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https://www.readbyqxmd.com/read/28231327/functionally-focused-algorithmic-analysis-of-high-resolution-microarray-cgh-genomic-landscapes-demonstrates-comparable-genomic-copy-number-aberrations-in-msi-and-mss-sporadic-colorectal-cancer
#1
Hamad Ali, Milad S Bitar, Ashraf Al Madhoun, Makia Marafie, Fahd Al-Mulla
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers...
2017: PloS One
https://www.readbyqxmd.com/read/28229366/mining-cancer-transcriptomes-bioinformatic-tools-and-the-remaining-challenges
#2
Thomas Milan, Brian T Wilhelm
The development of next-generation sequencing technologies has had a profound impact on the field of cancer genomics. With the enormous quantities of data being generated from tumor samples, researchers have had to rapidly adapt tools or develop new ones to analyse the raw data to maximize its value. While much of this effort has been focused on improving specific algorithms to get faster and more precise results, the accessibility of the final data for the research community remains a significant problem. Large amounts of data exist but are not easily available to researchers who lack the resources and experience to download and reanalyze them...
February 22, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28224495/hidden-markov-models-in-bioinformatics-snv-inference-from-next-generation-sequence
#3
Jiawen Bian, Xiaobo Zhou
The rapid development of next generation sequencing (NGS) technology provides a novel avenue for genomic exploration and research. Hidden Markov models (HMMs) have wide applications in pattern recognition as well as Bioinformatics such as transcription factor binding sites and cis-regulatory modules detection. An application of HMM is introduced in this chapter with the in-deep developing of NGS. Single nucleotide variants (SNVs) inferred from NGS are expected to reveal gene mutations in cancer. However, NGS has lower sequence coverage and poor SNV detection capability in the regulatory regions of the genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28223168/prognostic-alternative-mrna-splicing-signature-in-non-small-cell-lung-cancer
#4
Yuan Li, Nan Sun, Zhiliang Lu, Shouguo Sun, Jianbing Huang, Zhaoli Chen, Jie He
Alternative splicing provides a major mechanism to generate protein diversity. Increasing evidence suggests a link of dysregulation of splicing associated with cancer. Genome-wide alternative splicing profiling in lung cancer remains largely unstudied. We generated alternative splicing profiles in 491 lung adenocarcinoma (LUAD) and 471 lung squamous cell carcinoma (LUSC) patients in TCGA using RNA-seq data, prognostic models and splicing networks were built by integrated bioinformatics analysis. A total of 3,691 and 2,403 alternative splicing events were significantly associated with patient survival in LUAD and LUSC, respectively, including EGFR, CD44, PIK3C3, RRAS2, MAPKAP1 and FGFR2...
February 18, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28222670/microrna-223-3p-inhibits-human-bladder-cancer-cell-migration-and-invasion
#5
Ju Guo, Runfu Cao, Xingwei Yu, Zewen Xiao, Zhiwen Chen
The regulation of initiation and progression during carcinogenesis of bladder carcinoma is not completely elucidated. Dysregulation of microRNAs has been detected to play critical roles in the development of various cancers, including bladder carcinoma, whereas the involvement of miR-223-3p in the tumorigenesis of bladder carcinoma has not been studied. Here, we show that significantly higher levels of nuclear receptor coactivator 1 and significantly lower levels of miR-223-3p were detected in bladder carcinoma tissue, compared to the adjacent non-tumor tissue...
February 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28218742/mirna-expression-profiles-reveal-the-involvement-of-mir-26a-mir-548l-and-mir-34a-in-hepatocellular-carcinoma-progression-through-regulation-of-st3gal5
#6
Hongjiao Cai, Huimin Zhou, Yuan Miao, Nana Li, Lifen Zhao, Li Jia
MicroRNAs (miRNAs) have key roles in comprehensive physiological and pathological processes by targeting specific genes through translational repression. Identification of miRNAs related to metastasis enables us to obtain better insight into cancer development. In the current study, we investigated the miRNA expressional profiles in the highly invasive human hepatocellular carcinoma cell line MHCC97-H and MHCC97-L with lower metastatic potential using miRNA microarrays. By quantitative real-time PCR, we confirmed the results of miRNA experiments...
