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https://www.readbyqxmd.com/read/28549458/detection-of-alk-fusion-transcripts-in-ffpe-lung-cancer-samples-by-nanostring-technology
#1
Adriane F Evangelista, Maicon F Zanon, Adriana Cruvinel Carloni, Flávia E de Paula, Mariana Andozia Morini, Maressa Ferreira-Neto, Iberê Cauduro Soares, Jose Elias Miziara, Pedro de Marchi, Cristovam Scapulatempo-Neto, Rui M Reis
BACKGROUND: ALK-rearranged lung cancers exhibit specific pathologic and clinical features and are responsive to anti-ALK therapies. Therefore, the detection of ALK-rearrangement is fundamental for personalized lung cancer therapy. Recently, new molecular techniques, such as NanoString nCounter, have been developed to detect ALK fusions with more accuracy and sensitivity. METHODS: In the present study, we intended to validate a NanoString nCounter ALK-fusion panel in routine biopsies of FFPE lung cancer patients...
May 26, 2017: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/28549232/identification-and-characterization-of-transcription-factor-zmereb94-involved-in-starch-synthesis-in-maize
#2
Hui Li, Qianlin Xiao, Chunxia Zhang, Jia Du, Xiao Li, Huanhuan Huang, Bin Wei, Yangping Li, Guowu Yu, Hanmei Liu, Yufeng Hu, Yinghong Liu, Junjie Zhang, Yubi Huang
Maize is an important food crop and industrial material owing to its high starch content. However, the mechanism of starch synthesis is not fully elucidated, especially with regard to the expression and regulation of starch synthetic genes. The APETALA2/Ethylene Responsive Factor (AP2/ERF) family plays a crucial role in various biological processes via regulating gene expression. In this study, the ZmEREB94 gene was identified through co-expression analysis. Bioinformatics analysis confirmed that ZmEREB94 belongs to the AP2/ERF family...
May 4, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28543708/comprehensive-characterization-of-rspo-fusions-in-colorectal-traditional-serrated-adenomas
#3
Shigeki Sekine, Reiko Ogawa, Taiki Hashimoto, Motohiro Kojima, Hiroshi Yoshida, Hirokazu Taniguchi, Yutaka Saito, Yasuhiro Ohno, Atsushi Ochiai, Nobuyoshi Hiraoka
AIMS: Traditional serrated adenoma (TSA) is a rare but distinct type of colorectal polyp. Our previous study showed that PTPRK-RSPO3 fusions are frequent and characteristic genetic alterations in TSAs. This study aimed to comprehensively characterize the prevalence and variability of RSPO fusions in colorectal TSAs. METHODS AND RESULTS: We examined RSPO expression and explored novel RSPO fusions in 129 TSAs, including 66 lesions previously analyzed for WNT pathway gene mutations...
May 24, 2017: Histopathology
https://www.readbyqxmd.com/read/28539478/a-novel-epigenetic-aml1-eto-thap10-mir-383-mini-circuitry-contributes-to-t-8-21-leukaemogenesis
#4
Yonghui Li, Qiaoyang Ning, Jinlong Shi, Yang Chen, Mengmeng Jiang, Li Gao, Wenrong Huang, Yu Jing, Sai Huang, Anqi Liu, Zhirui Hu, Daihong Liu, Lili Wang, Clara Nervi, Yun Dai, Michael Q Zhang, Li Yu
DNA methylation patterns are frequently deregulated in t(8;21) acute myeloid leukaemia (AML), but little is known of the mechanisms by which specific gene sets become aberrantly methylated. Here, we found that the promoter DNA methylation signature of t(8;21)(+) AML blasts differs from that of t(8;21)(-) AMLs. This study demonstrated that a novel hypermethylated zinc finger-containing protein, THAP10, is a target gene and can be epigenetically suppressed by AML1-ETO at the transcriptional level in t(8;21) AML...
