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Genes, Chromosomes & Cancer

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https://www.readbyqxmd.com/read/28545165/highly-recurrent-h3f3a-mutations-with-additional-epigenetic-regulator-alterations-in-giant-cell-tumor-of-bone
#1
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) for clinical diagnosis have not been assessed...
May 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28512763/impact-of-mlh1-expression-on-tumour-evolution-after-curative-surgical-tumour-resection-in-a-murine-orthotopic-xenograft-model-for-human-msi-colon-cancer
#2
Katy Meunier, Marianne Ferron, Claire Calmel, Jean-François Fléjou, Marc Pocard, Françoise Praz
Colorectal cancers (CRCs) displaying microsatellite instability (MSI) most often result from MLH1 deficiency. The aim of this study was to assess the impact of MLH1 expression per se on tumour evolution after curative surgical resection using a xenograft tumour model. Transplantable tumours established with the human MLH1-deficient HCT116 cell line and its MLH1-complemented isogenic clone, mlh1-3, were implanted onto the caecum of NOD/SCID mice. Curative surgical resection was performed at day 10 in half of the animals...
May 16, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28510357/kif11-silencing-and-inhibition-induces-chromosome-instability-that-may-contribute-to-cancer
#3
Yasamin Asbaghi, Laura L Thompson, Zelda Lichtensztejn, Kirk J McManus
Understanding the aberrant pathways that contribute to oncogenesis and identifying the altered genes involved in these pathways is a critical first step to develop effective strategies to better combat cancer. Chromosome instability (CIN) is an aberrant phenotype that occurs in ∼80% of all cancer types and is associated with aggressive tumors, the acquisition of multi-drug resistance and poor patient prognosis. Despite these associations however, the aberrant genes and molecular defects underlying CIN remain poorly understood...
May 16, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28510278/tfg-met-fusion-in-an-infantile-spindle-cell-sarcoma-with-neural-features
#4
Uta Flucke, Max M van Noesel, Marc Wijnen, Lei Zhang, Chun-Liang Chen, Yun-Shao Sung, Cristina R Antonescu
An increasing number of congenital and infantile sarcomas displaying a primitive, monomorphic spindle cell phenotype have been characterized to harbor recurrent gene fusions, including infantile fibrosarcoma and congenital spindle cell rhabdomyosarcoma. Here we report an unusual spindle cell sarcoma presenting as a large and infiltrative pelvic soft tissue mass in a 4-month-old girl, which revealed a novel TFG-MET gene fusion by whole transcriptome RNA sequencing. The tumor resembled the morphology of an infantile fibrosarcoma with both fascicular and patternless growth, however, it expressed strong S100 protein immunoreactivity, while lacking SOX10 staining and retaining H3K27me3 expression...
May 16, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28466543/mutation-patterns-in-genes-encoding-interferon-signaling-and-antigen-presentation-a-pan-cancer-survey-with-implications-for-the-use-of-immune-checkpoint-inhibitors
#5
Jan Budczies, Michael Bockmayr, Frederick Klauschen, Volker Endris, Stefan Fröhling, Peter Schirmacher, Carsten Denkert, Albrecht Stenzinger
Blockade of immune checkpoints has become a powerful tool in cancer medicine, which is effective across various solid cancer types and hematologic malignancies. While immunohistochemical detection of PD-L1 expression in tumor cells, immune cells, or both has been introduced as predictive biomarker in several clinical trials, shortcomings and limitations of this approach were quickly recognized. As a single biomarker is unlikely to adequately reflect the complex interplay between immune cells and cancer, various genetic determinants of therapy success, including microsatellite instability, mutational burden, and PD-L1 amplification, are being investigated...
May 2, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28437838/prognostic-relevance-of-mir-124-3p-and-its-target-tp53inp1-in-pediatric-ependymoma
#6
Yulia Margolin-Miller, Natalia Yanichkin, Keren Shichrur, Helen Toledano, Anat Ohali, Theophilos Tzaridis, Shalom Michowitz, Suzana Fichman-Horn, Meora Feinmesser, Stefan M Pfister, Hendrik Witt, Uri Tabori, Eric Bouffet, Vijay Ramaswamy, Cynthia Hawkins, Michael D Taylor, Isaac Yaniv, Smadar Avigad
Ependymoma is a malignant pediatric brain tumor, often incurable under the current treatment regimen. We aimed to evaluate the expression of microRNAs (miRs) in pediatric ependymoma tumors in an attempt to identify prognostic molecular markers which would lead to potential therapeutic targets. Following miR-array expression analysis, we focused on 9 miRs that correlated with relapse which were further validated by quantitative real-time PCR (qRT-PCR) in a cohort of 67 patients. Western blotting and immunohistochemistry were used to measure target protein expression in 20 and 34 tumor samples, respectively...
