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https://www.readbyqxmd.com/read/28431272/specific-microrna-mrna-regulatory-network-of-colon-cancer-invasion-mediated-by-tissue-kallikrein-related-peptidase-6
#1
Earlphia Sells, Ritu Pandey, Hwudaurw Chen, Bethany A Skovan, Haiyan Cui, Natalia A Ignatenko
Metastatic colon cancer is a major cause of deaths among colorectal cancer (CRC) patients. Elevated expression of kallikrein 6 (KLK6), a member of a kallikrein subfamily of peptidase S1 family serine proteases, has been reported in CRC and is associated with low patient survival rates and poor disease prognosis. We knocked down KLK6 expression in HCT116 colon cancer cells to determine the significance of KLK6 expression for metastatic dissemination and to identify the KLK6-associated microRNAs (miRNAs) signaling networks in metastatic colon cancer...
April 18, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28430743/microrna-148a-promotes-apoptosis-and-suppresses-growth-of-breast-cancer-cells-by-targeting-b-cell-lymphoma-2
#2
Qunying Li, Pingping Ren, Pengfei Shi, Yihan Chen, Feixiang Xiang, Li Zhang, Jing Wang, Qing Lv, Mingxing Xie
MicroRNAs (miRNAs) contribute toward tumorigenesis through the modulation of tumor-related genes. MiR-148a has been characterized as a tumor-suppressing miRNA and its downregulation has been reported in tumors of a variety of cancers. However, the functional role of miR-148a in breast cancer is not yet fully understood. Using both in-vitro and in-vivo models, we confirmed that miR-148a acts to inhibit the proliferation of breast cancer cells. Through the use of bioinformatic approaches in miRNA target prediction, we determined that B-cell lymphoma 2 (BCL-2) is a likely target of miR-148a...
April 20, 2017: Anti-cancer Drugs
https://www.readbyqxmd.com/read/28430657/microrna-signatures-predict-prognosis-of-patients-with-glioblastoma-multiforme-through-the-cancer-genome-atlas
#3
Ying Yuan, Hua Zhang, Xuexia Liu, Zhongming Lu, Guojun Li, Meixia Lu, Xiaofeng Tao
MicroRNAs (miRNAs) play major roles in various biological processes and have been implicated in the pathogenesis and malignant progression of glioblastoma multiforme (GBM). The aim of this study was to assess the predictive values of miRNAs for overall survival (OS) of patients with GBM. MiRNA expression profiles and clinical information of 563 GBM patients were obtained from the Cancer Genome Atlas. The most significantly altered miRNAs were identified and miRNA expression profiles were performed, through principal component analysis, the least absolute shrinkage and selection operator method...
April 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28429075/toward-personalized-management-in-bladder-cancer-the-promise-of-novel-molecular-taxonomy
#4
REVIEW
Marie-Lisa Eich, Lars Dyrskjøt, George J Netto
Empowered by the recent advances in next generation sequencing and bioinformatics technology, an unprecedented wave of integrated transcriptomic and genomic studies have impacted the field of bladder cancer. These studies not only have confirmed previously charted genetic pathways in bladder cancer development but also have led to the discovery of numerous additional crucial driver genetic alterations. As a result, a novel genomic-based taxonomy is emerging that promises to better define clinically relevant intrinsic subtypes of bladder cancer...
April 21, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28428271/master-transcriptional-regulators-in-cancer-discovery-via-reverse-engineering-approaches-and-subsequent-validation
#5
REVIEW
Bruce Moran, Arman Rahman, Katja Palonen, Fiona T Lanigan, William M Gallagher
Reverse engineering of transcriptional networks using gene expression data enables identification of genes that underpin the development and progression of different cancers. Methods to this end have been available for over a decade and, with a critical mass of transcriptomic data in the oncology arena having been reached, they are ever more applicable. Extensive and complex networks can be distilled into a small set of key master transcriptional regulators (MTR), genes that are very highly connected and have been shown to be involved in processes of known importance in disease...
