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https://www.readbyqxmd.com/read/28341855/mir-503-promotes-bone-formation-in-distraction-osteogenesis-through-suppressing-smurf1-expression
#1
Yuxin Sun, Jia Xu, Liangliang Xu, Jinfang Zhang, Kaiming Chan, Xiaohua Pan, Gang Li
Distraction osteogenesis (DO) is a unique technique for promoting bone formation in clinical practice. However the underlying mechanism remains elusive. As epigenetic mediators, microRNAs have been reported to play important roles in regulating osteogenesis. In this study, after successfully established the DO model of rats, a microRNA microarray was performed to find molecular targets for DO. Total 100 microRNAs were identified as differently expressed, with miR-503 being one of the most significantly up-regulated miRNAs in DO...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28341746/leveraging-sequence-based-faecal-microbial-community-survey-data-to-identify-a-composite-biomarker-for-colorectal-cancer
#2
Manasi S Shah, Todd Z DeSantis, Thomas Weinmaier, Paul J McMurdie, Julia L Cope, Adam Altrichter, Jose-Miguel Yamal, Emily B Hollister
OBJECTIVE: Colorectal cancer (CRC) is the second leading cause of cancer-associated mortality in the USA. The faecal microbiome may provide non-invasive biomarkers of CRC and indicate transition in the adenoma-carcinoma sequence. Re-analysing raw sequence and metadata from several studies uniformly, we sought to identify a composite and generalisable microbial marker for CRC. DESIGN: Raw 16S rRNA gene sequence data sets from nine studies were processed with two pipelines, (1) QIIME closed reference (QIIME-CR) or (2) a strain-specific method herein termed SS-UP (Strain Select, UPARSE bioinformatics pipeline)...
March 24, 2017: Gut
https://www.readbyqxmd.com/read/28340574/myocyte-enhancer-factor-2d-provides-a-cross-talk-between-chronic-inflammation-and-lung-cancer
#3
Hai-Xing Zhu, Lin Shi, Yong Zhang, Yi-Chun Zhu, Chun-Xue Bai, Xiang-Dong Wang, Jie-Bai Zhou
BACKGROUND: Lung cancer is the leading cause of cancer-related morbidity and mortality worldwide. Patients with chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), are exposed to a higher risk of developing lung cancer. Chronic inflammation may play an important role in the lung carcinogenesis among those patients. The present study aimed at identifying candidate biomarker predicting lung cancer risk among patients with chronic respiratory diseases. METHODS: We applied clinical bioinformatics tools to analyze different gene profile datasets with a special focus on screening the potential biomarker during chronic inflammation-lung cancer transition...
March 24, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28339471/expression-quantitative-trait-loci-for-pax8-contributes-to-the-prognosis-of-hepatocellular-carcinoma
#4
Shijie Ma, Jianshui Yang, Ci Song, Zijun Ge, Jing Zhou, Guoxin Zhang, Zhibin Hu
Paired-box family member PAX8 encodes a transcription factor that has a role in cell differentiation and cell growth and may participate in the prognosis of hepatocellular carcinoma (HCC). By bioinformatics analysis, we identified several single nucleotide polymorphisms (SNPs) within a newly identified long non-coding RNA (lncRNA) AC016683.6 as expression quantitative trait loci (eQTLs) for PAX8. Hence, we hypothesized that PAX8eQTLs in lncRNA AC016683.6 may influence the HCC prognosis. We then performed a case-only study to assess the association between the two SNPs as well as the prognosis of HCC in 331 HBV-positive HCC patients without surgical treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28339176/identification-of-likely-associations-between-cerebral-folate-deficiency-and-complex-genetic-and-metabolic-pathogenesis-of-autism-spectrum-disorders-by-utilization-of-a-pilot-interaction-modeling-approach
#5
Daniel Krsička, Jan Geryk, Markéta Vlčková, Markéta Havlovicová, Milan Macek, Radka Pourová
Recently, cerebral folate deficiency (CFD) was suggested to be involved in the pathogenesis of autism spectrum disorders (ASD). However, the exact role of folate metabolism in the pathogenesis of ASD, identification of underlying pathogenic mechanisms and impaired metabolic pathways remain unexplained. The aim of our study was to develop and test a novel, unbiased, bioinformatics approach in order to identify links between ASD and disturbed cerebral metabolism by focusing on abnormal folate metabolism, which could foster patient stratification and novel therapeutic interventions...
March 24, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28339095/expression-of-yes-associated-protein%C3%A2-1-and-its-clinical-significance-in-ovarian-serous-cystadenocarcinoma
#6
Sang Yeon Cho, Kwanghun Kim, Min Soo Park, Mi Young Jang, Young Hwan Choi, Suyeon Han, Hyun Mo Shin, Chaeuk Chung, Hye Young Han, Jung Bo Yang, Young Bok Ko, Heon Jong Yoo
Yes-associated protein 1 (YAP1) is a key transcriptional regulator in the Hippo signaling pathway that plays a critical role in the development and progression of several types of malignancies, including ovarian cancer. Herein, we investigated the expression of YAP1 and its clinical significance in a large population of patients with ovarian serous cystadenocarcinoma (OSC), which is the most common form of epithelial ovarian neoplasm, using the TCGA database. Surprisingly, cross-cancer mRNA expression and alterations in YAP1 were higher in OSC than in those of other types of cancers in the TCGA database...
