keyword
https://read.qxmd.com/read/32849296/identification-of-a-prognostic-3-gene-risk-prediction-model-for-thyroid-cancer
#1
Haiping Zhao, Shiwei Zhang, Shijie Shao, Haixing Fang
Objective: We aimed to screen the genes associated with thyroid cancer (THCA) prognosis, and construct a poly-gene risk prediction model for prognosis prediction and improvement. Methods: The HTSeq-Counts data of THCA were accessed from TCGA database, including 505 cancer samples and 57 normal tissue samples. "edgeR" package was utilized to perform differential analysis, and weighted gene co-expression network analysis (WGCNA) was applied to screen the differential co-expression genes associated with THCA tissue types...
2020: Frontiers in Endocrinology
https://read.qxmd.com/read/31076498/a-ca2-atpase-regulates-e-cadherin-biogenesis-and-epithelial-mesenchymal-transition-in-breast-cancer-cells
#2
Donna K Dang, Monish Ram Makena, Jose P Llongueras, Hari Prasad, Myungjun Ko, Manuj Bandral, Rajini Rao
Progression of benign tumors to invasive, metastatic cancer is accompanied by the epithelial to mesenchymal transition (EMT), characterized by loss of the cell-adhesion protein E-cadherin. Although silencing mutations and transcriptional repression of the E-cadherin gene have been widely studied, not much is known about post-translational regulation of E-cadherin in tumors. We show that E-cadherin is tightly co-expressed with the secretory pathway Ca2+-ATPase isoform 2, SPCA2 (ATP2C2), in breast tumors. Loss of SPCA2 impairs surface expression of E-cadherin and elicits mesenchymal gene expression through disruption of cell adhesion in tumorspheres and downstream Hippo-YAP signaling...
May 10, 2019: Molecular Cancer Research: MCR
https://read.qxmd.com/read/30443032/rna-sequencing-based-analysis-of-the-laying-hen-uterus-revealed-the-novel-genes-and-biological-pathways-involved-in-the-eggshell-biomineralization
#3
Nirvay Sah, Donna Lee Kuehu, Vedbar Singh Khadka, Youping Deng, Karolina Peplowska, Rajesh Jha, Birendra Mishra
Eggshell is the outermost calcified covering of an egg that protects it from microbial invasion and physical damage, and is critical for egg quality. However, understanding of the genes/proteins and the biological pathways regulating the eggshell formation is still obscure. We hypothesized that the transcriptomic analysis of the chicken uteri using RNA-sequencing may reveal novel genes and biological pathways involved in the eggshell biomineralization. RNA-sequence analysis using uteri of laying hens at 15-20 h post-ovulation (layers, n = 3) and non-laying (non-layers, n = 3) hens was carried out...
November 15, 2018: Scientific Reports
https://read.qxmd.com/read/30003630/genome-wide-association-meta-analysis-of-age-at-first-cannabis-use
#4
Camelia C Minică, Karin J H Verweij, Peter J van der Most, Hamdi Mbarek, Manon Bernard, Kristel R van Eijk, Penelope A Lind, Meng Zhen Liu, Dominique F Maciejewski, Teemu Palviainen, Cristina Sánchez-Mora, Richard Sherva, Michelle Taylor, Raymond K Walters, Abdel Abdellaoui, Timothy B Bigdeli, Susan J T Branje, Sandra A Brown, Miguel Casas, Robin P Corley, George Davey-Smith, Gareth E Davies, Erik A Ehli, Lindsay Farrer, Iryna O Fedko, Iris Garcia-Martínez, Scott D Gordon, Catharina A Hartman, Andrew C Heath, Ian B Hickie, Matthew Hickman, Christian J Hopfer, Jouke Jan Hottenga, René S Kahn, Jaakko Kaprio, Tellervo Korhonen, Henry R Kranzler, Ken Krauter, Pol A C van Lier, Pamela A F Madden, Sarah E Medland, Michael C Neale, Wim H J Meeus, Grant W Montgomery, Ilja M Nolte, Albertine J Oldehinkel, Zdenka Pausova, Josep A Ramos-Quiroga, Vanesa Richarte, Richard J Rose, Jean Shin, Michael C Stallings, Tamara L Wall, Jennifer J Ware, Margaret J Wright, Hongyu Zhao, Hans M Koot, Tomas Paus, John K Hewitt, Marta Ribasés, Anu Loukola, Marco P Boks, Harold Snieder, Marcus R Munafò, Joel Gelernter, Dorret I Boomsma, Nicholas G Martin, Nathan A Gillespie, Jacqueline M Vink, Eske M Derks
BACKGROUND AND AIMS: Cannabis is one of the most commonly used substances among adolescents and young adults. Earlier age at cannabis initiation is linked to adverse life outcomes, including multi-substance use and dependence. This study estimated the heritability of age at first cannabis use and identified associations with genetic variants. METHODS: A twin-based heritability analysis using 8055 twins from three cohorts was performed. We then carried out a genome-wide association meta-analysis of age at first cannabis use in a discovery sample of 24 953 individuals from nine European, North American and Australian cohorts, and a replication sample of 3735 individuals...
