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Genes, Chromosomes & Cancer

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https://www.readbyqxmd.com/read/29127730/comprehensive-study-of-three-novel-cases-of-tfeb-amplified-renal-cell-carcinoma-and-review-of-the-literature-evidence-for-a-specific-entity-with-poor-outcome
#1
Lionel Mendel, Damien Ambrosetti, Yohan Bodokh, Mélanie Ngo-Mai, Matthieu Durand, Cécile Simbsler-Michel, Mickael Delhorbe, Jean Amiel, Florence Pedeutour
The first case of TFEB-amplified renal cell carcinoma was published in 2014. Since then, 29 additional cases have been described. The prognostic and therapeutic implications of this rare entity remain to be determined. We describe here the clinical, histological and genetic features of three novel cases, as well as the first complete literature review. Four tumors were examined from three patients selected from the large collection of genetically characterized renal tumors in our institution. The pathological and immunohistochemical features were centrally reviewed by a uropathologist...
November 11, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29119645/high-sensitivity-of-fish-analysis-in-detecting-homozygous-smarcb1-deletions-in-poorly-differentiated-chordoma-a-clinicopathologic-and-molecular-study-of-9-cases
#2
Adepitan A Owosho, Lei Zhang, Marc K Rosenblum, Cristina R Antonescu
Poorly differentiated chordomas (PDCs) represent a rare subset of notochordal neoplasms, affecting primarily children and associated with an aggressive outcome. In contrast to conventional chordomas, PDC show solid growth and increased cellularity, cytologic atypia, and mitotic activity. Recent studies have shown that PDCs are characterized by recurrent deletions encompassing the SMARCB1 locus, resulting in consistent loss of nuclear SMARCB1 expression. Thus PDC joined the expanding family of SMARCB1-deficient tumors characterized by various SMARCB1 structural abnormalities, ranging from large homozygous deletions to small intragenic mutations...
November 9, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29119627/colorectal-cancer-susceptibility-loci-as-predictive-markers-of-rectal-cancer-prognosis-after-surgery
#3
Yue Hu, Jochen Gaedcke, Georg Emons, Tim Beissbarth, Marian Grade, Peter Jo, Meredith Yeager, Stephen J Chanock, Hendrik Wolff, Jordi Camps, B Michael Ghadimi, Thomas Ried
To understand the molecular mechanism of rectal cancer and develop markers for disease prognostication, we generated and explored a dataset from 243 rectal cancer patients by gene expression microarray analysis of cancer samples and matched controls, and SNP-arrays of germline DNA. We found that two of the loci most strongly linked with colorectal cancer (CRC) risk, 8q24 (upstream of MYC) and 18q21 (in the intron of SMAD7), as well as 20q13 (in the intron of LAMA5), are tightly associated with the prognosis of rectal cancer patients...
November 9, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29057546/clinical-features-and-biological-implications-of-different-u2af1-mutation-types-in-myelodysplastic-syndromes
#4
Bing Li, Jinqin Liu, Yujiao Jia, Jingya Wang, Zefeng Xu, Tiejun Qin, Zhongxun Shi, Zhen Song, Shuailing Peng, Huijun Huang, Liwei Fang, Hongli Zhang, Lijuan Pan, Naibo Hu, Shiqiang Qu, Yue Zhang, Jian Wu, Na Liu, Kun Ru, Gang Huang, Zhijian Xiao
U2AF1 mutations (U2AF1MT) occur commonly in myelodysplastic syndromes (MDS) without ring sideroblasts. The aim of this study was to investigate the clinical and biological implications of different U2AF1 mutation types in MDS. We performed targeted gene sequencing in a cohort of 511 MDS patients. Eighty-six patients (17%) were found to have U2AF1MT, which occurred more common in younger patients (P=0.001) and represented ancestral lesions in a substantial proportion (71%) of cases. ASXL1MT and isolated +8 were significantly enriched in U2AF1MT-positive cases, whereas TP53MT, SF3B1MT and complex karyotypes were inversely associated with U2AF1MT...
October 23, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29052312/bleomycin-induced-chromosomal-damage-and-shortening-of-telomeres-in-peripheral-blood-lymphocytes-of-incident-cancer-patients
#5
Michal Kroupa, Zdenka Polivkova, Sivaramakrishna Rachakonda, Michaela Schneiderova, Sona Vodenkova, Tomas Buchler, Katerina Jiraskova, Marketa Urbanova, Ludmila Vodickova, Kari Hemminki, Rajiv Kumar, Pavel Vodicka
Disruption of genomic integrity due to deficient DNA repair capacity and telomere shortening constitute hallmarks of malignant diseases. Incomplete or deficient repair of DNA double-strand breaks (DSB) is manifested by chromosomal aberrations (CAs) and their frequency reflects inter-individual differences of response to exposure to mutagenic compounds. In this study, we investigated chromosomal integrity in peripheral blood lymphocytes (PBL) from newly diagnosed cancer patients, including 47 breast (BC) and 44 colorectal cancer (CRC) patients and 90 matched healthy controls...
