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Genes, Chromosomes & Cancer

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https://www.readbyqxmd.com/read/28063196/asxl2-mutations-are-frequently-found-in-pediatric-aml-patients-with-t-8-21-runx1-runx1t1-and-associated-with-a-better-prognosis
#1
Genki Yamato, Norio Shiba, Kenichi Yoshida, Yuichi Shiraishi, Yusuke Hara, Kentaro Ohki, Jun Okubo, Haruna Okuno, Kenichi Chiba, Hiroko Tanaka, Akitoshi Kinoshita, Hiroshi Moritake, Nobutaka Kiyokawa, Daisuke Tomizawa, Myoung-Ja Park, Manabu Sotomatsu, Takashi Taga, Souichi Adachi, Akio Tawa, Keizo Horibe, Hirokazu Arakawa, Satoru Miyano, Seishi Ogawa, Yasuhide Hayashi
ASXL2 is an epigenetic regulator involved in polycomb repressive complex regulation or recruitment. Clinical features of pediatric AML patients with ASXL2 mutations remain unclear. Thus, we investigated frequencies of ASXL1 and ASXL2 mutations, clinical features of patients with these mutations, correlations of these mutations with other genetic alterations including BCOR/BCORL1 and cohesin complex component genes, and prognostic impact of these mutations in 369 pediatric patients with de novo AML (0-17 years)...
January 7, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28063190/prognostic-impact-of-specific-molecular-profiles-in-pediatric-acute-megakaryoblastic-leukemia-in-non-down-syndrome
#2
Yusuke Hara, Norio Shiba, Kentaro Ohki, Ken Tabuchi, Genki Yamato, Myoung-Ja Park, Daisuke Tomizawa, Akitoshi Kinoshita, Akira Shimada, Hirokazu Arakawa, Akiko M Saito, Nobutaka Kiyokawa, Akio Tawa, Keizo Horibe, Takashi Taga, Souichi Adachi, Tomohiko Taki, Yasuhide Hayashi
Pediatric acute megakaryoblastic leukemia with non-Down syndrome (AMKL) is a unique subtype of acute myeloid leukemia (AML). Novel CBFA2T3-GLIS2 and NUP98-KDM5A fusions recurrently found in AMKL were recently reported as poor prognostic factors. However, their detailed clinical and molecular characteristics in patients treated with recent improved therapies remain uncertain. We analyzed molecular features of 44 AMKL patients treated on two recent Japanese AML protocols, the AML99 and AML-05 trials. We identified CBFA2T3-GLIS2, NUP98-KDM5A, RBM15-MKL1, and KMT2A rearrangements in 12 (27%), 4 (9%), 2 (5%), and 3 (7%) patients, respectively...
January 7, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28063177/comparable-clinical-outcomes-in-patients-with-her2-mutant-and-egfr-mutant-lung-adenocarcinomas
#3
Chien-Hung Gow, Hou-Tai Chang, Chor-Kuan Lim, Chao-Yu Liu, Jin-Shing Chen, Jin-Yuan Shih
HER2 is a major proliferative driver in lung cancer. HER2 gene aberrations impact the prognosis of lung adenocarcinoma (ADC). A one-step reverse transcription-polymerase chain reaction was performed using RNA samples from 888 Asian lung cancer patients to detect HER2, EGFR, KRAS, ALK, and ROS1 mutations. The demographic data and treatment outcomes of HER2 mutation-positive lung ADC patients were analyzed and compared to those with HER2 mutation-negative tumors. HER2 mutation was identified in 40 (4.5%) lung ADC patients...
January 7, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28052524/cross-species-analysis-of-the-canine-and-human-bladder-cancer-transcriptome-and-exome
#4
Stephen A Ramsey, Tanjin Xu, Cheri Goodall, Adelaide C Rhodes, Amita Kashyap, Jun He, Shay Bracha
We investigated the correspondence between transcriptome and exome alterations in canine bladder cancer and the correspondence between these alterations and cancer-driving genes and transcriptional alterations in human bladder cancer. We profiled canine bladder tumors using mRNA-seq and exome-seq and used a comparative oncology approach to investigate: (i) the similarity of transcriptional alterations in bladder cancer vs. normal bladder, in humans and canines, at the levels of gene functions, pathways, and cytogenetic regions; and (ii) the extent to which genic mutations in canine bladder cancer are associated with known cancer mutations (from human) as well as alterations in transcript levels in the canine tumor...
January 3, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28035718/thsd7a-expression-in-human-cancer
#5
Phillip R Stahl, Elion Hoxha, Thorsten Wiech, Cornelia Schröder, Ronald Simon, Rolf A K Stahl
We recently described a case of a Thrombospondin Type-1 Domain containing 7A (THSD7A) associated membranous nephropathy in a female patient who was synchronously suffering from a THSD7A-positive malignancy. We here investigated the role of THSD7A as a new potential tumor antigen by evaluating over 20,000 tissue spots in more than 70 different tumor entities by immunohistochemistry using tissue microarrays. THSD7A expression was highly variable in different neoplasias with differing staining patterns. Both gain and loss of THSD7A expression compared to expression status in non-tumor tissue were linked to tumor-specific markers in the different tumor entities and were of prognostic value...
