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https://www.readbyqxmd.com/read/29909697/identification-of-candidate-microrna-biomarkers-in-renal-fibrosis-a-meta-analysis-of-profiling-studies
#1
Alieh Gholaminejad, Hossein Abdul Tehrani, Mohammad Gholami Fesharaki
CONTEXT: The prognostic, diagnostic and therapeutic value of microRNA (miRNA) expression aberrations in renal fibrosis has been studied in recent years. However, the miRNA expression profiling efforts have led to inconsistent results between the studies. OBJECTIVE(S): The aim of this study was to perform a meta-analysis on the renal fibrosis miRNA expression profiling studies to identify candidate diagnostic biomarkers. MATERIALS AND METHODS: We performed comprehensive literature searches in several databases to identify miRNA expression studies of renal fibrosis in animal models and humans...
June 18, 2018: Biomarkers: Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals
https://www.readbyqxmd.com/read/29907662/expression-of-atresia-biomarkers-in-granulosa-cells-after-ovarian-stimulation-in-heifers
#2
David A Landry, Lia Rossi-Perazza, Simon Lafontaine, Marc-Andre Sirard
The use of younger gamete donors in dairy cattle genetic selection programs significantly accelerates genetic gains by decreasing the interval between generations. Ovarian stimulation and the practice of follicle-stimulating hormone (FSH) withdrawal, also known as coasting, are intensively used in pre-pubertal heifers without detrimental effects on subsequent reproductive performance but generally with lower embryo yields. However, recent data from embryo transfer programs showed similar embryo yields in younger and sexually mature animals but with a significant difference in the coasting period...
June 15, 2018: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/29899525/genome-wide-association-study-of-habitual-physical-activity-in-over-377-000-uk-biobank-participants-identifies-multiple-variants-including-cadm2-and-apoe
#3
Yann C Klimentidis, David A Raichlen, Jennifer Bea, David O Garcia, Nathan E Wineinger, Lawrence J Mandarino, Gene E Alexander, Zhao Chen, Scott B Going
BACKGROUND/OBJECTIVES: Physical activity (PA) protects against a wide range of diseases. Habitual PA appears to be heritable, motivating the search for specific genetic variants that may inform efforts to promote PA and target the best type of PA for each individual. SUBJECTS/METHODS: We used data from the UK Biobank to perform the largest genome-wide association study of PA to date, using three measures based on self-report (nmax  = 377,234) and two measures based on wrist-worn accelerometry data (nmax  = 91,084)...
June 13, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29898756/ndrg1-regulates-neutral-lipid-metabolism-in-breast-cancer-cells
#4
Christopher J Sevinsky, Faiza Khan, Leila Kokabee, Anza Darehshouri, Krishna Rao Maddipati, Douglas S Conklin
BACKGROUND: Altered lipid metabolism is an emerging hallmark of aggressive breast cancers. The N-myc downstream regulated gene (NDRG1) gene plays a critical role in peripheral nervous system myelination, as inactivating mutations cause severe demyelinating neuropathy. In breast cancer, elevated NDRG1 expression has been linked to clinical outcomes, but its functional role in breast cancer physiology has remained unclear. METHODS: A meta-analysis of NDRG1 expression in multiple large publicly available genomic databases was conducted...