October 20, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29044880/targeted-deep-sequencing-of-effusion-cytology-samples-is-feasible-informs-spatiotemporal-tumor-evolution-and-has-clinical-and-diagnostic-utility
#6
Jonas Leichsenring, Anna-Lena Volckmar, Martina Kirchner, Daniel Kazdal, Mark Kriegsmann, Fabian Stögbauer, Teresa Bockmayr, Frederick Klauschen, Felix J F Herth, Roland Penzel, Arne Warth, Peter Schirmacher, Volker Endris, Albrecht Stenzinger
During the course of disease, many cancer patients eventually present with metastatic disease including peritoneal or pleural spread. In this context, cytology specimens derived from ascites or pleural effusion may help to differentiate malignant from benign conditions and sometimes yield diagnosis of a malignancy. However, even when supported by immunohistochemistry, cytological interpretation can be challenging, especially if tumor cellularity is low. Here, we investigated whether targeted deep sequencing of formalin-fixed and paraffin embedded (FFPE) cytology specimens of cancer patients is feasible, and has diagnostic and clinical impact...
October 16, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29044863/identification-of-somatic-genetic-alterations-in-ovarian-clear-cell-carcinoma-with-next-generation-sequencing
#7
Yusuke Shibuya, Hideki Tokunaga, Sakae Saito, Kazurou Shimokawa, Fumiki Katsuoka, Li Bin, Kaname Kojima, Masao Nagasaki, Masayuki Yamamoto, Nobuo Yaegashi, Jun Yasuda
Ovarian clear cell carcinoma (OCCC) is the most refractory subtype of ovarian cancer and more prevalent in Japanese than Caucasians (25% and 5% of all ovarian cancer, respectively). The aim of this study is to discover the genomic alterations that may cause OCCC and effective molecular targets for chemotherapy. Paired genomic DNAs of 48 OCCC tissues and corresponding non-cancerous tissues were extracted from formalin-fixed, paraffin embedded specimens collected between 2007 and 2015 at Tohoku University Hospital...
October 16, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28960585/loss-of-heterozygosity-and-uniparental-disomy-of-chromosome-region-10q23-3-26-3-in-glioblastoma
#8
Ekaterina A Alekseeva, Ekaterina B Kuznetsova, Alexander S Tanas, Evgeny V Prozorenko, Anton M Zaytsev, Mikhail I Kurzhupov, Olga N Kirsanova, Viktoria V Rudenko, Vladimir V Strelnikov, Dmitry V Zaletaev
Glioblastoma is the most frequent and aggressive brain tumor in the adult population. Loss of heterozygosity (LOH) at markers of the long arm of chromosome 10 is the most common genetic alteration in glioblastoma, being detectable in up to 80% of cases. We have tested 124 glioblastoma samples for LOH by microsatellite analysis of the 10q23.3-26.3 region which contains the cancer related genes PTEN, FGFR2, MKI67, and MGMT. Then, a real-time quantitative microsatellite analysis (QuMA) was used to qualitatively estimate the change in copy number of this region in the samples with LOH...
September 27, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28940826/trichostatin-a-preferentially-reverses-the-upregulation-of-gene-expression-levels-induced-by-gain-of-chromosome-7-in-colorectal-cancer-cell-lines
#9
Floryne O Buishand, Eric Cardin, Yue Hu, Thomas Ried
Epithelial cancers are defined by a tumor-specific distribution of chromosomal aneuploidies that are maintained when cells metastasize and are conserved in cell lines derived from primary tumors. Correlations between genomic copy number and gene expression have been observed for different tumors including, colorectal (CRC), breast, and pancreatic cancer. These ploidy-driven transcriptional deregulations are characterized by low-level expression changes of most genes on the affected chromosomes. The emergence of these aberrations at an early stage of tumorigenesis and the strong selection for the maintenance of these aneuploidies suggest that aneuploidy-dependent transcriptional deregulations might contribute to cellular transformation and maintenance of the malignant phenotype...
September 23, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28913947/extreme-chromosome-17-copy-number-instability-is-a-prognostic-factor-in-patients-with-gastroesophageal-adenocarcinoma-a-retrospective-cohort-study
#10
Jacqueline E Birkness, Neal G Spada, Caitlyn Miller, James D Luketich, Katie S Nason, Weijing Sun, Jon M Davison
Gastric and esophageal cancers frequently show genomic instability and aneuploidy. Chromosomal copy number instability (CIN) is a form of genomic instability that exerts pleiotropic effects on cellular biology and is a source of genetic heterogeneity in a population of cells. CIN results in cell-to-cell variation in chromosome copy number which can be detected and quantified by fluorescence in situ hybridization (FISH). CIN is a biomarker associated with differential response to a number of chemotherapy compounds...
