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Guillaume Velasco, Giacomo Grillo, Nizar Touleimat, Laure Ferry, Ivana Ivkovic, Florence Ribierre, Jean-François Deleuze, Sophie Chantalat, Capucine Picard, Claire Francastel
Alterations of DNA methylation landscapes and machinery are a hallmark of many human diseases. A prominent case is the ICF syndrome, a rare autosomal recessive immunological/neurological disorder diagnosed by the loss of DNA methylation at (peri)centromeric repeats and its associated chromosomal instability. It is caused by mutations in the de novo DNA methyltransferase DNMT3B in about half of the patients (ICF1). In the remainder, the striking identification of mutations in factors devoid of DNA methyltransferase activity, ZBTB24 (ICF2), CDCA7 (ICF3) or HELLS (ICF4), raised key questions about common or distinguishing DNA methylation alterations downstream of these mutations and hence, about the functional link between the four factors...
April 12, 2018: Human Molecular Genetics
Niina Sandholm, Per-Henrik Groop
Diabetic kidney disease and other long-term complications are common in diabetes, and comprise the main cause of co-morbidity and premature mortality in individuals with diabetes. While familial clustering and heritability have been reported for all diabetic complications, the genetic background and the molecular mechanisms remain poorly understood. In recent years, genome-wide association studies have identified a few susceptibility loci for the renal complications as well as for diabetic retinopathy, diabetic cardiovascular disease and mortality...
February 13, 2018: Current Opinion in Genetics & Development
Christopher Jenness, Simona Giunta, Manuel M Müller, Hiroshi Kimura, Tom W Muir, Hironori Funabiki
Mutations in CDCA7, the SNF2 family protein HELLS (LSH), or the DNA methyltransferase DNMT3b cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. While it has been speculated that DNA methylation defects cause this disease, little is known about the molecular function of CDCA7 and its functional relationship to HELLS and DNMT3b. Systematic analysis of how the cell cycle, H3K9 methylation, and the mitotic kinase Aurora B affect proteomic profiles of chromatin in Xenopus egg extracts revealed that HELLS and CDCA7 form a stoichiometric complex on chromatin, in a manner sensitive to Aurora B...
January 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
Yu-Ting Huang, John O Mason, David J Price
BACKGROUND: We studied whether regulation of Cdca7 (Cell division cycle associated 7) expression by transcription factor Pax6 contributes to Pax6's cellular actions during corticogenesis. The function of Cdca7 in mediating Pax6's effects during corticogenesis has not been explored. Pax6 is expressed by radial glial progenitors in the ventricular zone of the embryonic cortical neuroepithelium, where it is required for the development of a normal complement of Tbr2-expressing intermediate progenitor cells in the subventricular zone...
June 5, 2017: BMC Neuroscience
Colin J Ross, Fadi Towfic, Jyoti Shankar, Daphna Laifenfeld, Mathis Thoma, Matthew Davis, Brian Weiner, Rebecca Kusko, Ben Zeskind, Volker Knappertz, Iris Grossman, Michael R Hayden
BACKGROUND: Copaxone is an efficacious and safe therapy that has demonstrated clinical benefit for over two decades in patients with relapsing forms of multiple sclerosis (MS). On an individual level, patients show variability in their response to Copaxone, with some achieving significantly higher response levels. The involvement of genes (e.g., HLA-DRB1*1501) with high inter-individual variability in Copaxone's mechanism of action (MoA) suggests the potential contribution of genetics to treatment response...
May 31, 2017: Genome Medicine
Eun Pyo Hong, Min Jin Go, Hyung-Lae Kim, Ji Wan Park
A complex interplay among host, pathogen, and environmental factors is believed to contribute to the risk of developing pulmonary tuberculosis (PTB). The lack of replication of published genome-wide association study (GWAS) findings limits the clinical utility of reported single nucleotide polymorphisms (SNPs). We conducted a GWAS using 467 PTB cases and 1,313 healthy controls obtained from two community-based cohorts in Korea. We evaluated the performance of PTB risk models based on different combinations of genetic and nongenetic factors and validated the results in an independent Korean population comprised of 179 PTB cases and 500 healthy controls...
