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https://www.readbyqxmd.com/read/29348692/genome-wide-search-for-higher-order-epistasis-as-modifiers-of-treatment-effects-on-bone-mineral-density-in-childhood-cancer-survivors
#1
Cindy Im, Kirsten K Ness, Sue C Kaste, Wassim Chemaitilly, Wonjong Moon, Yadav Sapkota, Russell J Brooke, Melissa M Hudson, Leslie L Robison, Yutaka Yasui, Carmen L Wilson
Single-nucleotide polymorphisms (SNPs) contributing to interactions between regulatory elements that modulate gene transcription may explain some of the uncharacterized variation for complex traits. We explored this hypothesis among 856 adult survivors of pediatric cancer exposed to curative treatments that adversely affect bone mineral density (BMD). To restrict our search to interactions among SNPs in regulatory elements, our analysis considered 75523 SNPs mapped to putative promoter or enhancer regions. In anticipation that power to detect higher order epistasis would be low using an exhaustive search and a Bonferroni-corrected threshold for genome-wide significance (e...
January 18, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29346510/viper-a-web-application-for-rapid-expert-review-of-variant-calls
#2
Marius Wöste, Martin Dugas
Summary: With the rapid development in next-generation sequencing, cost and time requirements for genomic sequencing are decreasing, enabling applications in many areas such as cancer research. Many tools have been developed to analyze genomic variation ranging from single nucleotide variants to whole chromosomal aberrations. As sequencing throughput increases, the number of variants called by such tools also grows. Often employed manual inspection of such calls is thus becoming a time-consuming procedure...
January 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29344888/perseus-a-bioinformatics-platform-for-integrative-analysis-of-proteomics-data-in-cancer-research
#3
Stefka Tyanova, Juergen Cox
Mass spectrometry-based proteomics is a continuously growing field marked by technological and methodological improvements. Cancer proteomics is aimed at pursuing goals such as accurate diagnosis, patient stratification, and biomarker discovery, relying on the richness of information of quantitative proteome profiles. Translating these high-dimensional data into biological findings of clinical importance necessitates the use of robust and powerful computational tools and methods. In this chapter, we provide a detailed description of standard analysis steps for a clinical proteomics dataset performed in Perseus, a software for functional analysis of large-scale quantitative omics data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344887/phosphoproteomics-based-profiling-of-kinase-activities-in-cancer-cells
#4
Jakob Wirbel, Pedro Cutillas, Julio Saez-Rodriguez
Cellular signaling, predominantly mediated by phosphorylation through protein kinases, is found to be deregulated in most cancers. Accordingly, protein kinases have been subject to intense investigations in cancer research, to understand their role in oncogenesis and to discover new therapeutic targets. Despite great advances, an understanding of kinase dysfunction in cancer is far from complete.A powerful tool to investigate phosphorylation is mass-spectrometry (MS)-based phosphoproteomics, which enables the identification of thousands of phosphorylated peptides in a single experiment...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344674/long-non-coding-rna-h1-promotes-cell-proliferation-and-invasion-by-acting-as-a-cerna-of-mir%C3%A2-138-and-releasing-ezh2-in-oral-squamous-cell-carcinoma
#5
Yonglong Hong, Haitao He, Wen Sui, Jingge Zhang, Shenfu Zhang, Dajiang Yang
Long non-coding RNAs (lncRNAs) have been shown to play pivotal roles in various types of human cancer, including oral squamous cell carcinoma (OSCC). However, the potential mechanisms of action of lncRNAs in OSCC remain to be fully elucidated. The aim of the present study was to further explore the potential mechanisms of action of lncRNAs in OSCC. We first analyzed Gene Expression Omnibus (GEO) datasets to investigate aberrantly expressed lncRNAs which may be involved in the development of OSCC. Reverse transcription‑quantitative PCR (RT‑qPCR) was performed to analyze the expression levels of lncRNA H19...
January 16, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29344557/in-colonic-%C3%AF-0-rho0-cells-reduced-mitochondrial-function-mediates-transcriptomic-alterations-associated-with-cancer
#6
Harrison M Penrose, Sandra Heller, Chloe Cable, Hani Nakhoul, Nate Ungerleider, Melody Baddoo, Zachary F Pursell, Erik K Flemington, Susan E Crawford, Suzana D Savkovic
Background: Mitochondrial reprogramming has emerged as a hallmark of cancer pathobiology. Although it is believed this reprogramming is essential for cancer cells to thrive, how it supports cancer pathobiology is unclear. We previously generated colonic ρ0 (rho0) cells with reduced mitochondrial energy function and acquired their transcriptional signature. Here, we utilized a bioinformatics approach to identify their changes linked to cancer pathobiology. Methods: Human colon cancer HCT116 cells, control and ρ0, were used for qPCR...
