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https://www.readbyqxmd.com/read/29150767/cell-migration-in-1d-and-2d-nanofiber-microenvironments
#1
Horacio M Estabridis, Aniket Jana, Amrinder Nain, David J Odde
Understanding how cells migrate in fibrous environments is important in wound healing, immune function, and cancer progression. A key question is how fiber orientation and network geometry influence cell movement. Here we describe a quantitative, modeling-based approach toward identifying the mechanisms by which cells migrate in fibrous geometries having well controlled orientation. Specifically, U251 glioblastoma cells were seeded onto non-electrospinning Spinneret based tunable engineering parameters fiber substrates that consist of networks of suspended 400 nm diameter nanofibers...
November 17, 2017: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/29150680/potential-landscape-of-high-dimensional-nonlinear-stochastic-dynamics-with-large-noise
#2
Ying Tang, Ruoshi Yuan, Gaowei Wang, Xiaomei Zhu, Ping Ao
Quantifying stochastic processes is essential to understand many natural phenomena, particularly in biology, including the cell-fate decision in developmental processes as well as the genesis and progression of cancers. While various attempts have been made to construct potential landscape in high dimensional systems and to estimate transition rates, they are practically limited to the cases where either noise is small or detailed balance condition holds. A general and practical approach to investigate real-world nonequilibrium systems, which are typically high-dimensional and subject to large multiplicative noise and the breakdown of detailed balance, remains elusive...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29147648/molecular-crosstalking-among-noncoding-rnas-a-new-network-layer-of-genome-regulation-in-cancer
#3
REVIEW
Marco Ragusa, Cristina Barbagallo, Duilia Brex, Angela Caponnetto, Matilde Cirnigliaro, Rosalia Battaglia, Davide Barbagallo, Cinzia Di Pietro, Michele Purrello
Over the past few years, noncoding RNAs (ncRNAs) have been extensively studied because of the significant biological roles that they play in regulation of cellular mechanisms. ncRNAs are associated to higher eukaryotes complexity; accordingly, their dysfunction results in pathological phenotypes, including cancer. To date, most research efforts have been mainly focused on how ncRNAs could modulate the expression of protein-coding genes in pathological phenotypes. However, recent evidence has shown the existence of an unexpected interplay among ncRNAs that strongly influences cancer development and progression...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29145449/estimation-of-the-proteomic-cancer-co-expression-sub-networks-by-using-association-estimators
#4
Cihat Erdoğan, Zeyneb Kurt, Banu Diri
In this study, the association estimators, which have significant influences on the gene network inference methods and used for determining the molecular interactions, were examined within the co-expression network inference concept. By using the proteomic data from five different cancer types, the hub genes/proteins within the disease-associated gene-gene/protein-protein interaction sub networks were identified. Proteomic data from various cancer types is collected from The Cancer Proteome Atlas (TCPA). Correlation and mutual information (MI) based nine association estimators that are commonly used in the literature, were compared in this study...
2017: PloS One
https://www.readbyqxmd.com/read/29143332/accurate-prediction-and-elucidation-of-drug-resistance-based-on-the-robust-and-reproducible-chemoresponse-communities
#5
Enyu Dai, Jing Wang, Feng Yang, Xu Zhou, Qian Song, Shuyuan Wang, Xuexin Yu, Dianming Liu, Qian Yang, Hong Dai, Wei Jiang, Hong Ling
Selecting the available treatment for each cancer patient from genomic context is a core goal of precision medicine, but innovative approaches with mechanism interpretation and improved performance are still highly needed. Through utilizing in vitro chemotherapy response data coupled with gene and miRNA expression profiles, we applied a network-based approach that identified markers not as individual molecules but as functional groups extracted from the integrated transcription factor and miRNA regulatory network...
November 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29142286/discovery-of-bladder-cancer-related-genes-using-integrative-heterogeneous-network-modeling-of-multi-omics-data
#6
Chen Peng, Ao Li, Minghui Wang
In human health, a fundamental challenge is the identification of disease-related genes. Bladder cancer (BC) is a worldwide malignant tumor, which has resulted in 170,000 deaths in 2010 up from 114,000 in 1990. Moreover, with the emergence of multi-omics data, more comprehensive analysis of human diseases become possible. In this study, we propose a multi-step approach for the identification of BC-related genes by using integrative Heterogeneous Network Modeling of Multi-Omics data (iHNMMO). The heterogeneous network model properly and comprehensively reflects the multiple kinds of relationships between genes in the multi-omics data of BC, including general relationships, unique relationships under BC condition, correlational relationships within each omics and regulatory relationships between different omics...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138955/the-impact-of-palliative-care-training-for-oncologists-and-integrative-palliative-service-in-a-public-funded-hospital-cluster-a-retrospective-cohort-study
#7
Pak-Lun Lam, Tai-Chung Lam, Cheuk-Wai Choi, Anne Wing-Mui Lee, Kwok-Keung Yuen, To-Wai Leung
PURPOSE: Oncological care of advanced cancer patients was provided by multiple departments in Hong Kong. One of these departments, the clinical oncology department (COD), introduced systematic palliative care training for its oncologists since 2002. The COD was recognized as a European Society for Medical Oncology (ESMO) Designated Centre of Integrated Oncology and Palliative Care since 2009. This retrospective cohort study aims to review the impact of integrative training and service on palliative care coverage and outcome...