February 20, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28218435/a-low-frequency-variant-in-smad7-modulates-tgf-%C3%AE-signaling-and-confers-risk-for-colorectal-cancer-in-chinese-population
#7
Jiaoyuan Li, Li Zou, Ying Zhou, Lu Li, Ying Zhu, Yang Yang, Yajie Gong, Jiao Lou, Juntao Ke, Yi Zhang, Jianbo Tian, Danyi Zou, Xiating Peng, Jiang Chang, Jing Gong, Rong Zhong, Xiaobo Zhou, Xiaoping Miao
The TGF-β pathway plays an essential role in regulating cell proliferation and differentiation. GWASs and candidate approaches have identified a battery of genetic variants in the TGF-β pathway contributing to colorectal cancer (CRC). However, most of the significant variants are common variants and their functions remain ambiguous. To identify causal variants with low-frequency in the TGF-β pathway contributing to CRC susceptibility in Chinese population, we performed targeted sequencing of 12 key genes in TGF-β signaling in CRC patients followed by a two-stage case-control study with a total of 5109 cases and 5169 controls...
February 20, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28218035/microrna-153-regulates-glutamine-metabolism-in-glioblastoma-through-targeting-glutaminase
#8
Zhenyang Liu, Junyu Wang, Yunjun Li, Juan Fan, Lihua Chen, Ruxiang Xu
Glioblastoma is the most aggressive manifestation of malignant gliomas and considered to be among the deadliest forms of human cancers. MicroRNAs are found to tightly regulate diverse biological processes and considered to play important roles in cancer etiology. In this study, we found that microRNA-153 was significantly downregulated in glioblastoma tissues compared to matched non-tumor tissues and in glioblastoma cell lines. To investigate the potential function of microRNA-153 in glioblastoma, we transfected glioblastoma cell line U87MG as well as U373MG with synthetic microRNA-153 oligos and observed decreased cell proliferation and increased apoptosis...
February 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28215562/gene-selection-for-tumor-classification-using-neighborhood-rough-sets-and-entropy-measures
#9
Yumin Chen, Zunjun Zhang, Jianzhong Zheng, Ying Ma, Yu Xue
With the development of bioinformatics, tumor classification from gene expression data becomes an important useful technology for cancer diagnosis. Since a gene expression data often contains thousands of genes and a small number of samples, gene selection from gene expression data becomes a key step for tumor classification. Attribute reduction of rough sets has been successfully applied to gene selection field, as it has the characters of data driving and requiring no additional information. However, traditional rough set method deals with discrete data only...
February 12, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28214999/e6-associated-protein-dependent-estrogen-receptor-regulation-of-protein-kinase-a-regulatory-subunit-r2a-expression-in-neuroblastoma
#10
Jean-Pierre Obeid, Youssef H Zeidan, Nawal Zafar, Jimmy El Hokayem
E6ap is a known transcriptional coregulator for estrogen receptor alpha (Er, Erα) in the presence of estrogen. Protein kinase A (PKA) contains two regulatory subunits derived from four genes. Recent evidence demonstrates that PKA regulates E6ap activity. Data generated in our lab indicated estrogen dependent regulation of Pkar2a levels. Our project sets to investigate a possible feedback mechanism constituting of Erα and E6ap transcriptional regulation of Pkar2a expression. Western blot evaluated protein regulation correlations with E2 in mouse neuroblastoma lines...
February 18, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28214218/implication-of-downregulation-and-prospective-pathway-signaling-of-microrna-375-in-lung-squamous-cell-carcinoma
#11
Wen-Jie Chen, Ting-Qing Gan, Hui Qin, Su-Ning Huang, Li-Hua Yang, Ye-Ying Fang, Zu-Yun Li, Lin-Jiang Pan, Gang Chen
BACKGROUND: Lung cancer is one of the most typical cancers in the world. Altered expression profiles of microRNA-375(miR-375) are linked to many diseases including lung cancer. However, the relationship between miR-375 and lung squamous cell carcinoma (LUSC) is controversial. METHODS: We first evaluated the 23 LUSCs and the paired normal lung tissues by qRT-PCR. Then we analyzed the LUSC samples with miR-375 expression based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO)...