July 13, 2018: Addiction
https://read.qxmd.com/read/29201552/-atp2c2-and-dyx1c1-are-putative-modulators-of-dyslexia-related-mmr
#5
Bent Müller, Gesa Schaadt, Johannes Boltze, Frank Emmrich, Michael A Skeide, Nicole E Neef, Indra Kraft, Jens Brauer, Angela D Friederici, Holger Kirsten, Arndt Wilcke
Background: Dyslexia is a specific learning disorder affecting reading and spelling abilities. Its prevalence is ~5% in German-speaking individuals. Although the etiology of dyslexia largely remains to be determined, comprehensive evidence supports deficient phonological processing as a major contributing factor. An important prerequisite for phonological processing is auditory discrimination and, thus, essential for acquiring reading and spelling skills. The event-related potential Mismatch Response (MMR) is an indicator for auditory discrimination capabilities with dyslexics showing an altered late component of MMR in response to auditory input...
November 2017: Brain and Behavior
https://read.qxmd.com/read/29191953/surfactant-protein-d-is-a-causal-risk-factor-for-copd-results-of-mendelian-randomisation
#6
Ma'en Obeidat, Xuan Li, Stephen Burgess, Guohai Zhou, Nick Fishbane, Nadia N Hansel, Yohan Bossé, Philippe Joubert, Ke Hao, David C Nickle, Maarten van den Berge, Wim Timens, Michael H Cho, Brian D Hobbs, Kim de Jong, Marike Boezen, Rayjean J Hung, Nicholas Rafaels, Rasika Mathias, Ingo Ruczinski, Terri H Beaty, Kathleen C Barnes, Peter D Paré, Don D Sin
Surfactant protein D (SP-D) is produced primarily in the lung and is involved in regulating pulmonary surfactants, lipid homeostasis and innate immunity. Circulating SP-D levels in blood are associated with chronic obstructive pulmonary disease (COPD), although causality remains elusive.In 4061 subjects with COPD, we identified genetic variants associated with serum SP-D levels. We then determined whether these variants affected lung tissue gene expression in 1037 individuals. A Mendelian randomisation framework was then applied, whereby serum SP-D-associated variants were tested for association with COPD risk in 11 157 cases and 36 699 controls and with 11 years decline of lung function in the 4061 individuals...
November 2017: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://read.qxmd.com/read/28473875/genome-wide-dna-methylation-analysis-reveals-loci-that-distinguish-different-types-of-adipose-tissue-in-obese-individuals
#7
Donia Macartney-Coxson, Miles C Benton, Ray Blick, Richard S Stubbs, Ronald D Hagan, Michael A Langston
BACKGROUND: Epigenetic mechanisms provide an interface between environmental factors and the genome and are known to play a role in complex diseases such as obesity. These mechanisms, including DNA methylation, influence the regulation of development, differentiation and the establishment of cellular identity. Here we employ two approaches to identify differential methylation between two white adipose tissue depots in obese individuals before and after gastric bypass and significant weight loss...
2017: Clinical Epigenetics
https://read.qxmd.com/read/28000910/-environmental-and-genetic-variables-related-with-alterations-in-language-acquisition-in-early-childhood
#8
REVIEW
A Moriano-Gutierrez, J Colomer-Revuelta, J Sanjuan, J M Carot-Sierra
INTRODUCTION: A great deal of research has addressed problems in the correct acquisition of language, but with few overall conclusions. The reasons for this lie in the individual variability, the existence of different measures for assessing language and the fact that a complex network of genetic and environmental factors are involved in its development. AIM: To review the environmental and genetic variables that have been studied to date, in order to gain a better under-standing of the causes of specific language impairment and create new evidence that can help in the development of screening systems for the early detection of these disorders...
January 1, 2017: Revista de Neurologia
https://read.qxmd.com/read/27017909/atp2c2-is-transcribed-from-a-unique-transcriptional-start-site-in-mouse-pancreatic-acinar-cells
#9
Melissa A Fenech, Caitlin M Sullivan, Lucimar T Ferreira, Rashid Mehmood, William A MacDonald, Peter B Stathopulos, Christopher L Pin
Proper regulation of cytosolic Ca(2+) is critical for pancreatic acinar cell function. Disruptions in normal Ca(2+) concentrations affect numerous cellular functions and are associated with pancreatitis. Membrane pumps and channels regulate cytosolic Ca(2+) homeostasis by promoting rapid Ca(2+) movement. Determining how expression of Ca(2+) modulators is regulated and the cellular alterations that occur upon changes in expression can provide insight into initiating events of pancreatitis. The goal of this study was to delineate the gene structure and regulation of a novel pancreas-specific isoform for Secretory Pathway Ca(2+) ATPase 2 (termed SPCA2C), which is encoded from the Atp2c2 gene...