May 24, 2017: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/28538183/runx1-eto-and-runx1-evi1-differentially-reprogram-the-chromatin-landscape-in-t-8-21-and-t-3-21-aml
#5
Justin Loke, Salam A Assi, Maria Rosaria Imperato, Anetta Ptasinska, Pierre Cauchy, Yura Grabovska, Natalia Martinez Soria, Manoj Raghavan, H Ruud Delwel, Peter N Cockerill, Olaf Heidenreich, Constanze Bonifer
Acute myeloid leukemia (AML) is a heterogeneous disease caused by mutations in transcriptional regulator genes, but how different mutant regulators shape the chromatin landscape is unclear. Here, we compared the transcriptional networks of two types of AML with chromosomal translocations of the RUNX1 locus that fuse the RUNX1 DNA-binding domain to different regulators, the t(8;21) expressing RUNX1-ETO and the t(3;21) expressing RUNX1-EVI1. Despite containing the same DNA-binding domain, the two fusion proteins display distinct binding patterns, show differences in gene expression and chromatin landscape, and are dependent on different transcription factors...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28537542/malonate-degradation-in-acinetobacter-baylyi-adp1-operon-organization-and-regulation-by-mdcr
#6
Julie L Stoudenmire, Alicia L Schmidt, Melissa P Tumen-Velasquez, Kathryn T Elliott, Nicole S Laniohan, S Walker Whitley, Nickolaus R Galloway, Melesse Nune, Michael West, Cory Momany, Ellen L Neidle, Anna C Karls
Transcriptional regulators in the LysR or GntR families are typically encoded in the genomic neighbourhood of bacterial genes for malonate degradation. While these arrangements have been evaluated using bioinformatics methods, experimental studies demonstrating co-transcription of predicted operons were lacking. Here, transcriptional regulation was characterized for a cluster of mdc genes that enable a soil bacterium, Acinetobacter baylyi ADP1, to use malonate as a carbon source. Despite previous assumptions that the mdc-gene set forms one operon, our studies revealed distinct promoters in two different regions of a nine-gene cluster...
May 25, 2017: Microbiology
https://www.readbyqxmd.com/read/28536267/the-ubiquitin-ligase-stub1-regulates-stability-and-activity-of-runx1-and-runx1-runx1t1
#7
Taishi Yonezawa, Hirotaka Takahashi, Shiori Shikata, Xiaoxiao Liu, Moe Tamura, Shuhei Asada, Tsuyoshi Fukushima, Tomofusa Fukuyama, Yosuke Tanaka, Tatsuya Sawasaki, Toshio Kitamura, Susumu Goyama
RUNX1 is a member of RUNX transcription factors and plays important roles in hematopoiesis. Disruption of RUNX1 activity has been implicated in the development of hematopoietic neoplasms. Chromosomal translocations involving the RUNX1 gene are associated with several types of leukemia, including acute myeloid leukemia driven by a leukemogenic fusion protein RUNX1-RUNX1T1. Previous studies have shown that RUNX1 is an unstable protein and is subjected to proteolytic degradation mediated by the ubiquitin-proteasome pathway...
May 23, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28536102/spa-proteins-affect-the-subcellular-localization-of-cop1-in-the-cop1-spa-ubiquitin-ligase-complex-during-photomorphogenesis
#8
Martin Balcerowicz, Konstantin Kerner, Christian Schenkel, Ute Hoecker
The Arabidopsis COP1/SPA ubiquitin ligase is a central repressor which suppresses light signaling in darkness by targeting positive regulators of the light response, mainly transcription factors, for degradation. Light inactivates COP1/SPA, in part by excluding COP1 from the nucleus. SPA proteins are essential cofactors of COP1, but their exact role in the COP1/SPA complex is thus far unknown. To unravel a potential role of SPA proteins in COP1 nucleocytoplasmic partitioning, we monitored the subcellular localization of COP1 in a spa1234 quadruple mutant (spaQn)...
May 23, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28533693/dna-methylation-at-the-mu-1-opioid-receptor-gene-oprm1-promoter-predicts-preoperative-acute-and-chronic-postsurgical-pain-after-spine-fusion
#9
Vidya Chidambaran, Xue Zhang, Lisa J Martin, Lili Ding, Matthew T Weirauch, Kristie Geisler, Bobbie L Stubbeman, Senthilkumar Sadhasivam, Hong Ji
INTRODUCTION: The perioperative pain experience shows great interindividual variability and is difficult to predict. The mu-1 opioid receptor gene (OPRM1) is known to play an important role in opioid-pain pathways. Since deoxyribonucleic acid (DNA) methylation is a potent repressor of gene expression, DNA methylation was evaluated at the OPRM1 promoter, as a predictor of preoperative, acute, and chronic postsurgical pain (CPSP). METHODS: A prospective observational cohort study was conducted in 133 adolescents with idiopathic scoliosis undergoing spine fusion under standard protocols...