January 22, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28214207/microrna-155-targets-map3k10-and-regulates-osteosarcoma-cell-growth
#12
Chuangjian Wang, Xiaobo Zhang, Chunlin Zhang, Fuying Zhai, Ying Li, Zongqiang Huang
Osteosarcoma is the most common type of bone cancer prevalent in young adults. Recent studies suggested that aberrant microRNA expression plays an essential role in osteosarcoma pathogenesis. In this study, we found miR-155 up-regulation in different osteosarcoma cell lines U2OS, Saos-2 and MG-63. Through bioinformatic prediction and analysis, we identified its target MAP3K10 that involved in cell proliferation and apoptosis. This work demonstrates novel interaction between microRNA, intercellular MAPK signaling and apoptosis in osteosarcoma, which will provide targets for therapeutic development...
February 1, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28214016/melk-expression-in-ovarian-cancer-correlates-with-poor-outcome-and-its-inhibition-by-otssp167-abrogates-proliferation-and-viability-of-ovarian-cancer-cells
#13
Reto S Kohler, Henriette Kettelhack, Alexandra M Knipprath-Mészaros, André Fedier, Andreas Schoetzau, Francis Jacob, Viola Heinzelmann-Schwarz
OBJECTIVE: Maternal embryonic leucine-zipper kinase (MELK) shows oncogenic properties in basal-like breast cancer, a cancer subtype sharing common molecular features with high-grade serous ovarian cancer. We examined the potential of MELK as a molecular and pharmacological target for treatment of epithelial ovarian cancer (EOC). METHODS/MATERIALS: Bioinformatic analysis was performed on nine OC transcriptomic data sets totaling 1241 patients. Effects of MELK depletion by shRNA or inhibition by OTSSP167 in cell lines were assessed by colony formation and MTT (proliferation) assays, Western blotting (apoptosis), and flow cytometry (cell cycle analysis)...
February 14, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28213656/dual-functional-microrna-186-5p-targets-both-fgf2-and-rela-to-suppress-tumorigenesis-of-glioblastoma-multiforme
#14
Fachen Wang, Hui Jiang, Shanjun Wang, Bing Chen
Glioblastoma multiforme (GBM) is one of the most malignant cancers. MicroRNAs (miRs) were reported to play important roles in GBM recently. However, the role of a novel miR-186-5p in GBM tumorigenesis is still elusive. Using bioinformatics, miR-186-5p was identified as potential regulators of both fibroblast growth factor (FGF)-2 and NF-κB subunit RelA. Luciferase reporter assay was used to confirm the direct recognition FGF2 and RelA mRNAs by miR-186-5p. Invasion and migration assays were employed to study the effect of miR-186-5p on GBM cell growth in vitro...
February 17, 2017: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/28213554/hypoxia-selectively-enhances-integrin-receptor-expression-to-promote-metastasis
#15
Julia A Ju, Ines Godet, I Chae Ye, Jungmin Byun, Hasini Jayatilaka, Sun Joo Lee, Lisha Xiang, Debangshu Samanta, Meng Horng Lee, Pei-Hsun Wu, Denis Wirtz, Gregg L Semenza, Daniele M Gilkes
: Metastasis is the leading cause of breast cancer (BCa)mortality. Previous studies have implicated hypoxia-induced changes in the composition and stiffness of the extracellular matrix (ECM) in the metastatic process. Therefore, the contribution of potential ECM binding receptors in this process was explored. Using a bioinformatics approach the expression of all integrin receptor subunits, in two independent BCa patient data sets, were analyzed to determine if integrin status correlates with a validated hypoxiainducible gene signature...
February 17, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28212810/chromosomal-instability-analysis-and-regional-tumor-heterogeneity-in-colon-cancer
#16
Vincenza Barresi, Sergio Castorina, Nicolò Musso, Carmela Capizzi, Tonia Luca, Giovanna Privitera, Daniele Filippo Condorelli
Chromosomal instability (CIN) is classically defined as an increase in the rate at which numerical or structural chromosomal aberrations are acquired in a cancer cell. The number of somatic copy number abnormalities (CNAs) revealed by high resolution genomic array can be considered as a surrogate marker for CIN, but several points, related to sample processing and data analysis, need to be standardized. In this work we analyzed 51 CRC samples and matched normal mucosae by whole genome SNP arrays and compared different bioinformatics tools in order to identify broad (>25% of a chromosomal arm) and focal somatic copy number abnormalities (BCNAs and FCNAs respectively)...