December 2016: Journal of Cellular Physiology
https://read.qxmd.com/read/25448322/language-impairment-and-dyslexia-genes-influence-language-skills-in-children-with-autism-spectrum-disorders
#10
John D Eicher, Jeffrey R Gruen
Language and communication development is a complex process influenced by numerous environmental and genetic factors. Many neurodevelopment disorders include deficits in language and communication skills in their diagnostic criteria, including autism spectrum disorders (ASD), language impairment (LI), and dyslexia. These disorders are polygenic and complex with a significant genetic component contributing to each. The similarity of language phenotypes and comorbidity of these disorders suggest that they may share genetic contributors...
April 2015: Autism Research: Official Journal of the International Society for Autism Research
https://read.qxmd.com/read/25296922/deletion-of-16q24-1-supports-a-role-for-the-atp2c2-gene-in-specific-language-impairment
#11
Amena W Smith, Kenton R Holden, Alka Dwivedi, Barbara R Dupont, Michael J Lyons
A 10-year-old boy presented with a history of significant delay in language acquisition as well as receptive and expressive language impairment that persisted into elementary school. In school, he exhibited difficulty with reading comprehension, telling and understanding narratives, and making inferences. Other aspects of his neurodevelopment were normal, with no history of significant medical concerns. He did not have hearing impairment, oromotor dysfunction, or specific neurologic abnormalities. He did not meet testing criteria for autism...
March 2015: Journal of Child Neurology
https://read.qxmd.com/read/24940735/gene-expression-correlations-in-human-cancer-cell-lines-define-molecular-interaction-networks-for-epithelial-phenotype
#12
Kurt W Kohn, Barry M Zeeberg, William C Reinhold, Yves Pommier
Using gene expression data to enhance our knowledge of control networks relevant to cancer biology and therapy is a challenging but urgent task. Based on the premise that genes that are expressed together in a variety of cell types are likely to functions together, we derived mutually correlated genes that function together in various processes in epithelial-like tumor cells. Expression-correlated genes were derived from data for the NCI-60 human tumor cell lines, as well as data from the Broad Institute's CCLE cell lines...
2014: PloS One
https://read.qxmd.com/read/23228431/decoding-the-genetics-of-speech-and-language
#13
REVIEW
Sarah A Graham, Simon E Fisher
Researchers are beginning to uncover the neurogenetic pathways that underlie our unparalleled capacity for spoken language. Initial clues come from identification of genetic risk factors implicated in developmental language disorders. The underlying genetic architecture is complex, involving a range of molecular mechanisms. For example, rare protein-coding mutations of the FOXP2 transcription factor cause severe problems with sequencing of speech sounds, while common genetic risk variants of small effect size in genes like CNTNAP2, ATP2C2 and CMIP are associated with typical forms of language impairment...
February 2013: Current Opinion in Neurobiology
https://read.qxmd.com/read/22365959/defining-the-genetic-architecture-of-human-developmental-language-impairment
#14
REVIEW
Ning Li, Christopher W Bartlett
Language is a uniquely human trait, which poses limitations on animal models for discovering biological substrates and pathways. Despite this challenge, rapidly developing biotechnology in the field of genomics has made human genetics studies a viable alternative route for defining the molecular neuroscience of human language. This is accomplished by studying families that transmit both normal and disordered language across generations. The language disorder reviewed here is specific language impairment (SLI), a developmental deficiency in language acquisition despite adequate opportunity, normal intelligence, and without any apparent neurological etiology...
April 9, 2012: Life Sciences
https://read.qxmd.com/read/22240025/structural-evolution-and-tissue-specific-expression-of-tetrapod-specific-second-isoform-of-secretory-pathway-ca2-atpase
#15
Nikolay B Pestov, Ruslan I Dmitriev, Maria B Kostina, Tatyana V Korneenko, Mikhail I Shakhparonov, Nikolai N Modyanov
Secretory pathway Ca-ATPases are less characterized mammalian calcium pumps than plasma membrane Ca-ATPases and sarco-endoplasmic reticulum Ca-ATPases. Here we report analysis of molecular evolution, alternative splicing, tissue-specific expression and subcellular localization of the second isoform of the secretory pathway Ca-ATPase (SPCA2), the product of the ATP2C2 gene. The primary structure of SPCA2 from rat duodenum deduced from full-length transcript contains 944 amino acid residues, and exhibits 65% sequence identity with known SPCA1...
