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Results: 1312
Genome-wide Estrogen Receptor-α activation is sustained, not cyclical.
Estrogen Receptor-alpha (ER) drives 75% of breast cancers. Stimulation of the ER by estra-2-diol forms a transcriptionally-active chromatin-bound complex. Previous studies reported that ER binding follows a cyclical pattern....
Estrogen estrogen receptor MCF7 Breast Cancer Chromosomes Computational Biology endocrine Gene Expression human Systems Biology Base Sequence Binding Sites Estradiol Estrogen Receptor alpha Female Gene Expression Regulation Neoplastic Genome Human Genome-Wide Association Study Humans MCF-7 Cells Neoplasm Proteins Promoter Regions Genetic Protein Binding Receptors CXCR Signal Transduction Sorting Nexins Trefoil Factor-1
Genetic and environmental risk factors for atherosclerosis regulate transcription of phosphatase and actin regulating gene PHACTR1.
Michael E Reschen, Da Lin, Anil Chalisey, Elizabeth J Soilleux, Christopher A O'Callaghan
Dec 17, 2018
BACKGROUND AND AIMS: Coronary artery disease (CAD) risk is associated with non-coding genetic variants at the phosphatase and actin regulating protein 1(PHACTR1) gene locus. The PHACTR1 gene encodes an actin-binding protein with...
Atherosclerosis Expression quantitative trait locus (eQTL) Functional genomics genetic disease Genetic polymorphism Genomics Low-density lipoprotein (LDL) Myocardial Infarction Oxidized low density lipoprotein (oxLDL) PHACTR1 Adult Aged Alleles Atherosclerosis Coronary Artery Disease Coronary Vessels Endothelial Cells Gene Expression Regulation Gene-Environment Interaction Genotype Humans Inflammation Lipopolysaccharides MACROPHAGES Microfilament Proteins Middle Aged Muscle Smooth Vascular Polymorphism Single Nucleotide Tumor Necrosis Factor-alpha Young Adult
f-scLVM
Florian Buettner, Naruemon Pratanwanich, Davis J McCarthy, John C Marioni, Oliver Stegle
Mar 26, 2018
Single-cell RNA-sequencing (scRNA-seq) allows studying heterogeneity in gene expression in large cell populations. Such heterogeneity can arise due to technical or biological factors, making decomposing sources of variation...
Gene set annotations Single-cell RNA-seq Sparse factor analysis Animals Computer Simulation Databases as Topic Factor Analysis Statistical Gene Expression Regulation Mice Models Theoretical Mouse embryonic stem cells Neurons Reproducibility of Results Sequence Analysis RNA Single-Cell Analysis Software
SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete.
BACKGROUND: Sox proteins encompass an evolutionarily conserved family of transcription factors with critical roles in animal development and stem cell biology. In common with vertebrates, the Drosophila group B proteins SoxNeuro...
Early loss of Crebbp confers malignant stem cell properties on lymphoid progenitors.
Sarah J Horton, George Giotopoulos, Haiyang Yun, Shabana Vohra, Olivia Sheppard, Rachael Bashford-Rogers, Mamunur Rashid, Alexandra Clipson, Wai-In Chan, Daniel Sasca, Loukia Yiangou, Hikari Osaki, Faisal Basheer, Paolo Gallipoli, Natalie Burrows, Ayşegül Erdem, Anastasiya Sybirna, Sarah Foerster, Wanfeng Zhao, Tonci Sustic, Anna Petrunkina Harrison, Elisa Laurenti, Jessica Okosun, Daniel Hodson, Penny Wright, Ken G Smith, Patrick Maxwell, Jude Fitzgibbon, Ming Q Du, David J Adams, Brian JP Huntly
Apr 06, 2018
Loss-of-function mutations of cyclic-AMP response element binding protein, binding protein (CREBBP) are prevalent in lymphoid malignancies. However, the tumour suppressor functions of CREBBP remain unclear. We demonstrate that...
Acetylation Animals CREB-Binding Protein Cell Proliferation Cell Self Renewal Cell Transformation Neoplastic Cells Cultured DNA Damage Epigenesis Genetic Gene Expression Regulation Neoplastic Genetic Predisposition to Disease Histones Lymphangiogenesis Lymphoid Progenitor Cells Lymphoma lymphopoiesis Methylation Mice Mice Inbred C57BL Mice Knockout Mutation Neoplastic Stem Cells Phenotype Signal Transduction Time Factors Transcription Genetic Tumor Suppressor Protein p53
Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos.
