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Genes, Chromosomes & Cancer

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https://www.readbyqxmd.com/read/29318692/promoter-hypermethylation-inactivate-tumour-suppressor-fam134b-and-is-associated-with-poor-prognosis-in-colorectal-cancer
#1
Farhadul Islam, Vinod Gopalan, Suja Pillai, Cu-Tai Lu, Kais Kasem, Alfred King-Yin Lam
The present study aims to examine promoter methylation status of FAM134B in a large cohort of patients with colorectal adenocarcinomas. The clinical significances and correlations of FAM134B promoter methylation with its expression are also analysed. Methylation-specific high-resolution melt-curve analysis followed by sequencing was used to identify FAM134B promoter methylation in colorectal adenomas (n=32), colorectal adenocarcinomas (n=164), matched adjacent non-neoplastic colorectal mucosae (n=83) and colon cancer cell lines (n=4)...
January 10, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29315962/multiple-dicer1-related-tumors-in-a-child-with-a-large-interstitial-14q32-deletion
#2
Leanne de Kock, Dominique Geoffrion, Barbara Rivera, Rabea Wagener, Nelly Sabbaghian, Susanne Bens, Benjamin Ellezam, Dorothée Bouron-Dal Soglio, Jessica Ordóñez, Stephanie Sacharow, Jose Fernando Polo Nieto, R Paul Guillerman, Gordan M Vujanic, John R Priest, Reiner Siebert, William D Foulkes
Germ-line interstitial deletions involving the 14q32 chromosomal region, resulting in 14q32 deletion syndrome, are rare. DICER1 is a recently described cancer-predisposition gene located at 14q32.13. We report the case of a male child with an approximately 5.8 Mbp 14q32.13q32.2 germ-line deletion, which included the full DICER1 locus. We reviewed available clinical and pathological material, and conducted genetic analyses. In addition to having congenital dysmorphic features, the child developed multiple DICER1 syndrome-related tumors before age 5 years: a pediatric cystic nephroma (pCN), a ciliary body medulloepithelioma (CBME), and a small lung cyst (consistent with occult pleuropulmonary blastoma Type I/Ir cysts seen in DICER1 mutation carriers)...
January 9, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29277949/development-and-clinical-validation-of-a-circulating-tumor-dna-test-for-the-identification-of-clinically-actionable-mutations-in-non-small-cell-lung-cancer
#3
Liping Liu, Han Liu, Di Shao, Zu Liu, Jingjing Wang, Qiuhua Deng, Hailing Tang, Haihong Yang, Yalei Zhang, Yuan Qiu, Fei Cui, Meihua Tan, Pan Zhang, Zhilong Li, Jilong Liu, Wenhua Liang, Yuying Wang, Zhiyu Peng, Jian Wang, Huanming Yang, Mao Mao, Karsten Kristiansen, Mingzhi Ye, Jianxing He
Molecular analysis of potentially actionable mutations has become routine practice in oncological pathology. However, testing a wide range of oncogenes and mutations can be technically challenging because of limitations associated with tumor biopsy. Circulating tumor DNA (ctDNA) is a potential tool for the noninvasive profiling of tumors. In this study, we developed a next-generation sequencing (NGS)-based test for the detection of clinically relevant mutations in ctDNA and evaluated the feasibility of using this ctDNA NGS-based assay as an alternative to tissue genotyping...
December 26, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29266774/rreb1-mkl2-fusion-in-biphenotypic-oropharyngeal-sarcoma-new-entity-or-part-of-the-spectrum-of-biphenotypic-sinonasal-sarcomas
#4
Aurore Siegfried, Claire Romary, Fréderic Escudié, Yvan Nicaise, David Grand, Philippe Rochaix, Béatrice Barres, Sébastien Vergez, Christine Chevreau, Jean-Michel Coindre, Emmanuelle Uro-Coste, Sophie Le Guellec
An increasing number of sarcomas displaying a primitive, monomorphic spindle cell phenotype have been shown to harbor recurrent gene fusions, including biphenotypic sinonasal sarcoma (SNS). Occurring in the sinonasal area of middle-aged patients, SNS is a locally aggressive tumor harboring in 90% of cases recurrent gene fusions involving the PAX3 gene, in which the chimeric transcription factor induces an aberrant dual myogenic and neural phenotype. Here, we report an unusual oropharyngeal monomorphic spindle cell sarcoma in a 53-year-old man that revealed a novel RREB1-MKL2 gene fusion by RNA sequencing with the Illumina TruSight RNA Fusion Panel...
December 20, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29226599/microrna-transcription-factor-interactions-and-their-combined-effect-on-target-gene-expression-in-colon-cancer-cases
#5
Lila E Mullany, Jennifer S Herrick, Roger K Wolff, John R Stevens, Wade Samowitz, Martha L Slattery
Transcription factors (TFs) and microRNAs (miRNAs) regulate gene expression: TFs by influencing messenger RNA (mRNA) transcription and miRNAs by influencing mRNA translation and transcript degradation. Additionally, miRNAs and TFs alter each other's expression, making it difficult to ascertain the effect either one has on target gene (TG) expression. In this investigation, we use a two-way interaction model with the TF and miRNA as independent variables to investigate whether miRNAs and TFs work together to influence TG expression levels in colon cancer subjects...
