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Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis

Andrew E. Teschendorff, Michel Journée, Pierre A. Absil, Rodolphe Sepulchre, Carlos Caldas
2007 PLoS Computational Biology  
Citation: Teschendorff AE, Journée M, Absil PA, Sepulchre R, Caldas C (2007) Elucidating the altered transcriptional programs in breast cancer using Independent Component Analysis.  ...  In addition, we find associations linking the activity levels of biological pathways and transcription factors (NF1 and NFAT) with clinical outcome in breast cancer.  ...  The scientific responsibility rests with its authors. We would like to thank Jason Carroll for useful discussions.  ... 
doi:10.1371/journal.pcbi.0030161 pmid:17708679 pmcid:PMC1950343 fatcat:v4f2uhlzyre6xfqfpvnllerzqm

An In Vitro Model of Mast Cell Recruitment and Activation by Breast Cancer Cells Supports Anti-Tumoral Responses

Angélica Aponte-López, Jennifer Enciso, Samira Muñoz-Cruz, Ezequiel M. Fuentes-Pananá
2020 International Journal of Molecular Sciences  
Breast cancer (BrC) affects millions of women yearly. Mast cells (MCs) are common components of breast tumors with documented agonistic and antagonistic roles in tumor progression.  ...  We used aggressive and non-aggressive BrCC to model the progressive staging of the disease over HMC1 and LAD-2 human MC lines.  ...  (B) Overall survival plots comparing high or low expression of relevant genes found in the array analysis using breast cancer public databases. In (A) data represent three independent experiments.  ... 
doi:10.3390/ijms21155293 pmid:32722549 fatcat:2wbxxipig5fh3mgiefnjbankiq

Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

Chenjie Zeng, Xingyi Guo, Jirong Long, Karoline B. Kuchenbaecker, Arnaud Droit, Kyriaki Michailidou, Maya Ghoussaini, Siddhartha Kar, Adam Freeman, John L. Hopper, Roger L. Milne, Manjeet K. Bolla (+225 others)
2016 Breast Cancer Research  
Acknowledgements We thank all the individuals who took part in these studies and all the researchers, study staff, clinicians and other healthcare providers, technicians and administrative staff who have  ...  In particular, we would like to thank Terence 'Jack' Martin (St Vincents Institute, Melbourne, Australia) for carefully reviewing this manuscript. COGS  ...  Studies with a large sample size are needed to elucidate the association between this locus and breast cancer risk in African descendants.  ... 
doi:10.1186/s13058-016-0718-0 pmid:27459855 pmcid:PMC4962376 fatcat:zaw4gvaj4jejlfiezd7cxmxpye

Bioinformatics identification of dysregulated microRNAs in triple negative breast cancer based on microRNA expression profiling

Junqing Chen, Zhanhong Chen, Jian Huang, Feng Chen, Weiwu Ye, Guojun Ding, Xiaojia Wang
2017 Oncology Letters  
In the present study, the miRNA expression profiles of the human breast cancer cell line, MDA-MB-231, and MCF-7 cells, was evaluated by using miRNA microarray analysis.  ...  In addition, gene ontology analysis and pathway enrichment analysis revealed that the dysregulated miRNAs and predicted targets were found to be involved in the mitogen-activated protein kinase, Wnt, and  ...  LQ13H160016), the Medical Science and Technology Program of Zhejiang Province (grant nos. 2013KYA026 and 2015DTA004) to JQ Chen, the Foundation of Science and Technology Department of Zhejiang Province  ... 
doi:10.3892/ol.2017.7707 pmid:29435032 pmcid:PMC5778821 fatcat:fuwtgwlsyjam3pdiw53oytf2ly

Global Transcriptional Changes Following Statin Treatment in Breast Cancer

O. Bjarnadottir, S. Kimbung, I. Johansson, S. Veerla, M. Jonsson, P.-O. Bendahl, D. Grabau, I. Hedenfalk, S. Borgquist
2015 Clinical Cancer Research  
The Systematic Motif Analysis Retrieval Tool (SMART) was used to identify enriched transcription-factor-bindingsites.  ...  The results were confirmed in vitro in breast cancer cell lines.  ...  To further explore the potential functional significance of the altered genes, we Analysis of transcription factor binding sites enriched in genes altered by statin treatment The TFBS analysis program  ... 
doi:10.1158/1078-0432.ccr-14-1403 pmid:25840970 fatcat:eqs22mqhe5dmhbprdsdnhmhzvi

