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https://www.readbyqxmd.com/read/28345463/computational-and-mechanistic-studies-on-the-effect-of-galactoxyloglucan-imatinib-nanoconjugate-in-imatinib-resistant-k562-cells
#1
Alphy Rose James, B S Unnikrishnan, R Priya, Manu M Joseph, T K Manojkumar, K Raveendran Pillai, R Shiji, G U Preethi, P Kusumakumary, T T Sreelekha
Imatinib mesylate, a BCR/ABL fusion protein inhibitor, is the first-line treatment against chronic myelogenous leukemia. In spite of its advantageous viewpoints, imatinib still has genuine impediments like undesirable side effects and tumor resistance during chemotherapy. Nanoparticles with sustainable release profile will help in targeted delivery of anticancer drugs while minimizing deleterious side effects and drug resistance. The use of biopolymers like galactoxyloglucan (PST001) for the fabrication of imatinib mesylate nanoparticles could impart its use in overcoming multidrug resistance in chronic myelogenous leukemia patients with minimal side effects...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28345460/coactivator-associated-arginine-methyltransferase-1-promotes-cell-growth-and-is-targeted-by-microrna-195-5p-in-human-colorectal-cancer
#2
Meifeng Zhang, Wei Wu, Ming Gao, Jie Zhang, Xinde Ding, Ronghua Zhu, Haiqun Chen, Zhewei Fei
The pathogenesis of colorectal cancer remains poorly understood. Here, we show that coactivator-associated arginine methyltransferase 1 is frequently upregulated in colorectal cancer tissues and promotes cell growth in vitro and in vivo. Using bioinformatics-based prediction and luciferase reporter system, we found that coactivator-associated arginine methyltransferase 1 is post-transcriptionally targeted by microRNA-195-5p in colorectal cancer. Ectopic expression of microRNA-195-5p led to the suppression of the coactivator-associated arginine methyltransferase 1 3'-untranslated regions activity and downregulation of the endogenous coactivator-associated arginine methyltransferase 1 protein in colorectal cancer cells...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28341746/leveraging-sequence-based-faecal-microbial-community-survey-data-to-identify-a-composite-biomarker-for-colorectal-cancer
#3
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/28341036/advanced-methodologies-in-high-throughput-sequencing-of-immune-repertoires
#4
REVIEW
Simon Friedensohn, Tarik A Khan, Sai T Reddy
In recent years, major efforts have been made to develop sophisticated experimental and bioinformatic workflows for sequencing adaptive immune repertoires. The immunological insight gained has been applied to fields as varied as lymphocyte biology, immunodiagnostics, vaccines, cancer immunotherapy, and antibody engineering. In this review, we provide a detailed overview of these advanced methodologies, focusing specifically on strategies to reduce sequencing errors and bias and to achieve high-throughput pairing of variable regions (e...
March 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28340574/myocyte-enhancer-factor-2d-provides-a-cross-talk-between-chronic-inflammation-and-lung-cancer
#5
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
#6
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/28339095/expression-of-yes-associated-protein%C3%A2-1-and-its-clinical-significance-in-ovarian-serous-cystadenocarcinoma
#7
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
#8
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/28339011/reduction-of-mir%C3%A2-132%C3%A2-3p-contributes-to-gastric-cancer-proliferation-by-targeting-muc13
#9
Liang He, Linlin Qu, Lijing Wei, Yan Chen, Jian Suo
Abnormal expression of epidermal growth factor receptor (EGFR) signaling and microRNAs (miRNAs) has been widely seen in gastric cancer. The present study focused on the miRNAs that regulate human epidermal growth factor receptor (HER) activation through mucin 13 (MUC13). The protein level of MUC13 was demonstrated to be significantly increased in gastric cancer tissues compared with normal tissues by western blot analysis and immunohistochemistry. TargetScan bioinformatic predictions indicated that miRNA (miR)‑212‑3p and miR‑132‑3p may bind to the 3'‑untranslated region of MUC13...
March 22, 2017: Molecular Medicine 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
#10
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/28337276/microrna-9-regulates-non-small-cell-lung-cancer-cell-invasion-and-migration-by-targeting-eukaryotic-translation-initiation-factor-5a2
#11
Guodong Xu, Guofeng Shao, Qiaoling Pan, Lebo Sun, Dawei Zheng, Minghui Li, Ni Li, Huoshun Shi, Yiming Ni
MicroRNAs (miRNAs) play a critical role in cancer development and progression. Bioinformatics analyses has identified eukaryotic translation initiation factor 5A2 (eIF5A2) as a target of miR-9. In this study, we attempted to determine whether miR-9 regulates non-small cell lung cancer (NSCLC) cell invasion and migration by targeting eIF5A2 We examined eIF5A2 expression using reverse transcription-quantitative PCR (RT-qPCR) and subsequently transfected A549 and NCI-H1299 NSCLC cells with a miR-9 mimic or miR-9 inhibitor to determine the migration and invasive capability of the cells via wound healing assay and Transwell invasion assay, respectively...