April 24, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28420034/a-fluorescence-in-situ-hybridization-based-screen-allows-rapid-detection-of-adverse-cytogenetic-alterations-in-patients-with-acute-myeloid-leukemia
#7
Nadine Sandhöfer, Klaus H Metzeler, Purvi M Kakadia, Zlatana Pasalic, Wolfgang Hiddemann, Michaela Neusser, Ortrud Steinlein, Michael Fiegl, Marion Subklewe, Karsten Spiekermann, Stefan K Bohlander, Stephanie Schneider, Jan Braess
In adult acute myeloid leukemia (AML), the karyotype of the leukemic cell is among the strongest prognostic factors. The Medical Research Council (MRC) and the European LeukemiaNet (ELN) classifications distinguish between favorable, intermediate and adverse cytogenetic risk patients who differ in their treatment response and overall survival. Conventional cytogenetic analyses are a mandatory component of AML diagnostics but they are time-consuming; therefore, therapeutic decisions in elderly patients are often delayed...
April 18, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28398700/differential-requirements-for-dna-repair-proteins-in-immortalized-cell-lines-using-alternative-lengthening-of-telomere-mechanisms
#8
Alaina R Martinez, Zeenia Kaul, Jeffrey D Parvin, Joanna Groden
Cancer cells require telomere maintenance to enable uncontrolled growth. Most often telomerase is activated, although a subset of human cancers are telomerase-negative and depend on recombination-based mechanisms known as ALT (Alternative Lengthening of Telomeres). ALT depends on proteins that are essential for homologous recombination, including BLM and the MRN complex, to extend telomeres. This study surveyed the requirement for requisite homologous recombination proteins, yet to be studied in human ALT cell lines, by protein depletion using RNA interference...
April 11, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28395118/etv6-runx1-like-acute-lymphoblastic-leukemia-a-novel-b-cell-precursor-leukemia-subtype-associated-with-the-cd27-cd44-immunophenotype
#9
Marketa Zaliova, Michaela Kotrova, Silvia Bresolin, Jan Stuchly, Jan Stary, Ondrej Hrusak, Geertruy Te Kronnie, Jan Trka, Jan Zuna, Martina Vaskova
We have shown previously that ETV6/RUNX1-positive acute lymphoblastic leukemia (ALL) is distinguishable from other ALL subtypes by CD27(pos) /CD44(low-neg) immunophenotype. During diagnostic immunophenotyping of 573 childhood B-cell precursor ALL (BCP-ALL), we identified eight cases with this immunophenotype among "B-other ALL" (BCP-ALL cases negative for routinely tested chromosomal/genetic aberrations). We aimed to elucidate whether these cases belong to the recently described ETV6/RUNX1-like ALL defined by the ETV6/RUNX1-specific gene expression profile (GEP), harboring concurrent ETV6 and IKZF1 lesions...
April 10, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28393427/hnrnpm-and-cd44s-expression-affects-tumor-aggressiveness-and-predicts-poor-prognosis-in-breast-cancer-with-axillary-lymph-node-metastases
#10
Huizhi Sun, Tieju Liu, Dongwang Zhu, Xueyi Dong, Fang Liu, Xiaohui Liang, Chen Chen, Bing Shao, Meili Wang, Yi Wang
HnRNPM is an essential splicing factor and its expression is closely correlated with invasion and metastasis of tumor cells. The CD44 cell adhesion molecule is aberrantly expressed in many breast tumors and CD44 splice variants have been implicated in specific oncogenic signaling pathways. To investigate the clinical significance and biological function of hnRNPM, immunohistochemistry, quantitative, and semiquantitative polymerase chain reaction, lentiviral transfection system and transwell invasion assays were performed...
April 10, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28316110/proteasome-ubiquitin-receptor-psmd4-is-an-amplification-target-in-breast-cancer-and-may-predict-sensitivity-to-parpi
#11
Marlena S Fejzo, Lee Anderson, Hsiao-Wang Chen, Enrique Guandique, Ondrej Kalous, Dylan Conklin, Dennis J Slamon
Poly (ADP-ribose) polymerase 1 (PARP1) is an enzyme involved in DNA repair under investigation as a chemotherapeutic target. Current randomized phase three trials of PARPi in metastatic breast cancer are limited to patients with documented BRCA1/2 mutations and no biomarker of PARPi beyond BRCA status is available. In an effort to identify novel biomarkers for PARP inhibition, we created a cell line (HCC1187/TALRES) resistant to the PARP1 inhibitor talazoparib. Herein we show by array-CGH that HCC1187/TALRES has a selective loss of the proteasome ubiquitin receptor PSMD4 amplicon resulting in significant down-regulation of PSMD4...
