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https://www.readbyqxmd.com/read/29045811/top2a-induces-malignant-character-of-pancreatic-cancer-through-activating-%C3%AE-catenin-signaling-pathway
#1
Yao-Fei Pei, Xi-Min Yin, Xi-Qiang Liu
It has been reported that Topoisomerase II alpha (TOP2A) could induce tumor development and progression in many cancer types. Herein, through analysis of different independent cohorts, we found TOP2A was up-regulated in pancreatic cancer as compared with non-tumor tissues. Moreover, the up-regulation of TOP2A was significantly correlated with tumor metastasis and shorter survival in patients with pancreatic cancer. Knockdown of TOP2A in pancreatic cancer cell lines inhibited cell proliferation and migration...
October 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29044514/ccdc6-the-identity-of-a-protein-known-to-be-partner-in-fusion
#2
REVIEW
Aniello Cerrato, Francesco Merolla, Francesco Morra, Angela Celetti
Coiled Coil Domain Containing 6 gene, CCDC6, was initially isolated as part of a tumorigenic DNA originated by the fusion of CCDC6 with the tyrosine kinase of RET receptor, following a paracentric inversion of chromosome 10. For a long time CCDC6 has been considered as an accidental partner of the RET protooncogene, providing the promoter and the first 101 aa necessary for the constitutive activation of the oncogenic Tyrosine Kinase (TK) RET in thyroid cells. With the advent of more refined diagnostic tools and bioinformatic algorithms, an exponential growth in fusion genes discoveries has allowed the identification of CCDC6 as partner of genes other than RET in different tumor types...
October 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29042947/mir-124-inhibits-proliferation-migration-and-invasion-of-malignant-melanoma-cells-via-targeting-versican
#3
Ping Yang, Pingyuan Bu, Chengyuan Li
MicroRNA (miR)-124 has been implicated in malignant melanoma (MM). However, the detailed regulatory mechanism of miR-124 in the malignant phenotypes of MM cells has remained largely elusive. A total of 68 pairs of MM tissues and adjacent tissues were collected. Reverse-transcription quantitative polymerase chain reaction was used to examine the mRNA expression of versican as well as the expression of miR-124, and the protein expression of versican was assessed by western blot analysis. MTT, wound healing and Transwell assays were used to determine cell proliferation, migration and invasion, respectively...
October 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29042587/mir-302b-suppresses-osteosarcoma-cell-migration-and-invasion-by-targeting-runx2
#4
Yuanlong Xie, Wenchao Sun, Zhouming Deng, Xiaobin Zhu, Chao Hu, Lin Cai
Osteosarcoma patients with lung metastasis and local invasion remain challenging to treat despite the significant contribution of the combination of surgery and neo-adjuvant chemotherapy. Our previous microarray study demonstrated that miR-302b had significantly lower expression in osteosarcoma cell lines than in osteoblast cell lines. In the present study, we further elucidated the role of miR-302b in regulating the migration and invasiveness of osteosarcoma. MiR-302b expression was markedly down-regulated in osteosarcoma cell lines and clinical tumour tissues...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29041922/institute-collection-and-analysis-of-nanobodies-ican-a-comprehensive-database-and-analysis-platform-for-nanobodies
#5
Jing Zuo, Jian Li, Rongxin Zhang, Longsheng Xu, Hanhan Chen, Xiaohuan Jia, Zhipeng Su, Linhong Zhao, Xing Huang, Wei Xie
BACKGROUND: Nanobodies are single-domain antibodies that contain the unique structural and functional properties of naturally-occurring heavy chain in camelidae. As a novel class of antibody, they show many advantages compared with traditional antibodies such as smaller size, higher stability, improved specificity, more easily expressed in microorganisms. These unusual hallmarks make them as promising tools in basic research and clinical practice. Although thousands of nanobodies are known to be published, no single database provides searchable, unified annotation and integrative analysis tools for these various nanobodies...
