scholarly journals Bottom-up, integrated -omics analysis identifies broadly dosage-sensitive genes in breast cancer samples from TCGA

PLoS ONE ◽  
2019 ◽  
Vol 14 (1) ◽  
pp. e0210910 ◽  
Author(s):  
Bobak D. Kechavarzi ◽  
Huanmei Wu ◽  
Thompson N. Doman
Keyword(s):  
Breast Cancer ◽  
Bottom Up ◽  
Omics Analysis ◽  
Integrated Omics

scholarly journals FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer

2016 ◽  
Vol 113 (43) ◽  
pp. E6600-E6609 ◽  
Author(s):  
Xiaoyong Fu ◽  
Rinath Jeselsohn ◽  
Resel Pereira ◽  
Emporia F. Hollingsworth ◽  
Chad J. Creighton ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Endocrine Resistance ◽  
Cancer Cell Line ◽  
Estrogen Receptor Α ◽  
Resistant Cell ◽  
Transcriptional Reprogramming ◽  
Er Positive ◽  
Integrated Omics ◽  
And Function

Forkhead box protein A1 (FOXA1) is a pioneer factor of estrogen receptor α (ER)–chromatin binding and function, yet its aberration in endocrine-resistant (Endo-R) breast cancer is unknown. Here, we report preclinical evidence for a role of FOXA1 in Endo-R breast cancer as well as evidence for its clinical significance. FOXA1 is gene-amplified and/or overexpressed in Endo-R derivatives of several breast cancer cell line models. Induced FOXA1 triggers oncogenic gene signatures and proteomic profiles highly associated with endocrine resistance. Integrated omics data reveal IL8 as one of the most perturbed genes regulated by FOXA1 and ER transcriptional reprogramming in Endo-R cells. IL-8 knockdown inhibits tamoxifen-resistant cell growth and invasion and partially attenuates the effect of overexpressed FOXA1. Our study highlights a role of FOXA1 via IL-8 signaling as a potential therapeutic target in FOXA1-overexpressing ER-positive tumors.

scholarly journals A Bottom-Up Synthesis Approach to Silver Nanoparticles Induces Anti-Proliferative and Apoptotic Activities Against MCF-7, MCF-7/TAMR-1 and MCF-10A Human Breast Cell Lines

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4332
Author(s):  
Nurul Izzati Zulkifli ◽  
Musthahimah Muhamad ◽  
Nur Nadhirah Mohamad Zain ◽  
Wen-Nee Tan ◽  
Noorfatimah Yahaya ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Silver Nanoparticles ◽  
Cell Lines ◽  
Leaf Extract ◽  
Breast Cancer Cell Lines ◽  
Face Centered Cubic ◽  
Human Breast ◽  
Bottom Up ◽  
Mcf 7

A bottom-up approach for synthesizing silver nanoparticles (AgNPs-GA) phytomediated by Garcinia atroviridis leaf extract is described. Under optimized conditions, the AgNPs-GA were synthesized at a concentration of 0.1 M silver salt and 10% (w/v) leaf extract, 1:4 mixing ratio of reactants, pH 3, temperature 32 °C and 72 h reaction time. The AgNPs-GA were characterized by various analytical techniques and their size was determined to be 5–30 nm. FTIR spectroscopy indicates the role of phenolic functional groups in the reduction of silver ions into AgNPs-GA and in supporting their subsequent stability. The UV-Visible spectrum showed an absorption peak at 450 nm which reflects the surface plasmon resonance (SPR) of AgNPs-GA and further supports the stability of these biosynthesized nanoparticles. SEM, TEM and XRD diffractogram analyses indicate that AgNPs-GA were spherical and face-centered-cubic in shape. This study also describes the efficacy of biosynthesized AgNPs-GA as anti-proliferative agent against human breast cancer cell lines, MCF-7 and MCF-7/TAMR-1. Our findings indicate that AgNPs-GA possess significant anti-proliferative effects against both the MCF-7 and MCF-7/TAMR-1 cell lines, with inhibitory concentration at 50% (IC50 values) of 2.0 and 34.0 µg/mL, respectively, after 72 h of treatment. An induction of apoptosis was evidenced by flow cytometry using Annexin V-FITC and propidium iodide staining. Therefore, AgNPs-GA exhibited its anti-proliferative activity via apoptosis on MCF-7 and MCF-7/TAMR-1 breast cancer cells in vitro. Taken together, the leaf extract from Garcinia atroviridis was found to be highly capable of producing AgNPs-GA with favourable physicochemical and biological properties.

