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https://www.readbyqxmd.com/read/28049421/placental-transcriptome-co-expression-analysis-reveals-conserved-regulatory-programs-across-gestation
#1
Sam Buckberry, Tina Bianco-Miotto, Stephen J Bent, Vicki Clifton, Cheryl Shoubridge, Kartik Shankar, Claire T Roberts
BACKGROUND: Mammalian development in utero is absolutely dependent on proper placental development, which is ultimately regulated by the placental genome. The regulation of the placental genome can be directly studied by exploring the underlying organisation of the placental transcriptome through a systematic analysis of gene-wise co-expression relationships. RESULTS: In this study, we performed a comprehensive analysis of human placental co-expression using RNA sequencing and intergrated multiple transcriptome datasets spanning human gestation...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28045622/use-of-minimal-residual-disease-assessment-to-redefine-induction-failure-in-pediatric-acute-lymphoblastic-leukemia
#2
David O'Connor, Anthony V Moorman, Rachel Wade, Jeremy Hancock, Ronald M R Tan, Jack Bartram, John Moppett, Claire Schwab, Katharine Patrick, Christine J Harrison, Rachael Hough, Nick Goulden, Ajay Vora, Sujith Samarasinghe
Purpose Our aim was to determine the role of end-of-induction (EOI) minimal residual disease (MRD) assessment in the identification and stratification of induction failure in patients with pediatric acute lymphoblastic leukemia (ALL) and to identify genetic abnormalities that drive disease in these patients. Patients and Methods Analysis included 3,113 patients who were treated in the Medical Research Council UKALL2003 multicenter randomized trial (NCT00222612) between 2003 and 2011. MRD was measured by using standardized real-time quantitative PCR...
January 3, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28010895/platelet-derived-growth-factor-receptors-pdgfrs-fusion-genes-involvement-in-hematological-malignancies
#3
REVIEW
Kwaku Appiah-Kubi, Ting Lan, Ying Wang, Hai Qian, Min Wu, Xiaoyuan Yao, Yan Wu, Yongchang Chen
PURPOSE: To investigate oncogenic platelet-derived growth factor receptor(PDGFR) fusion genes involvement in hematological malignancies, the advances in the PDGFR fusion genes diagnosis and development of PDGFR fusions inhibitors. METHODS: Literature search was done using terms "PDGFR and Fusion" or "PDGFR and Myeloid neoplasm" or 'PDGFR and Lymphoid neoplasm' or "PDGFR Fusion Diagnosis" or "PDGFR Fusion Targets" in databases including PubMed, ASCO.org, and Medscape...
January 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/27983964/functional-consequences-of-i56ii-dlx-enhancer-deletion-in-the-developing-mouse-forebrain
#4
S Fazel Darbandi, L Poitras, S Monis, S Lindtner, M Yu, G Hatch, J L Rubenstein, M Ekker
Dlx homeobox genes encode a group of transcription factors that play an essential role during developmental processes including maintaining the differentiation, proliferation and migration of GABAergic interneurons. The Dlx1/2 and Dlx5/6 genes are expressed in the forebrain and are arranged in convergently transcribed bigene clusters, with I12a/I12b and I56i/I56ii cis-regulatory elements (CREs) located in the intergenic region of each cluster respectively. We have characterized the phenotypic consequences of deleting I56ii on forebrain development and spatial patterning of corridor cells that are involved in guiding thalamocortical projections...