April 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28427494/characterization-and-expression-analysis-of-peroxiredoxin-genes-in-nnk-induced-v79-cells
#6
Gui Qin Shi, Wen Shan Zhou, Meng Li, Fei Ren, Ya Wei Han
4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is a potent and prevalent nitrosamine procarcinogen found in cigarette smoke. The aim of this work is to study alterations in peroxiredoxin (Prx) expression induced by NNK during carcinogenesis. Characterization of Prx genes from hamster was performed using bioinformatics. V79 cells were induced with different concentrations of NNK (0.1-0.4 mg/mL), and the expression levels of six Prx genes (Prx1-Prx6) were measured by qRT-PCR 24 h following NNK treatment...
March 2017: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/28427212/high-myc-expression-and-transcription-activity-underlies-intra-tumoral-heterogeneity-in-triple-negative-breast-cancer
#7
Nidhi Gupta, Karen Jung, Chengsheng Wu, Abdulraheem Alshareef, Hind Alqahtani, Sambasivarao Damaraju, John R Mackey, Sunita Ghosh, Siham Sabri, Bassam S Abdulkarim, Gilbert Bigras, Raymond Lai
We have previously identified a novel intra-tumoral dichotomy in triple-negative breast cancer (TNBC) based on the differential responsiveness to a reporter containing the Sox2 regulatory region-2 (SRR2), with reporter responsive (RR) cells being more stem-like than reporter unresponsive (RU) cells. Using bioinformatics, we profiled the protein-DNA binding motifs of SRR2 and identified Myc as one of the potential transcription factors driving SRR2 activity. In support of its role, Myc was found to be highly expressed in RR cells as compared to RU cells...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28427206/mir-146a-and-mir-146b-promote-proliferation-migration-and-invasion-of-follicular-thyroid-carcinoma-via-inhibition-of-st8sia4
#8
Wei Ma, Xuzi Zhao, Leilei Liang, Guangzhi Wang, Yanyan Li, Xiaolong Miao, Yongfu Zhao
Follicular thyroid carcinoma (FTC) is a more aggressive form of thyroid cancer than the common papillary type. Alpha-2,8-sialyltransferase (ST8SIA) family members are expressed in various cancers and may be associated with FTC progression. In this study, we measured ST8SIA family expression in two FTC cell lines with different invasive potentials (FTC-133 and FTC-238) and Nthy-ori 3-1 cell lines, as well as FTC and normal thyroid tissues. ST8SIA4 was downregulated in the highly invasive FTC-238 cells and FTC tissues...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28427159/genome-wide-analysis-of-long-noncoding-rna-and-mrna-co-expression-profile-in-intrahepatic-cholangiocarcinoma-tissue-by-rna-sequencing
#9
Wenhui Yang, Yuan Li, Xia Song, Jun Xu, Jun Xie
Long noncoding RNAs (lncRNAs), which are pervasively transcribed in the genome, are emerging in molecular biology as crucial regulators of cancer. RNA-seq data were downloaded from GEO of NCBI and further analyzed to identify novel targets in intrahepatic cholangiocarcinoma (iCCA).We investigated differences in lncRNA and mRNA profiles between 7 pairs of iCCA and adjacent normal tissues. 230 lncRNAs were differentially expressed more than four-fold change in iCCA tissues. Among these, 97 were upregulated and 133 downregulated relatively to normal tissues...
February 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28425505/novel-interactions-of-the-von-hippel-lindau-pvhl-tumor-suppressor-with-the-cdkn1-family-of-cell-cycle-inhibitors
#10
Giovanni Minervini, Raffaele Lopreiato, Raissa Bortolotto, Antonella Falconieri, Geppo Sartori, Silvio C E Tosatto
Germline inactivation of the von Hippel-Lindau (VHL) tumor suppressor predisposes patients to develop different highly vascularized cancers. pVHL targets the hypoxia-inducible transcription factor (HIF-1α) for degradation, modulating the activation of various genes involved in hypoxia response. Hypoxia plays a relevant role in regulating cell cycle progression, inducing growth arrest in cells exposed to prolonged oxygen deprivation. However, the exact molecular details driving this transition are far from understood...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424428/global-mirna-expression-profiling-of-domestic-cat-livers-following-acute-toxoplasma-gondii-infection
#11
Wei Cong, Xiao-Xuan Zhang, Jun-Jun He, Fa-Cai Li, Hany M Elsheikha, Xing-Quan Zhu
Although microRNAs (miRNAs) play an important role in liver homeostasis, the extent to which they can be altered by Toxoplasma gondii infection is unknown. Here, we utilized small RNA sequencing and bioinformatic analyses to characterize miRNA expression profiles in the liver of domestic cats at 7 days after oral infection with T. gondii (Type II) strain. A total of 384 miRNAs were identified and 82 were differentially expressed, of which 33 were up-regulated and 49 down-regulated. Also, 5690 predicted host gene targets for the differentially expressed miRNAs were identified using the bioinformatic algorithm miRanda...