December 30, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28033648/characterisation-of-the-genomic-landscape-of-crlf2-rearranged-acute-lymphoblastic-leukemia
#6
Lisa J Russell, Lisa Jones, Amir Enshaei, Stefano Tonin, Sarra L Ryan, Jeyanthy Eswaran, Sirintra Nakjang, Elli Papaemmanuil, Jose M C Tubio, Adele K Fielding, Ajay Vora, Peter J Campbell, Anthony V Moorman, Christine J Harrison
Deregulated expression of the type I cytokine receptor, CRLF2, is observed in 5-15% of precursor B-cell acute lymphoblastic leukaemia (B-ALL). We aimed to determine the clinical and genetic landscape of those with IGH-CRLF2 or P2RY8-CRLF2 (CRLF2-r) using multiple genomic approaches. Clinical and demographic features of CRLF2-r patients were characteristic of B-ALL. Patients with IGH-CRLF2 were older (14yrs v 4yrs, P<0.001), while the incidence of CRLF2-r among Down syndrome patients was high (50/161, 31%)...
December 29, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27997717/sequential-analysis-of-18-genes-in-polycythemia-vera-and-essential-thrombocythemia-reveals-an-association-between-mutational-status-and-clinical-outcome
#7
Damien Luque Paz, Aurélie Chauveau, Françoise Boyer, Caroline Buors, Laura Samaison, Laurane Cottin, Valérie Seegers, Claude Férec, Cédric Le Maréchal, Paul Gueguen, Eric Lippert, Jean-Christophe Ianotto, Valérie Ugo
Philadelphia-negative classical myeloproliferative neoplasms (MPN) are clonal diseases characterized by driver mutations of JAK2, MPL, or CALR. Additional mutations may occur in epigenetic regulators, signaling, or splicing genes that may be useful in the prognostic assessment of MPN patients. In primary myelofibrosis, molecular-based prognostic scoring systems have been recently proposed, but few data are available to date for polycythemia vera (PV) and essential thrombocythemia (ET). In this study, we used a next generation sequencing-based 18-gene panel in 50 JAK2V617F positive PV and JAK2V617F positive ET patients from an institutional cohort investigated at diagnosis and at 3-year follow-up (3y)...
December 20, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27997714/genomic-and-transcriptomic-analysis-of-imatinib-resistance-in-gastrointestinal-stromal-tumors
#8
Tsuyoshi Takahashi, Asmaa Elzawahry, Sachiyo Mimaki, Eisaku Furukawa, Rie Nakatsuka, Hiromi Nakamura, Takahiko Nishigaki, Satoshi Serada, Tetsuji Naka, Seiichi Hirota, Tatsuhiro Shibata, Katsuya Tsuchihara, Toshirou Nishida, Mamoru Kato
Gastrointestinal stromal tumors represent the most common mesenchymal tumor of the digestive tract, driven by gain-of-function mutations in KIT. Despite its proven benefits, half of the patients treated with imatinib show disease progression within 2 years due to secondary resistance mutations in KIT. It remains unclear how the genomic and transcriptomic features change during the acquisition of imatinib resistance. Here, we performed exome sequencing and microarray transcription analysis for four imatinib-resistant cell lines and one cell line briefly exposed to imatinib...
December 20, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27925331/the-mirna-landscape-of-colorectal-polyps
#9
Martha L Slattery, Jennifer S Herrick, Roger K Wolff, Lila E Mullany, John R Stevens, Wade Samowitz
The genomic landscape of adenomas and polyps may help define disease pathways. Expression of miRNAs in adenomas and polyps may importantly contribute to these pathways. We evaluated miRNA expression in 293 polyp-normal colorectal mucosa pairs. Polyps were classified as either adenomatous polyp (AD), hyperplastic polyp (HP), or sessile serrated polyp (SSP). We compared these miRNA expression profiles in polyps to miRNA expression in microsatellite unstable (MSI) and stable (MSS) tumors. A False Discovery Rate (FDR) of 0...
December 7, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27914109/bcor-upregulation-in-a-poorly-differentiated-synovial-sarcoma-with-ss18l1-ssx1-fusion-a-pathologic-and-molecular-pitfall
#10
Yu-Chien Kao, Yun-Shao Sung, Lei Zhang, Samuel Kenan, Samuel Singer, William D Tap, David Swanson, Brendan C Dickson, Cristina R Antonescu
The diagnosis of poorly differentiated synovial sarcoma (PD-SS) may be challenging due to overlapping morphologic features with other undifferentiated round cell sarcomas (URCS). Particularly relevant is the histologic overlap and shared BCOR overexpression between a subset of SS and URCS with various BCOR genetic abnormalities. Here we report a case of PD-SS lacking the canonical SS18-SSX gene fusion, but showing strong BCOR immunoreactivity and BCOR gene abnormalities by FISH which were misinterpreted as a URCS with BCOR gene rearrangements...
