2, encoding Exostosin Glycosyltransferase 2, are associated with multiple osteochondromas (MO), an autosomal dominant disease characterized by the development of multiple peripheral cartilaginous benign tumors with a weak risk of malignant transformation. We report here a family with a remarkable clinical presentation characterized by the development of isolated chondrosarcomas, mostly located in ribs. Comparative analysis of exomes from two third-degree affected relatives led us to identify a single common disruptive variation, corresponding to a stop mutation (c...
September 16, 2016: Genes, Chromosomes & Cancer
Tobias Herold, Klaus H Metzeler, Sebastian Vosberg, Luise Hartmann, Vindi Jurinovic, Sabrina Opatz, Nikola P Konstandin, Stephanie Schneider, Evelyn Zellmeier, Bianka Ksienzyk, Alexander Graf, Stefan Krebs, Helmut Blum, Maria Cristina Sauerland, Thomas Büchner, Wolfgang E Berdel, Bernhard J Wörmann, Ulrich Mansmann, Wolfgang Hiddemann, Stefan K Bohlander, Karsten Spiekermann, Philipp A Greif
Deletions of the long arm of chromosome 9 [del(9q)] are a rare but recurring aberration in acute myeloid leukemia (AML). Del(9q) can be found as the sole abnormality or in combination with other cytogenetic aberrations such as t(8;21) and t(15;17). TLE1 and TLE4 were identified to be critical genes contained in the 9q region. We performed whole exome sequencing of 5 patients with del(9q) as the sole abnormality followed by targeted amplicon sequencing of 137 genes of 26 patients with del(9q) as sole or combined with other aberrations...
September 16, 2016: Genes, Chromosomes & Cancer
Jiafeng Li, Jinsheng Zhao, Yue Li
Overexpression of the nucleoporin NUP88 has been observed in a large number of tumors and has been experimentally proven to promote tumorigenesis. However, the mechanism underlying the tumor-promoting activity of overexpressed NUP88 is not clear. To investigate the potential pathways that drive tumorigenesis under NUP88 overexpressed condition, we applied a proteomic approach to identify NUP88-associated proteins at a subcellular compartment level. Gene ontology analysis revealed significant associations between NUP88 interactome and biological processes that are related to nuclear transport, RNA processing, cell cycle progression, metabolic regulation, and viral infection...
September 16, 2016: Genes, Chromosomes & Cancer
Kristina Karrman, Bertil Johansson
The most common pediatric malignancy is acute lymphoblastic leukemia (ALL), of which T-cell ALL (T-ALL) comprises 10-15% of cases. T-ALL arises in the thymus from an immature thymocyte as a consequence of a stepwise accumulation of genetic and epigenetic aberrations. Crucial biological processes such as differentiation, self-renewal capacity, proliferation, and apoptosis are targeted and deranged by several types of neoplasia-associated genetic alteration, for example translocations, deletions, and mutations of genes that code for proteins involved in signaling transduction, epigenetic regulation, and transcription...
September 16, 2016: Genes, Chromosomes & Cancer
Ge Gao, Sarah H Johnson, George Vasmatzis, Christina E Pauley, Nicole M Tombers, Jan L Kasperbauer, David I Smith
Common fragile sites (CFS) are chromosome regions that are prone to form gaps or breaks in response to DNA replication stress. They are often found as hotspots for sister chromatid exchanges, deletions and amplifications in different cancers. Many of the CFS regions are found to span genes whose genomic sequence is greater than 1 Mb, some of which have been demonstrated to function as important tumor suppressors. CFS regions are also hotspots for human papillomavirus (HPV) integrations in cervical cancer. We used mate-pair sequencing to examine HPV integration events and chromosomal structural variations in 34 oropharyngeal squamous cell carcinoma (OPSCC)...
September 16, 2016: Genes, Chromosomes & Cancer
Chiara Varamo, Marcella Occelli, Daniela Vivenza, Marco Merlano, Cristiana Lo Nigro
Malignant melanoma (MM) is a highly aggressive skin cancer with high incidence worldwide. It originates from melanocytes and is characterized by invasion, early metastasis and despite the use of new drugs it is still characterized by high mortality. Since an early diagnosis determines a better prognosis, it is important to explore novel prognostic markers in the management of patients with MM. microRNAs (miRNAs) are small (∼22 nucleotides) single-stranded non-coding RNAs that negatively regulate the expression of more than 60% of human genes...
August 25, 2016: Genes, Chromosomes & Cancer
Lucia Nacci, Roberto Valli, Rita Maria Pinto, Marco Zecca, Marco Cipolli, Jacopo Morini, Simone Cesaro, Emanuela Boveri, Vittorio Rosti, Paola Corti, Maura Ambroni, Francesco Pasquali, Cesare Danesino, Emanuela Maserati, Antonella Minelli
Shwachman-Diamond syndrome (SDS) (OMIM 260400) is a rare autosomal recessive disease characterized by exocrine pancreatic insufficiency, skeletal and haematological abnormalities and bone marrow (BM) dysfunction. Mutations in the SBDS gene cause SDS. Clonal chromosome anomalies are often present in BM, i(7)(q10) and del(20)(q) being the most frequent ones. We collected 6 SDS cases with del(20)(q): a cluster of imprinted genes, including L3MBTL1 and SGK2 is present in the deleted region. Only the paternal allele is expressed for these genes...
August 24, 2016: Genes, Chromosomes & Cancer
Yu-Chien Kao, Yun-Shao Sung, Lei Zhang, Chun-Liang Chen, Shih-Chiang Huang, Cristina R Antonescu
Ossifying fibromyxoid tumor (OFMT) is an uncommon mesenchymal neoplasm of uncertain differentiation and intermediate malignant potential. Recurrent gene fusions involving either PHF1 or BCOR have been found in 85% of OFMT, including typical and malignant examples. As a subset of OFMT still lack known genetic abnormalities, we identified two OFMTs negative for PHF1 and BCOR rearrangements, which were subjected to transcriptome analysis for fusion discovery. The RNA sequencing found a novel CREBBP-BCORL1 fusion candidate in an axillary mass of a 51 year-old male and a KDM2A-WWTR1 in a thigh mass of a 36 year-old male...
August 18, 2016: Genes, Chromosomes & Cancer
Paula Marrano, Meredith S Irwin, Paul S Thorner
Amplification of the MYCN gene in neuroblastoma is associated with a poor prognosis and is considered to remain unchanged in post-treatment specimens and metastases. While heterogeneity of MYCN copy number in tumor cells has been reported, serial samples have only been studied in a limited way, and the biologic relevance of this finding is not well understood. We used in situ hybridization on paraffin sections of 102 specimens from 30 patients with MYCN-amplified neuroblastoma to determine MYCN copy number in the primary tumor, pre- and post-treatment, and in metastatic samples...
July 28, 2016: Genes, Chromosomes & Cancer
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