March 18, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28383167/hspa8-as-a-novel-fusion-partner-of-nr4a3-in-extraskeletal-myxoid-chondrosarcoma
#12
Milena Urbini, Annalisa Astolfi, Maria Abbondanza Pantaleo, Salvatore Serravalle, Angelo Paolo Dei Tos, Piero Picci, Valentina Indio, Marta Sbaraglia, Stefania Benini, Alberto Righi, Marco Gambarotti, Alessandro Gronchi, Chiara Colombo, Gian Paolo Dagrada, Silvana Pilotti, Roberta Maestro, Maurizio Polano, Maristella Saponara, Giuseppe Tarantino, Andrea Pession, Guido Biasco, Paolo Giovanni Casali, Silvia Stacchiotti
Extraskeletal myxoid chondrosarcoma (EMC) is a very rare sarcoma most often arising in the soft tissue. Rare EMC of the bone have been reported. EMC exhibits distinctive clinico-pathological and genetic features; however, despite the name, it lacks any feature of cartilaginous differentiation. EMC is characterized by the rearrangement of the NR4A3, which, in most cases (about 62-75%), is fused with EWSR1 and less frequently with other partners, including TAF15 (27%), TCF12 (4%), TFG, and FUS. We herein report the identification by whole-transcriptome sequencing of HSPA8 as a novel fusion partner of NR4A3 in a case of EMC...
July 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28379620/genome-wide-copy-number-variation-pattern-analysis-and-a-classification-signature-for-non-small-cell-lung-cancer
#13
Zhe-Wei Qiu, Jia-Hao Bi, Adi F Gazdar, Kai Song
The accurate classification of non-small cell lung carcinoma (NSCLC) into lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) is essential for both clinical practice and lung cancer research. Although the standard WHO diagnosis of NSCLC on biopsy material is rapid and economic, more than 13% of NSCLC tumors in the USA are not further classified. The purpose of this study was to analyze the genome-wide pattern differences in copy number variations (CNVs) and to develop a CNV signature as an adjunct test for the routine histopathologic classification of NSCLCs...
July 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28378892/distinct-prognostic-roles-and-heterogeneity-of-ttf1-copy-number-and-ttf1-protein-expression-in-non-small-cell-lung-cancer
#14
Katsuhiro Yoshimura, Yusuke Inoue, Kazutaka Mori, Yuji Iwashita, Tomoaki Kahyo, Akikazu Kawase, Masayuki Tanahashi, Hiroshi Ogawa, Naoki Inui, Kazuhito Funai, Kazuya Shinmura, Hiroshi Niwa, Takafumi Suda, Haruhiko Sugimura
Thyroid transcription factor 1 (TTF1) located on chromosome band 14q13.3 is an oncogene and a suppressor gene in non-small cell lung cancer (NSCLC). The prognostic relevance of TTF1 copy number alterations (CNAs) and their association with TTF1 protein expression are poorly understood. Here, we assessed TTF1 CNAs and protein expression using microarrays in a cohort of 636 NSCLC, including 423 adenocarcinoma (ADC) and 171 squamous cell carcinoma (SCC). In addition, fluorescent in situ hybridization and immunohistochemistry were performed...
July 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28295846/the-enigmatic-oncogene-and-tumor-suppressor-like-properties-of-rad54b-insights-into-genome-instability-and-cancer
#15
REVIEW
Erin N McAndrew, Kirk J McManus
One of the major challenges to the cell is to ensure genome stability, which can be compromised through endogenous errors or exogenous DNA damaging agents, such as ionizing radiation or common chemotherapeutic agents. To maintain genome stability the cell has a multifaceted line of defense, including cell cycle checkpoints and DNA damage repair pathways. RAD54B is involved in many of these pathways and thus exhibits a role in maintaining and repairing genome stability following DNA damage. RAD54B is involved in cell cycle regulation after DNA damage and participates in homologous recombinational repair, which ensures the precise repair of the most deleterious DNA lesions, double-stranded breaks...