Rachel E Jennings, Andrew A Berry, David T Gerrard, Stephen J Wearne, James Strutt, Sarah Withey, Mariya Chhatriwala, Karen Piper Hanley, Ludovic Vallier, Nicoletta Bobola, Neil A Hanley
May 14, 2018
CTCF maintains regulatory homeostasis of cancer pathways.
Sarah J Aitken, Ximena Ibarra-Soria, Elissavet Kentepozidou, Paul Flicek, Christine Feig, John C Marioni, Duncan T Odom
Sep 20, 2018
CTCF Cancer Chromatin architecture chromatin state Hemizygosity Transcription Animals Breast Neoplasms CCCTC-Binding Factor Cell Line Chromatin DNA Neoplasm Enhancer Elements Genetic Female FIBROBLASTS Gene Expression Regulation Neoplastic Genome Hemizygote Homeostasis Humans Liver Neoplasms Experimental Mice Mice Inbred C57BL Mice Transgenic Protein Binding Signal Transduction Uterine Neoplasms
Transcriptional regulation of mammalian autophagy at a glance.
Macroautophagy, hereafter referred to as autophagy, is a catabolic process that results in the lysosomal degradation of cytoplasmic contents ranging from abnormal proteins to damaged cell organelles. It is activated under...
The proneural wave in the Drosophila optic lobe is driven by an excitable reaction-diffusion mechanism.
David J Jörg, Elizabeth E Caygill, Anna E Hakes, Esteban G Contreras, Andrea H Brand, Benjamin D Simons
Feb 15, 2019
D. melanogaster developmental biology Optic Lobe physics of living systems proneural wave reaction-diffusion system sequential patterning Animals Cell Differentiation Drosophila Drosophila Proteins ErbB Receptors Gene Expression Regulation Developmental Neuroepithelial Cells Neurons Optic Lobe Nonmammalian Receptors Invertebrate Peptide Signal Transduction
PAGA
F Alexander Wolf, Fiona K Hamey, Mireya Plass, Jordi Solana, Joakim S Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, Fabian J Theis
Feb 18, 2019
Quantitative analysis of auxin sensing in leaf primordia argues against proposed role in regulating leaf dorsoventrality.
Dorsoventrality in leaves has been shown to depend on the pre-patterned expression of KANADI and HD-ZIPIII genes within the plant shoot apical meristem (SAM). However, it has also been proposed that asymmetric auxin levels...
A. thaliana Auxin developmental biology dorsal Leaf plant plant biology polarity ventral Arabidopsis Arabidopsis Proteins Cell Nucleus Gene Expression Regulation Plant Green Fluorescent Proteins Homeodomain Proteins Indoleacetic Acids Meristem Microscopy Confocal Mutation Plant Leaves Plant Shoots Transcription Factors Transgenes
Comparative analysis reveals a role for TGF-β in shaping the residency-related transcriptional signature in tissue-resident memory CD8+ T cells.
Artika P Nath, Asolina Braun, Scott C Ritchie, Francis R Carbone, Laura K Mackay, Thomas Gebhardt, Michael Inouye
Mar 19, 2019
Tissue-resident CD8+ memory T (TRM) cells are immune cells that permanently reside at tissue sites where they play an important role in providing rapid protection against reinfection. They are not only phenotypically and...
Coupling between dynamic 3D tissue architecture and BMP morphogen signaling during Drosophila wing morphogenesis.
Jinghua Gui, Yunxian Huang, Martin Montanari, Daniel Toddie-Moore, Kenji Kikushima, Stephanie Nix, Yukitaka Ishimoto, Osamu Shimmi
Mar 26, 2019
At the level of organ formation, tissue morphogenesis drives developmental processes in animals, often involving the rearrangement of two-dimensional (2D) structures into more complex three-dimensional (3D) tissues. These...
bone morphogenetic protein Drosophila Epithelial morphogenesis live-imaging three-dimensional architecture Animals Bone Morphogenetic Proteins Cell Differentiation Cell Proliferation Drosophila Proteins Drosophila melanogaster Epithelium Gene Expression Regulation Developmental Gene Knockdown Techniques Morphogenesis Signal Transduction Wings Animal
Tensorial blind source separation for improved analysis of multi-omic data.
There is an increased need for integrative analyses of multi-omic data. We present and benchmark a novel tensorial independent component analysis (tICA) algorithm against current state-of-the-art methods. We find that tICA...
Cancer dimensional reduction Epigenome-wide association study Independent Component Analysis Multi-omic Tensor mQTL Algorithms DNA Copy Number Variations DNA Methylation Epigenesis Genetic Epigenomics Gene Expression Regulation Neoplastic Genetic Markers Genome-Wide Association Study Humans Neoplasms Quantitative Trait Loci
A ChIP-chip approach reveals a novel role for transcription factor IRF1 in the DNA damage response.