October 27, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27979924/tumor-suppressors-btg1-and-ikzf1-cooperate-during-mouse-leukemia-development-and-increase-relapse-risk-in-b-cell-precursor-acute-lymphoblastic-leukemia-patients
#5
Blanca Scheijen, Judith M Boer, Rene' Marke, Esther Tijchon, Dorette van Ingen Schenau, Esme' Waanders, Liesbeth van Emst, Laurens T van der Meer, Rob Pieters, Gabriele Escherich, Martin A Horstmann, Edwin Sonneveld, Nicola Venn, Rosemary Sutton, Luciano Dalla-Pozza, Roland P Kuiper, Peter M Hoogerbrugge, Monique L den Boer, Frank N van Leeuwen
Deletions and mutations affecting lymphoid transcription factor IKZF1 (IKAROS) are associated with an increased relapse risk and poor outcome in B-cell precursor acute lymphoblastic leukemia. However, additional genetic events may either enhance or negate the effects of IKZF1 deletions on prognosis. In a large discovery cohort of 533 childhood B-cell precursor acute lymphoblastic leukemia patients, we observed that single copy losses of BTG1 were significantly enriched in IKZF1-deleted B-cell precursor acute lymphoblastic leukemia (P=0...
December 15, 2016: Haematologica
https://www.readbyqxmd.com/read/27924221/targeting-mll1-h3k4-methyltransferase-activity-to-guide-cardiac-lineage-specific-reprogramming-of-fibroblasts
#6
Liu Liu, Ienglam Lei, Hacer Karatas, Yangbing Li, Li Wang, Leonid Gnatovskiy, Yali Dou, Shaomeng Wang, Li Qian, Zhong Wang
Generation of induced cardiomyocytes (iCMs) directly from fibroblasts offers a great opportunity for cardiac disease modeling and cardiac regeneration. A major challenge of iCM generation is the low conversion rate. To address this issue, we attempted to identify small molecules that could potentiate the reprogramming ability towards cardiac fate by removing inhibitory roadblocks. Using mouse embryonic fibroblasts as the starting cell source, we first screened 47 cardiac development related epigenetic and transcription factors, and identified an unexpected role of H3K4 methyltransferase Mll1 and related factor Men1 in inhibiting iCM reprogramming...
2016: Cell Discovery
https://www.readbyqxmd.com/read/27923118/cutting-out-the-middle-man-in-light-hormone-interactions
#7
Anna N Stepanova, Jose M Alonso
In this issue of Developmental Cell, Shi et al. (2016a) show that red-light-activated phytochrome B interacts with transcriptional regulators of ethylene signaling, EIN3/EIL1, triggering their degradation by bringing the F-box proteins EBF1 and 2 to the complex. These findings provide a paradigm for crosstalk between light and hormone signaling pathways.
December 5, 2016: Developmental Cell
https://www.readbyqxmd.com/read/27918534/multiethnic-genome-wide-meta-analysis-of-ectopic-fat-depots-identifies-loci-associated-with-adipocyte-development-and-differentiation
#8
Audrey Y Chu, Xuan Deng, Virginia A Fisher, Alexander Drong, Yang Zhang, Mary F Feitosa, Ching-Ti Liu, Olivia Weeks, Audrey C Choh, Qing Duan, Thomas D Dyer, John D Eicher, Xiuqing Guo, Nancy L Heard-Costa, Tim Kacprowski, Jack W Kent, Leslie A Lange, Xinggang Liu, Kurt Lohman, Lingyi Lu, Anubha Mahajan, Jeffrey R O'Connell, Ankita Parihar, Juan M Peralta, Albert V Smith, Yi Zhang, Georg Homuth, Ahmed H Kissebah, Joel Kullberg, René Laqua, Lenore J Launer, Matthias Nauck, Michael Olivier, Patricia A Peyser, James G Terry, Mary K Wojczynski, Jie Yao, Lawrence F Bielak, John Blangero, Ingrid B Borecki, Donald W Bowden, John Jeffrey Carr, Stefan A Czerwinski, Jingzhong Ding, Nele Friedrich, Vilmunder Gudnason, Tamara B Harris, Erik Ingelsson, Andrew D Johnson, Sharon L R Kardia, Carl D Langefeld, Lars Lind, Yongmei Liu, Braxton D Mitchell, Andrew P Morris, Thomas H Mosley, Jerome I Rotter, Alan R Shuldiner, Bradford Towne, Henry Völzke, Henri Wallaschofski, James G Wilson, Matthew Allison, Cecilia M Lindgren, Wolfram Goessling, L Adrienne Cupples, Matthew L Steinhauser, Caroline S Fox
Variation in body fat distribution contributes to the metabolic sequelae of obesity. The genetic determinants of body fat distribution are poorly understood. The goal of this study was to gain new insights into the underlying genetics of body fat distribution by conducting sample-size-weighted fixed-effects genome-wide association meta-analyses in up to 9,594 women and 8,738 men of European, African, Hispanic and Chinese ancestry, with and without sex stratification, for six traits associated with ectopic fat (hereinafter referred to as ectopic-fat traits)...