2017: PloS One
M L van den Boogaard, P E Thijssen, C Aytekin, F Licciardi, A A Kıykım, L Spossito, V A S H Dalm, G J Driessen, R Kersseboom, F de Vries, M M van Ostaijen-Ten Dam, A Ikinciogullari, F Dogu, M Oleastro, E Bailardo, L Daxinger, E Nain, S Baris, M J D van Tol, C Weemaes, S M van der Maarel
BACKGROUND: Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is a rare, genetically heterogeneous, autosomal recessive disorder. Patients suffer from recurrent infections caused by reduced levels or absence of serum immunoglobulins. Genetically, 4 subtypes of ICF syndrome have been identified to date: ICF1 (DNMT3B mutations), ICF2 (ZBTB24 mutations), ICF3 (CDCA7 mutations), and ICF4 (HELLS mutations). AIM: To study the mutation spectrum in ICF syndrome...
October 2017: Clinical Genetics
Haoyu Wu, Peter E Thijssen, Eleonora de Klerk, Kelly K D Vonk, Jun Wang, Bianca den Hamer, Caner Aytekin, Silvère M van der Maarel, Lucia Daxinger
For genetically heterogeneous diseases a better understanding of how the underlying gene defects are functionally interconnected will be important for dissecting disease etiology. The Immunodeficiency, Centromeric instability, Facial anomalies (ICF) syndrome is a chromatin disorder characterized by mutations in DNMT3B, ZBTB24, CDCA7 or HELLS Here, we generated a Zbtb24 BTB domain deletion mouse and found that loss of functional Zbtb24 leads to early embryonic lethality. Transcriptome analysis identified Cdca7 as the top down-regulated gene in Zbtb24 homozygous mutant mESCs, which can be restored by ectopic ZBTB24 expression...
September 15, 2016: Human Molecular Genetics
Peter E Thijssen, Yuya Ito, Giacomo Grillo, Jun Wang, Guillaume Velasco, Hirohisa Nitta, Motoko Unoki, Minako Yoshihara, Mikita Suyama, Yu Sun, Richard J L F Lemmers, Jessica C de Greef, Andrew Gennery, Paolo Picco, Barbara Kloeckener-Gruissem, Tayfun Güngör, Ismail Reisli, Capucine Picard, Kamila Kebaili, Bertrand Roquelaure, Tsuyako Iwai, Ikuko Kondo, Takeo Kubota, Monique M van Ostaijen-Ten Dam, Maarten J D van Tol, Corry Weemaes, Claire Francastel, Silvère M van der Maarel, Hiroyuki Sasaki
No abstract text is available yet for this article.
2016: Nature Communications
Caixia Cheng, Yong Zhou, Hongyi Li, Teng Xiong, Shuaicheng Li, Yanghui Bi, Pengzhou Kong, Fang Wang, Heyang Cui, Yaoping Li, Xiaodong Fang, Ting Yan, Yike Li, Juan Wang, Bin Yang, Ling Zhang, Zhiwu Jia, Bin Song, Xiaoling Hu, Jie Yang, Haile Qiu, Gehong Zhang, Jing Liu, Enwei Xu, Ruyi Shi, Yanyan Zhang, Haiyan Liu, Chanting He, Zhenxiang Zhao, Yu Qian, Ruizhou Rong, Zhiwei Han, Yanlin Zhang, Wen Luo, Jiaqian Wang, Shaoliang Peng, Xukui Yang, Xiangchun Li, Lin Li, Hu Fang, Xingmin Liu, Li Ma, Yunqing Chen, Shiping Guo, Xing Chen, Yanfeng Xi, Guodong Li, Jianfang Liang, Xiaofeng Yang, Jiansheng Guo, JunMei Jia, Qingshan Li, Xiaolong Cheng, Qimin Zhan, Yongping Cui
Comprehensive identification of somatic structural variations (SVs) and understanding their mutational mechanisms in cancer might contribute to understanding biological differences and help to identify new therapeutic targets. Unfortunately, characterization of complex SVs across the whole genome and the mutational mechanisms underlying esophageal squamous cell carcinoma (ESCC) is largely unclear. To define a comprehensive catalog of somatic SVs, affected target genes, and their underlying mechanisms in ESCC, we re-analyzed whole-genome sequencing (WGS) data from 31 ESCCs using Meerkat algorithm to predict somatic SVs and Patchwork to determine copy-number changes...
