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https://www.readbyqxmd.com/read/29555671/a-screening-approach-to-identify-clinically-actionable-variants-causing-congenital-heart-disease-in-exome-data
#1
Justin O Szot, Hartmut Cuny, Gillian M Blue, David T Humphreys, Eddie Ip, Katrina Harrison, Gary F Sholler, Eleni Giannoulatou, Paul Leo, Emma L Duncan, Duncan B Sparrow, Joshua W K Ho, Robert M Graham, Nicholas Pachter, Gavin Chapman, David S Winlaw, Sally L Dunwoodie
BACKGROUND: Congenital heart disease (CHD)-structural abnormalities of the heart that arise during embryonic development-is the most common inborn malformation, affecting ≤1% of the population. However, currently, only a minority of cases can be explained by genetic abnormalities. The goal of this study was to identify disease-causal genetic variants in 30 families affected by CHD. METHODS: Whole-exome sequencing was performed with the DNA of multiple family members...
March 2018: Circulation. Genomic and precision medicine
https://www.readbyqxmd.com/read/29518627/zfp36l2-a-novel-aml1-target-gene-induces-aml-cells-apoptosis-and-inhibits-cell-proliferation
#2
Jia Liu, Wenting Lu, Shuang Liu, Ying Wang, Saisai Li, Yingxi Xu, Haiyan Xing, Kejing Tang, Zheng Tian, Qing Rao, Min Wang, Jianxiang Wang
The t(8;21)(q22;q22) translocation generated the fusion protein AML1-ETO. AML1-ETO recruits histone deacetylase (HDAC) complex via its ETO part to repress AML1-mediated transactivation. Our previous study demonstrated that HDAC inhibitor phenylbutyrate (PB) could induce AML1-ETO positive leukemia cell line Kasumi-1 cells to undergo differentiation and apoptosis accompanied by significant changes in gene expression profile. ZFP36L2 was one of the up-regulated genes in Kasumi-1 cells induced by PB treatment. In this study, ZFP36L2 was found to express at a lower level in acute myeloid leukemia (AML) patients with t(8;21) compared to AML patients without t(8;21)...
February 27, 2018: Leukemia Research
https://www.readbyqxmd.com/read/29449217/zfp36l2-is-a-cell-cycle-regulated-ccch-protein-necessary-for-dna-lesion-induced-s-phase-arrest
#3
Aya Noguchi, Shungo Adachi, Naoto Yokota, Tomohisa Hatta, Tohru Natsume, Hiroyuki Kawahara
ZFP36L2 promotes the destruction of AU-rich element-containing transcripts, while its regulation and functional significance in cell cycle control are scarcely identified. We show that ZFP36L2 is a cell cycle-regulated CCCH protein whose abundance is regulated post-translationally at the respective stages of the cell cycle. Indeed, ZFP36L2 protein was eliminated after release from M phase, and ZYG11B-based E3 ligase plays a role in its polyubiquitination in interphase. Although ZFP36L2 is dispensable for normal cell cycle progression, we found that endogenous ZFP36L2 played a key role in cisplatin-induced S-phase arrest, a process in which the suppression of G1/S cyclins is necessary...
February 15, 2018: Biology Open
https://www.readbyqxmd.com/read/29426877/zfp36l1-and-zfp36l2-inhibit-cell-proliferation-in-a-cyclin-d-dependent-and-p53-independent-manner
#4
Fat-Moon Suk, Chi-Ching Chang, Ren-Jye Lin, Shyr-Yi Lin, Shih-Chen Liu, Chia-Feng Jau, Yu-Chih Liang
ZFP36 family members include ZFP36, ZFP36L1, and ZFP36L2, which belong to CCCH-type zinc finger proteins with two tandem zinc finger (TZF) regions. Whether ZFP36L1 and ZFP36L2 have antiproliferative activities similar to that of ZFP36 is unclear. In this study, when ZFP36L1 or ZFP36L2 was overexpressed in T-REx-293 cells, cell proliferation was dramatically inhibited and the cell cycle was arrested at the G1 phase. The levels of cell-cycle-related proteins, including cyclin B, cyclin D, cyclin A, and p21, decreased; however, p53 increased in ZFP36L1-or ZFP36L2-overexpressing T-REx-293 cells...