June 14, 2018: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29896277/-mlh1-promoter-methylation-and-prediction-prognosis-of-gastric-cancer-a-systematic-review-and-meta-and-bioinformatic-analysis
#5
Shixuan Shen, Xiaohui Chen, Hao Li, Liping Sun, Yuan Yuan
Background: The promoter methylation of MLH1 gene and gastric cancer (GC)has been investigated previously. To get a more credible conclusion, we performed a systematic review and meta and bioinformatic analysis to clarify the role of MLH1 methylation in the prediction and prognosis of GC. Methods: Eligible studies were targeted after searching the PubMed, Web of Science, Embase, BIOSIS, CNKI and Wanfang Data to collect the information of MLH1 methylation and GC. The link strength between the two was estimated by odds ratio with its 95% confidence interval...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29896212/meta-analysis-of-the-effect-of-overexpression-of-dehydration-responsive-element-binding-family-genes-on-temperature-stress-tolerance-and-related-responses
#6
Chao Dong, Yuanchun Ma, Dan Zheng, Michael Wisniewski, Zong-Ming Cheng
Dehydration-responsive element binding proteins are transcription factors that play a critical role in plant response to temperature stress. Over-expression of DREB genes has been demonstrated to enhance temperature stress tolerance. A series of physiological and biochemical modifications occur in a complex and integrated way when plants respond to temperature stress, which makes it difficult to assess the mechanism underlying the DREB enhancement of stress tolerance. A meta-analysis was conducted of the effect of DREB overexpression on temperature stress tolerance and the various parameters modulated by overexpression that were statistically quantified in 75 published articles...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29892015/multi-ethnic-genome-wide-association-study-for-atrial-fibrillation
#7
Carolina Roselli, Mark D Chaffin, Lu-Chen Weng, Stefanie Aeschbacher, Gustav Ahlberg, Christine M Albert, Peter Almgren, Alvaro Alonso, Christopher D Anderson, Krishna G Aragam, Dan E Arking, John Barnard, Traci M Bartz, Emelia J Benjamin, Nathan A Bihlmeyer, Joshua C Bis, Heather L Bloom, Eric Boerwinkle, Erwin B Bottinger, Jennifer A Brody, Hugh Calkins, Archie Campbell, Thomas P Cappola, John Carlquist, Daniel I Chasman, Lin Y Chen, Yii-Der Ida Chen, Eue-Keun Choi, Seung Hoan Choi, Ingrid E Christophersen, Mina K Chung, John W Cole, David Conen, James Cook, Harry J Crijns, Michael J Cutler, Scott M Damrauer, Brian R Daniels, Dawood Darbar, Graciela Delgado, Joshua C Denny, Martin Dichgans, Marcus Dörr, Elton A Dudink, Samuel C Dudley, Nada Esa, Tonu Esko, Markku Eskola, Diane Fatkin, Stephan B Felix, Ian Ford, Oscar H Franco, Bastiaan Geelhoed, Raji P Grewal, Vilmundur Gudnason, Xiuqing Guo, Namrata Gupta, Stefan Gustafsson, Rebecca Gutmann, Anders Hamsten, Tamara B Harris, Caroline Hayward, Susan R Heckbert, Jussi Hernesniemi, Lynne J Hocking, Albert Hofman, Andrea R V R Horimoto, Jie Huang, Paul L Huang, Jennifer Huffman, Erik Ingelsson, Esra Gucuk Ipek, Kaoru Ito, Jordi Jimenez-Conde, Renee Johnson, J Wouter Jukema, Stefan Kääb, Mika Kähönen, Yoichiro Kamatani, John P Kane, Adnan Kastrati, Sekar Kathiresan, Petra Katschnig-Winter, Maryam Kavousi, Thorsten Kessler, Bas L Kietselaer, Paulus Kirchhof, Marcus E Kleber, Stacey Knight, Jose E Krieger, Michiaki Kubo, Lenore J Launer, Jari Laurikka, Terho Lehtimäki, Kirsten Leineweber, Rozenn N Lemaitre, Man Li, Hong Euy Lim, Henry J Lin, Honghuang Lin, Lars Lind, Cecilia M Lindgren, Marja-Liisa Lokki, Barry London, Ruth J F Loos, Siew-Kee Low, Yingchang Lu, Leo-Pekka Lyytikäinen, Peter W Macfarlane, Patrik K Magnusson, Anubha Mahajan, Rainer Malik, Alfredo J Mansur, Gregory M Marcus, Lauren Margolin, Kenneth B Margulies, Winfried März, David D McManus, Olle Melander, Sanghamitra Mohanty, Jay A Montgomery, Michael P Morley, Andrew P Morris, Martina Müller-Nurasyid, Andrea Natale, Saman Nazarian, Benjamin Neumann, Christopher Newton-Cheh, Maartje N Niemeijer, Kjell Nikus, Peter Nilsson, Raymond Noordam, Heidi Oellers, Morten S Olesen, Marju Orho-Melander, Sandosh Padmanabhan, Hui-Nam Pak, Guillaume Paré, Nancy L Pedersen, Joanna Pera, Alexandre Pereira, David Porteous, Bruce M Psaty, Sara L Pulit, Clive R Pullinger, Daniel J Rader, Lena Refsgaard, Marta Ribasés, Paul M Ridker, Michiel Rienstra, Lorenz Risch, Dan M Roden, Jonathan Rosand, Michael A Rosenberg, Natalia Rost, Jerome I Rotter, Samir Saba, Roopinder K Sandhu, Renate B