November 2017: Oncoscience
https://www.readbyqxmd.com/read/29344215/mir-203a-suppresses-cell-proliferation-by-targeting-e2f-transcription-factor-3-in-human-gastric-cancer
#7
Huiqin Yang, Lixia Wang, Xiaoli Tang, Wenmei Bai
MicroRNAs (miRs) are a class of short non-coding RNAs that serve an essential role in the tumorigenesis of gastric cancer (GC). MiR-203a has been reported as a tumor repressor in various types of human cancer. In the present study, the function of miR-203a on the proliferation of GC cells was investigated. Bioinformatics analyses revealed that miR-203a targets the 3'-untranslated region of E2F transcription factor 3 (E2F3) messenger RNA. A luciferase reporter assay and western blot analysis were performed to confirm whether E2F3 was a target of miR-203a...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344185/downregulation-of-mir-30a-is-associated-with-proliferation-and-invasion-via-targeting-mef2d-in-cervical-cancer
#8
Jing Zhao, Bo Li, Chuqiang Shu, Yun Ma, Yingping Gong
Accumulating studies have revealed that microRNAs serve crucial roles in cancer development and progression. MicroRNA-30a (miR-30a) has been implicated in various cancer types. However, the role of miR-30a in cervical cancer remains unclear. In the current study, a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay revealed that miR-30a was significantly downregulated in cervical cancer tissues compared with adjacent normal tissues, and in the cervical cancer cell lines HeLa, SiHa and Ca-Ski compared with GH329 normal cervical epithelial cells...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344174/expression-profile-of-cytokines-in-gastric-cancer-patients-using-proteomic-antibody-microarray
#9
Xiaoqiang Quan, Yi Ding, Ruo Feng, Xiaoyan Zhu, Qinxian Zhang
Gastric cancer (GC) is often a deadly disease due to the late diagnosis and chemoresistance that characterizes many cases of this disease. The aim of this study was to explore a panel of candidate cytokines as diagnostic and predictive biomarkers for GC. Sixteen tissue samples of GC and adjacent noncancerous mucosa were selected from GC patients (n=8) for antibody microarray analysis. Proteomic chip-based analysis was performed to simultaneously identify 507 cytokines using a cytokine antibody array in the gastric tissues to screen for differential proteins related in cases of GC...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344135/identification-of-differentially-expressed-genes-in-oral-squamous-cell-carcinoma-tca8113-cells
#10
Jun Wang, Lifeng Li, Lina Gao, Chao Guan, Kexin Su, Linlin Li, Wenping Luo, Hongying Chen, Ping Ji
Previous studies have demonstrated that cancer cells with increased levels of aldehyde dehydrogenase 'bright' activity (ALDHbr) exhibit stem cell properties compared with cells exhibiting decreased ALDH activity (ALDHlow). To screen possible biomarkers of cancer stem cells in tongue squamous cell carcinoma, ALDHbr and ALDHlow cells were isolated from the tongue squamous cell carcinoma TCA8113 cell line, and suppression subtractive hybridization was performed to identify differentially expressed genes in the two subpopulations...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343974/identification-of-key-pathways-and-genes-in-tp53-mutation-acute-myeloid-leukemia-evidence-from-bioinformatics-analysis
#11
Rui Huang, Xiwen Liao, Qiaochuan Li
Background: Tumor protein p53 (TP53) mutations are not only a risk factor in acute myeloid leukemia (AML) but also a potential biomarker for individualized treatment options. This study aimed to investigate potential pathways and genes associated with TP53 mutations in adult de novo AML. Methods: An RNA sequencing dataset of adult de novo AML was downloaded from The Cancer Genome Atlas database. Differentially expressed genes (DEGs) were identified by edgeR of the R platform...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29342301/subtyping-bladder-cancers-biology-vs-bioinformatics
#12
David J McConkey, Woonyoung Choi
No abstract text is available yet for this article.
January 12, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29342249/splice-expression-variation-analysis-seva-for-inter-tumor-heterogeneity-of-gene-isoform-usage-in-cancer
#13
Bahman Afsari, Theresa Guo, Michael Considine, Liliana Florea, Luciane T Kagohara, Genevieve L Stein-O'Brien, Dylan Kelley, Emily Flam, Kristina D Zambo, Patrick K Ha, Donald Geman, Michael F Ochs, Joseph A Califano, Daria A Gaykalova, Alexander V Favorov, Elana J Fertig
Motivation: Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in normal tissues, which have stable regulation of gene splicing. Pathological conditions, such as cancer, can have broken regulation of splicing that increases the heterogeneity of the expression of splice variants. Inferring events with such differential heterogeneity in gene isoform usage requires new statistical approaches...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#14
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29341215/microrna181c-inhibits-prostate-cancer-cell-growth-and-invasion-by-targeting-multiple-erk-signaling-pathway-components
#15
Zhengzheng Su, Mengni Zhang, Miao Xu, Xinglan Li, Junya Tan, Yunyi Xu, Xiuyi Pan, Ni Chen, Xueqin Chen, Qiao Zhou
BACKGROUND: The ERK signaling pathway is frequently deregulated in tumorigenesis, mostly by classical mechanisms such as gene mutation of its components (eg, RAS and RAF). However, whether and how multiple key components of ERK pathway are regulated by microRNAs are not clear. METHODS: We firstly predicted post-transcriptional regulation of multiple key components of the ERK signaling pathway by miR181c through bioinformatics analysis, and then confirmed the post-transcriptional regulation by dual luciferase reporter gene assays and Western blot analysis...