February 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29408237/chromatin-modification-and-global-transcriptional-silencing-in-the-oocyte-mediated-by-the-mrna-decay-activator-zfp36l2
#5
Jennifer N Dumdie, Kyucheol Cho, Madhuvanthi Ramaiah, David Skarbrevik, Sergio Mora-Castilla, Deborah J Stumpo, Jens Lykke-Andersen, Louise C Laurent, Perry J Blackshear, Miles F Wilkinson, Heidi Cook-Andersen
Global transcriptional silencing is a highly conserved mechanism central to the oocyte-to-embryo transition. We report the unexpected discovery that global transcriptional silencing in oocytes depends on an mRNA decay activator. Oocyte-specific loss of ZFP36L2 an RNA-binding protein that promotes AU-rich element-dependent mRNA decay prevents global transcriptional silencing and causes oocyte maturation and fertilization defects, as well as complete female infertility in the mouse. Single-cell RNA sequencing revealed that ZFP36L2 downregulates mRNAs encoding transcription and chromatin modification regulators, including a large group of mRNAs for histone demethylases targeting H3K4 and H3K9, which we show are bound and degraded by ZFP36L2...
February 5, 2018: Developmental Cell
https://www.readbyqxmd.com/read/29295643/the-genomic-landscape-of-two-burkitt-lymphoma-cases-and-derived-cell-lines-comparison-between-primary-and-relapse-samples
#6
Claudia M Wever, Dominique Geoffrion, Bruno M Grande, Stephen Yu, Miguel Alcaide, Maryse Lemaire, Yasser Riazalhosseini, Josée Hébert, Christina Gavino, Donald C Vinh, Tina Petrogiannis-Haliotis, Svetlana Dmitrienko, Koren K Mann, Ryan D Morin, Nathalie A Johnson
Relapse occurs in 10-40% of Burkitt lymphoma (BL) patients that have completed intensive chemotherapy regimens and is typically fatal. While treatment-naive BL has been characterized, the genomic landscape of BL at the time of relapse (rBL) has never been reported. Here, we present a genomic characterization of two rBL patients. The diagnostic samples had mutations common in BL, including MYC and CCND3. Additional mutations were detected at relapse, affecting important pathways such as NFκB (IKBKB) and MEK/ERK (NRAS) signaling, glutamine metabolism (SIRT4), and RNA processing (ZFP36L2)...
January 3, 2018: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28882690/toxicogenomic-and-bioinformatics-platforms-to-identify-key-molecular-mechanisms-of-a-curcumin-analogue-dm-1-toxicity-in-melanoma-cells
#7
Érica Aparecida de Oliveira, Diogenes Saulo de Lima, Lucas Esteves Cardozo, Garcia Ferreira de Souza, Nayane de Souza, Debora Kristina Alves-Fernandes, Fernanda Faião-Flores, José Agustín Pablo Quincoces, Silvia Berlanga de Moraes Barros, Helder I Nakaya, Gisele Monteiro, Silvya Stuchi Maria-Engler
Melanoma is a highly invasive and metastatic cancer with high mortality rates and chemoresistance. Around 50% of melanomas are driven by activating mutations in BRAF that has led to the development of potent anti-BRAF inhibitors. However resistance to anti-BRAF therapy usually develops within a few months and consequently there is a need to identify alternative therapies that will bypass BRAF inhibitor resistance. The curcumin analogue DM-1 (sodium 4-[5-(4-hydroxy-3-methoxy-phenyl)-3-oxo-penta-1,4-dienyl]-2-methoxy-phenolate) has substantial anti-tumor activity in melanoma, but its mechanism of action remains unclear...