Schnabel, Katharina Schramm, Heribert Schunkert, Claudia Schurman, Stuart A Scott, Ilkka Seppälä, Christian Shaffer, Svati Shah, Alaa A Shalaby, Jaemin Shim, M Benjamin Shoemaker, Joylene E Siland, Juha Sinisalo, Moritz F Sinner, Agnieszka Slowik, Albert V Smith, Blair H Smith, J Gustav Smith, Jonathan D Smith, Nicholas L Smith, Elsayed Z Soliman, Nona Sotoodehnia, Bruno H Stricker, Albert Sun, Han Sun, Jesper H Svendsen, Toshihiro Tanaka, Kahraman Tanriverdi, Kent D Taylor, Maris Teder-Laving, Alexander Teumer, Sébastien Thériault, Stella Trompet, Nathan R Tucker, Arnljot Tveit, Andre G Uitterlinden, Pim Van Der Harst, Isabelle C Van Gelder, David R Van Wagoner, Niek Verweij, Efthymia Vlachopoulou, Uwe Völker, Biqi Wang, Peter E Weeke, Bob Weijs, Raul Weiss, Stefan Weiss, Quinn S Wells, Kerri L Wiggins, Jorge A Wong, Daniel Woo, Bradford B Worrall, Pil-Sung Yang, Jie Yao, Zachary T Yoneda, Tanja Zeller, Lingyao Zeng, Steven A Lubitz, Kathryn L Lunetta, Patrick T Ellinor
Atrial fibrillation (AF) affects more than 33 million individuals worldwide 1 and has a complex heritability 2 . We conducted the largest meta-analysis of genome-wide association studies (GWAS) for AF to date, consisting of more than half a million individuals, including 65,446 with AF. In total, we identified 97 loci significantly associated with AF, including 67 that were novel in a combined-ancestry analysis, and 3 that were novel in a European-specific analysis. We sought to identify AF-associated genes at the GWAS loci by performing RNA-sequencing and expression quantitative trait locus analyses in 101 left atrial samples, the most relevant tissue for AF...
June 11, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29891108/the-clinical-significance-of-platelet-derived-growth-factors-pdgfs-and-their-receptors-pdgfrs-in-gastric-cancer-a-systematic-review-and-meta-analysis
#8
REVIEW
Hai Qian, Kwaku Appiah-Kubi, Ying Wang, Min Wu, Yan Tao, Yan Wu, Yongchang Chen
BACKGROUND: The overexpression and mutation of platelet-derived growth factors (PDGFs) and their receptors (PDGFRs) are widespread in cancers and have been recognized as attractive oncologic targets with diverse therapeutic targets. Reports of the overexpression of genes, proteins and mutations of PDGFs/PDGFRs in gastric cancer and their associations with clinicopathological features, Western and Asian patients, as well as prognostic role have shown variable outcomes. This study sought to employ meta-analysis to evaluate PDGFs/PDGFRs status prognostic significance and their association with clinicopathological features of gastric cancer...
July 2018: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/29887872/stable-qtls-for-plant-height-on-chromosome-a09-identified-from-two-mapping-populations-in-peanut-arachis-hypogaea-l
#9
Jianwei Lv, Nian Liu, Jianbin Guo, Zhijun Xu, Xinping Li, Zhendong Li, Huaiyong Luo, Xiaoping Ren, Li Huang, Xiaojing Zhou, Yuning Chen, Weigang Chen, Yong Lei, Jinxing Tu, Huifang Jiang, Boshou Liao
The peanut ( Arachis hypogaea L.) is an important grain legume extensively cultivated worldwide, supplying edible oil and protein for human consumption. As in many other crops, plant height is a crucial factor in determining peanut architecture traits and has a unique effect on resistance to lodging and efficiency of mechanized harvesting as well as yield. Currently, the genetic basis underlying plant height remains unclear in peanut, which have hampered marker-assisted selection in breeding. In this study, we conducted a quantitative trait locus (QTL) analysis for peanut plant height by using two recombinant inbred line (RIL) populations including "Yuanza 9102 × Xuzhou 68-4 (YX)" and "Xuhua 13 × Zhonghua 6 (XZ)"...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29884137/a-systematic-review-and-meta-analyses-of-the-relationship-between-glutathione-s-transferase-gene-polymorphisms-and-renal-cell-carcinoma-susceptibility
#10
Zhiqing Zhong, Hongyan Li, Hongzhen Zhong, Tianbiao Zhou, Weiji Xie, Zhijun Lin
BACKGROUND: Association of GSTM1- and GSTT1-null genotypes, GSTP1 A/G gene polymorphism with renal cell carcinoma (RCC) susceptibility was detected, and the relationship between the GSTM1/GSTT1-null genotype and clinical TNM stages of RCC was assessed, using meta-analysis method. METHODS: Association investigations according to eligibility criteria were searched and identified from the databases of Cochrane Library, PubMed, and Embase from establishment time of databases to July 1, 2017, and eligible reports were analyzed by meta-analysis...