November 14, 2017: Supportive Care in Cancer: Official Journal of the Multinational Association of Supportive Care in Cancer
https://www.readbyqxmd.com/read/29138501/targeting-sxip-eb1-interaction-an-integrated-approach-to-the-discovery-of-small-molecule-modulators-of-dynamic-binding-sites
#8
T B Almeida, A J Carnell, I L Barsukov, N G Berry
End binding protein 1 (EB1) is a key element in the complex network of protein-protein interactions at microtubule (MT) growing ends, which has a fundamental role in MT polymerisation. EB1 is an important protein target as it is involved in regulating MT dynamic behaviour, and has been associated with several disease states, such as cancer and neuronal diseases. Diverse EB1 binding partners are recognised through a conserved four amino acid motif, (serine-X-isoleucine-proline) which exists within an intrinsically disordered region...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29137232/integration-of-metabolomics-transcriptomics-and-microrna-expression-profiling-reveals-a-mir-143-hk2-glucose-network-underlying-zinc-deficiency-associated-esophageal-neoplasia
#9
Louise Y Fong, Ruiyan Jing, Karl J Smalley, Cristian Taccioli, Johannes Fahrmann, Dinesh K Barupal, Hansjuerg Alder, John L Farber, Oliver Fiehn, Carlo M Croce
Esophageal squamous cell carcinoma (ESCC) in humans is a deadly disease associated with dietary zinc (Zn)-deficiency. In the rat esophagus, Zn-deficiency induces cell proliferation, alters mRNA and microRNA gene expression, and promotes ESCC. We investigated whether Zn-deficiency alters cell metabolism by evaluating metabolomic profiles of esophageal epithelia from Zn-deficient and replenished rats vs sufficient rats, using untargeted gas chromatography time-of-flight mass spectrometry (n = 8/group). The Zn-deficient proliferative esophagus exhibits a distinct metabolic profile with glucose down 153-fold and lactic acid up 1...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29136207/linkedomics-analyzing-multi-omics-data-within-and-across-32-cancer-types
#10
Suhas V Vasaikar, Peter Straub, Jing Wang, Bing Zhang
The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29136180/bcntb-bioinformatics-the-next-evolutionary-step-in-the-bioinformatics-of-breast-cancer-tissue-banking
#11
Emanuela Gadaleta, Stefano Pirrò, Abu Zafer Dayem Ullah, Jacek Marzec, Claude Chelala
Here, we present an update of Breast Cancer Now Tissue Bank bioinformatics, a rich platform for the sharing, mining, integration and analysis of breast cancer data. Its modalities provide researchers with access to a centralised information gateway from which they can access a network of bioinformatic resources to query findings from publicly available, in-house and experimental data generated using samples supplied from the Breast Cancer Now Tissue Bank. This in silico environment aims to help researchers use breast cancer data to their full potential, irrespective of any bioinformatics barriers...
October 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29135110/pathway-cross-talk-network-strategy-reveals-key-pathways-in-non-small-cell-lung-cancer
#12
Meng-Li Zheng, Nai-Kang Zhou, De-Liang Huang, Cheng-Hua Luo
PURPOSE: The purpose of this study was to explore the pathway cross-talks and key pathways in non-small cell lung cancer (NSCLC) to better understand the underlying pathological mechanism. METHODS: Integrated gene expression data, pathway data and protein-protein interaction (PPI) data were assessed to identify the pathway regulatory interactions in NSCLC, and constructed the background and disease pathway crosstalk networks, respectively. In this work, the attractor method was implemented to identified the differential pathways, and the rank product (RP) algorithm was used to determine the importance of pathways...
September 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/29132683/-impairment-of-dna-damage-response-and-cancer
#13
REVIEW
Chloé Rancoule, Alexis Vallard, Jean-Baptiste Guy, Sophie Espenel, Sylvie Sauvaigo, Claire Rodriguez-Lafrasse, Nicolas Magné
Maintaining the genetic integrity is a key process in cell viability and is enabled by a wide network of repair pathways. When this system is defective, it generates genomic instability and results in an accumulation of chromosomal aberrations and mutations that may be responsible for various clinical phenotypes, including susceptibility to develop cancer. Indeed, these defects can promote not only the initiation of cancer, but also allow the tumor cells to rapidly acquire mutations during their evolution. Several genes are involved in these damage repair systems and particular polymorphisms are predictive of the onset of cancer, the best described of them being BRCA...