January 2017: Nature Genetics
https://www.readbyqxmd.com/read/27913602/clonal-conversion-of-b-lymphoid-leukemia-reveals-cross-lineage-transfer-of-malignant-states
#9
Rajesh Somasundaram, Josefine Åhsberg, Kazuki Okuyama, Jonas Ungerbäck, Henrik Lilljebjörn, Thoas Fioretos, Tobias Strid, Mikael Sigvardsson
Even though leukemia is considered to be confined to one specific hematopoietic cell type, cases of acute leukemia of ambiguous lineage and patients relapsing in phenotypically altered disease suggest that a malignant state may be transferred between lineages. Because B-cell leukemia is associated with mutations in transcription factors of importance for stable preservation of lineage identity, we here investigated the potential lineage plasticity of leukemic cells. We report that primary pro-B leukemia cells from mice carrying heterozygous mutations in either or both the Pax5 and Ebf1 genes, commonly mutated in human leukemia, can be converted into T lineage leukemia cells...
November 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/27911806/permissive-roles-of-cytokines-interleukin-7-and-flt3-ligand-in-mouse-b-cell-lineage-commitment
#10
Lilly von Muenchow, Llucia Alberti-Servera, Fabian Klein, Giuseppina Capoferri, Daniela Finke, Rhodri Ceredig, Antonius Rolink, Panagiotis Tsapogas
Hematopoietic cells are continuously generated throughout life from hematopoietic stem cells, thus making hematopoiesis a favorable system to study developmental cell lineage commitment. The main factors incorporating environmental signals to developing hematopoietic cells are cytokines, which regulate commitment of hematopoietic progenitors to the different blood lineages by acting either in an instructive or a permissive manner. Fms-like tyrosine kinase-3 (Flt3) ligand (FL) and Interleukin-7 (IL-7) are cytokines pivotal for B-cell development, as manifested by the severely compromised B-cell development in their absence...
December 13, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27889898/the-transcription-factors-ebf1-and-ebf2-are-positive-regulators-of-myelination-in-schwann-cells
#11
Diego Moruzzo, Lucilla Nobbio, Bruno Sterlini, G Giacomo Consalez, Fabio Benfenati, Angelo Schenone, Anna Corradi
Myelin formation by Schwann cells is tightly controlled by multiple pathways and regulatory molecules. The Ebf2 gene, belonging to the Ebf family of transcription factors regulating cell development and differentiation, is expressed in Schwann cells, and Ebf2 knockout mice show peripheral nerve defects. We also found that Ebf1 is expressed in Schwann cells. To investigate Ebf function in myelination, we silenced Ebf genes in myelinating dorsal root ganglia cultures. Combined downregulation of Ebf genes leads to a severe impairment of myelin formation that is completely rescued by their specific overexpression, suggesting that the expression level of Ebf genes strongly influences axon myelination...