September 4, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28860350/identification-of-distinct-mutational-patterns-and-new-driver-genes-in-oesophageal-squamous-cell-carcinomas-and-adenocarcinomas
#8
De-Chen Lin, Huy Q Dinh, Jian-Jun Xie, Anand Mayakonda, Tiago Chedraoui Silva, Yan-Yi Jiang, Ling-Wen Ding, Jian-Zhong He, Xiu-E Xu, Jia-Jie Hao, Ming-Rong Wang, Chunquan Li, Li-Yan Xu, En-Min Li, Benjamin P Berman, H Phillip Koeffler
OBJECTIVES: Oesophageal squamous cell carcinoma (OSCC) and adenocarcinoma (OAC) are distinct cancers in terms of a number of clinical and epidemiological characteristics, complicating the design of clinical trials and biomarker developments. We analysed 1048 oesophageal tumour-germline pairs from both subtypes, to characterise their genomic features, and biological and clinical significance. DESIGN: Previously exome-sequenced samples were re-analysed to identify significantly mutated genes (SMGs) and mutational signatures...
August 31, 2017: Gut
https://www.readbyqxmd.com/read/28671688/the-genomic-landscape-of-pediatric-and-young-adult-t-lineage-acute-lymphoblastic-leukemia
#9
Yu Liu, John Easton, Ying Shao, Jamie Maciaszek, Zhaoming Wang, Mark R Wilkinson, Kelly McCastlain, Michael Edmonson, Stanley B Pounds, Lei Shi, Xin Zhou, Xiaotu Ma, Edgar Sioson, Yongjin Li, Michael Rusch, Pankaj Gupta, Deqing Pei, Cheng Cheng, Malcolm A Smith, Jaime Guidry Auvil, Daniela S Gerhard, Mary V Relling, Naomi J Winick, Andrew J Carroll, Nyla A Heerema, Elizabeth Raetz, Meenakshi Devidas, Cheryl L Willman, Richard C Harvey, William L Carroll, Kimberly P Dunsmore, Stuart S Winter, Brent L Wood, Brian P Sorrentino, James R Downing, Mignon L Loh, Stephen P Hunger, Jinghui Zhang, Charles G Mullighan
Genetic alterations that activate NOTCH1 signaling and T cell transcription factors, coupled with inactivation of the INK4/ARF tumor suppressors, are hallmarks of T-lineage acute lymphoblastic leukemia (T-ALL), but detailed genome-wide sequencing of large T-ALL cohorts has not been carried out. Using integrated genomic analysis of 264 T-ALL cases, we identified 106 putative driver genes, half of which had not previously been described in childhood T-ALL (for example, CCND3, CTCF, MYB, SMARCA4, ZFP36L2 and MYCN)...
August 2017: Nature Genetics
https://www.readbyqxmd.com/read/28455422/impact-of-rna-structure-on-zfp36l2-interaction-with-luteinizing-hormone-receptor-mrna
#10
Christopher B Ball, Amanda C Solem, Rita M Meganck, Alain Laederach, Silvia B V Ramos
ZFP36L2 (L2) destabilizes AU-rich element (ARE)-containing transcripts and has been implicated in female fertility. We have shown that only one of three putative AREs within the 3' UTR of murine luteinizing hormone receptor mRNA, ARE2197 (UAUUUAU), is capable of interacting with L2. To assess whether structural elements of ARE2197 could explain this unique binding ability, we performed whole-transcript SHAPE-MaP (selective 2' hydroxyl acylation by primer extension-mutational profiling) of the full-length mLHR mRNA...
August 2017: RNA
https://www.readbyqxmd.com/read/27862697/zfp36l2-promotes-cancer-cell-aggressiveness-and-is-regulated-by-antitumor-microrna-375-in-pancreatic-ductal-adenocarcinoma
#11
Keiichi Yonemori, Naohiko Seki, Hiroshi Kurahara, Yusaku Osako, Tetsuya Idichi, Takayuki Arai, Keiichi Koshizuka, Yoshiaki Kita, Kosei Maemura, Shoji Natsugoe
Due to its aggressive nature, pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal and hard-to-treat malignancies. Recently developed targeted molecular strategies have contributed to remarkable improvements in the treatment of several cancers. However, such therapies have not been applied to PDAC. Therefore, new treatment options are needed for PDAC based on current genomic approaches. Expression of microRNA-375 (miR-375) was significantly reduced in miRNA expression signatures of several types of cancers, including PDAC...