October 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29040639/the-medical-science-dmz-a-network-design-pattern-for-data-intensive-medical-science
#6
Sean Peisert, Eli Dart, William Barnett, Edward Balas, James Cuff, Robert L Grossman, Ari Berman, Anurag Shankar, Brian Tierney
Objective: We describe a detailed solution for maintaining high-capacity, data-intensive network flows (eg, 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations. Materials and Methods: High-end networking, packet-filter firewalls, network intrusion-detection systems. Results: We describe a "Medical Science DMZ" concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give 3 detailed descriptions of implemented Medical Science DMZs...
October 6, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29039502/long-non%C3%A2-coding-rna-hottip-promotes-hepatocellular-carcinoma-tumorigenesis-and-development-a-comprehensive-investigation-based-on-bioinformatics-qrt%C3%A2-pcr-and-meta%C3%A2-analysis-of-393-cases
#7
Yu Zhang, Jia-Cheng Huang, Kai-Teng Cai, Xi-Bing Yu, You-Rong Chen, Wen-Ya Pan, Ze-Liang He, Jun Lv, Zhen-Bo Feng, Gang Chen
HOTTIP functions as an independent biomarker in multiple cancers. However, the role of HOTTIP in hepatocellular carcinoma (HCC) remains unclear. In this study, we sought to investigate the HOTTIP expression in HCC and normal liver. We combined quantitative reverse transcription-polymerase chain reactions (qRT‑PCR), Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), Multi Experiment Matrix (MEM) and Oncomine database to assess the clinical role and the potential molecular mechanism of HOTTIP in HCC...
October 16, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/29036643/glass-assisted-and-standardized-assessment-of-gene-variations-from-sanger-sequence-trace-data
#8
Karol Pal, Vojtech Bystry, Tomas Reigl, Martin Demko, Adam Krejci, Tasoula Touloumenidou, Evangelia Stalika, Boris Tichy, Paolo Ghia, Kostas Stamatopoulos, Sarka Pospisilova, Jitka Malcikova, Nikos Darzentas
Motivation: Sanger sequencing is still being employed for sequence variant detection by many laboratories, especially in a clinical setting. However, chromatogram interpretation often requires manual inspection and in some cases, considerable expertise. Results: We present GLASS, a web-based Sanger sequence trace viewer, editor, aligner and variant caller, built to assist with the assessment of variations in 'curated' or user-provided genes. Critically, it produces a standardized variant output as recommended by the Human Genome Variation Society...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036588/a-novel-data-structure-to-support-ultra-fast-taxonomic-classification-of-metagenomic-sequences-with-k-mer-signatures
#9
Xinan Liu, Ye Yu, Jinpeng Liu, Corrine F Elliott, Chen Qian, Jinze Liu
Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand. Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036298/myvcf-a-desktop-application-for-high-throughput-mutations-data-management
#10
Alessandro Pietrelli, Luca Valenti
Summary: Next-generation sequencing technologies have become the most powerful tool to discover genetic variants associated with human diseases. Although the dramatic reductions in the costs facilitate the use in the wet-lab and clinics, the huge amount of data generated renders their management by non-expert researchers and physicians extremely difficult. Therefore, there is an urgent need of novel approaches and tools aimed at getting the 'end-users' closer to the sequencing data, facilitating the access by non-bioinformaticians, and to speed-up the functional interpretation of genetic variants...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29034544/cyp2u1-activity-is-altered-by-missense-mutations-in-hereditary-spastic-paraplegia-56
#11
Christelle M Durand, Laura Dhers, Christelle Tesson, Alessandra Tessa, Laetitia Fouillen, Stéphanie Jacqueré, Laure Raymond, Isabelle Coupry, Giovanni Benard, Frédéric Darios, Khalid H El-Hachimi, Guja Astrea, François Rivier, Guillaume Banneau, Claire Pujol, Didier Lacombe, Alexandra Durr, Patrick J Babin, Filippo M Santorelli, Nicolas Pietrancosta, Jean-Luc Boucher, Daniel Mansuy, Giovanni Stevanin, Cyril Goizet
Hereditary Spastic Paraplegia (HSP) is an inherited disorder of the central nervous system mainly characterized by gradual spasticity and weakness of the lower limbs. SPG56 is a rare autosomal recessive early onset complicated form of HSP caused by mutations in CYP2U1. The CYP2U1 enzyme was shown to catalyze the hydroxylation of arachidonic acid. Here, we report two further SPG56 families carrying 3 novel CYP2U1 missense variants and the development of an in vitro biochemical assay to determine the pathogenicity of missense variants of uncertain clinical significance...