2017: Pharmacogenomics and Personalized Medicine
https://www.readbyqxmd.com/read/28531838/antimicrobial-agents-triclosan-chloroxylenol-methylisothiazolinone-and-borax-used-in-cleaning-had-genotoxic-and-histopathologic-effects-on-rainbow-trout
#10
Erol Capkin, Tuna Ozcelep, Sevki Kayis, Ilhan Altinok
Triclosan (TRC), chloroxylenol (PCMX) and methylisothiazolinone (MIT) have been commonly used as an antimicrobial in soaps while borax (BRX) is used in household cleaning. After using these chemicals, they are washed down drains and getting into the aquatic ecosystem in which they may affect aquatic living organisms. In the present study, the chronic effects of TRC, PCMX, MIT and BRX on genotoxicity, gene expression and histopathology of rainbow trout (Oncorhynchus mykiss) were evaluated for 40 days under semi static condition...
May 15, 2017: Chemosphere
https://www.readbyqxmd.com/read/28531348/plant-derived-transcription-factors-for-orthologous-regulation-of-gene-expression-in-the-yeast-saccharomyces-cerevisiae
#11
Gita Naseri, Salma Balazadeh, Fabian Machens, Iman Kamranfar, Katrin Messerschmidt, Bernd Mueller-Roeber
Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects where tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harbouring cognate cis-regulatory motifs driving a yEGFP reporter...
May 22, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28527402/a-rare-e13a3-b2a3-bcr-abl1-fusion-transcript-with-normal-karyotype-in-chronic-myeloid-leukemia-the-challenges-in-diagnosis-and-monitoring-minimal-residual-disease-mrd
#12
M-H Duan, H Li, H Cai
Patients with chronic myeloid leukemia (CML) have a t (9;22)(q34;q11.2) or variant translocation that results in a BCR-ABL1 fusion gene. For many years, conventional karyotyping has been used as the standard diagnostic tool for t (9;22) (q34;q11.2). However, it has several limitations that may lead to failure for detecting BCR-ABL1 gene rearrangements in around 5% of all CML patients. Although reverse transcription polymerase chain reaction (RT-PCR) has evolved as a sensitive method for detecting BCR-ABL1 translocation, this method fail to detect certain BCR-ABL1 fusion transcript type, such as e13a3 (also known as b2a3), as a result of many commercially available and laboratory-developed primer sets...
May 12, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28525538/chimeraviz-a-tool-for-visualizing-chimeric-rna
#13
Stian Lågstad, Sen Zhao, Andreas M Hoff, Bjarne Johannessen, Ole Christian Lingjærde, Rolf I Skotheim
Summary: Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and this can be helped by a visualization framework that automatically integrates RNA data with known genomic features. Here we present chimeraviz , a Bioconductor package that automates the creation of chimeric RNA visualizations...
May 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28522867/movement-protein-of-apple-chlorotic-leaf-spot-virus-is-genetically-unstable-and-negatively-regulated-by-ribonuclease-e-in-e-coli
#14
Rahul Mohan Singh, Dharam Singh, Vipin Hallan
Movement protein (MP) of Apple chlorotic leaf spot virus (ACLSV) belongs to "30 K" superfamily of proteins and members of this family are known to show a wide array of functions. In the present study this gene was found to be genetically unstable in E. coli when transformed DH5α cells were grown at 28 °C and 37 °C. However, genetic instability was not encountered at 20 °C. Heterologous over expression failed despite the use of different transcriptional promoters and translational fusion constructs...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28521055/tying-the-knot-occurrence-and-possible-significance-of-gene-fusions-in-plant-metabolism-and-beyond
#15
Jillian M Hagel, Peter J Facchini
Gene fusions have recently attracted attention especially in the field of plant specialized metabolism. The occurrence of a gene fusion, in which originally separate gene products are combined into a single polypeptide, often corresponds to the functional association of individual components within a single metabolic pathway. Examples include gene fusions implicated in benzylisoquinoline alkaloid (BIA), terpenoid, and amino acid biosynthetic pathways, in which distinct domains within a fusion catalyze consecutive, yet independent reactions...