January 2017: Cancer Science
https://www.readbyqxmd.com/read/27566829/the-rna-binding-proteins-zfp36l1-and-zfp36l2-enforce-the-thymic-%C3%AE-selection-checkpoint-by-limiting-dna-damage-response-signaling-and-cell-cycle-progression
#12
Katharina U Vogel, Lewis S Bell, Alison Galloway, Helena Ahlfors, Martin Turner
The RNA-binding proteins Zfp36l1 and Zfp36l2 act redundantly to enforce the β-selection checkpoint during thymopoiesis, yet their molecular targets remain largely unknown. In this study, we identify these targets on a genome-wide scale in primary mouse thymocytes and show that Zfp36l1/l2 regulate DNA damage response and cell cycle transcripts to ensure proper β-selection. Double-negative 3 thymocytes lacking Zfp36l1/l2 share a gene expression profile with postselected double-negative 3b cells despite the absence of intracellular TCRβ and reduced IL-7 signaling...
October 1, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27182009/functional-analysis-of-zfp36-proteins-in-keratinocytes
#13
Frauke Prenzler, Annunziata Fragasso, Angelika Schmitt, Barbara Munz
The ZFP36 family of zinc finger proteins, including ZFP36, ZFP36L1, and ZFP36L2, regulates the production of growth factors and cytokines via destabilization of the respective mRNAs. We could recently demonstrate that in cultured keratinocytes, expression of the ZFP36, ZFP36L1, and ZFP36L2 genes is induced by growth factors and cytokines and that ZFP36L1 is a potent regulator of keratinocyte VEGF production. We now further analyzed the localization and function of ZFP36 proteins in the skin, specifically in epidermal keratinocytes...
August 2016: European Journal of Cell Biology
https://www.readbyqxmd.com/read/27102483/rna-binding-proteins-zfp36l1-and-zfp36l2-promote-cell-quiescence
#14
Alison Galloway, Alexander Saveliev, Sebastian Łukasiak, Daniel J Hodson, Daniel Bolland, Kathryn Balmanno, Helena Ahlfors, Elisa Monzón-Casanova, Sara Ciullini Mannurita, Lewis S Bell, Simon Andrews, Manuel D Díaz-Muñoz, Simon J Cook, Anne Corcoran, Martin Turner
Progression through the stages of lymphocyte development requires coordination of the cell cycle. Such coordination ensures genomic integrity while cells somatically rearrange their antigen receptor genes [in a process called variable-diversity-joining (VDJ) recombination] and, upon successful rearrangement, expands the pools of progenitor lymphocytes. Here we show that in developing B lymphocytes, the RNA-binding proteins (RBPs) ZFP36L1 and ZFP36L2 are critical for maintaining quiescence before precursor B cell receptor (pre-BCR) expression and for reestablishing quiescence after pre-BCR-induced expansion...
April 22, 2016: Science
https://www.readbyqxmd.com/read/26493225/emergence-and-evolution-of-zfp36l3
#15
Timothy J Gingerich, Deborah J Stumpo, Wi S Lai, Thomas A Randall, Scott J Steppan, Perry J Blackshear
In most mammals, the Zfp36 gene family consists of three conserved members, with a fourth member, Zfp36l3, present only in rodents. The ZFP36 proteins regulate post-transcriptional gene expression at the level of mRNA stability in organisms from humans to yeasts, and appear to be expressed in all major groups of eukaryotes. In Mus musculus, Zfp36l3 expression is limited to the placenta and yolk sac, and is important for overall fecundity. We sequenced the Zfp36l3 gene from more than 20 representative species, from members of the Muridae, Cricetidae and Nesomyidae families...