October 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/29030962/lncrna-dgcr5-promotes-lung-adenocarcinoma-luad-progression-via-inhibiting-hsa-mir-22-3p
#12
Hui-Xing Dong, Ren Wang, Jian Zeng, Jing Pan
Long non-coding RNAs (lncRNAs) serve critical roles in the pathogenesis of various cancers, including lung adenocarcinoma (LUAD). Herein, in this study, we aimed to investigate the biological and clinical significance of lncRNA DiGeorge syndrome critical region gene 5 (DGCR5) in LUAD. It was observed that DGCR5 was upregulated in LUAD tissues and LUAD cell lines. Inhibition of DGCR5 can prevent LUAD progression via playing anti-apoptosis roles. Both mRNA expression and protein levels of BCL-2 were increased by DGCR5 downregulation while reversely BAX was increased...
October 14, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29030400/microrna-signature-of-cigarette-smoking-and-evidence-for-a-putative-causal-role-of-micrornas-in-smoking-related-inflammation-and-target-organ-damage
#13
Christine M Willinger, Jian Rong, Kahraman Tanriverdi, Paul L Courchesne, Tianxiao Huan, Gregory A Wasserman, Honghuang Lin, Josée Dupuis, Roby Joehanes, Matthew R Jones, George Chen, Emelia J Benjamin, George T O'Connor, Joseph P Mizgerd, Jane E Freedman, Martin G Larson, Daniel Levy
BACKGROUND: Cigarette smoking increases risk for multiple diseases. MicroRNAs regulate gene expression and may play a role in smoking-induced target organ damage. We sought to describe a microRNA signature of cigarette smoking and relate it to smoking-associated clinical phenotypes, gene expression, and lung inflammatory signaling. METHODS AND RESULTS: Expression profiling of 283 microRNAs was conducted on whole blood-derived RNA from 5023 Framingham Heart Study participants (54...
October 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29029429/twist1-is-highly-expressed-in-cancer-associated-fibroblasts-of-esophageal-squamous-cell-carcinoma-with-a-prognostic-significance
#14
So-Young Yeo, Sang-Yun Ha, Keun-Woo Lee, Yan Cui, Zhao-Ting Yang, Yan-Hua Xuan, Seok-Hyung Kim
Cancer-associated fibroblasts (CAFs) play important roles in cancer progression. Twist1 was recently reported to be a key regulator of CAFs in gastric cancer, but its role in other types of cancer remains unclear, especially for esophageal squamous cell carcinoma (ESCC). We assessed the Twist1 expression on stromal fibroblasts using immunohistochemistry in 169 tissue specimens from ESCC patients, and performed in vitro and in vivo experiments to confirm the role of Twist1 in CAFs of ESCC. And we investigated the biological pathways that are activated in Twist1-high ESCC using The Cancer Genome Atlas (TCGA) data...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29028907/oncomir-an-online-resource-for-exploring-pan-cancer-microrna-dysregulation
#15
Nathan W Wong, Yuhao Chen, Shuai Chen, Xiaowei Wang
Summary: Dysregulation of microRNAs (miRNAs) is extensively associated with cancer development and progression. miRNAs have been shown to be biomarkers for predicting tumor formation and outcome. However, identification of the relationships between miRNA expression and tumor characteristics can be difficult and time-consuming without appropriate bioinformatics expertise. To address this issue, we present OncomiR, an online resource for exploring miRNA dysregulation in cancer. Using combined miRNA-seq, RNA-seq, and clinical data from The Cancer Genome Atlas, we systematically performed statistical analyses to identify dysregulated miRNAs that are associated with tumor development and progression in most major cancer types...