November 26, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27889482/the-red-light-receptor-phytochrome-b-directly-enhances-substrate-e3-ligase-interactions-to-attenuate-ethylene-responses
#12
Hui Shi, Xing Shen, Renlu Liu, Chang Xue, Ning Wei, Xing Wang Deng, Shangwei Zhong
Plants germinating under subterranean darkness assume skotomorphogenesis, a developmental program strengthened by ethylene in response to mechanical pressure of soil. Upon reaching the surface, light triggers a dramatic developmental transition termed de-etiolation that requires immediate termination of ethylene responses. Here, we report that light activation of photoreceptor phyB results in rapid degradation of EIN3, the master transcription factor in the ethylene signaling pathway. As a result, light rapidly and efficiently represses ethylene actions...
December 5, 2016: Developmental Cell
https://www.readbyqxmd.com/read/27876533/multiple-single-nucleotide-polymorphisms-in-the-first-intron-of-the-il2ra-gene-affect-transcription-factor-binding-and-enhancer-activity
#13
Anton M Schwartz, Denis E Demin, Ilya E Vorontsov, Artem S Kasyanov, Lidia V Putlyaeva, Karina A Tatosyan, Ivan V Kulakovskiy, Dmitry V Kuprash
IL2RA gene encodes the alpha subunit of a high-affinity receptor for interleukin-2 which is expressed by several distinct populations of lymphocytes involved in autoimmune processes. A large number of polymorphic alleles of the IL2RA locus are associated with the development of various autoimmune diseases. With bioinformatics analysis we the dissected the first intron of the IL2RA gene and selected several single nucleotide polymorphisms (SNPs) that may influence the regulation of the IL2RA gene in cell types relevant to autoimmune pathology...
February 20, 2017: Gene
https://www.readbyqxmd.com/read/27855558/diagnostic-evaluation-of-rna-sequencing-for-the-detection-of-genetic-abnormalities-associated-with-ph-like-acute-lymphoblastic-leukemia-all
#14
Kai Lee Yap, Larissa V Furtado, Kazuma Kiyotani, Emily Curran, Wendy Stock, Jennifer L McNeer, Sabah Kadri, Jeremy P Segal, Yusuke Nakamura, Michelle M Le Beau, Sandeep Gurbuxani, Gordana Raca
Philadelphia (Ph)-like acute lymphoblastic leukemia (ALL) is a molecular subtype of high-risk B-cell ALL characterized by formation of abnormal gene fusions involving tyrosine kinase (TK) and cytokine receptor genes and activation of TK signaling. Because of the diversity of associated genetic changes, the detection of Ph-like ALL cases currently requires multiple cytogenetic and molecular assays; thus, our goal was to develop a consolidated workflow for detecting genetic abnormalities in Ph-like ALL. We found that total and targeted RNA sequencing (RNAseq)-based approach allowed the detection of abnormal fusion transcripts (EBF1-PDGFRB, P2RY8-CRLF2, RCSD1-ABL1, and RCSD1-ABL2)...
November 17, 2016: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/27822221/activation-of-hls1-by-mechanical-stress-via-ethylene-stabilized-ein3-is-crucial-for-seedling-soil-emergence
#15
Xing Shen, Yanli Li, Ying Pan, Shangwei Zhong
The seeds of terrestrial flowering plants often start their life cycle in subterranean darkness. To protect the fragile apical meristematic tissues and cotyledons from mechanical injuries during soil penetration, dicotyledonous seedlings form an elegant apical hook at the top of the hypocotyl. The apical hook has been considered as an adaption structure to the subterranean environment. However, the role of the apical hook in seedling emergence and the molecular mechanism of apical hook formation under real-life conditions remain highly speculative...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27816938/genome-wide-association-study-of-parental-life-span
#16
Toshiko Tanaka, Ambarish Dutta, Luke C Pilling, Luting Xue, Kathryn L Lunetta, Joanne M Murabito, Stefania Bandinelli, Robert Wallace, David Melzer, Luigi Ferrucci
BACKGROUND: Having longer lived parents has been shown to be an important predictor of health trajectories and life span. As such, parental life span is an important phenotype that may uncover genes that affect longevity. METHODS: A genome-wide association study of parental life span in participants of European and African ancestry from the Health and Retirement Study was conducted. RESULTS: A genome-wide significant association was observed for rs35715456 (log10BF = 6...