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
#12
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/28334343/pathwaymapper-a-collaborative-visual-web-editor-for-cancer-pathways-and-genomic-data
#13
Istemi Bahceci, Ugur Dogrusoz, Konnor C La, Özgün Babur, Jianjiong Gao, Nikolaus Schultz
Motivation: While existing network visualization tools enable the exploration of cancer genomics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many manuscripts from The Cancer Genome Atlas (TCGA). These pathway diagrams typically summarize how a pathway is altered in individual cancer types, including alteration frequencies for each gene. Results: To address this need, we developed the web-based tool PathwayMapper, which runs in most common web browsers...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334134/a-compilation-of-web-based-research-tools-for-mirna-analysis
#14
Vaibhav Shukla, Vinay Koshy Varghese, Shama Prasada Kabekkodu, Sandeep Mallya, Kapaettu Satyamoorthy
Since the discovery of microRNAs (miRNAs), a class of noncoding RNAs that regulate the gene expression posttranscriptionally in sequence-specific manner, there has been a release of number of tools useful for both basic and advanced applications. This is because of the significance of miRNAs in many pathophysiological conditions including cancer. Numerous bioinformatics tools that have been developed for miRNA analysis have their utility for detection, expression, function, target prediction and many other related features...
February 25, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28334049/mmp1-expression-is-activated-by-slug-and-enhances-multi-drug-resistance-mdr-in-breast-cancer
#15
Ching-Ju Shen, Yu-Ling Kuo, Chien-Chung Chen, Ming-Jenn Chen, Ya-Min Cheng
High matrix metalloproteinase 1 (MMP1) expression is associated with enhanced breast cancer growth and metastasis and also might predict poor prognosis. In this study, we further investigated the functional role of MMP1 and how it is upregulated in multi-drug resistant (MDR) breast cancer cells. By retrieving microarray data in GEO datasets and the survival data in the Kaplan Meier plotter, we observed that MMP1 is significantly upregulated in MCF-7/ADR cells compared to the parental MCF-7 cells, while high MMP1 expression is associated with worse overall survival (OS) and recurrence free survival (RFS) in breast cancer patients after systematic therapy...
2017: PloS One
https://www.readbyqxmd.com/read/28333300/comparison-of-global-gene-expression-profiles-of-microdissected-human-foetal-leydig-cells-with-their-normal-and-hyperplastic-adult-equivalents
#16
Grete Lottrup, Kirstine Belling, Henrik Leffers, John E Nielsen, Marlene D Dalgaard, Anders Juul, Niels E Skakkebæk, Søren Brunak, Ewa Rajpert-De Meyts
STUDY QUESTION: Do human adult Leydig cells (ALCs) within hyperplastic micronodules display characteristics of foetal LCs (FLCs)? SUMMARY ANSWER: The gene expression profiles of FLCs and all ALC subgroups were clearly different, but there were no significant differences in expressed genes between the normally clustered and hyperplastic ALCs. WHAT IS KNOWN ALREADY: LCs are the primary androgen producing cells in males throughout development and appear in chronologically distinct populations; FLCs, neonatal LCs and ALCs...
March 17, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28333152/radiation-inducible-mir-770-5p-sensitizes-tumors-to-radiation-through-direct-targeting-of-pdz-binding-kinase
#17
Hyung Chul Lee, Nam-Gu Her, Donghee Kang, Seung Hee Jung, Jinwook Shin, Minyoung Lee, In Hwa Bae, Young-Nyun Kim, Heon Joo Park, Young-Gyu Ko, Jae-Seon Lee
Radiotherapy represents the most effective non-surgical modality in cancer treatment. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression, and are involved in many biological processes and diseases. To identify miRNAs that influence the radiation response, we performed miRNA array analysis using MCF7 cells at 2, 8, and 24 h post irradiation. We demonstrated that miR-770-5p is a novel radiation-inducible miRNA. When miR-770-5p was overexpressed, relative cell number was reduced due to increased apoptosis in MCF7 and A549 cells...
March 23, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28330108/identification-of-novel-snps-in-differentially-expressed-genes-and-its-association-with-horn-cancer-of-bos-indicus-bullocks-by-next-generation-sequencing
#18
P G Koringa, S J Jakhesara, D N Rank, C G Joshi
The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328815/strobe-compliant-integrin-through-focal-adhesion-involve-in-cancer-stem-cell-and-multidrug-resistance-of-ovarian-cancer
#19
Luwei Wei, Fuqiang Yin, Wei Zhang, Li Li
Cancer stem cells (CSCs) are considered to be the root of carcinoma relapse and drug resistance in ovarian cancer. Hunting for the potential CSC genes and explain their functions would be a feasible strategy to meet the challenge of the drug resistance in ovarian cancer. In this study, we performed bioinformatic approaches such as biochip data extraction and pathway enrichment analyses to elucidate the mechanism of the CSC genes in regulation of drug resistance. Potential key genes, integrins, were identified to be related to CSC in addition to their associations with drug resistance and prognosis in ovarian cancer...
March 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28327945/enhancing-knowledge-discovery-from-cancer-genomics-data-with-galaxy
#20
Marco A Albuquerque, Bruno M Grande, Elie J Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K Grewal, Sohrab P Shah, Paul C Boutros, Ryan D Morin
The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data...
March 9, 2017: GigaScience
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