February 4, 2016: American Journal of Human Genetics
Q L Wang, X Chen, M H Zhang, Q H Shen, Z M Qin
The objective of this paper was to identify hub genes and pathways associated with retinoblastoma using centrality analysis of the co-expression network and pathway-enrichment analysis. The co-expression network of retinoblastoma was constructed by weighted gene co-expression network analysis (WGCNA) based on differentially expressed (DE) genes, and clusters were obtained through the molecular complex detection (MCODE) algorithm. Degree centrality analysis of the co-expression network was performed to explore hub genes present in retinoblastoma...
2015: Genetics and Molecular Research: GMR
Peter E Thijssen, Yuya Ito, Giacomo Grillo, Jun Wang, Guillaume Velasco, Hirohisa Nitta, Motoko Unoki, Minako Yoshihara, Mikita Suyama, Yu Sun, Richard J L F Lemmers, Jessica C de Greef, Andrew Gennery, Paolo Picco, Barbara Kloeckener-Gruissem, Tayfun Güngör, Ismail Reisli, Capucine Picard, Kamila Kebaili, Bertrand Roquelaure, Tsuyako Iwai, Ikuko Kondo, Takeo Kubota, Monique M van Ostaijen-Ten Dam, Maarten J D van Tol, Corry Weemaes, Claire Francastel, Silvère M van der Maarel, Hiroyuki Sasaki
The life-threatening Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome is a genetically heterogeneous autosomal recessive disorder. Twenty percent of patients cannot be explained by mutations in the known ICF genes DNA methyltransferase 3B or zinc-finger and BTB domain containing 24. Here we report mutations in the cell division cycle associated 7 and the helicase, lymphoid-specific genes in 10 unexplained ICF cases. Our data highlight the genetic heterogeneity of ICF syndrome; however, they provide evidence that all genes act in common or converging pathways leading to the ICF phenotype...
2015: Nature Communications
Xiangjun Song, Xiaomin Zhao, Yong Huang, Hailing Xiang, Wenlong Zhang, Dewen Tong
Transmissible gastroenteritis virus (TGEV) is a member of Coronaviridae family. TGEV infection has emerged as a major cause of severe gastroenteritis and leads to alterations of many cellular processes. Meanwhile, the pathogenic mechanism of TGEV is still unclear. microRNAs (miRNAs) are a novel class of small non-coding RNAs which are involved in the regulation of numerous biological processes such as viral infection and cell apoptosis. Accumulating data show that miRNAs are involved in the process of coronavirus infection such as replication of severe acute respiratory syndrome coronavirus (SARS-CoV)...
2015: International Journal of Biological Sciences
Jordi Guiu, Dylan J M Bergen, Emma De Pater, Abul B M M K Islam, Verónica Ayllón, Leonor Gama-Norton, Cristina Ruiz-Herguido, Jessica González, Nuria López-Bigas, Pablo Menendez, Elaine Dzierzak, Lluis Espinosa, Anna Bigas
Hematopoietic stem cell (HSC) specification occurs in the embryonic aorta and requires Notch activation; however, most of the Notch-regulated elements controlling de novo HSC generation are still unknown. Here, we identify putative direct Notch targets in the aorta-gonad-mesonephros (AGM) embryonic tissue by chromatin precipitation using antibodies against the Notch partner RBPj. By ChIP-on-chip analysis of the precipitated DNA, we identified 701 promoter regions that were candidates to be regulated by Notch in the AGM...
November 17, 2014: Journal of Experimental Medicine
TacGhee Yi, Wang-Kyun Kim, Joon-Seok Choi, Seung Yong Song, Juhee Han, Ji Hye Kim, Won-Serk Kim, Sang Gyu Park, Hyun-Joo Lee, Yun Kyoung Cho, Sung-Joo Hwang, Sun U Song, Jong-Hyuk Sung
OBJECTIVE: Adipose-derived stem cells (ASCs) isolated from subcutaneous adipose tissue have been tested in clinical trials. However, ASCs isolated by enzyme digestion and centrifugation are heterogeneous and exhibit wide variation in regenerative potential and clinical outcomes. Therefore, we developed a new method for isolating clonal ASCs (cASCs) that does not use enzyme digestion or centrifugation steps. RESEARCH DESIGN AND METHODS: In addition to cell surface markers and differentiation potential, we compared the mitogenic, paracrine and hair growth-promoting effects of ASCs isolated by the gradient centrifugation method (GCM) or by the new subfractionation culturing method (SCM)...
