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Prediction of epigenetically regulated genes in breast cancer cell lines

Leandro A Loss, Anguraj Sadanandam, Steffen Durinck, Shivani Nautiyal, Diane Flaucher, Victoria EH Carlton, Martin Moorhead, Yontao Lu, Joe W Gray, Malek Faham, Paul Spellman, Bahram Parvin
2010 BMC Bioinformatics  
The computational pipeline for identification of epigenetically regulated genes from a panel of breast cancer cell lines.  ...  Conclusions In this paper, we proposed a computational pipeline for identifying epigenetically regulated genes for a panel of breast cancer cell lines.  ...  SN, DF, VC, MM, YL and MF conducted the experiments resulting in available data from the ICBP panel of breast cancer cell lines. All authors read and approved the final manuscript. Table 2 .  ... 
doi:10.1186/1471-2105-11-305 pmid:20525369 pmcid:PMC2903569 fatcat:7yjwpo5cjfhqlnucsklmfhsy7i

MicroRNAs and Epigenetics Strategies to Reverse Breast Cancer

Mohammad Mijanur Rahman, Andrew C. Brane, Trygve O. Tollefsbol
2019 Cells  
The accrued scientific findings strongly suggest epigenetic dysregulation in breast cancer pathogenesis though genomic instability is central to breast cancer hallmarks.  ...  microRNAs (miRNAs) of gene expression profiles.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cells8101214 pmid:31597272 pmcid:PMC6829616 fatcat:4yhgdorxpbaxvfrfttccs22rwu

Analysis of H3K4me3-ChIP-Seq and RNA-Seq data to understand the putative role of miRNAs and their target genes in breast cancer cell lines

Aneesh Kotipalli, Ruma Banerjee, Sunitha Manjari Kasibhatla, Rajendra Joshi
2021 Genomics & Informatics  
Acknowledgments The authors thank the BRAF facility of C-DAC for HPC infrastructure. The authors would also like to deeply thank Dr. Janaki C.H. for her scientific review and critical comments.  ...  Epigenetic regulation via histone modification of microRNA (miRNA) pro-Breast cancer is one of the leading causes of cancer in women all over the world and accounts for ~25% of newly observed cancers in  ...  , PTRF, RUNX2, UGT8, CFB, CSF3, HEG1, PLAU, PTER, S100A3, SNURF, and WIPF1) Table 5 . 5 Predicted gene targets of differentially regulated miRNAs in breast cancer cell lines (TNBC and luminal-A) proposed  ... 
doi:10.5808/gi.21020 fatcat:5wj5vpm7kvd63heu5j72ngqopq

Epigenetic regulation of kallikrein-related peptidases: there is a whole new world out there

Maria D. Pasic, Ekaterina Olkhov, Bharati Bapat, George M. Yousef
2012 Biological chemistry  
Epigenetic regulation of KLKs holds promise for an array of therapeutic applications in many diseases including cancer.  ...  Target prediction showed that KLKs are potential targets of miRNAs that are dysregulated in tumors, including prostate, kidney and ovarian cancers, with downstream effect on tumor proliferation.  ...  . , 2009 KLK6 promoter methylation is associated with the downregulation of the gene in breast cancer cell lines and a small number of patients.  ... 
doi:10.1515/hsz-2011-0273 pmid:22505515 fatcat:lolrab53b5gthhf222bbllp3jy

Epigenetic targeting in breast cancer: Therapeutic impact and future direction

M.B. Lustberg, B. Ramaswamy
2009 Drug News and Perspectives  
and prognostic tools in breast cancer.  ...  DNA methylation and histone modifications are the two major epigenetic changes that influence gene expression in cancer.  ...  Epigenetic regulation of BRCA genes There is evidence for epigenetic regulation of BRCA1 and BRCA2 genes in both sporadic and hereditary breast cancers.  ... 
doi:10.1358/dnp.2009.22.7.1405072 pmid:19890494 pmcid:PMC3658161 fatcat:bsi5oejzubbqzhgi4f5hrs2g2a