January 27, 2012: Biochemical and Biophysical Research Communications
https://read.qxmd.com/read/21674634/secretory-pathway-stress-responses-as-possible-mechanisms-of-disease-involving-golgi-ca2-pump-dysfunction
#16
REVIEW
Gary E Shull, Marian L Miller, Vikram Prasad
In mammalian tissues, uptake of Ca(2+) and Mn(2+) by Golgi membranes is mediated by the secretory pathway Ca(2+) -ATPases, SPCA1 and SPCA2, encoded by the ATP2C1 and ATP2C2 genes. Loss of one copy of the ATP2C1 gene, which causes SPCA1 haploinsufficiency, leads to squamous cell tumors of keratinized epithelia in mice and to Hailey-Hailey disease, an acantholytic skin disease, in humans. Although the disease phenotypes resulting from SPCA1 haploinsufficiency in mice and humans are quite different, each species-specific phenotype is remarkably similar to those arising as a result of null mutations in one copy of the ATP2A2 gene, encoding SERCA2, the endoplasmic reticulum (ER) Ca(2+) pump...
May 2011: BioFactors
https://read.qxmd.com/read/21457949/dcdc2-kiaa0319-and-cmip-are-associated-with-reading-related-traits
#17
Tom S Scerri, Andrew P Morris, Lyn-Louise Buckingham, Dianne F Newbury, Laura L Miller, Anthony P Monaco, Dorothy V M Bishop, Silvia Paracchini
BACKGROUND: Several susceptibility genes have been proposed for dyslexia (reading disability; RD) and specific language impairment (SLI). RD and SLI show comorbidity, but it is unclear whether a common genetic component is shared. METHODS: We have investigated whether candidate genes for RD and SLI affect specific cognitive traits or have broad effect on cognition. We have analyzed common risk variants within RD (MRPL19/C2ORF3, KIAA0319, and DCDC2) and language impairment (CMIP and ATP2C2) candidate loci in the Avon Longitudinal Study of Parents and Children cohort (n = 3725), representing children born in southwest England in the early 1990s...
August 1, 2011: Biological Psychiatry
https://read.qxmd.com/read/21165691/investigation-of-dyslexia-and-sli-risk-variants-in-reading-and-language-impaired-subjects
#18
D F Newbury, S Paracchini, T S Scerri, L Winchester, L Addis, Alex J Richardson, J Walter, J F Stein, J B Talcott, A P Monaco
Dyslexia (or reading disability) and specific language impairment (or SLI) are common childhood disorders that show considerable co-morbidity and diagnostic overlaps and have been suggested to share some genetic aetiology. Recently, genetic risk variants have been identified for SLI and dyslexia enabling the direct evaluation of possible shared genetic influences between these disorders. In this study we investigate the role of variants in these genes (namely MRPL19/C20RF3, ROBO1, DCDC2, KIAA0319, DYX1C1, CNTNAP2, ATP2C2 and CMIP) in the aetiology of SLI and dyslexia...
January 2011: Behavior Genetics
https://read.qxmd.com/read/20955937/genetic-advances-in-the-study-of-speech-and-language-disorders
#19
REVIEW
D F Newbury, A P Monaco
Developmental speech and language disorders cover a wide range of childhood conditions with overlapping but heterogeneous phenotypes and underlying etiologies. This characteristic heterogeneity hinders accurate diagnosis, can complicate treatment strategies, and causes difficulties in the identification of causal factors. Nonetheless, over the last decade, genetic variants have been identified that may predispose certain individuals to different aspects of speech and language difficulties. In this review, we summarize advances in the genetic investigation of stuttering, speech-sound disorder (SSD), specific language impairment (SLI), and developmental verbal dyspraxia (DVD)...
October 21, 2010: Neuron
https://read.qxmd.com/read/20599950/mist1-regulates-the-pancreatic-acinar-cell-expression-of-atp2c2-the-gene-encoding-secretory-pathway-calcium-atpase-2
#20
Victoria C Garside, Agnes S Kowalik, Charis L Johnson, Daniel DiRenzo, Stephen F Konieczny, Christopher L Pin
MIST1 is a transcription factor expressed in pancreatic acinar cells and other serous exocrine cells. Mice harboring a targeted deletion of the Mist1 gene (Mist1(-/-)) exhibit alterations in acinar regulated exocytosis and aberrant Ca(2+) signaling that are normally controlled by acinar cell Ca(2+)-ATPases. Previous studies indicated that total sarcoendoplasmic reticulum Ca(2+)-ATPases (SERCA) and plasma membrane Ca(2+)-ATPases (PMCA) remained unaffected in Mist1(-/-) acinar cultures. Therefore, we have assessed the expression of Atp2c2, the gene that encodes the secretory pathway Ca(2+)-ATPase 2 (SPCA2)...
October 15, 2010: Experimental Cell Research
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