January 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28212580/network-pharmacology-based-and-clinically-relevant-prediction-of-the-active-ingredients-and-potential-targets-of-chinese-herbs-in-metastatic-breast-cancer-patients
#17
Yu Mao, Jian Hao, Zi-Qi Jin, Yang-Yang Niu, Xue Yang, Dan Liu, Rui Cao, Xiong-Zhi Wu
Chinese Herbal Medicine (CHM) plays a significant role in breast cancer treatment. We conduct the study to ascertain the relative molecular targets of effective Chinese herbs in treating stage IV breast cancer.Survival benefit of CHM was verified by Kaplan-Meier method and Cox regression analysis. A bivariate correlation analysis was used to find and establish the effect of herbs in complex CHM formulas. A network pharmacological approach was adopted to explore the potential mechanisms of CHM.Patients in the CHM group had a median survival time of 55 months, which was longer than the 23 months of patients in the non-CHM group...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28210664/fibronectin-and-androgen-receptor-expression-data-in-prostate-cancer-obtained-from-a-rna-sequencing-bioinformatics-analysis
#18
Dibash K Das, Thahmina Ali, Konstantinos Krampis, Olorunseun O Ogunwobi
Prostate cancer is the second most commonly diagnosed male cancer in the world. The molecular mechanisms underlying its development and progression are still unclear. Here we show analysis of a prostate cancer RNA-sequencing dataset that was originally generated by Ren et al. [3] from the prostate tumor and adjacent normal tissues of 14 patients. The data presented here was analyzed using our RNA-sequencing bioinformatics analysis pipeline implemented on the bioinformatics web platform, Galaxy. The relative expression of fibronectin (FN1) and the androgen receptor (AR) were calculated in fragments per kilobase of transcript per million mapped reads, and represented in FPKM unit...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28210267/mir-30-family-potentially-targeting-pi3k-siah2-predicted-interaction-network-represents-a-novel-putative-theranostic-panel-in-non-small-cell-lung-cancer
#19
Lawrence W C Chan, Fengfeng Wang, Fei Meng, Lili Wang, Sze Chuen Cesar Wong, Joseph S K Au, Sijun Yang, William C S Cho
Non-small cell lung cancer (NSCLC) comprises about 84% of all lung cancers. Many treatment options are available but the survival rate is still very low due to drug resistance. It has been found that phosphoinositide-3-kinase (PI3K) affects sensitivity to tyrosine kinase inhibitors (TKIs), including gefitinib and erlotinib. Expression level of seven in absentia homolog 2 (SIAH2), an E3 ubiquitin-protein ligase, is upregulated in NSCLC and correlated with tumor grade. However, the relationship between PI3K and SIAH2 remains unclear and therefore it is not known whether they can act as treatment co-targets and theranostic dual markers for overcoming TKI resistance...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28209205/long-noncoding-agap2-as1-is-activated-by-sp1-and-promotes-cell-proliferation-and-invasion-in-gastric-cancer
#20
Fuzhen Qi, Xianghua Liu, Hao Wu, Xiang Yu, Chenchen Wei, Xiaodan Huang, Guozhong Ji, Fengqi Nie, Keming Wang
BACKGROUND: Long noncoding RNAs (lncRNAs) have emerged as important regulators of tumorigenesis and cancer progression. Recently, the lncRNA AGAP2-AS1 was identified as an oncogenic lncRNA in human non-small cell lung cancer (NSCLC) and its elevated expression was linked to NSCLC development and progression. However, the expression pattern and molecular mechanism of AGAP2-AS1 in gastric cancer (GC) have not been characterized. METHODS: Bioinformatic analysis was performed to determine AGAP2-AS1 expression levels in the GC and normal tissues using gene profiling data from the Gene Expression Omnibus...
February 16, 2017: Journal of Hematology & Oncology
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