scholarly journals Integrated ‘omics analysis reveals new drug-induced mitochondrial perturbations in human hepatocytes

2018 ◽  
Vol 289 ◽  
pp. 1-13 ◽  
Author(s):  
Jarno E.J. Wolters ◽  
Simone G.J. van Breda ◽  
Jonas Grossmann ◽  
Claudia Fortes ◽  
Florian Caiment ◽  
...  
Keyword(s):  
Human Hepatocytes ◽  
Drug Induced ◽  
New Drug ◽  
Omics Analysis ◽  
Integrated Omics

Multiple omics analysis of the protective effects of SFN on estrogen-dependent breast cancer cells

2020 ◽  
Vol 47 (5) ◽  
pp. 3331-3346
Author(s):  
Hui Huang ◽  
Shuyuan Cao ◽  
Zhan Zhang ◽  
Lei Li ◽  
Feng Chen ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Cells ◽  
Breast Cancer Cells ◽  
Protective Effects ◽  
Omics Analysis

scholarly journals A Bottom-Up Review of Image Analysis Methods for Suspicious Region Detection in Mammograms

2021 ◽  
Vol 7 (9) ◽  
pp. 190
Author(s):  
Parita Oza ◽  
Paawan Sharma ◽  
Samir Patel ◽  
Alessandro Bruno
Keyword(s):  
Breast Cancer ◽  
Biomedical Imaging ◽  
Critical Role ◽  
Breast Mri ◽  
Image Features ◽  
Mass Detection ◽  
Bottom Up ◽  
Region Detection ◽  
Suspicious Region ◽  
Pros And Cons

Breast cancer is one of the most common death causes amongst women all over the world. Early detection of breast cancer plays a critical role in increasing the survival rate. Various imaging modalities, such as mammography, breast MRI, ultrasound and thermography, are used to detect breast cancer. Though there is a considerable success with mammography in biomedical imaging, detecting suspicious areas remains a challenge because, due to the manual examination and variations in shape, size, other mass morphological features, mammography accuracy changes with the density of the breast. Furthermore, going through the analysis of many mammograms per day can be a tedious task for radiologists and practitioners. One of the main objectives of biomedical imaging is to provide radiologists and practitioners with tools to help them identify all suspicious regions in a given image. Computer-aided mass detection in mammograms can serve as a second opinion tool to help radiologists avoid running into oversight errors. The scientific community has made much progress in this topic, and several approaches have been proposed along the way. Following a bottom-up narrative, this paper surveys different scientific methodologies and techniques to detect suspicious regions in mammograms spanning from methods based on low-level image features to the most recent novelties in AI-based approaches. Both theoretical and practical grounds are provided across the paper sections to highlight the pros and cons of different methodologies. The paper’s main scope is to let readers embark on a journey through a fully comprehensive description of techniques, strategies and datasets on the topic.

scholarly journals Integrated omics analysis of sweat reveals an aberrant amino acid metabolism pathway in Vogt–Koyanagi–Harada disease

2020 ◽  
Vol 200 (3) ◽  
pp. 250-259
Author(s):  
X. Cui ◽  
G. Su ◽  
L. Zhang ◽  
S. Yi ◽  
Q. Cao ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Metabolism Pathway ◽  
Omics Analysis ◽  
Integrated Omics

scholarly journals Integrated omics-analysis reveals Wnt-mediated NAD+ metabolic reprogramming in cancer stem-like cells

Oncotarget ◽  
2016 ◽  
Vol 7 (30) ◽  
pp. 48562-48576 ◽  
Author(s):  
Jueun Lee ◽  
Hyun Jung Kee ◽  
Soonki Min ◽  
Ki Cheong Park ◽  
Sunho Park ◽  
...  
Keyword(s):  
Metabolic Reprogramming ◽  
Omics Analysis ◽  
Integrated Omics
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