January 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/26180518/functional-regulation-of-zfp36l1-and-zfp36l2-in-response-to-lipopolysaccharide-in-mouse-raw264-7-macrophages
#16
Kuan-Ting Wang, Hsin-Hui Wang, Yan-Yun Wu, Yu-Lun Su, Pei-Yu Chiang, Nien-Yi Lin, Shun-Chang Wang, Geen-Dong Chang, Ching-Jin Chang
BACKGROUND: The tristetraprolin (TTP) family of mRNA-binding proteins contains three major members, Ttp, Zfp36l1, and Zfp36l2. Ttp down-regulates the stability of AU-rich element-containing mRNAs and functions as an anti-inflammation regulator. METHODS: To examine whether other TTP family proteins also play roles in the inflammatory response, their expression profiles and the possible mRNA targets were determined in the knockdown cells. RESULTS: Ttp mRNA and protein were highly induced by lipopolysaccharide (LPS), whereas Zfp36l1 and Zfp36l2 mRNAs were down-regulated and their proteins were phosphorylated during early lipopolysaccharide stimulation...
2015: Journal of Inflammation
https://www.readbyqxmd.com/read/25875247/identification-of-common-regulators-of-genes-in-co-expression-networks-affecting-muscle-and-meat-properties
#17
Siriluck Ponsuksili, Puntita Siengdee, Yang Du, Nares Trakooljul, Eduard Murani, Manfred Schwerin, Klaus Wimmers
Understanding the genetic contributions behind skeletal muscle composition and metabolism is of great interest in medicine and agriculture. Attempts to dissect these complex traits combine genome-wide genotyping, expression data analyses and network analyses. Weighted gene co-expression network analysis (WGCNA) groups genes into modules based on patterns of co-expression, which can be linked to phenotypes by correlation analysis of trait values and the module eigengenes, i.e. the first principal component of a given module...
2015: PloS One
https://www.readbyqxmd.com/read/25565391/immune-system-related-differentially-expressed-genes-transcription-factors-and-micrornas-in-post-menopausal-females-with-osteopenia
#18
M Ma, S Luo, X Chen, F Yuan, J Cai, L Lu, F Yin
This study was to identify differentially expressed genes (DEGs) in post-menopausal females with osteopenia and further screened the potentially involved transcription factors (TFs) and microRNAs (miRNAs). Data set GSE13850 of circulating B lymphocytes from post-menopausal females with low or high bone mineral density (BMD) was downloaded from Gene Expression Omnibus. Limma package in R was used to identify DEGs following raw data processing. Enrichment analysis was performed using DAVID (Database for Annotation, Visualization and Integrated Discovery) and visualized using plug-in EnrichmentMap of Cytoscape software...
March 2015: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/25505318/an-rna-binding-protein-promotes-axonal-integrity-in-peripheral-neurons-by-destabilizing-rest
#19
Francesca Cargnin, Tamilla Nechiporuk, Karin Müllendorff, Deborah J Stumpo, Perry J Blackshear, Nurit Ballas, Gail Mandel
The RE1 Silencing Transcription Factor (REST) acts as a governor of the mature neuronal phenotype by repressing a large consortium of neuronal genes in non-neuronal cells. In the developing nervous system, REST is present in progenitors and downregulated at terminal differentiation to promote acquisition of mature neuronal phenotypes. Paradoxically, REST is still detected in some regions of the adult nervous system, but how REST levels are regulated, and whether REST can still repress neuronal genes, is not known...
December 10, 2014: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/25486926/breakpoint-heterogeneity-in-2-3-p15-23-q26-translocations-involving-evi1-in-myeloid-hemopathies
#20
Marc De Braekeleer, Nadia Guéganic, Corine Tous, Marie-Josée Le Bris, Audrey Basinko, Frédéric Morel, Nathalie Douet-Guilbert
Several chromosomal rearrangements involving band 3q26 are known to induce EVI1 overexpression. They include inv(3)(q21q26), t(3;3)(q21;q26), t(3;21)(q26;q22) and t(3;12)(q26;p13). Translocations involving the short arm of chromosome 2 and 3q26 have been reported in more than 50 patients with myeloid disorders. However, although the breakpoints on 2p are scattered over a long segment, their distribution had only been analyzed in 9 patients. We performed fluorescent in situ hybridization with a library of BAC (Bacterial Artificial Chromosome) clones in 4 patients with t(2;3)(p15-23;q26)...
February 2015: Blood Cells, Molecules & Diseases
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