Comprehensive epigenetic analyses reveal master regulators driving lung metastasis of breast cancer

Kening Li, Congling Xu, Yuxin Du, Muhammad Junaid, Aman-Chandra Kaushik, Dong-Qing Wei
2019 Journal of Cellular and Molecular Medicine  
However, the epigenetic reprogramming and regulatory mechanisms in lung metastasis of breast cancer remain unclear.  ...  breast cancer cells.  ...  The regulation relationships between TFs and target genes were listed in Table S6 . We predicted the interactions between TFs based on their shared target genes in each cell line.  ... 
doi:10.1111/jcmm.14424 pmid:31215771 pmcid:PMC6653217 fatcat:rglpilee3bejzeszjhqpjuno7a

Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for TNBC and gene set prediction combination

Hyoung-Min Park, HuiSu Kim, Kang-Hoon Lee, Je-Yoel Cho
2020 BMB Reports  
BMB Rep. 2020; 53(5): 266-271 Opposing histone modifications in TNBC Hyoung-Min Park, et al. 267 BMB Reports  ...  DUSP6 and VSNL1 gene expressions were significantly down-regulated in HER2+ and TNBC breast cancer cell lines.  ...  For example, gene expressions of NOVA1, SOX5 and NAT8L were found higher in the TNBC cell line than in the normal cell line while expressed lower in overall breast cancer than the healthy population (  ... 
doi:10.5483/bmbrep.2020.53.5.045 fatcat:wnhos2wphfgs7lzch5pvashtfm

Epigenetic Biomarkers in Cancer

Ramon Cacabelos
2015 Clinical & Medical Biochemistry Open Access  
Nasopharyngeal carcinoma associated gene 6 (NGX6) is down-regulated in most colon cancer cell lines and tumor tissues.  ...  The impact of epigenetic events in oncogenic genes has been documented in many different types of cancer.  ... 
doi:10.4172/2471-2663.1000e101 fatcat:fydp2pcm7fgulllkunt6oh7vmi

Overview on Epigenetic Re-programming: A Potential Therapeutic Intervention in Triple Negative Breast Cancers

Ezanee Azlina Mohamad Hanif, Shamsul Azhar Shah
2018 Asian Pacific Journal of Cancer Prevention  
Acknowledgements This work was funded by grants from Ministry of Higher Education Malaysia (MoHE), and Geran Galakan Penyelidik Muda (GGPM-2017-103).  ...  Figure 5 . 5 Apoptosis Driven by Activation of FOXO1 and Phosphorylated Protein Kinase B to Regulate BIM in Triple Negative Breast Cancer Cell Lines.  ...  Epigenetic regulation is one of the key players in silencing expressions of genes in estrogen receptor (ER) positive in breast cancer, as research discovered a highly methylated promoter region in the  ... 
doi:10.31557/apjcp.2018.19.12.3341 fatcat:35icij67r5gsxi4o6g7tojzmqq

Crocodylus porosus Sera a Potential Source to Identify Novel Epigenetic Targets: In Silico Analysis

Ruqaiyyah Siddiqui, Jibran Sualeh Muhammad, Sutherland K. Maciver, Naveed Ahmed Khan
2022 Veterinary Sciences  
The purpose of this study was to use in silico analysis to identify genes that might be epigenetically modulated in cells treated with crocodile serum and to understand the role of potential genes as novel  ...  Furthermore, we present a comprehensive overview of relevant studies on epigenetic regulation of these genes along with an insight into their clinical implications.  ...  Acknowledgments: The authors are grateful to the University of Sharjah to support this work. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/vetsci9050210 pmid:35622738 pmcid:PMC9144183 fatcat:hlodur3s2ncjvjwgg4xcxphzmq

Comparative epigenetic analyses reveal distinct patterns of oncogenic pathways activation in breast cancer subtypes