September 14, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28891274/breast-cancer-risk-and-germline-genomic-profiling-of-women-with-neurofibromatosis-type-1-who-developed-breast-cancer
#11
Xia Wang, Jamie K Teer, Renee N Tousignant, Albert M Levin, David Boulware, Dhananjay A Chitale, Brandon M Shaw, Zhihua Chen, Yonghong Zhang, Jaishri O Blakeley, Maria T Acosta, Ludwine M Messiaen, Bruce R Korf, Michael A Tainsky
NF1 mutations predispose to neurofibromatosis type 1 (NF1) and women with NF1 have a moderately elevated risk for breast cancer, especially under age 50. Germline genomic analysis may better define the risk so screening and prevention can be applied to the individuals who benefit the most. Survey conducted in several neurofibromatosis clinics in the United States has demonstrated a 17.2% lifetime risk of breast cancer in women affected with NF1. Cumulated risk to age 50 is estimated to be 9.27%. For genomic profiling, fourteen women with NF1 and a history of breast cancer were recruited and underwent whole exome sequencing (WES), targeted genomic DNA based and RNA-based analysis of the NF1 gene...
September 10, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28857319/transcription-factors-intricate-players-of-the-bone-morphogenetic-protein-signaling-pathway
#12
REVIEW
M Ampuja, Anne Kallioniemi
Bone morphogenetic proteins (BMPs) are a family of growth factors, some of which are known by the name growth and differentiation factor (GDF). BMPs were discovered in the 1960s in an attempt to find factors capable of inducing bone formation. By the end of 1980s, several different BMPs had been found and to date, around 20 members are known. Together with TGFβ, nodal, and activins, they comprise the TGFβ superfamily. BMPs are known to regulate cell fate both in development and adult tissues, and as such they are also involved in many disease states...
August 31, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28845532/mutational-analysis-using-sanger-and-next-generation-sequencing-in-sporadic-spindle-cell-hemangiomas-a-study-of-19-cases
#13
Roel W Ten Broek, Elise M Bekers, Wendy W J de Leng, Eric Strengman, Bastiaan B J Tops, Heinz Kutzner, Jan Willem Leeuwis, Joost M van Gorp, David H Creytens, Thomas Mentzel, Paul J van Diest, Astrid Eijkelenboom, Uta Flucke
Spindle cell hemangioma (SCH) is a distinct vascular soft-tissue lesion characterized by cavernous blood vessels and a spindle cell component mainly occurring in the distal extremities of young adults. The majority of cases harbor heterozygous mutations in IDH1/2 sporadically or rarely in association with Maffucci syndrome. However, based on mosaicism and accordingly a low percentage of lesional cells harboring a mutant allele, detection can be challenging. We tested 19 sporadic SCHs by Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), conventional next generation sequencing (NGS), and NGS using a single molecule molecular inversion probes (smMIP)-based library preparation to compare their diagnostic value...
August 28, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28675510/the-co-regulatory-networks-of-tumor-suppressor-genes-oncogenes-and-mirnas-in-colorectal-cancer
#14
Martha L Slattery, Jennifer S Herrick, Lila E Mullany, Wade S Samowitz, John R Sevens, Lori Sakoda, Roger K Wolff
Tumor suppressor genes (TSGs) and oncogenes (OG) are involved in carcinogenesis. MiRNAs also contribute to cellular pathways leading to cancer. We use data from 217 colorectal cancer (CRC) cases to evaluate differences in TSGs and OGs expression between paired CRC and normal mucosa and evaluate how TSGs and OGs are associated with miRNAs. Gene expression data from RNA-Seq and miRNA expression data from Agilent Human miRNA Microarray V19.0 were used. We focus on genes most strongly associated with CRC (fold change (FC) of ≥1...
November 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28736828/genomic-and-metabolic-characterization-of-a-chromophobe-renal-cell-carcinoma-cell-line-model-uok276
#15
Youfeng Yang, Cathy D Vocke, Christopher J Ricketts, Darmood Wei, Hesed M Padilla-Nash, Martin Lang, Carole Sourbier, J Keith Killian, Shawna L Boyle, Robert Worrell, Paul S Meltzer, Thomas Ried, Maria J Merino, Adam R Metwalli, W Marston Linehan
Chromophobe renal cell carcinoma (ChRCC) represents 5% of all RCC cases and frequently demonstrates multiple chromosomal losses and an indolent pattern of local growth, but can demonstrate aggressive features and resistance to treatment in a metastatic setting. Cell line models are an important tool for the investigation of tumor biology and therapeutic drug efficacy. Currently, there are few ChRCC-derived cell lines and none is well characterized. This study characterizes a novel ChRCC-derived cell line model, UOK276...