October 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29020999/beneficial-effects-of-heqi-san-on-rat-model-of-polycystic-ovary-syndrome-through-the-pi3k-akt-pathway
#16
Hengxia Zhao, Daocheng Zhou, Ye Chen, Deliang Liu, Shufang Chu, Shimao Zhang
BACKGROUND: Heqi San, a traditional Chinese medicine (TCM) has been reported to regulate hormone levels in patients with metabolic disease, suggesting a potential clinical application. In the current study, we aimed to elucidate the effect of Heqi San on rat model of polycystic ovary syndrome (PCOS). METHOD: PCOS model was established in female SD rats. Rats were randomly divided into four groups: the control, untreated PCOS model, Heqi San treated PCOS model (8...
October 11, 2017: Daru: Journal of Faculty of Pharmacy, Tehran University of Medical Sciences
https://www.readbyqxmd.com/read/29017577/elevated-expression-of-par3-promotes-prostate-cancer-metastasis-by-forming-a-par3-apkc-kibra-complex-and-inactivating-the-hippo-pathway
#17
Pei-Jie Zhou, Wei Xue, Jinliang Peng, Yanqing Wang, Lianzi Wei, Ziqiang Yang, Helen He Zhu, Yu-Xiang Fang, Wei-Qiang Gao
BACKGROUND: Prostate cancer (PCa) is one of the most frequent tumors and leading cause of cancer deaths among males worldwide. The majority of deaths are due to recurrence and subsequent development of the metastatic cancer. Although loss or dislocalization of polarity proteins has been implicated in embryogenesis deficiency and tumorigenesis, association of polarity protein expression levels with tumor metastasis remains unclear. METHODS: Bioinformatics, qRT-PCR, western blot and immunohistochemical (IHC) analyses were used to examine expression of Par3, a key component of polarity-associated partitioning defective (PAR) complex, in primary and metastatic clinical PCa samples...
October 10, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28993196/long-non-coding-rna-expression-profiles-in-different-severity-ev71-infected-hand-foot-and-mouth-disease-patients
#18
Jun Meng, Zhenyu Yao, Yaqing He, Renli Zhang, Hong Yang, Xiangjie Yao, Long Chen, Hailong Zhang, Jinquan Cheng
Enterovirus 71 (EV71) is associated with the severe hand foot and mouth disease (HFMD) outcomes, however the host-virus interaction mechanism and the pathogenesis remain poorly understood. Long non-coding RNAs (lncRNAs) are involved in variety physiological and pathological processes, but the functions of lncRNAs in EV71 infection remain elusive. Here we profiled the expression of lncRNAs in peripheral blood mononuclear cells (PBMCs) from EV71-infected mild patients, severe patients as well as the healthy controls, and identified 8541 lncRNAs were differentially expressed...
October 6, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28990809/proteomic-interrogation-of-hsp90-and-insights-for-medical-research
#19
Lorenz Weidenauer, Tai Wang, Suhasini Joshi, Gabriela Chiosis, Manfredo R Quadroni
Heat shock protein 90 (HSP90) regulates protein homeostasis in eukaryotes. As a "professional interactor", HSP90 binds to and chaperones many proteins and has both housekeeping and disease-related functions but its regulation remains in part elusive. HSP90 complexes are a target for therapy, notably against cancer, and several inhibitors are currently in clinical trials. Proteomic studies have revealed the vast interaction network of HSP90 and, in doing so, the extent of cellular processes the chaperone takes part in, especially in yeast and human cells...
October 9, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28988258/moving-beyond-descriptions-of-diversity-clinical-and-research-implications-of-bacterial-imbalance-in-chronic-rhinosinusitis
#20
B Wagner Mackenzie, D W Waite, M Hoggard, M W Taylor, K Biswas, R G Douglas
Chronic rhinosinusitis (CRS) is a debilitating disease which affects 5-16% of the general population and involves long-term inflammation of the sinonasal cavity. While microbial involvement in the pathogenesis of CRS has long been suspected, the exact role of microbes remains unclear. Recent application of cultivation-independent, molecular methods has provided much new information, taking advantage of developments in both laboratory- and bioinformatics-based analyses. The aim of this mini-review is to present a variety of available bioinformatics approaches, such as data classification techniques and network analyses, with proven applications in other aspects of human microbiome health and disease research...
October 8, 2017: Rhinology
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