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https://www.readbyqxmd.com/read/28841467/chronological-age-prediction-based-on-dna-methylation-massive-parallel-sequencing-and-random-forest-regression
#1
Jana Naue, Huub C J Hoefsloot, Olaf R F Mook, Laura Rijlaarsdam-Hoekstra, Marloes C H van der Zwalm, Peter Henneman, Ate D Kloosterman, Pernette J Verschure
The use of DNA methylation (DNAm) to obtain additional information in forensic investigations showed to be a promising and increasing field of interest. Prediction of the chronological age based on age-dependent changes in the DNAm of specific CpG sites within the genome is one such potential application. Here we present an age-prediction tool for whole blood based on massive parallel sequencing (MPS) and a random forest machine learning algorithm. MPS allows accurate DNAm determination of pre-selected markers and neighboring CpG-sites to identify the best age-predictive markers for the age-prediction tool...
August 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28830460/gene-mutational-pattern-and-expression-level-in-560-acute-myeloid-leukemia-patients-and-their-clinical-relevance
#2
Yong-Mei Zhu, Pan-Pan Wang, Jin-Yan Huang, Yun-Shuo Chen, Bing Chen, Yu-Jun Dai, Han Yan, Yi Hu, Wen-Yan Cheng, Ting-Ting Ma, Sai-Juan Chen, Yang Shen
BACKGROUND: Cytogenetic aberrations and gene mutations have long been regarded as independent prognostic markers in AML, both of which can lead to misexpression of some key genes related to hematopoiesis. It is believed that the expression level of the key genes is associated with the treatment outcome of AML. METHODS: In this study, we analyzed the clinical features and molecular aberrations of 560 newly diagnosed non-M3 AML patients, including mutational status of CEBPA, NPM1, FLT3, C-KIT, NRAS, WT1, DNMT3A, MLL-PTD and IDH1/2, as well as expression levels of MECOM, ERG, GATA2, WT1, BAALC, MEIS1 and SPI1...
August 22, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28782694/co-regulation-of-micrornas-and-transcription-factors-in-cardiomyocyte-specific-differentiation-of-murine-embryonic-stem-cells-an-aspect-from-transcriptome-analysis
#3
Lin Gan, Bernd Denecke
The differentiation process of embryonic stem cells is a comprehensive process regulated by a variety of factors in response to stimulus. Studies of this process can be focused on cell biology as well as on molecular biology level. In this paper we identified the co-regulation of molecular regulators and their interactions during cardiomyocyte specific differentiation of mouse embryonic stem cells based on parallel genome wide transcriptome analyses of mRNA and microRNA. Differentially expressed mRNAs and microRNAs were identified according to their expression profiles...
August 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28751478/novel-gene-and-network-associations-found-for-lymphoblastic-leukemia-using-case-control-and-family-based-studies-in-multi-ethnic-populations
#4
Priyanka Nakka, Natalie P Archer, Heng Xu, Philip J Lupo, Benjamin J Raphael, Jun J Yang, Sohini Ramachandran
BACKGROUND: Acute lymphoblastic leukemia (ALL) is the most common childhood cancer, suggesting that germline variants influence ALL risk. Although multiple genome-wide association (GWA) studies have identified variants predisposing children to ALL, it remains unclear whether genetic heterogeneity affects ALL susceptibility and how interactions within and among genes containing ALL-associated variants influence ALL risk. METHODS: Here we jointly analyze two published datasets of case-control GWA summary statistics along with germline data from ALL case-parent trios...
July 27, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28745213/emerging-roles-of-meis1-in-cardiac-regeneration-stem-cells-and-cancer
#5
Merve Aksoz, Raife Dilek Turan, Esra Albayrak, Fatih Kocabas
Meis1 is a member of three-amino-acid loop extension (TALE) homeodomain transcription factors. Studies in the last decade have shown that Meis1 has crucial roles in cardiac regeneration, stem cell function, and tumorigenesis. We have recently demonstrated that knocking out of Meis1 in adult cardiomyocytes resulted in the induction of cardiomyocyte proliferation. This suggests that targeting of Meis1 might be utilized in the manipulation of cardiomyocyte cell cycle post cardiac injuries. In addition, hematopoietic stem cell (HSC) specific deletion of Meis1 leads to in vivo expansion of HSCs pool...