October 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28639284/soft-tissue-angiofibroma-clinicopathologic-immunohistochemical-and-molecular-analysis-of-14-cases
#16
Elise M Bekers, Patricia Jta Groenen, Marian Aj Verdijk, Winny L Raaijmakers-van Geloof, Paul Roepman, Robert Vink, Nathalie Db Gilhuijs, Joost M van Gorp, Judith Vmg Bovée, David H Creytens, Adrienne M Flanagan, Albert Jh Suurmeijer, Thomas Mentzel, Elsa Arbajian, Uta Flucke
Soft tissue angiofibroma is rare and has characteristic histomorphological and genetic features. For diagnostic purposes, there are no specific antibodies available. Fourteen lesions (6 females, 8 males; age range 7-67 years) of the lower extremities (12) and trunk (2) were investigated by immunohistochemistry, including for the first time NCOA2. NCOA2 was also tested in a control group of other spindle cell lesions. The known fusion-genes (AHRR-NCOA2 and GTF2I-NCOA2) were examined using RT-PCR in order to evaluate their diagnostic value...
October 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28639280/mutational-profiles-of-brenner-tumors-show-distinctive-features-uncoupling-urothelial-carcinomas-and-ovarian-carcinoma-with-transitional-cell-histology
#17
Nicole Pfarr, Silvia Darb-Esfahani, Jonas Leichsenring, Eliane Taube, Melanie Boxberg, Ioana Braicu, Moritz Jesinghaus, Roland Penzel, Volker Endris, Aurelia Noske, Wilko Weichert, Peter Schirmacher, Carsten Denkert, Albrecht Stenzinger
Brenner tumors (BT) are rare ovarian tumors encompassing benign, borderline, and malignant variants. While the histopathology of BTs and their clinical course is well described, little is known about the underlying genetic defects. We employed targeted next generation sequencing to analyze the mutational landscape in a cohort of 23 BT cases (17 benign, 2 borderline, and 4 malignant) and 3 ovarian carcinomas with transitional cell histology (TCC). Copy number variations (CNV) were validated by fluorescence in-situ hybridization (FISH) and quantitative PCR-based copy number assays...
October 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28597942/copy-number-alterations-determined-by-single-nucleotide-polymorphism-array-testing-in-the-clinical-laboratory-are-indicative-of-gene-fusions-in-pediatric-cancer-patients
#18
Tracy M Busse, Jacquelyn J Roth, Donna Wilmoth, Luanne Wainwright, Laura Tooke, Jaclyn A Biegel
Gene fusions resulting from structural rearrangements are an established mechanism of tumorigenesis in pediatric cancer. In this clinical cohort, 1,350 single nucleotide polymorphism (SNP)-based chromosomal microarrays from 1,211 pediatric cancer patients were evaluated for copy number alterations (CNAs) associated with gene fusions. Karyotype or fluorescence in situ hybridization studies were performed in 42% of the patients. Ten percent of the bone marrow or solid tumor specimens had SNP array-associated CNAs suggestive of a gene fusion...
October 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28545165/highly-recurrent-h3f3a-mutations-with-additional-epigenetic-regulator-alterations-in-giant-cell-tumor-of-bone
#19
Koichi Ogura, Fumie Hosoda, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Shoko Ohashi, Hirofumi Rokutan, Erina Takai, Shinichi Yachida, Akira Kawai, Sakae Tanaka, Tatsuhiro Shibata
Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next-generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) samples for clinical diagnosis have not been assessed...
October 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28560743/occurrence-of-bap1-germline-mutations-in-cutaneous-melanocytic-tumors-with-loss-of-bap1-expression-a-pilot-study
#20
Odile Cabaret, Emilie Perron, Brigitte Bressac-de Paillerets, Nadem Soufir, Arnaud de la Fouchardière
Melanocytic BAP1-associated intradermal tumors (MBAITs) can either be sporadic or associated with a cancer-predisposition syndrome. In this study we explored the clinical status of 136 patients in which at least one MBAIT was found. 49/136 (36%) of them gave their signed consent for an oncogenetic BAP1 blood test. 28/136 patients (20%) diagnosed with an MBAIT had other MBAITs and/or a personal or familial history of BAP1-related cancers that could clinically designate them as potential carriers of a BAP1 germline mutation...
September 2017: Genes, Chromosomes & Cancer
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