Prolactin Alters the Mammary Epithelial Hierarchy, Increasing Progenitors and Facilitating Ovarian Steroid Action

Kathleen A. O'Leary, Michael P. Shea, Stephanie Salituro, Courtney E. Blohm, Linda A. Schuler
2017 Stem Cell Reports  
Hormones drive mammary development and function and play critical roles in breast cancer.  ...  Our findings demonstrate that PRL can powerfully influence the epithelial hierarchy alone and temper the actions of ovarian steroids, which may underlie its role in the development of breast cancer.  ...  Mirroring the epidemiologic data establishing that the relationship of PRL levels to breast cancer in women is independent from estrogen (Tworoger and Hankinson, 2008) , cancers in NRL-PRL females can  ... 
doi:10.1016/j.stemcr.2017.08.011 pmid:28919264 pmcid:PMC5639259 fatcat:i7fgqciciffvrgesoimlks62su

Molecular signatures of metaplastic carcinoma of the breast by large-scale transcriptional profiling: identification of genes potentially related to epithelial–mesenchymal transition

H C Lien, Y H Hsiao, Y S Lin, Y T Yao, H F Juan, W H Kuo, Mien-Chie Hung, K J Chang, F J Hsieh
2007 Oncogene  
We performed transcriptional profiling using half-agenome oligonucleotide microarrays to elucidate genetic profiles of MCBs and their differences to those of ductal carcinoma of breasts (DCBs) using discarded  ...  Metaplastic carcinoma of the breast (MCB) is a poorly understood subtype of breast cancer.  ...  We performed transcriptional profiling using half-agenome oligonucleotide microarrays to elucidate genetic profiles of MCBs and their differences to those of ductal carcinoma of breasts (DCBs) using discarded  ... 
doi:10.1038/sj.onc.1210593 pmid:17603561 fatcat:em2fonlvlvcnjerlgzyvvgvir4

Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

Krista Marie Vincent, Scott D. Findlay, Lynne Marie Postovit
2015 Breast Cancer Research  
Gene set enrichment analysis suggests that cancer cell lines have enhanced proliferation and glycolysis independent of stromal and immune contributions compared with breast cancer cells in situ.  ...  Results: We found the transcriptional characteristics of breast cancer cell lines to mirror those of the tumours.  ...  Acknowledgements This work was supported by an Alberta Innovates -Health Solutions Translational Health Chair in cancer and a Canadian Breast Cancer Foundation operating grant (to LMP).  ... 
doi:10.1186/s13058-015-0613-0 pmid:26289960 pmcid:PMC4545915 fatcat:4btg5hxgv5ezfhhbyxrolityfi

Indole-3-Carbinol and 3-3′-Diindolylmethane Antiproliferative Signaling Pathways Control Cell-Cycle Gene Transcription in Human Breast Cancer Cells by Regulating Promoter–Sp1 Transcription Factor Interactions

Gary L. Firestone, Leonard F. Bjeldanes
2003 Journal of Nutrition  
Mutagenic analysis of the p21 Waf1/Cip1 promoter reveals that in transfected breast cancer cells, DIM (as well as I3C) stimulates p21 Waf1/Cip1 transcription through an indole-responsive region of the  ...  Mutagenic analysis reveals that I3C signaling targets a composite transcriptional element in the Cdk6 promoter that requires both Sp1 and Ets transcription factors for transactivation function.  ...  ACKNOWLEDGMENTS We thank Carolyn Cover, Erin Cram, Chibo Hong and Richard Staub for their direct contributions to the work summarized in this article.  ... 
doi:10.1093/jn/133.7.2448s pmid:12840223 fatcat:7pzmanmszzgxbciwlr7zpvzv6a

Use of gene expression profiling to understand the transcriptional program associated with estrogen-induced uterine growth

J. G. Moggs, D. G. Deavall, G. Orphanides
2003 Pure and Applied Chemistry  
The use of gene expression data in predictive and mechanistic toxicology is hindered by a lack of information on the relationships between transcriptional events and physiological and pathological changes  ...  We discuss the analysis of these relationships using the rodent uterotrophic response as a model experimental system for estrogen-induced uterine growth.  ...  A similar kinetic approach was used to reveal the co-expression of DNA replication fork genes during estrogen-induced mitogenesis in a human breast cancer cell line [17] .  ... 
doi:10.1351/pac200375112429 fatcat:osdsq35vzff2ro2tokge7cokve

Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine

Lance D Miller, Edison T Liu
2007 Breast Cancer Research  
Genome-wide expression microarray studies have revealed that the biological and clinical heterogeneity of breast cancer can be partly explained by information embedded within a complex but ordered transcriptional  ...  Emerging 'hypothesis-driven' strategies that incorporate knowledge of pathways and other biological phenomena in the signature discovery process are linking prognosis and therapy prediction with transcriptional  ...  Acknowledgements The authors are supported by the Singapore Agency for Science, Technology and Research (A*STAR).  ... 
doi:10.1186/bcr1662 pmid:17397520 pmcid:PMC1868923 fatcat:jvzoro26afeclj5cpa2jmaex74

LRH-1 controls proliferation in breast tumor cells by regulating CDKN1A gene expression

S Bianco, M Jangal, D Garneau, N Gévry
2014 Oncogene  
This study reveals a novel mechanism of control of cell proliferation by LRH-1 regulating CDKN1A transcription in breast cancer cells, independent of ERα and p53 status.  ...  Analysis of breast cancer samples reveals that a high LRH-1 level is inversely correlated with CDKN1A expression in breast cancer patients and is associated with poor prognosis.  ...  This work was supported with fund from the Canadian Institute of Health Research (CIHR) to NG. SB was the recipient of a postdoctoral fellowship from the Réseau Québécois en Reproduction (RQR).  ... 
doi:10.1038/onc.2014.382 pmid:25435372 fatcat:lxmjklqv6bhtjaviwhkm65io7i

Tumor-extracellular matrix interactions: Identification of tools associated with breast cancer progression

Marta Giussani, Giuseppe Merlino, Vera Cappelletti, Elda Tagliabue, Maria Grazia Daidone
2015 Seminars in Cancer Biology  
Stroma and ECM-related signatures proved to influence breast cancer progression, and to contribute to the identification of tumor phenotypes resistant to cytotoxic and hormonal treatments.  ...  Several evidences support the concept that cancer development and progression are not entirely cancer cell-autonomous processes, but may be influenced, and possibly driven, by cross-talk between cancer  ...  Acknowledgments This work was supported by the Italian Association for Cancer Research (AIRC), Special Program "EDERA" Tumor microenvironment-related changes as new tools for early detection and assessment  ... 
doi:10.1016/j.semcancer.2015.09.012 pmid:26416466 fatcat:gjyre7cb5jevdkk4ofl2la2kj4

Splicing Factors in Breast Cancer: Drivers of the Breast Tumor Fate [chapter]

Felipe A. C. da Luz, Paula C. Brigido, Alberto S. Moraes, Rogerio A. Araujo, Marcelo J.B. Silva
2017 Breast Cancer - From Biology to Medicine  
These concepts will elucidate their role in tumorigenesis and a prospective use as biomarkers in breast cancer.  ...  Growing data show deregulation of splicing events in cancer, being breast cancer the most studied. This aberrant pattern of splicing has an important role in breast tumor progression.  ...  Acknowledgements We gratefully acknowledge financial support from the Brazilian Agencies CAPES, FAPEMIG and MCT/CNPq, and NUPPEC-Cancer Hospital of Uberlândia/Grupo Luta pela Vida.  ... 
doi:10.5772/66162 fatcat:sxrqfxnwgrbdxeed2vv4a35vwe

Mining for regulatory programs in the cancer transcriptome

Daniel R Rhodes, Shanker Kalyana-Sundaram, Vasudeva Mahavisno, Terrence R Barrette, Debashis Ghosh, Arul M Chinnaiyan
2005 Nature Genetics  
D.R.R. was supported by the Medical Scientist Training Program and the Cancer Biology Training Program, and A.M.C. is a Pew Scholar.  ...  This research is supported in part by the National Institutes of Health through the University of Michigan's Cancer Center Support Grant, pilot funds from the Dean's Office and the Department of Pathology  ...  Other known E2F targets activated in many cancer CRPs include TFDP1, CDC25, RPA1 and USP13. The near universal Overview of the method used to elucidate CRPs.  ... 
doi:10.1038/ng1578 pmid:15920519 fatcat:3gwgcimzijh4lgliobov6qjkz4
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