Yongsheng Li, Shengli Li, Juan Chen, Tingting Shao, Chunjie Jiang, Yuan Wang, Hong Chen, Juan Xu, Xia Li
2014 Human Molecular Genetics  
And these epigenetic alterations regulated corresponding gene expression in a synergetic way in both subtypes.  ...  Breast cancer is a highly heterogeneous disease that is characterized by genetic and epigenetic aberrations; however, our knowledge of epigenetic alterations of breast cancer subtypes remains limited.  ...  Additionally, as epigenetic regulation of gene expression is a dynamic and reversible process, assessment of the epigenetic patterns may predict more subtype-specific epigenetic drugs.  ... 
doi:10.1093/hmg/ddu256 pmid:24871326 fatcat:huqkvy5nxre35b4jsx23as7kny

Pathway landscapes and epigenetic regulation in breast cancer and melanoma cell lines

Mariama El Baroudi, Dario La Sala, Caterina Cinti, Enrico Capobianco
2014 Theoretical Biology and Medical Modelling  
Epigenetic variation is a main regulation mechanism of gene expression in various cancer histotypes, and due to its reversibility, the potential impact in therapy can be very relevant. Methods.  ...  Based on a selected pair, breast cancer (BC) and melanoma, we conducted inference analysis in parallel on a few cell lines (MCF-7 for BC and A375 for melanoma).  ...  In Table 3 , we reported pathways that we found commonly enriched among up-regulated genes in one cancer cell line and down-regulated genes in the other cell line.  ... 
doi:10.1186/1742-4682-11-s1-s8 pmid:25077705 pmcid:PMC4108926 fatcat:dbltoctln5d7jes52sislxpyui

Epigenetic regulation of ZEB1-RAB25/ESRP1 axis plays a critical role in phenylbutyrate treatment-resistant breast cancer

Mariko Kikuchi, Keishi Yamashita, Mina Waraya, Naoko Minatani, Hideki Ushiku, Ken Kojo, Akira Ema, Yoshimasa Kosaka, Hiroshi Katoh, Norihiko Sengoku, Takumo Enomoto, Hirokazu Tanino (+2 others)
2015 OncoTarget  
In this study, we used 7 breast cancer cell lines to identify biomarker candidates that predict PB sensitivity in breast cancer.  ...  The genes associated with PB sensitivity are downstream targets of ZEB1. Epigenetic regulation of ZEB1 may prove valuable as a critical biomarker for predicting resistance to breast cancer therapies.  ...  Epigenetic regulation of ZEB1 may serve as a critical biomarker for predicting resistance to breast cancer treatments.  ... 
doi:10.18632/oncotarget.6480 pmid:26646320 pmcid:PMC4811494 fatcat:qnhziyad2repfhad5qytjmlgyy

Reversing Hormone Therapy Resistance: A Novel Era of Epigenetic Therapy in Breast and Prostate Cancers

Nguyen Minh Nam
2015 Journal of Steroids & Hormonal Science  
In breast cancer, methylation of CpG islands within the promoter of the gene encoding ER-α is one of the main causes of the loss of ER expression in ER-negative breast cancer cells.  ...  Efforts should be directed to find biological markers and epigenetic gene signatures that could predict the efficacy of a specific inhibitor.  ...  In breast cancer, methylation of CpG islands within the promoter of the gene encoding ER-α is one of the main causes of the loss of ER expression in ER-negative breast cancer cells.  ... 
doi:10.4172/2157-7536.1000-e116 fatcat:6o5v5ga43jcuvecsn7imtpgemm

Novel mediators of breast cancer bone metastasis—insights from studies of gene-regulation and the global proteome

Janet E. Brown, Steven L. Wood
2018 Annals of Translational Medicine  
CAPG enhances breast cancer metastasis by competing with PRMT5 to modulate STC-1 transcription.  ...  Footnote Conflicts of Interest: The authors have no conflicts of interest to declare.  ...  Epigenetic regulation of HGF/Met signalling results in both anoikis resistance and stem-cell characteristics characteristic of epithelial-mesenchymal transition (EMT) in metastatic breast cancer.  ... 
doi:10.21037/atm.2018.10.41 pmid:30613646 pmcid:PMC6291541 fatcat:opdvjc3doba53n7cihhetjgmqe
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