November 10, 2017: Bulletin du Cancer
https://www.readbyqxmd.com/read/29126202/activedriverdb-human-disease-mutations-and-genome-variation-in-post-translational-modification-sites-of-proteins
#14
Michal Krassowski, Marta Paczkowska, Kim Cullion, Tina Huang, Irakli Dzneladze, B F Francis Ouellette, Joseph T Yamada, Amelie Fradet-Turcotte, Jüri Reimand
Interpretation of genetic variation is needed for deciphering genotype-phenotype associations, mechanisms of inherited disease, and cancer driver mutations. Millions of single nucleotide variants (SNVs) in human genomes are known and thousands are associated with disease. An estimated 21% of disease-associated amino acid substitutions corresponding to missense SNVs are located in protein sites of post-translational modifications (PTMs), chemical modifications of amino acids that extend protein function. ActiveDriverDB is a comprehensive human proteo-genomics database that annotates disease mutations and population variants through the lens of PTMs...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29123978/deep-sequencing-and-comprehensive-expression-analysis-identifies-several-molecules-potentially-related-to-human-poorly-differentiated-hepatocellular-carcinoma
#15
Ping Shao, Deguang Sun, Liming Wang, Rong Fan, Zhenming Gao
Hepatocellular carcinoma (HCC) that is graded histologically as poorly differentiated has a high recurrence, metastasis and poor prognosis. We sought to determine the regulatory mechanisms of HCC tumorigenesis and to identify molecules closely related to poorly differentiated HCC. High-throughput sequencing was used to construct microRNA (miRNA) and mRNA expression profiles for poorly differentiated HCC tissues and adjacent tissues. Network analysis was carried out to study miRNA-target interactions. Integrating the miRNA and mRNA data of HCC with four tumor grades from The Cancer Genome Atlas (TCGA) portal enabled the identification of potential closely related molecules for early diagnosis of poorly differentiated HCC...
November 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/29119509/a-network-based-integrative-workflow-to-unravel-mechanisms-underlying-disease-progression
#16
Faiz M Khan, Mehdi Sadeghi, Shailendra K Gupta, Olaf Wolkenhauer
Unraveling mechanisms underlying diseases has motivated the development of systems biology approaches. The key challenges for the development of mathematical models and computational tool are (1) the size of molecular networks, (2) the nonlinear nature of spatio-temporal interactions, and (3) feedback loops in the structure of interaction networks. We here propose an integrative workflow that combines structural analyses of networks, high-throughput data, and mechanistic modeling. As an illustration of the workflow, we use prostate cancer as a case study with the aim of identifying key functional components associated with primary to metastasis transitions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29118934/exploring-conserved-mrna-mirna-interactions-in-colon-and-lung-cancers
#17
Fereshteh Izadi, Mona Zamanian-Azodi, Vahid Mansouri, Mahsa Khodadoostan, Nosratollah Naderi
Aim: The main goal of this analysis was prioritization of co-expressed genes and miRNAs that are thought to have important influences in the pathogenesis of colon and lung cancers. Background: MicroRNAs (miRNAs) as small and endogenous noncoding RNAs which regulate gene expression by repressing mRNA translation or decreasing stability of mRNAs; they have proven pivotal roles in different types of cancers. Accumulating evidence indicates the role of miRNAs in a wide range of biological processes from oncogenesis and tumor suppressors to contribution to tumor progression...
2017: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/29113851/impact-of-academic-facility-type-and-volume-on-post-surgical-outcomes-following-diagnosis-of-glioblastoma
#18
Alan Hauser, Sunil W Dutta, Timothy N Showalter, Jason P Sheehan, Surbhi Grover, Daniel M Trifiletti
OBJECTIVE: To identify if facility type and/or facility volume impact overall survival (OS) following diagnosis of glioblastoma (GBM). We also sought to compare early post-surgical outcomes based on these factors. METHODS: The National Cancer Database was queried for patients with GBM diagnosed from 2004 to 2013 with known survival. Patients were grouped based on facility type and facility volume. Multivariable analyses were performed to investigate factors associated OS following diagnosis and Chi-square tests were used to compare early post-surgical outcomes...
November 4, 2017: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
https://www.readbyqxmd.com/read/29113250/comparison-of-mirna-and-gene-expression-profiles-between-metastatic-and-primary-prostate-cancer
#19
Kaimin Guo, Zuowen Liang, Fubiao Li, Hongliang Wang
The present study aimed to identify the regulatory mechanisms associated with the metastasis of prostate cancer (PC). The microRNA (miRNA/miR) microarray dataset GSE21036 and gene transcript dataset GSE21034 were downloaded from the Gene Expression Omnibus database. Following pre-processing, differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs) between samples from patients with primary prostate cancer (PPC) and metastatic prostate cancer (MPC) with |log2 fold change (FC)| >1 and a false discovery rate <0...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29113170/screening-of-potential-therapy-targets-for-prostate-cancer-using-integrated-analysis-of-two-gene-expression-profiles
#20
Rui Zhao, Yao Wang, Muchun Zhang, Xinquan Gu, Weihua Wang, Jiufeng Tan, Xin Wei, Ning Jin
The aim of the present study was to analyze potential therapy targets for prostate cancer using integrated analysis of two gene expression profiles. First, gene expression profiles GSE38241 and GSE3933 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between prostate cancer and normal control samples were identified using the Linear Models for Microarray Data package. Pathway enrichment analysis of DEGs was performed using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes...
November 2017: Oncology Letters
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