March 21, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28339092/macc1-decreases-the-chemosensitivity-of-gastric-cancer-cells-to-oxaliplatin-by-regulating-fasn-expression
#7
Jiangman Duan, Lishan Chen, Minyu Zhou, Jingwen Zhang, Li Sun, Na Huang, Jianping Bin, Yulin Liao, Wangjun Liao
The effect of chemotherapeutic agents is limited as a result of drug resistance, which demands prompt solutions provided by clinical studies. To date, the underlying mechanisms of chemotherapy resistance are relatively unknown. Metastasis-associated in colon cancer 1 (MACC1) is an oncogene associated with the progression and prognosis of gastric cancer (GC). Bioinformatic analysis revealed that MACC1 is positively associated with fatty acid synthase (FASN), a major enzyme of lipogenesis, and drives chemoresistance to oxaliplatin in GC...
March 22, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28338236/hsa-mir-3199-2-and-hsa-mir-1293-as-novel-prognostic-biomarkers-of-papillary-renal-cell-carcinoma-by-cox-ratio-risk-regression-model-screening
#8
Wen Luo, Lei Wang, Mao-Hua Luo, Yu-Zhu Huang, Hua Yang, Yu Zhou, Hong-Tao Jia, Xiu-Xin Wang
Papillary renal cell carcinoma(PRCC) is the second most common and aggressive renal cell carcinoma. Identification of novel microRNA biomarkers could be beneficial for the diagnosis and prognosis of PRCCpatients.We aimed to screen differentially expressed miRNAs that can act as prognostic factors and to predict the survival of PRCC patients. High-throughput data of miRNAs of 274 PRCC samples were downloaded from TCGA(The Cancer Genome Atlas) dataset and interested miRNAs were identified. Hierarchical clustering and principal component analysis (PCA) were performed on these miRNAs...
March 24, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28337302/different-impairment-of-immune-and-inflammation-functions-in-short-and-long-term-after-ischemic-stroke
#9
Wen-Xing Li, Fei Qi, Jia-Qian Liu, Gong-Hua Li, Shao-Xing Dai, Tao Zhang, Fei Cheng, Dahai Liu, Song Guo Zheng
Ischemic stroke therapy and prognosis outcomes largely depend on the time periods after symptom onset. This study aims to explore the difference of global gene expression profiles and impairment of biological functions between short-term and long-term after stroke onset. We compared three short-term (3 h, 5 h and 24 h) and a long-term (6-month) gene expression levels by a multi-platform microarray data integration method. RankProd was used to calculate the differentially expressed genes between stroke patients and controls...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28337072/precision-metagenomics-rapid-metagenomic-analyses-for-infectious-disease-diagnostics-and-public-health-surveillance
#10
Ebrahim Afshinnekoo, Chou Chou, Noah Alexander, Sofia Ahsanuddin, Audrey N Schuetz, Christopher E Mason
Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear...
March 21, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28336453/a-bioinformatic-analysis-of-micrornas-role-in-osteoarthritis
#11
Lin Cong, Yue Zhu, Guanjun Tu
OBJECTIVE: To evaluate the underlying function of miRNAs in osteoarthritis (OA). DESIGN: A bioinformatic analysis of miRNAs-OA studies was completed in multiple databases. All identified articles were assessed using specific inclusion and exclusion criteria (Eligible case-control studies for the present study included those which investigated miRNAs differential expression in cartilage tissues and cells of OA and controls. Abstracts, case reports, conference presentations, editorials, and expert opinions were excluded...
March 21, 2017: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/28336429/insight-into-stereochemistry-of-a-new-imp-allelic-variant-imp-55-metallo-%C3%AE-lactamase-identified-in-a-clinical-strain-of-acinetobacter-baumannii
#12
Mohammad Reza Shakibaie, Omid Azizi, Fereshteh Shahcheraghi
Metallo-β-lactamases (MBLs) such as IMPs are broad-spectrum β-lactamases that inactivate virtually all β-lactam antibiotics including carbapenems. In this study, we investigated the hydrolytic activity, phylogenetic relationship, three dimensional (3D) structure including zinc binding motif of a new IMP variant (IMP-55) identified in a clinical strain of Acinetobacter baumannii (AB). AB strain 56 was isolated from an adult ICU of a teaching hospital in Kerman, Iran. It exhibited MIC 32μg/ml to imipenem and showed MBL activity...