July 24, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28735443/retinoic-acid-regulates-avian-lung-branching-through-a-molecular-network
#6
Hugo Fernandes-Silva, Patrícia Vaz-Cunha, Violina Baranauskaite Barbosa, Carla Silva-Gonçalves, Jorge Correia-Pinto, Rute Silva Moura
Retinoic acid (RA) is of major importance during vertebrate embryonic development and its levels need to be strictly regulated otherwise congenital malformations will develop. Through the action of specific nuclear receptors, named RAR/RXR, RA regulates the expression of genes that eventually influence proliferation and tissue patterning. RA has been described as crucial for different stages of mammalian lung morphogenesis, and as part of a complex molecular network that contributes to precise organogenesis; nonetheless, nothing is known about its role in avian lung development...
July 22, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28707666/-identification-of-proteins-associated-with-transcription-factors-hoxa9-and-e2a-pbx1-by-tandem-affinity-purification
#7
E A Shestakova, M Boutin, S Bourassa, E Bonneil, J J Bijl
Chimeric transcription factor E2A-PBX1 induces the development of acute lymphoblastic B-cell leukemia in children. Using a transgenic mouse model, we previously demonstrated that homeobox (HOX) gene HOXA9 genetically interact with E2A-PBX1 gene in the development of B-cell leukemia in mice. HOXA9 itself is a potent oncogene resulting in myeloid leukemia when overexpressed, which is strongly accelerated by its collaborator Meis1. HOX, PBX1 and MEIS1 proteins have been shown to form hetero dimeric or trimeric complexes in different combinations...
May 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28695622/sleep-disturbance-by-pramipexole-is-modified-by-meis1-in-mice
#8
Aaro V Salminen, Barbara Schormair, Cornelia Flachskamm, Miguel Torres, Bertram Müller-Myhsok, Mayumi Kimura, Juliane Winkelmann
Meis homeobox 1 (Meis1) is a transcription factor functioning in the development of the nervous system and the cardiovascular system. Both common and rare variants within the gene have been associated with restless legs syndrome (RLS), while its association with symptoms of insomnia has also been discovered recently. RLS is associated with sleep disturbances, and while Meis1 haploinsufficiency is one of the most promising strategies for an RLS animal model, sleep phenotyping of Meis1 knockout mice has never been conducted...
July 11, 2017: Journal of Sleep Research
https://www.readbyqxmd.com/read/28687780/nuclear-receptors-connect-progenitor-transcription-factors-to-cell-cycle-control
#9
Marta Neto, Marina Naval-Sánchez, Delphine Potier, Paulo S Pereira, Dirk Geerts, Stein Aerts, Fernando Casares
The specification and growth of organs is controlled simultaneously by networks of transcription factors. While the connection between these transcription factors with fate determinants is increasingly clear, how they establish the link with the cell cycle is far less understood. Here we investigate this link in the developing Drosophila eye, where two transcription factors, the MEIS1 homologue hth and the Zn-finger tsh, synergize to stimulate the proliferation of naïve eye progenitors. Experiments combining transcriptomics, open-chromatin profiling, motif analysis and functional assays indicate that these progenitor transcription factors exert a global regulation of the proliferation program...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28664166/lentiviral-fluorescent-genetic-barcoding-for-multiplex-fate-tracking-of-leukemic-cells
#10
Tobias Maetzig, Jens Ruschmann, Lea Sanchez Milde, Courteney K Lai, Niklas von Krosigk, R Keith Humphries
Tracking the behavior of leukemic samples both in vitro and in vivo plays an increasingly large role in efforts to better understand the leukemogenic processes and the effects of potential new therapies. Such work can be accelerated and made more efficient by methodologies enabling the characterization of leukemia samples in multiplex assays. We recently developed three sets of lentiviral fluorescent genetic barcoding (FGB) vectors that create 26, 14, and 6 unique immunophenotyping-compatible color codes from GFP-, yellow fluorescent protein (YFP)-, and monomeric kusabira orange 2 (mKO2)-derived fluorescent proteins...
September 15, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28663367/genome-wide-temporal-profiling-of-transcriptome-and-open-chromatin-of-early-cardiomyocyte-differentiation-derived-from-hipscs-and-hescs
#11
Qing Liu, Chao Jiang, Jin Xu, Ming-Tao Zhao, Kevin Van Bortle, Xun Cheng, Guangwen Wang, Howard Y Chang, Joseph C Wu, Michael P Snyder
RATIONALE: Recent advances have improved our ability to generate cardiomyocytes from human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs). However, our understanding of the transcriptional regulatory networks underlying early stages (ie, from mesoderm to cardiac mesoderm) of cardiomyocyte differentiation remains limited. OBJECTIVE: To characterize transcriptome and chromatin accessibility during early cardiomyocyte differentiation from hiPSCs and hESCs...