March 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423738/lncrna-snhg1-a-non-degradable-sponge-for-mir-338-promotes-expression-of-proto-oncogene-cst3-in-primary-esophageal-cancer-cells
#12
Yan Yan, Qingxia Fan, Liping Wang, Yue Zhou, Jianhua Li, Kun Zhou
Competing endogenous RNA (ceRNA) is a newly proposed mechanism that describes a crosstalk among lncRNAs, mRNAs and their shared miRNAs. In this study, the role of miR-338-3p (miR-338) in the progression of esophageal cancer and its involve in the ceRNA regulatory circuit lncRNA-Snhg1/CST3 were explored. MiR-338 displayed a 30% decreased expression in esophageal squamous cell carcinoma tissues compared with the adjacent. Then, proto-oncogene CST3 was predicted and validated as a target gene of miR-338. Gain-and-loss-function experiments indicated that miR-338 suppressed expression of CST3 protein (also Cystatin C, CysC), promoted expression of apoptotic proteins caspase-8/3, attenuated esophageal carcinoma cell growth and induced its apoptosis...
March 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423715/a-functional-variant-at-the-mirna-binding-site-in-hmgb1-gene-is-associated-with-risk-of-oral-squamous-cell-carcinoma
#13
Chiao-Wen Lin, Ying-Erh Chou, Chia-Ming Yeh, Shun-Fa Yang, Chun-Yi Chuang, Yu-Fan Liu
Oral squamous cell carcinoma (OSCC) is a common malignancy that has been causally associated with both hereditary and acquired factors. The high mobility group box 1 (HMGB1) gene plays an important role as a DNA chaperone to help maintain nuclear homeostasis. Altered expression of HMGB1 has been implicated in a wide range of pathological processes, including inflammation and cancer. The present study explores the impact of HMGB1 gene polymorphisms, combined with environmental risks regarding susceptibility to oral tumorigenesis...
March 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423702/experience-with-precision-genomics-and-tumor-board-indicates-frequent-target-identification-but-barriers-to-delivery
#14
Alan H Bryce, Jan B Egan, Mitesh J Borad, A Keith Stewart, Grzegorz S Nowakowski, Asher Chanan-Khan, Mrinal M Patnaik, Stephen M Ansell, Michaela S Banck, Steven I Robinson, Aaron S Mansfield, Eric W Klee, Gavin R Oliver, Jennifer B McCormick, Norine E Huneke, Colleen M Tagtow, Robert B Jenkins, Kandelaria M Rumilla, Sarah E Kerr, Jean-Pierre A Kocher, Scott A Beck, Martin E Fernandez-Zapico, Gianrico Farrugia, Konstantinos N Lazaridis, Robert R McWilliams
BACKGROUND: The ability to analyze the genomics of malignancies has opened up new possibilities for off-label targeted therapy in cancers that are refractory to standard therapy. At Mayo Clinic these efforts are organized through the Center for Individualized Medicine (CIM). RESULTS: Prior to GTB, datasets were analyzed and integrated by a team of bioinformaticians and cancer biologists. Therapeutically actionable mutations were identified in 65% (92/141) of the patients tested with 32% (29/92) receiving genomically targeted therapy with FDA approved drugs or in an independent clinical trial with 45% (13/29) responding...
March 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423643/pole-and-pold1-screening-in-155-patients-with-multiple-polyps-and-early-onset-colorectal-cancer
#15
Clara Esteban-Jurado, David Giménez-Zaragoza, Jenifer Muñoz, Sebastià Franch-Expósito, Miriam Álvarez-Barona, Teresa Ocaña, Miriam Cuatrecasas, Sabela Carballal, María López-Cerón, Maria Marti-Solano, Marcos Díaz-Gay, Tom van Wezel, Antoni Castells, Luis Bujanda, Judith Balmaña, Victoria Gonzalo, Gemma Llort, Clara Ruiz-Ponte, Joaquín Cubiella, Francesc Balaguer, Rosa Aligué, Sergi Castellví-Bel
Germline mutations in POLE and POLD1 have been shown to cause predisposition to colorectal multiple polyposis and a wide range of neoplasms, early-onset colorectal cancer being the most prevalent. In order to find additional mutations affecting the proofreading activity of these polymerases, we sequenced its exonuclease domain in 155 patients with multiple polyps or an early-onset colorectal cancer phenotype without alterations in the known hereditary colorectal cancer genes. Interestingly, none of the previously reported mutations in POLE and POLD1 were found...