March 20, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28336332/how-to-use-and-integrate-bioinformatics-tools-to-compare-proteomic-data-from-distinct-conditions-a-tutorial-using-the-pathological-similarities-between-aortic-valve-stenosis-and-coronary-artery-disease-as-a-case-study
#13
Fábio Trindade, Rita Ferreira, Beatriz Magalhães, Adelino Leite-Moreira, Inês Falcão-Pires, Rui Vitorino
Nowadays we are surrounded by a plethora of bioinformatics tools, powerful enough to deal with the large amounts of data arising from proteomic studies, but whose application is sometimes hard to find. Therefore, we used a specific clinical problem - to discriminate pathophysiology and potential biomarkers between two similar cardiovascular diseases, aortic valve stenosis (AVS) and coronary artery disease (CAD) - to make a step-by-step guide through four bioinformatics tools: STRING, DisGeNET, Cytoscape and ClueGO...
March 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28334716/downregulation-of-ubap2l-inhibits-the-epithelial-mesenchymal-transition-via-snail1-regulation-in-hepatocellular-carcinoma-cells
#14
Tao Ye, Jing Xu, Ling Du, Wenhui Mo, Yiming Liang, Jinglin Xia
BACKGROUND/AIMS: Dysregulation of ubiquitin-associated protein 2-like (UBAP2L) has been reported in tumors, but its role in hepatocellular carcinoma (HCC) progression is unclear. METHODS: The expression levels of UBAP2L in HCC tissues and HCC cell lines were detected by western blot and quantitative real-time (qRT) PCR. The effects of UBAP2L expression on HCC cell biological traits, including migration and invasion, were investigated by wound healing assay and matrigel transwell assay...
March 27, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28334291/smartr-an-open-source-platform-for-interactive-visual-analytics-for-translational-research-data
#15
Sascha Herzinger, Wei Gu, Venkata Satagopam, Serge Eifes, Kavita Rege, Adriano Barbosa Da Silva, Reinhard Schneider
In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical, or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies...
March 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334267/resistomap-online-visualization-of-human-gut-microbiota-antibiotic-resistome
#16
Konstantin S Yarygin, Boris A Kovarsky, Tatyana S Bibikova, Damir S Melnikov, Alexander V Tyakht, Dmitry G Alexeev
Summary: We created ResistoMap - a Web-based interactive visualization of the presence of genetic determinants conferring resistance to antibiotics, biocides and heavy metals in human gut microbiota. ResistoMap displays the data on more than 1500 published gut metagenomes of world populations including both healthy subjects and patients. Multiparameter display filters allow visual assessment of the associations between the meta-data and proportions of resistome. The geographic map navigation layer allows to state hypotheses regarding the global trends of antibiotic resistance and correlate the gut resistome variations with the national clinical guidelines on antibiotics application...
March 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334266/phenopolis-an-open-platform-for-harmonization-and-analysis-of-genetic-and-phenotypic-data
#17
Nikolas Pontikos, Jing Yu, Ismail Moghul, Lucy Withington, Fiona Blanco-Kelly, Tom Vulliamy, Tsz Lun Wong, Cian Murphy, Valentina Cipriani, Alessia Fiorentino, Gavin Arno, Daniel Greene, Julius Ob Jacobsen, Tristan Clark, David S Gregory, Andrea Nemeth, Stephanie Halford, Chris F Inglehearn, Susan Downes, Graeme C Black, Andrew R Webster, Alison J Hardcastle, Vincent Plagnol
Summary: Phenopolis is an open-source web server providing an intuitive interface to genetic and phenotypic databases. It integrates analysis tools such as variant filtering and gene prioritisation based on phenotype. The Phenopolis platform will accelerate clinical diagnosis, gene discovery and encourage wider adoption of the Human Phenotype Ontology in the study of rare genetic diseases. Availability and Implementation: A demo of the website is available at https://phenopolis...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28327897/towards-a-global-cancer-knowledge-network-dissecting-the-current-international-cancer-genomic-sequencing-landscape
#18
D J Vis, J Lewin, R G Liao, M Mao, F Andre, R L Ward, F Calvo, B T Teh, A A Camargo, B M Knoppers, C Sawyers, L F A Wessels, M Lawler, L L Siu, E Voest
Background: While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. Methods: A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally...
February 3, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#19
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28327201/detecting-gene-signature-activation-in-breast-cancer-in-an-absolute-single-patient-manner
#20
E R Paquet, R Lesurf, A Tofigh, V Dumeaux, M T Hallett
BACKGROUND: The ability to reliably identify the state (activated, repressed, or latent) of any molecular process in the tumor of a patient from an individual whole-genome gene expression profile obtained from microarray or RNA sequencing (RNA-seq) promises important clinical utility. Unfortunately, all previous bioinformatics tools are only applicable in large and diverse panels of patients, or are limited to a single specific pathway/process (e.g. proliferation). METHODS: Using a panel of 4510 whole-genome gene expression profiles from 10 different studies we built and selected models predicting the activation status of a compendium of 1733 different biological processes...
March 21, 2017: Breast Cancer Research: BCR
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