November 2014: Expert Opinion on Biological Therapy
Elinor Sawyer, Rebecca Roylance, Christos Petridis, Mark N Brook, Salpie Nowinski, Efterpi Papouli, Olivia Fletcher, Sarah Pinder, Andrew Hanby, Kelly Kohut, Patricia Gorman, Michele Caneppele, Julian Peto, Isabel Dos Santos Silva, Nichola Johnson, Ruth Swann, Miriam Dwek, Katherine-Anne Perkins, Cheryl Gillett, Richard Houlston, Gillian Ross, Paolo De Ieso, Melissa C Southey, John L Hopper, Elena Provenzano, Carmel Apicella, Jelle Wesseling, Sten Cornelissen, Renske Keeman, Peter A Fasching, Sebastian M Jud, Arif B Ekici, Matthias W Beckmann, Michael J Kerin, Federick Marme, Andreas Schneeweiss, Christof Sohn, Barbara Burwinkel, Pascal Guénel, Therese Truong, Pierre Laurent-Puig, Pierre Kerbrat, Stig E Bojesen, Børge G Nordestgaard, Sune F Nielsen, Henrik Flyger, Roger L Milne, Jose Ignacio Arias Perez, Primitiva Menéndez, Javier Benitez, Hermann Brenner, Aida Karina Dieffenbach, Volker Arndt, Christa Stegmaier, Alfons Meindl, Peter Lichtner, Rita K Schmutzler, Magdalena Lochmann, Hiltrud Brauch, Hans-Peter Fischer, Yon-Dschun Ko, Heli Nevanlinna, Taru A Muranen, Kristiina Aittomäki, Carl Blomqvist, Natalia V Bogdanova, Thilo Dörk, Annika Lindblom, Sara Margolin, Arto Mannermaa, Vesa Kataja, Veli-Matti Kosma, Jaana M Hartikainen, Georgia Chenevix-Trench, Kconfab Investigators, Diether Lambrechts, Caroline Weltens, Erik Van Limbergen, Sigrid Hatse, Jenny Chang-Claude, Anja Rudolph, Petra Seibold, Dieter Flesch-Janys, Paolo Radice, Paolo Peterlongo, Bernardo Bonanni, Sara Volorio, Graham G Giles, Gianluca Severi, Laura Baglietto, Catriona A McLean, Christopher A Haiman, Brian E Henderson, Fredrick Schumacher, Loic Le Marchand, Jacques Simard, Mark S Goldberg, France Labrèche, Martine Dumont, Vessela Kristensen, Robert Winqvist, Katri Pylkäs, Arja Jukkola-Vuorinen, Saila Kauppila, Irene L Andrulis, Julia A Knight, Gord Glendon, Anna Marie Mulligan, Peter Devillee, Rob A E M Tollenaar, Caroline M Seynaeve, Mieke Kriege, Jonine Figueroa, Stephen J Chanock, Mark E Sherman, Maartje J Hooning, Antoinette Hollestelle, Ans M W van den Ouweland, Carolien H M van Deurzen, Jingmei Li, Kamila Czene, Keith Humphreys, Angela Cox, Simon S Cross, Malcolm W R Reed, Mitul Shah, Anna Jakubowska, Jan Lubinski, Katarzyna Jaworska-Bieniek, Katarzyna Durda, Anthony Swerdlow, Alan Ashworth, Nicholas Orr, Minouk Schoemaker, Fergus J Couch, Emily Hallberg, Anna González-Neira, Guillermo Pita, M Rosario Alonso, Daniel C Tessier, Daniel Vincent, Francois Bacot, Manjeet K Bolla, Qin Wang, Joe Dennis, Kyriaki Michailidou, Alison M Dunning, Per Hall, Doug Easton, Paul Pharoah, Marjanka K Schmidt, Ian Tomlinson, Montserrat Garcia-Closas
Invasive lobular breast cancer (ILC) accounts for 10-15% of all invasive breast carcinomas. It is generally ER positive (ER+) and often associated with lobular carcinoma in situ (LCIS). Genome-wide association studies have identified more than 70 common polymorphisms that predispose to breast cancer, but these studies included predominantly ductal (IDC) carcinomas. To identify novel common polymorphisms that predispose to ILC and LCIS, we pooled data from 6,023 cases (5,622 ILC, 401 pure LCIS) and 34,271 controls from 36 studies genotyped using the iCOGS chip...