IRF1 is a transcription factor that regulates key processes in the immune system and in tumour suppression. To gain further insight into IRF1's role in these processes, we searched for new target genes by performing chromatin...
Binding Sites Cell Line Tumor Cells Cultured Chromatin Immunoprecipitation Cross-Linking Reagents DNA Damage DNA Repair DNA-Binding Proteins Fanconi Anemia Complementation Group Proteins FIBROBLASTS Gene Expression Regulation Humans Interferon Regulatory Factor-1 Interferon-gamma Melphalan Oligonucleotide Array Sequence Analysis RNA Helicases RNA Interference Regulatory Elements Transcriptional Reproducibility of Results
Hepatocyte expression and prognostic importance of senescence marker p21 in liver histopathology samples from dogs with chronic hepatitis.
Andre J Kortum, Emilie A Cloup, Tim L Williams, Fernendo Constantino-Casas, Penny J Watson
Sep 10, 2018
αE-catenin is a candidate tumor suppressor for the development of E-cadherin-expressing lobular-type breast cancer.
Jolien S de Groot, Max Ak Ratze, Miranda van Amersfoort, Tanja Eisemann, Eva J Vlug, Mijanou T Niklaas, Suet-Feung Chin, Carlos Caldas, Paul J van Diest, Jos Jonkers, Johan de Rooij, Patrick WB Derksen
Sep 10, 2018
Although mutational inactivation of E-cadherin (CDH1) is the main driver of invasive lobular breast cancer (ILC), approximately 10-15% of all ILCs retain membrane-localized E-cadherin despite the presence of an apparent...
E-cadherin Rho/Rock lobular breast cancer mouse model α-catenin (CTNNA1) Actomyosin Adherens Junctions Animals Anoikis Antigens CD Breast Neoplasms Cadherins Carcinoma Lobular Cell Adhesion Cell Proliferation Cell Shape Female Gene Expression Regulation Neoplastic Genetic Predisposition to Disease Humans MCF-7 Cells Mice Knockout Mutation Neoplasm Invasiveness Phenotype Signal Transduction Tumor Suppressor Protein p53 Tumor Suppressor Proteins alpha Catenin rho GTP-Binding Proteins rho-Associated Kinases
Integrative Kinome Profiling Identifies mTORC1/2 Inhibition as Treatment Strategy in Ovarian Clear Cell Carcinoma.
Joseph J Caumanns, Katrien Berns, G Bea A Wisman, Rudolf SN Fehrmann, Tushar Tomar, Harry Klip, Gert J Meersma, E Marielle Hijmans, Annemiek MC Gennissen, Evelien W Duiker, Desiree Weening, Hiroaki Itamochi, Roelof JC Kluin, Anna KL Reyners, Michael J Birrer, Helga B Salvesen, Ignace Vergote, Els Van Nieuwenhuysen, James Brenton, E Ioana Braicu, Jolanta Kupryjanczyk, Beata Spiewankiewicz, Lorenza Mittempergher, René Bernards, Ate GJ van der Zee, Steven de Jong
Sep 10, 2018
Purpose: Advanced-stage ovarian clear cell carcinoma (OCCC) is unresponsive to conventional platinum-based chemotherapy. Frequent alterations in OCCC include deleterious mutations in the tumor suppressor ARID1A and activating...
Adenocarcinoma Clear Cell Animals Cell Line Tumor Cell Proliferation Class I Phosphatidylinositol 3-Kinases DNA-Binding Proteins Female Gene Expression Regulation Neoplastic Heterografts Humans Mechanistic Target of Rapamycin Complex 1 Mechanistic Target of Rapamycin Complex 2 Mice Morpholines Mutation Nuclear Proteins Ovarian Neoplasms Signal Transduction Transcription Factors
DeepSynergy
Kristina Preuer, Richard PI Lewis, Sepp Hochreiter, Andreas Bender, Krishna C Bulusu, Günter Klambauer
Nov 05, 2018
MOTIVATION: While drug combination therapies are a well-established concept in cancer treatment, identifying novel synergistic combinations is challenging due to the size of combinatorial space. However, computational approaches...
Injury-induced perivascular niche supports alternative differentiation of adult rodent CNS progenitor cells.