January 16, 2018: Prostate
https://www.readbyqxmd.com/read/29340066/clinicopathological-and-prognostic-significance-of-sdc1-overexpression-in-breast-cancer
#16
Xiangrong Cui, Xuan Jing, Qin Yi, Chunlan Long, Jie Tian, Jing Zhu
Background: Breast cancer is the leading cause of cancer death among global women, and its early diagnosis and treatment are very urgent. Syndecan-1 (SDC1) is a heparin sulfate proteoglycan, which has been linked with the prognosis and treatment response in a various tumor type. To investigate whether SDC1 can serve as a prognostic indictor in breast cancer, bioinformatic analyses were performed in the present study. Methods: SDC1 expression was assessed using Oncomine analysis...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340059/microrna-95-promotes-myogenic-differentiation-by-down-regulation-of-aminoacyl-trna-synthase-complex-interacting-multifunctional-protein-2
#17
Biao Li, Shanshan Xie, Chunbo Cai, Lili Qian, Shengwang Jiang, Dezun Ma, Gaojun Xiao, Ting Gao, Jinzeng Yang, Wentao Cui
MicroRNA-95 (miR-95) is well known for its ability to promote the proliferation of a variety of cancer cells, but its function in skeletal muscle development has not been reported so far. Our laboratory has recently generated genetically engineered Meishan pigs containing a loss-of-function myostatin (MSTN) mutant (MSTN-/-). These MSTN-/- pigs grow and develop normally but show clear double muscle phenotype as observed in Belgian cattle. We observed that the expression of miR-95 was up-regulated in the longissimus dorsi from MSTN-/- Meishan pigs at day 65 during embryo development...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340028/high-resolution-microbiome-profiling-uncovers-fusobacterium-nucleatum-lactobacillus-gasseri-johnsonii-and-lactobacillus-vaginalis-associated-to-oral-and-oropharyngeal-cancer-in-saliva-from-hpv-positive-and-hpv-negative-patients-treated-with-surgery-and-chemo
#18
Rafael Guerrero-Preston, James Robert White, Filipa Godoy-Vitorino, Arnold Rodríguez-Hilario, Kelvin Navarro, Herminio González, Christina Michailidi, Anne Jedlicka, Sierra Canapp, Jessica Bondy, Amanda Dziedzic, Barbara Mora-Lagos, Gustavo Rivera-Alvarez, Carmen Ili-Gangas, Priscilla Brebi-Mieville, William Westra, Wayne Koch, Hyunseok Kang, Luigi Marchionni, Young Kim, David Sidransky
Microbiome studies show altered microbiota in head and neck squamous cell carcinoma (HNSCC), both in terms of taxonomic composition and metabolic capacity. These studies utilized a traditional bioinformatics methodology, which allows for accurate taxonomic assignment down to the genus level, but cannot accurately resolve species level membership. We applied Resphera Insight, a high-resolution methodology for 16S rRNA taxonomic assignment that is able to provide species-level context in its assignments of 16S rRNA next generation sequencing (NGS) data...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339925/mir-136-targets-mien1-and-involves-the-metastasis-of-colon-cancer-by-suppressing-epithelial-to-mesenchymal-transition
#19
Haipeng Ren, Yuanling Qi, Xiaoyan Yin, Jianfeng Gao
MIEN1 is a novel oncogene, and it involves tumor progression in various cancer types, including colon cancer. However, the definite molecular mechanisms of MIEN1 in colon cancer progression remain to be completely elucidated. In the present study, bioinformatics prediction showed that miR-136 could be an upstream regulator of MIEN1; a luciferase assay and Western blot assay revealed that miR-136 negatively regulates MIEN1 expression via directly targeting its 3'-untranslated region sequence. Moreover, a functional assay using wound healing and transwell invasion showed that overexpressed miR-136 inhibited cell migration and invasion, and overexpression of MIEN1 partly rescued the above-mentioned effects of miR-136 in colon cancer cells...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29337373/making-use-of-cancer-genomic-databases
#20
Chad J Creighton
The vast amounts of genomic data now deposited in public repositories represent rich resources for cancer researchers. Large-scale genomics initiatives such as The Cancer Genome Atlas have made available data from multiple molecular profiling platforms (e.g., somatic mutation, RNA and protein expression, and DNA methylation) for the same set of over 10,000 human tumors. There has been much collective effort toward providing user-friendly software tools for biologists lacking computational skills to ask questions of large-scale genomic datasets...
January 16, 2018: Current Protocols in Molecular Biology
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