April 2014: PLoS Genetics
Jiang He, Tanika N Kelly, Qi Zhao, Hongfan Li, Jianfeng Huang, Laiyuan Wang, Cashell E Jaquish, Yun Ju Sung, Lawrence C Shimmin, Fanghong Lu, Jianjun Mu, Dongsheng Hu, Xu Ji, Chong Shen, Dongshuang Guo, Jixiang Ma, Renping Wang, Jinjin Shen, Shengxu Li, Jing Chen, Hao Mei, Chung-Shiuan Chen, Shufeng Chen, Jichun Chen, Jianxin Li, Jie Cao, Xiangfeng Lu, Xigui Wu, Treva K Rice, C Charles Gu, Karen Schwander, L Lee Hamm, Depei Liu, Dabeeru C Rao, James E Hixson, Dongfeng Gu
BACKGROUND: Blood pressure (BP) responses to dietary sodium and potassium intervention and cold pressor test vary considerably among individuals. We aimed to identify novel genetic variants influencing individuals' BP responses to dietary intervention and cold pressor test. METHODS AND RESULTS: We conducted a genome-wide association study of BP responses in 1881 Han Chinese and de novo genotyped top findings in 698 Han Chinese. Diet-feeding study included a 7-day low-sodium (51...
December 2013: Circulation. Cardiovascular Genetics
Niina Sandholm, Amy Jayne McKnight, Rany M Salem, Eoin P Brennan, Carol Forsblom, Valma Harjutsalo, Ville-Petteri Mäkinen, Gareth J McKay, Denise M Sadlier, Winfred W Williams, Finian Martin, Nicolae Mircea Panduru, Lise Tarnow, Jaakko Tuomilehto, Karl Tryggvason, Gianpaolo Zerbini, Mary E Comeau, Carl D Langefeld, Catherine Godson, Joel N Hirschhorn, Alexander P Maxwell, Jose C Florez, Per-Henrik Groop
Sex and genetic variation influence the risk of developing diabetic nephropathy and ESRD in patients with type 1 diabetes. We performed a genome-wide association study in a cohort of 3652 patients from the Finnish Diabetic Nephropathy (FinnDiane) Study with type 1 diabetes to determine whether sex-specific genetic risk factors for ESRD exist. A common variant, rs4972593 on chromosome 2q31.1, was associated with ESRD in women (P<5×10(-8)) but not in men (P=0.77). This association was replicated in the meta-analysis of three independent type 1 diabetes cohorts (P=0...
October 2013: Journal of the American Society of Nephrology: JASN
E Kaitlynn Allen, Wei-Min Chen, Daniel E Weeks, Fang Chen, Xuanlin Hou, José L Mattos, Josyf C Mychaleckyj, Fernando Segade, Margaretha L Casselbrant, Ellen M Mandel, Robert E Ferrell, Stephen S Rich, Kathleen A Daly, Michèle M Sale
Chronic otitis media with effusion (COME) and recurrent otitis media (ROM) have been shown to be heritable, but candidate gene and linkage studies to date have been equivocal. Our aim was to identify genetic susceptibility factors using a genome-wide association study (GWAS). We genotyped 602 subjects from 143 families with 373 COME/ROM subjects using the Illumina Human CNV370-Duo DNA Bead Chip (324,748 SNPs). We carried out the GWAS scan and imputed SNPs at the regions with the most significant associations...
December 2013: Journal of the Association for Research in Otolaryngology: JARO
Haiping Zhao, Yumin Luo, Xiangrong Liu, Rongliang Wang, Feng Yan, Xiaomeng Liu, Sijie Li, Rehana K Leak, Xunming Ji
Neuronal cell cycle re-entry is pro-apoptotic. The neuroprotective effects and anti-apoptosis of ischemic postconditioning (IPostC) are well established but the underlying mechanism is still unknown. We explored this critical gap in the present study by genomic comparison of ischemic rat cortex following transient middle cerebral artery occlusion (tMCAO) alone and tMCAO+IPostC. The gene expression profiles of ipsilateral cortices were subjected to microarray analysis. RT-PCR, immunoblotting, and immunofluorescence were subsequently used to quantify or localize the cell proliferation marker proliferating cell nuclear antigen (PCNA), positive and negative cell cycle regulators, and related signaling molecules...
May 1, 2013: CNS & Neurological Disorders Drug Targets
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