May 18, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28516957/asxl2-is-essential-for-haematopoiesis-and-acts-as-a-haploinsufficient-tumour-suppressor-in-leukemia
#16
Jean-Baptiste Micol, Alessandro Pastore, Daichi Inoue, Nicolas Duployez, Eunhee Kim, Stanley Chun-Wei Lee, Benjamin H Durham, Young Rock Chung, Hana Cho, Xiao Jing Zhang, Akihide Yoshimi, Andrei Krivtsov, Richard Koche, Eric Solary, Amit Sinha, Claude Preudhomme, Omar Abdel-Wahab
Additional sex combs-like (ASXL) proteins are mammalian homologues of additional sex combs (Asx), a regulator of trithorax and polycomb function in Drosophila. While there has been great interest in ASXL1 due to its frequent mutation in leukemia, little is known about its paralog ASXL2, which is frequently mutated in acute myeloid leukemia patients bearing the RUNX1-RUNX1T1 (AML1-ETO) fusion. Here we report that ASXL2 is required for normal haematopoiesis with distinct, non-overlapping effects from ASXL1 and acts as a haploinsufficient tumour suppressor...
May 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28515143/cyclin-c-influences-the-timing-of-mitosis-in-fission-yeast
#17
Gabor Banyai, Zsolt Szilagyi, Vera Baraznenok, Olga Khorosjutina, Claes M Gustafsson
The multiprotein Mediator complex is required for the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator contains the Cdk8 regulatory subcomplex, which directs periodic transcription and influences cell cycle progression in fission yeast. We here investigate the role of CycC, the cognate cyclin partner of Cdk8, in cell cycle control. Previous reports suggested that CycC interact with other cellular Cdks, but a fusion of CycC to Cdk8 reported here did not cause any obvious cell cycle phenotypes...
May 17, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28513875/incidence-clinicopathologic-features-and-fusion-transcript-landscape-of-translocation-renal-cell-carcinomas
#18
Xiao-Tong Wang, Qiu-Yuan Xia, Xiao-Jun Zhou, Qiu Rao
The recent article entitled "Incidence, clinicopathologic features, and fusion transcript landscape of translocation renal cell carcinomas" by Marion Classe and colleagues has been accepted in January 2017 by Histopathology(1) . The authors aimed to describe the landscape of fusion transcript in a large single institution series of interphase fluorescence in situ hybridization (FISH) confirmed translocation renal cell carcinomas (RCCs). They also identified two new fusion partners, GRIPAP1 and MED15, in Xp11 translocation RCCs...
May 17, 2017: Histopathology
https://www.readbyqxmd.com/read/28512179/cooperative-regulatory-functions-of-mir858-and-myb83-during-cyst-nematode-parasitism
#19
Sarbottam Piya, Christina Kihm, J Hollis Rice, Thomas J Baum, Tarek Hewezi
microRNAs (miRNAs) recently have been established as key regulators of transcriptome reprogramming that defines cell function and identity. Nevertheless, the molecular functions of the greatest number of miRNA genes remain to be determined. Here, we report cooperative regulatory functions of miR858 and its MYB83 transcription factor target gene in transcriptome reprogramming during Heterodera cyst nematode parasitism of Arabidopsis. Gene expression analyses and promoter-GUS fusion assays documented a role of miR858 in post-transcriptional regulation of MYB83 in the Heterodera schachtii-induced feeding sites, the syncytia...
May 16, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28507416/pathotypic-characterization-of-newcastle-disease-virus-isolated-from-vaccinated-chicken-in-west-java-indonesia
#20
Dwi Desmiyeni Putri, Ekowati Handharyani, Retno Damajanti Soejoedono, Agus Setiyono, Ni Luh Putu Ika Mayasari, Okti Nadia Poetri
AIM: This research was conducted to differentiate and characterize eight Newcastle disease virus (NDV) isolates collected from vaccinated chicken at commercial flocks in West Java, Indonesia, in 2011, 2014 and 2015 by pathotype specific primers. MATERIALS AND METHODS: A total of eight NDV isolates collected from clinical outbreaks among commercial vaccinated flocks in West Java, Indonesia, in 2011, 2014, and 2015 were used in this study. Reverse transcription-polymerase chain reaction was used to detect and differentiate virulence of NDV strains, using three sets of primers targeting their M and F gene...
April 2017: Veterinary World
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