August 4, 2017: Circulation Research
https://www.readbyqxmd.com/read/28645892/meis1-effects-on-motor-phenotypes-and-the-sensorimotor-system-in-mice
#12
Aaro V Salminen, Lillian Garrett, Barbara Schormair, Jan Rozman, Florian Giesert, Kristina M Niedermeier, Lore Becker, Birgit Rathkolb, Ildikó Rácz, Martin Klingenspor, Thomas Klopstock, Eckhard Wolf, Andreas Zimmer, Valérie Gailus-Durner, Miguel Torres, Helmut Fuchs, Martin Hrabě de Angelis, Wolfgang Wurst, Sabine M Hölter, Juliane Winkelmann
MEIS1 encodes a developmental transcription factor and has been linked to restless legs syndrome (RLS) in genome-wide association studies. RLS is a movement disorder leading to severe sleep reduction and has a substantial impact on the quality of life of patients. In genome-wide association studies, MEIS1 has consistently been the gene with the highest effect size and functional studies suggest a disease-relevant downregulation. Therefore, haploinsufficiency of Meis1 could be the system with the most potential for modeling RLS in animals...
August 1, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28626420/restless-legs-syndrome-from-pathophysiology-to-clinical-diagnosis-and-management
#13
REVIEW
Shiyi Guo, Jinsha Huang, Haiyang Jiang, Chao Han, Jie Li, Xiaoyun Xu, Guoxin Zhang, Zhicheng Lin, Nian Xiong, Tao Wang
Restless legs syndrome (RLS), a common neurological sensorimotor disorder in western countries, has gained more and more attention in Asian countries. The prevalence of RLS is higher in older people and females. RLS is most commonly related to iron deficiency, pregnancy and uremia. The RLS symptoms show a significant circadian rhythm and a close relationship to periodic limb movements (PLMs) in clinical observations, while the pathophysiological pathways are still unknown. The diagnostic criteria have been revised in 2012 to improve the validity of RLS diagnosis...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28604731/genome-wide-association-analysis-of-insomnia-complaints-identifies-risk-genes-and-genetic-overlap-with-psychiatric-and-metabolic-traits
#14
Anke R Hammerschlag, Sven Stringer, Christiaan A de Leeuw, Suzanne Sniekers, Erdogan Taskesen, Kyoko Watanabe, Tessa F Blanken, Kim Dekker, Bart H W Te Lindert, Rick Wassing, Ingileif Jonsdottir, Gudmar Thorleifsson, Hreinn Stefansson, Thorarinn Gislason, Klaus Berger, Barbara Schormair, Juergen Wellmann, Juliane Winkelmann, Kari Stefansson, Konrad Oexle, Eus J W Van Someren, Danielle Posthuma
Persistent insomnia is among the most frequent complaints in general practice. To identify genetic factors for insomnia complaints, we performed a genome-wide association study (GWAS) and a genome-wide gene-based association study (GWGAS) in 113,006 individuals. We identify three loci and seven genes associated with insomnia complaints, with the associations for one locus and five genes supported by joint analysis with an independent sample (n = 7,565). Our top association (MEIS1, P < 5 × 10(-8)) has previously been implicated in restless legs syndrome (RLS)...
June 12, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28599093/clinical-and-molecular-cytogenetic-characterization-of-four-unrelated-patients-carrying-2p14-microdeletions
#15
Marie-Laure Mathieu, Caroline Demily, Sandra Chantot-Bastaraud, Alexandra Afenjar, Cyril Mignot, Joris Andrieux, Marion Gerard, Jaume Catala-Mora, Pierre Simon Jouk, Audrey Labalme, Patrick Edery, Damien Sanlaville, Massimiliano Rossi
We report the clinical and molecular cytogenetic characterization of four unrelated patients from France and Spain, carrying 2p14 microdeletions and presenting with intellectual disability and dysmorphisms. 2p14 microdeletions are very rare. Seven patients have been reported so far harboring deletions including 2p14p15 and encompassing OTX1, whose haploinsufficiency is frequently associated with genitourinary defects. To date, only one patient has been reported carrying a more proximal 2p14 microdeletion which does not include OTX1...