November 5, 2016: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/27807034/interaction-of-ccr4-not-with-ebf1-regulates-gene-specific-transcription-and-mrna-stability-in-b-lymphopoiesis
#17
Cheng-Yuan Yang, Senthilkumar Ramamoorthy, Sören Boller, Marc Rosenbaum, Alfonso Rodriguez Gil, Gerhard Mittler, Yumiko Imai, Keiji Kuba, Rudolf Grosschedl
Transcription factor EBF1 (early B-cell factor 1) regulates early B-cell differentiation by poising or activating lineage-specific genes and repressing genes associated with alternative cell fates. To identify proteins that regulate the diverse functions of EBF1, we used SILAC (stable isotope labeling by amino acids in cell culture)-based mass spectrometry of proteins associated with endogenous EBF1 in pro-B cells. This analysis identified most components of the multifunctional CCR4-NOT complex, which regulates transcription and mRNA degradation...
October 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/27744667/replication-of-early-b-cell-factor-1-ebf1-gene-by-psychosocial-stress-interaction-effects-on-central-adiposity-in-a-korean-population
#18
Hyun-Jin Kim, Jin-Young Min, Kyoung-Bok Min
OBJECTIVES: Central obesity plays a major role in the development of many chronic diseases, including cardiovascular disease and cancer. Chronic stress may be involved in the pathophysiology of central obesity. Although several large-scale genome-wide association studies have reported susceptibility genes for central adiposity, the effects of interactions between genes and psychosocial stress on central adiposity have rarely been examined. A recent study focusing on Caucasians discovered the novel gene early B-cell factor 1 (EBF1), which was associated with central obesity-related traits via interactions with stress levels...
September 2016: Journal of Preventive Medicine and Public Health, Yebang Ŭihakhoe Chi
https://www.readbyqxmd.com/read/27664237/superenhancer-reprogramming-drives-a-b-cell-epithelial-transition-and-high-risk-leukemia
#19
Yeguang Hu, Zhihong Zhang, Mariko Kashiwagi, Toshimi Yoshida, Ila Joshi, Nilamani Jena, Rajesh Somasundaram, Akinola Olumide Emmanuel, Mikael Sigvardsson, Julien Fitamant, Nabeel El-Bardeesy, Fotini Gounari, Richard A Van Etten, Katia Georgopoulos
IKAROS is required for the differentiation of highly proliferative pre-B-cell precursors, and loss of IKAROS function indicates poor prognosis in precursor B-cell acute lymphoblastic leukemia (B-ALL). Here we show that IKAROS regulates this developmental stage by positive and negative regulation of superenhancers with distinct lineage affiliations. IKAROS defines superenhancers at pre-B-cell differentiation genes together with B-cell master regulators such as PAX5, EBF1, and IRF4 but is required for a highly permissive chromatin environment, a function that cannot be compensated for by the other transcription factors...
September 1, 2016: Genes & Development
https://www.readbyqxmd.com/read/27539385/gene-expression-analysis-of-developing-cell-groups-in-the-pretectal-region-of-xenopus-laevis
#20
Ruth Morona, José Luis Ferran, Luis Puelles, Agustín González
Our previous analysis of progenitor domains in the pretectum of Xenopus revealed three molecularly distinct anteroposterior subdivisions, identified as precommissural (PcP), juxtacommissural (JcP), and commissural (CoP) histogenetic domains (Morona et al. [2011] J Comp Neurol 519:1024-1050). Here we analyzed at later developmental stages the nuclei derived from these areas, attending to their gene expression patterns and histogenesis. Transcription-factor gene markers were used to selectively map derivatives of each domain: Pax7 and Pax6 (CoP); Foxp1 and Six3 (JcP); and Xiro1, VGlut2, Ebf1, and Ebf3 (PcP)...
August 19, 2016: Journal of Comparative Neurology
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