March 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422960/predicting-the-impact-of-lynch-syndrome-causing-missense-mutations-from-structural-calculations
#16
Sofie V Nielsen, Amelie Stein, Alexander B Dinitzen, Elena Papaleo, Michael H Tatham, Esben G Poulsen, Maher M Kassem, Lene J Rasmussen, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen
Accurate methods to assess the pathogenicity of mutations are needed to fully leverage the possibilities of genome sequencing in diagnosis. Current data-driven and bioinformatics approaches are, however, limited by the large number of new variations found in each newly sequenced genome, and often do not provide direct mechanistic insight. Here we demonstrate, for the first time, that saturation mutagenesis, biophysical modeling and co-variation analysis, performed in silico, can predict the abundance, metabolic stability, and function of proteins inside living cells...
April 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28422721/functional-analysis-implicating-the-snp-rs61552325-in-erbb2-as-an-effector-for-androgen-insensitive-prostate-cancer-cell-invasion
#17
Xianxiang Xin, Yinmin Gu, Yang Chen, Yuanjie Huang, Zengnan Mo, Yanling Hu
BACKGROUND: As one of the most common cancers in men, the pathogenesis of prostate cancer has been widely researched. Aberrant activation of the erb-b2 receptor tyrosine kinase 2 (ERBB2) has been found to play a critical role in metastatic prostate cancer. In our previous study, we demonstrated that rs61552325 (Pro1140Ala) located in ERBB2 is strongly correlated to prostate cancer. Therefore, we initially studied the effect of rs61552325 on androgen-independent prostate cancer cell metastasis...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422088/clustering-by-fast-search-and-merge-of-local-density-peaks-for-gene-expression-microarray-data
#18
Rashid Mehmood, Saeed El-Ashram, Rongfang Bie, Hussain Dawood, Anton Kos
Clustering is an unsupervised approach to classify elements based on their similarity, and it is used to find the intrinsic patterns of data. There are enormous applications of clustering in bioinformatics, pattern recognition, and astronomy. This paper presents a clustering approach based on the idea that density wise single or multiple connected regions make a cluster, in which density maxima point represents the center of the corresponding density region. More precisely, our approach firstly finds the local density regions and subsequently merges the density connected regions to form the meaningful clusters...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28420412/intersect-then-combine-approach-improving-the-performance-of-somatic-variant-calling-in-whole-exome-sequencing-data-using-multiple-aligners-and-callers
#19
Maurizio Callari, Stephen-John Sammut, Leticia De Mattos-Arruda, Alejandra Bruna, Oscar M Rueda, Suet-Feung Chin, Carlos Caldas
Bioinformatic analysis of genomic sequencing data to identify somatic mutations in cancer samples is far from achieving the required robustness and standardisation. In this study we generated a whole exome sequencing benchmark dataset using the platinum genome sample NA12878 and developed an intersect-then-combine (ITC) approach to increase the accuracy in calling single nucleotide variants (SNVs) and indels in tumour-normal pairs. We evaluated the effect of alignment, base quality recalibration, mutation caller and filtering on sensitivity and false positive rate...
April 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28419837/identification-and-molecular-cloning-of-novel-transcripts-of-the-human-kallikrein-related-peptidase-10-klk10-gene-using-next-generation-sequencing
#20
Panagiotis G Adamopoulos, Christos K Kontos, Andreas Scorilas
Kallikreins (KLKs) form the largest group of serine proteases in the human genome sharing many structural and functional characteristics. Multiple alternative transcripts have been reported for most human KLKs, while many of them have been found aberrantly expressed in various human malignancies, thus possessing significant prognostic or/and diagnostic value. Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity, as it affects cell cycle control, proliferation, apoptosis, invasion, and metastasis...
April 15, 2017: Biochemical and Biophysical Research Communications
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