July 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28295819/variants-in-bak1-spry4-and-gab2-are-associated-with-pediatric-germ-cell-tumors-a-report-from-the-children-s-oncology-group
#16
Erin L Marcotte, Nathan Pankratz, James F Amatruda, A Lindsay Frazier, Mark Krailo, Stella Davies, Jacqueline R Starr, Ching C Lau, Michelle Roesler, Erica Langer, Caroline Hallstrom, Anthony J Hooten, Jenny N Poynter
Germ cell tumors (GCT) are a rare form of childhood cancer that originate from the primordial germ cell. Recent genome-wide association studies (GWAS) have identified susceptibility alleles for adult testicular GCT (TGCT). We test whether these SNPs are associated with GCT in pediatric and adolescent populations. This case-parent triad study includes individuals with GCT diagnosed between ages 0 and 19. We evaluated 26 SNPs from GWAS of adult TGCT and estimated main effects for pediatric GCT within complete trios (N = 366) using the transmission disequilibrium test...
July 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28281307/integrated-expression-analysis-identifies-transcription-networks-in-mouse-and-human-gastric-neoplasia
#17
Zheng Chen, Mohammed Soutto, Bushra Rahman, Muhammad W Fazili, DunFa Peng, Maria Blanca Piazuelo, Heidi Chen, M Kay Washington, Yu Shyr, Wael El-Rifai
Gastric cancer (GC) is a leading cause of cancer-related deaths worldwide. The Tff1 knockout (KO) mouse model develops gastric lesions that include low-grade dysplasia (LGD), high-grade dysplasia (HGD), and adenocarcinomas. In this study, we used Affymetrix microarrays gene expression platforms for analysis of molecular signatures in the mouse stomach [Tff1-KO (LGD) and Tff1 wild-type (normal)] and human gastric cancer tissues and their adjacent normal tissue samples. Combined integrated bioinformatics analysis of mouse and human datasets indicated that 172 genes were consistently deregulated in both human gastric cancer samples and Tff1-KO LGD lesions (P < ...
July 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28236351/genomic-array-as-compared-to-karyotyping-in-myelodysplastic-syndromes-in-a-prospective-clinical-trial
#18
Marian J Stevens-Kroef, Daniel Olde Weghuis, Najat ElIdrissi-Zaynoun, Bert van der Reijden, Eline M P Cremers, Canan Alhan, Theresia M Westers, Heleen A Visser-Wisselaar, Dana A Chitu, Sonia M Cunha, Edo Vellenga, Saskia K Klein, Pierre Wijermans, Georgine E de Greef, M Ron Schaafsma, Petra Muus, Gert J Ossenkoppele, Arjan A van de Loosdrecht, Joop H Jansen
Karyotyping is considered as the gold standard in the genetic subclassification of myelodysplastic syndrome (MDS). Oligo/SNP-based genomic array profiling is a high-resolution tool that also enables genome wide analysis. We compared karyotyping with oligo/SNP-based array profiling in 104 MDS patients from the HOVON-89 study. Oligo/SNP-array identified all cytogenetically defined genomic lesions, except for subclones in two cases and balanced translocations in three cases. Conversely, oligo/SNP-based genomic array profiling had a higher success rate, showing 55 abnormal cases, while an abnormal karyotype was found in only 35 patients...
July 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28233365/etv-transcriptional-upregulation-is-more-reliable-than-rna-sequencing-algorithms-and-fish-in-diagnosing-round-cell-sarcomas-with-cic-gene-rearrangements
#19
Yu-Chien Kao, Yun-Shao Sung, Chun-Liang Chen, Lei Zhang, Brendan C Dickson, David Swanson, Sumathi Vaiyapuri, Farida Latif, Abdullah Alholle, Shih-Chiang Huang, Jason L Hornick, Cristina R Antonescu
CIC rearrangements have been reported in two-thirds of EWSR1-negative small blue round cell tumors (SBRCTs). However, a number of SBRCTs remain unclassified despite exhaustive analysis. Fourteen SBRCTs lacking driver genetic events by RNA sequencing (RNAseq) analysis were collected. Unsupervised hierarchical clustering was performed using samples from our RNAseq database, including 13 SBRCTs with non-CIC genetic abnormalities and 2 CIC-rearranged angiosarcomas among others. Remarkably, all 14 study cases showed high mRNA levels of ETV1/4/5, and by unsupervised clustering most grouped into a distinct cluster, separate from other tumors...
June 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28233357/promotion-of-invasion-by-mutant-ras-is-dependent-on-activation-of-the-wasf3-metastasis-promoter-gene
#20
Yong Teng, Lambert Ngoka, John K Cowell
Metastasis represents an end stage in the evolution of cancer progression and has been related to specific genetic pathways. Overexpression of mutant RAS in particular appears to promote invasion and metastasis, although exactly how this occurs has not been well characterized. It was previously showed that activation of the WASF3 protein regulates actin cytoskeleton dynamics that promote invasion. In this report, how WASF3 overexpression interacts with mutant RAS to increase invasion and metastasis was investigated...
June 2017: Genes, Chromosomes & Cancer
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