Justyna Ulanska-Poutanen, Jakub Mieczkowski, Chao Zhao, Katarzyna Konarzewska, Beata Kaza, Hartmut Bf Pohl, Lukasz Bugajski, Bozena Kaminska, Robin Jm Franklin, Malgorzata Zawadzka
Nov 19, 2018
Schwann Cells adult CNS progenitors neuroscience perivascular niche rat remyelination Animals Astrocytes Bone Morphogenetic Proteins Cell Differentiation Cellular Microenvironment Central Nervous System Demyelinating Diseases Endothelial Cells Gene Expression Regulation Ligands Oligodendroglia Peripheral Nervous System RNA Messenger Rats Stem Cell Niche Stem Cells Wnt Signaling Pathway Wounds and Injuries
Common genetic variation drives molecular heterogeneity in human iPSCs.
Helena Kilpinen, Angela Goncalves, Andreas Leha, Vackar Afzal, Kaur Alasoo, Sofie Ashford, Sendu Bala, Dalila Bensaddek, Francesco Paolo Casale, Oliver J Culley, Petr Danecek, Adam Faulconbridge, Peter W Harrison, Annie Kathuria, Davis McCarthy, Shane A McCarthy, Ruta Meleckyte, Yasin Memari, Nathalie Moens, Filipa Soares, Alice Mann, Ian Streeter, Chukwuma A Agu, Alex Alderton, Rachel Nelson, Sarah Harper, Minal Patel, Alistair White, Sharad R Patel, Laura Clarke, Reena Halai, Christopher M Kirton, Anja Kolb-Kokocinski, Philip Beales, Ewan Birney, Davide Danovi, Angus I Lamond, Willem H Ouwehand, Ludovic Vallier, Fiona M Watt, Richard Durbin, Oliver Stegle, Daniel J Gaffney
Nov 20, 2018
Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS...
Genome-wide association study implicates immune dysfunction in the development of Hodgkin lymphoma.
Amit Sud, Hauke Thomsen, Giulia Orlando, Asta Försti, Philip J Law, Peter Broderick, Rosie Cooke, Fadi Hariri, Tomi Pastinen, Douglas F Easton, Paul DP Pharoah, Alison M Dunning, Julian Peto, Federico Canzian, Rosalind Eeles, Zsofia Kote-Jarai, Kenneth Muir, Nora Pashayan, Daniele Campa, Per Hoffmann, Markus M Nöthen, Karl-Heinz Jöckel, Elke Pogge von Strandmann, Anthony J Swerdlow, Andreas Engert, Nick Orr, Kari Hemminki, Richard S Houlston
Nov 21, 2018
Quantitative Temporal Proteomic Analysis of Vaccinia Virus Infection Reveals Regulation of Histone Deacetylases by an Interferon Antagonist.
Lior Soday, Yongxu Lu, Jonas D Albarnaz, Colin TR Davies, Robin Antrobus, Geoffrey L Smith, Michael P Weekes
Apr 16, 2019
Histone deacetylase host-pathogen interaction Immune Evasion innate immunity interferon Poxvirus quantitative proteomics restriction factor systems virology tandem mass tag Cytomegalovirus Down-Regulation Gene Expression Regulation Viral Herpesvirus 1 Human Histone Deacetylases Host-Pathogen Interactions Humans Immune Evasion Interferons Membrane Proteins Proteasome Endopeptidase Complex Proteolysis Proteomics Time Factors Vaccinia vaccinia virus Viral Proteins
Dicer1 is required for pigment cell and craniofacial development in zebrafish.
Andrea MJ Weiner, Nadia L Scampoli, Tomás J Steeman, Christopher M Dooley, Elisabeth M Busch-Nentwich, Robert N Kelsh, Nora B Calcaterra
Apr 29, 2019
The multidomain RNase III endoribonuclease DICER is required for the generation of most functional microRNAs (miRNAs). Loss of Dicer affects developmental processes at different levels. Here, we characterized the zebrafish...
Neural Crest Zebrafish miRNAs Sox10 3' Untranslated Regions Animals Apoptosis Cartilage Embryo Nonmammalian Gene Expression Regulation Head Larva Melanocytes Microphthalmia-Associated Transcription Factor Monophenol Monooxygenase Mutation Neural Crest Ribonuclease III SOXE Transcription Factors Zebrafish Zebrafish Proteins
Therapeutic relevance of the PP2A-B55 inhibitory kinase MASTL/Greatwall in breast cancer.
Mónica Álvarez-Fernández, María Sanz-Flores, Belén Sanz-Castillo, María Salazar-Roa, David Partida, Elisabet Zapatero-Solana, H Raza Ali, Eusebio Manchado, Scott Lowe, Todd VanArsdale, David Shields, Carlos Caldas, Miguel Quintela-Fandino, Marcos Malumbres
Apr 29, 2019
PP2A is a major tumor suppressor whose inactivation is frequently found in a wide spectrum of human tumors. In particular, deletion or epigenetic silencing of genes encoding the B55 family of PP2A regulatory subunits is a common...
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