December 11, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29218853/rna-sequencing-identifies-novel-greb1-ncoa2-fusion-gene-in-a-uterine-sarcoma-with-the-chromosomal-translocation-t-2-8-p25-q13
#6
Marta Brunetti, Ioannis Panagopoulos, Ludmila Gorunova, Ben Davidson, Sverre Heim, Francesca Micci
Sarcomas account for 3% of all uterine malignancies and many of them are characterized by acquired, specific fusion genes whose detection has increased pathogenetic knowledge and diagnostic precision. We describe a novel fusion gene, GREB1-NCOA2, detected by transcriptome sequencing and validated by RT-PCR and Sanger sequencing in an undifferentiated uterine sarcoma. The chimeric transcript was an in-frame fusion between exon 3 of GREB1 and exon 15 of NCOA2. The fusion is reported here for the first time, but it involves the GREB1 gene, an important promoter of tumor growth and progression, and NCOA2 which is known to be involved in transcriptional regulation...
December 8, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29218825/in-vivo-evidence-supporting-a-metastasis-suppressor-role-for-stard13-dlc2-in-erbb2-neu-oncogene-induced-mouse-mammary-tumours
#7
Pratima Basak, Heather Leslie, Rachelle L Dillon, William J Muller, Afshin Raouf, Michael Ra Mowat
Overexpression of dominant oncogenes and the loss of tumor suppressor genes are basic genetic events in the acquisition of the malignant phenotype. The erb-b2 receptor tyrosine kinase 2 (ERBB-2) proto-oncogene is overexpressed in 20-30% of human breast cancers. The StAR related lipid transfer domain containing 13 gene (STARD13), also known as Deleted in Liver Cancer-2 (DLC-2), maps to chromosome band 13q12.3 and is frequently downregulated in human cancers, including 72% of breast cancers. It encodes a RhoGAP protein with sterile α motif (SAM) and StAR-related lipid transfer (START) domains...
December 8, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29205637/a-field-guide-for-cancer-diagnostics-using-cell-free-dna-from-principles-to-practice-and-clinical-applications
#8
REVIEW
Anna-Lena Volckmar, Holger Sültmann, Anja Riediger, Thoas Fioretos, Peter Schirmacher, Volker Endris, Albrecht Stenzinger, Steffen Dietz
Recently, many genome-wide profiling studies provided insights into the molecular background of major cancer types. The deeper understanding of the genetic alterations and their functional consequences leveraged the discovery of novel therapeutic opportunities, improving clinical management of cancer patients. While tissue-based molecular patient stratification is the gold standard for precision medicine, it has certain limitations: Tissue biopsies are risky invasive sampling procedures and may not represent the entire tumor due to genetic heterogeneity...
December 5, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29181884/mir-221-222-cluster-expression-improves-clinical-stratification-of-non-muscle-invasive-bladder-cancer-tat1-patients-risk-for-short-term-relapse-and-progression
#9
Foteini D Tsikrika, Margaritis Avgeris, Panagiotis K Levis, Theodoros Tokas, Konstantinos Stravodimos, Andreas Scorilas
Clinical heterogeneity of bladder cancer prognosis requires the identification of bladder tumors' molecular profile to improve the prediction value of the established and clinically used markers. In the present study, we have analyzed miR-221/222 cluster expression in bladder tumors and its clinical significance for patients' prognosis and disease outcome. The study included 387 tissue specimens. Following extraction, total RNA was polyadenylated at 3΄-end and reversed transcribed. SYBR-Green based qPCR assays were performed for the quantification of miR-221/222 expression...
November 27, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29181864/functions-of-the-multi-interacting-protein-kidins220-arms-in-cancer-and-other-pathologies
#10
REVIEW
Muhammad-Zawwad Raza, Simone Allegrini, Charles Dumontet, Lars Petter Jordheim
Development of an organ and subsequently the whole system from an embryo is a highly integrated process. Although there is evidence that different systems are interconnected during developmental stages, the molecular understanding of this relationship is either not known or only to a limited extent. Nervous system development, amongst all, is maybe the most crucial and complex process. It relies on the correct distribution of specific neuronal growth factors and hormones to the specific receptors. Among the plethora of proteins that are involved in downstream signalling of neuronal growth factors, we find the kinase-D interacting substrate of 220 kDa (KIDINS220), also known as ankyrin-rich repeat membrane spanning (ARMS) protein...
November 27, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29181861/aneuploidy-tp53-mutation-and-amplification-of-myc-correlate-with-increased-intratumor-heterogeneity-and-poor-prognosis-of-breast-cancer-patients
#11
Johanna Oltmann, Kerstin Heselmeyer-Haddad, Leanora S Hernandez, Rüdiger Meyer, Irianna Torres, Yue Hu, Natalie Doberstein, J Keith Killian, David Petersen, Y Jack Zhu, Daniel C Edelman, Paul S Meltzer, Russell Schwartz, E Michael Gertz, Alejandro A Schäffer, Gert Auer, Jens K Habermann, Thomas Ried
The clinical course of breast cancer varies from one patient to another. Currently, the choice of therapy relies on clinical parameters and histological and molecular tumor features. Alas, these markers are informative in only a subset of patients. Therefore, additional predictors of disease outcome would be valuable for treatment stratification. Extensive studies showed that the degree of variation of the nuclear DNA content, i.e., aneuploidy determines prognosis. Our aim was to further elucidate the molecular basis of aneuploidy...
November 27, 2017: Genes, Chromosomes & Cancer
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
#12
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
#13
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
#14
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
#15
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
#16
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/28845532/mutational-analysis-using-sanger-and-next-generation-sequencing-in-sporadic-spindle-cell-hemangiomas-a-study-of-19-cases
#17
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...
December 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28675510/the-co-regulatory-networks-of-tumor-suppressor-genes-oncogenes-and-mirnas-in-colorectal-cancer
#18
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/29044880/targeted-deep-sequencing-of-effusion-cytology-samples-is-feasible-informs-spatiotemporal-tumor-evolution-and-has-clinical-and-diagnostic-utility
#19
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
#20
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
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