June 8, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29876898/methods-of-analysis-and-meta-analysis-for-identifying-differentially-expressed-genes
#11
Panagiota I Kontou, Athanasia Pavlopoulou, Pantelis G Bagos
Microarray approaches are widely used high-throughput techniques to assess simultaneously the expression of thousands of genes under certain conditions and study the effects of certain treatments, diseases, and developmental stages. The traditional way to perform such experiments is to design oligonucleotide hybridization probes that correspond to specific genes and then measure the expression of the genes in order to determine which of them are up- or down-regulated compared to a condition that is used as a control...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29872345/association-of-mrna-expression-of-tp53-and-the-tp53-codon-72-arg-pro-gene-polymorphism-with-colorectal-cancer-risk-in-asian-population-a-bioinformatics-analysis-and-meta-analysis
#12
Zhiyong Dong, Longzhi Zheng, Weimin Liu, Cunchuan Wang
Background: The relationship between TP53 codon 72 Pro/Arg gene polymorphism and colorectal cancer risk in Asians is still controversial, and this bioinformatics analysis and meta-analysis was performed to assess the associations. Methods: The association studies were identified from PubMed, and eligible reports were included. RevMan 5.3.1 software, Oncolnc, cBioPortal, and Oncomine online tools were used for statistical analysis. A random/fixed effects model was used in meta-analysis...
2018: Cancer Management and Research
https://www.readbyqxmd.com/read/29871690/a-survey-of-microrna-single-nucleotide-polymorphisms-identifies-novel-breast-cancer-susceptibility-loci-in-a-case-control-population-based-study-of-african-american-women
#13
Jeannette T Bensen, Mariaelisa Graff, Kristin L Young, Praveen Sethupathy, Joel Parker, Chad V Pecot, Kevin Currin, Stephen A Haddad, Edward A Ruiz-Narváez, Christopher A Haiman, Chi-Chen Hong, Lara E Sucheston-Campbell, Qianqian Zhu, Song Liu, Song Yao, Elisa V Bandera, Lynn Rosenberg, Kathryn L Lunetta, Christine B Ambrosone, Julie R Palmer, Melissa A Troester, Andrew F Olshan
BACKGROUND: MicroRNAs (miRNAs) regulate gene expression and influence cancer. Primary transcripts of miRNAs (pri-miRNAs) are poorly annotated and little is known about the role of germline variation in miRNA genes and breast cancer (BC). We sought to identify germline miRNA variants associated with BC risk and tumor subtype among African-American (AA) women. METHODS: Under the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, genotyping and imputed data from four studies on BC in AA women were combined into a final dataset containing 224,188 miRNA gene single nucleotide polymorphisms (SNPs) for 8350 women: 3663 cases and 4687 controls...
June 5, 2018: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29867970/meta-analysis-of-maternal-and-fetal-transcriptomic-data-elucidates-the-role-of-adaptive-and-innate-immunity-in-preterm-birth
#14
Bianca Vora, Aolin Wang, Idit Kosti, Hongtai Huang, Ishan Paranjpe, Tracey J Woodruff, Tippi MacKenzie, Marina Sirota
Preterm birth (PTB) is the leading cause of newborn deaths around the world. Spontaneous preterm birth (sPTB) accounts for two-thirds of all PTBs; however, there remains an unmet need of detecting and preventing sPTB. Although the dysregulation of the immune system has been implicated in various studies, small sizes and irreproducibility of results have limited identification of its role. Here, we present a cross-study meta-analysis to evaluate genome-wide differential gene expression signals in sPTB. A comprehensive search of the NIH genomic database for studies related to sPTB with maternal whole blood samples resulted in data from three separate studies consisting of 339 samples...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29866053/rna-seq-meta-analysis-identifies-genes-in-skeletal-muscle-associated-with-gain-and-intake-across-a-multi-season-study-of-crossbred-beef-steers
#15
Brittney N Keel, Christina M Zarek, John W Keele, Larry A Kuehn, Warren M Snelling, William T Oliver, Harvey C Freetly, Amanda K Lindholm-Perry
BACKGROUND: Feed intake and body weight gain are economically important inputs and outputs of beef production systems. The purpose of this study was to discover differentially expressed genes that will be robust for feed intake and gain across a large segment of the cattle industry. Transcriptomic studies often suffer from issues with reproducibility and cross-validation. One way to improve reproducibility is by integrating multiple datasets via meta-analysis. RNA sequencing (RNA-Seq) was performed on longissimus dorsi muscle from 80 steers (5 cohorts, each with 16 animals) selected from the outside fringe of a bivariate gain and feed intake distribution to understand the genes and pathways involved in feed efficiency...