June 9, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28572861/genome-wide-dna-methylation-profiling-integrated-with-gene-expression-profiling-identifies-pax9-as-a-novel-prognostic-marker-in-chronic-lymphocytic-leukemia
#16
Lata Rani, Nitin Mathur, Ritu Gupta, Ajay Gogia, Gurvinder Kaur, Jaspreet Kaur Dhanjal, Durai Sundar, Lalit Kumar, Atul Sharma
BACKGROUND: In chronic lymphocytic leukemia (CLL), epigenomic and genomic studies have expanded the existing knowledge about the disease biology and led to the identification of potential biomarkers relevant for implementation of personalized medicine. In this study, an attempt has been made to examine and integrate the global DNA methylation changes with gene expression profile and their impact on clinical outcome in early stage CLL patients. RESULTS: The integration of DNA methylation profile (n = 14) with the gene expression profile (n = 21) revealed 142 genes as hypermethylated-downregulated and; 62 genes as hypomethylated-upregulated in early stage CLL patients compared to CD19+ B-cells from healthy individuals...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28545608/differential-regulation-analysis-reveals-dysfunctional-regulatory-mechanism-involving-transcription-factors-and-micrornas-in-gastric-carcinogenesis
#17
Quanxue Li, Junyi Li, Wentao Dai, Yi-Xue Li, Yuan-Yuan Li
Gastric cancer (GC) is one of the most incident malignancies in the world. Although lots of featured genes and microRNAs (miRNAs) have been identified to be associated with gastric carcinogenesis, underlying regulatory mechanisms still remain unclear. In order to explore the dysfunctional mechanisms of GC, we developed a novel approach to identify carcinogenesis relevant regulatory relationships, which is characterized by quantifying the difference of regulatory relationships between stages. Firstly, we applied the strategy of differential coexpression analysis (DCEA) to transcriptomic datasets including paired mRNA and miRNA of gastric samples to identify a set of genes/miRNAs related to gastric cancer progression...
March 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28469672/stemness-maintenance-properties-in-human-oral-stem-cells-after-long-term-passage
#18
Francesca Diomede, Thangavelu Soundara Rajan, Valentina Gatta, Marco D'Aurora, Ilaria Merciaro, Marco Marchisio, Aurelio Muttini, Sergio Caputi, Placido Bramanti, Emanuela Mazzon, Oriana Trubiani
Background. Neural crest-derived mesenchymal stem cells (MSCs) from human oral tissues possess immunomodulatory and regenerative properties and are emerging as a potential therapeutic tool to treat diverse diseases, such as multiple sclerosis, myocardial infarction, and connective tissue damages. In addition to cell-surface antigens, dental MSCs express embryonic stem cell markers as neural crest cells originate from the ectoderm layer. In vitro passages may eventually modify these embryonic marker expressions and other stemness properties, including proliferation...
2017: Stem Cells International
https://www.readbyqxmd.com/read/28462489/role-of-maml1-and-meis1-in-esophageal-squamous-cell-carcinoma-depth-of-invasion
#19
Mohammad Reza Abbaszadegan, Meysam Moghbeli
Homeobox (HOX) transcription factors and NOTCH signaling pathway are critical regulators of stem cell functions, cell fate in development and homeostasis of gastrointestinal tissues. In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. Fifty one ESCC cases were enrolled to assess the levels of Meis1 and Maml1 mRNA expression using real-time polymerase chain reaction (PCR)...
May 1, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28425489/meis1-variant-as-a-determinant-of-autonomic-imbalance-in-restless-legs-syndrome
#20
Jérôme Thireau, Charlotte Farah, Nicolas Molinari, Fabrice Bouilloux, Lucas Torreilles, Juliane Winkelmann, Sabine Scholz, Sylvain Richard, Yves Dauvilliers, Frédéric Marmigère
Restless Legs Syndrome (RLS) is a genetically complex neurological disorder in which overlapping genetic risk factors may contribute to the diversity and heterogeneity of the symptoms. The main goal of the study was to investigate, through analysis of heart rate variability (HRV), whether in RLS patients the MEIS1 polymorphism at risk influences the sympathovagal regulation in different sleep stages. Sixty-four RLS patients with periodic leg movement index above 15 per hour, and 38 controls underwent one night of video-polysomnographic recording...
April 20, 2017: Scientific Reports
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