December 3, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27859935/single-nucleotide-polymorphisms-within-micrornas-microrna-targets-and-microrna-biogenesis-genes-and-their-impact-on-colorectal-cancer-survival
#11
Lila E Mullany, Jennifer S Herrick, Roger K Wolff, Martha L Slattery
We have shown that single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, miRNA target genes, and miRNA biogenesis genes minimally contribute to colon cancer risk. It is possible that these SNPs alter survival. We analyzed 565 SNPs in or adjacent to microRNAs, target genes, or biogenesis genes, using 1115 cases and 1173 controls; 837 cases had survival information. We tested SNPs for associations with colorectal cancer (CRC) survival using a Cox proportional hazard model adjusting for age, study center, gender, AJCC disease stage, and MSI tumor status...
November 18, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27910166/anchored-multiplex-pcr-for-targeted-next-generation-sequencing-reveals-recurrent-and-novel-usp6-fusions-and-upregulation-of-usp6-expression-in-aneurysmal-bone-cyst
#12
Natalya V Guseva, Omar Jaber, Munir R Tanas, Aaron A Stence, Ramakrishna Sompallae, Jenna Schade, Allison N Fillman, Benjamin J Miller, Aaron D Bossler, Deqin Ma
Primary aneurysmal bone cyst (ABC) is a neoplastic process due to recurrent translocations involving the USP6 gene. By fluorescence in situ hybridization, up to 69% of primary ABCs harbored USP6 translocations; no USP6 translocation was found in secondary ABC or giant cell tumor of bone (GCT). GCT can recur locally, metastasize to the lungs in some cases, and rarely undergo malignant transformation. Differentiating primary ABC from its mimics is important for treatment and prognosis. We evaluated USP6 fusion and expression in 13 cases of primary and 1 case of secondary ABC, and 9 cases of GCT using nucleic acid extracted from formalin-fixed, paraffin-embedded tissue and a next generation sequencing (NGS)-based assay...
November 7, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27870151/ph-like-acute-lymphoblastic-leukemia-with-a-novel-pax5-kidins220-fusion-transcript
#13
Kenichi Sakamoto, Toshihiko Imamura, Takuyo Kanayama, Mio Yano, Daisuke Asai, Takao Deguchi, Yoshiko Hashii, Akihiko Tanizawa, Yusei Ohshima, Nobutaka Kiyokawa, Keizo Horibe, Atsushi Sato
Although "paired box 5" (PAX5)-related fusion genes are well documented in childhood B-cell precursor acute lymphoblastic leukemia (ALL), these types of fusion with the exception of PAX5-JAK2 are rarely seen in patients with gene expression profiles similar to those of BCR-ABL1 (Philadelphia)-positive ALL (Ph-like ALL). We report a novel fusion of the genes PAX5 and "kinase D-interacting substrate of 220 kDa" (KIDINS220, also known as ARMS) in a Ph-like ALL. As PAX5 is a master regulator of B-lymphocyte differentiation, PAX5 rearrangements induce a differentiation block in B lymphocytes...
November 7, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27792260/targeted-next-generation-sequencing-enables-reliable-detection-of-her2-erbb2-status-in-breast-cancer-and-provides-ancillary-information-of-clinical-relevance
#14
Nicole Pfarr, Roland Penzel, Volker Endris, Clemens Lier, Christa Flechtenmacher, Anna-Lena Volckmar, Martina Kirchner, Jan Budczies, Jonas Leichsenring, Esther Herpel, Aurelia Noske, Wilko Weichert, Andreas Schneeweiss, Peter Schirmacher, Hans-Peter Sinn, Albrecht Stenzinger
HER2-positive breast cancers are a heterogeneous group of tumors, which share amplification and overexpression of HER2. In routine diagnostics, the HER2 (ERBB2) status is currently assessed by immunohistochemistry (IHC) and in-situ hybridization (ISH). Data on targeted next-generation sequencing (NGS) approaches that could be used to determine the HER2 status are sparse. Employing two breast cancer-related gene panels, we performed targeted NGS of 41 FFPE breast cancers for which full pathological work-up including ISH and IHC results were available...
October 28, 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27718540/germline-bap1-alterations-in-familial-uveal-melanoma
#15
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 H 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...
February 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27717206/epigenetic-silencing-of-mir-200c-in-breast-cancer-is-associated-with-aggressiveness-and-is-modulated-by-zeb1
#16
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)...
February 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27717083/t-cell-acute-lymphoblastic-leukemia-in-infants-has-distinct-genetic-and-epigenetic-features-compared-to-childhood-cases
#17
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...
February 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27637012/prognostic-significance-of-p2ry8-crlf2-and-crlf2-overexpression-may-vary-across-risk-subgroups-of-childhood-b-cell-acute-lymphoblastic-leukemia
#18
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...
February 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27636706/familial-solitary-chondrosarcoma-resulting-from-germline-ext2-mutation
#19
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...
February 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27636375/multiple-biological-processes-may-be-associated-with-tumorigenesis-under-nup88-overexpressed-condition
#20
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...
February 2017: Genes, Chromosomes & Cancer
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