June 4, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29862346/-de-novo-assembly-and-characterizing-of-the-culm-derived-meta-transcriptome-from-the-polyploid-sugarcane-genome-based-on-coding-transcripts
#16
Nam V Hoang, Agnelo Furtado, Prathima P Thirugnanasambandam, Frederik C Botha, Robert J Henry
Sugarcane biomass has been used for sugar, bioenergy and biomaterial production. The majority of the sugarcane biomass comes from the culm, which makes it important to understand the genetic control of biomass production in this part of the plant. A meta-transcriptome of the culm was obtained in an earlier study by using about one billion paired-end (150 bp) reads of deep RNA sequencing of samples from 20 diverse sugarcane genotypes and combining de novo assemblies from different assemblers and different settings...
March 2018: Heliyon
https://www.readbyqxmd.com/read/29861410/rankprod-combined-with-genetic-algorithm-optimized-artificial-neural-network-establishes-a-diagnostic-and-prognostic-prediction-model-that-revealed-c1qtnf3-as-a-biomarker-for-prostate-cancer
#17
Qi Hou, Zhi-Tong Bing, Cheng Hu, Mao-Yin Li, Ke-Hu Yang, Zu Mo, Xiang-Wei Xie, Ji-Lin Liao, Yan Lu, Shigeo Horie, Ming-Wu Lou
Prostate cancer (PCa) is the most commonly diagnosed cancer in males in the Western world. Although prostate-specific antigen (PSA) has been widely used as a biomarker for PCa diagnosis, its results can be controversial. Therefore, new biomarkers are needed to enhance the clinical management of PCa. From publicly available microarray data, differentially expressed genes (DEGs) were identified by meta-analysis with RankProd. Genetic algorithm optimized artificial neural network (GA-ANN) was introduced to establish a diagnostic prediction model and to filter candidate genes...
May 31, 2018: EBioMedicine
https://www.readbyqxmd.com/read/29852038/cost-effectiveness-of-osimertinib-in-the-first-line-treatment-of-patients-with-egfr-mutated-advanced-non-small-cell-lung-cancer
#18
Pedro N Aguiar, Benjamin Haaland, Wungki Park, Pui San Tan, Auro Del Giglio, Gilberto de Lima Lopes
Importance: The survival of patients with advanced non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) gene mutations has improved substantially in the last decade with the development of targeted tyrosine kinase inhibitors (TKIs). Osimertinib, a third-generation TKI that is approved by the US Food and Drug Administration for the treatment of patients who develop EGFR T790M mutations, has recently shown improved clinical outcomes compared with gefitinib and erlotinib for treatment-naive patients...
May 31, 2018: JAMA Oncology
https://www.readbyqxmd.com/read/29844132/glycosyltransferase-gene-expression-identifies-a-poor-prognostic-colorectal-cancer-subtype-associated-with-mismatch-repair-deficiency-and-incomplete-glycan-synthesis
#19
Masaru Noda, Hirokazu Okayama, Kazunoshin Tachibana, Wataru Sakamoto, Katsuharu Saito, Aung Kyi Thar Min, Mai Ashizawa, Takahiro Nakajima, Keita Aoto, Tomoyuki Momma, Kyoko Katakura, Shinji Ohki, Koji Kono
PURPOSE: We aimed to discover glycosyltransferase gene (glycogene)-derived molecular subtypes of colorectal cancer (CRC) associated with patient outcomes. EXPERIMENTAL DESIGN: Transcriptomic and epigenomic datasets of non-tumor, pre-cancerous, cancerous tissues and cell lines with somatic mutations, mismatch repair status, clinicopathological and survival information, were assembled (n=4223) and glycogene profiles were analyzed. Immunohistochemistry for a glycogene, GALNT6, was conducted in adenoma and carcinoma specimens (n=403)...
May 29, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29843660/gene-expression-profiling-of-1200-pancreatic-ductal-adenocarcinoma-reveals-novel-subtypes
#20
Lan Zhao, Hongya Zhao, Hong Yan
BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer related death in the world with a five-year survival rate of less than 5%. Not all PDAC are the same, because there exist intra-tumoral heterogeneity between PDAC, which poses a great challenge to personalized treatments for PDAC. METHODS: To dissect the molecular heterogeneity of PDAC, we performed a retrospective meta-analysis on whole transcriptome data from more than 1200 PDAC patients...
May 29, 2018: BMC Cancer
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