423
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Transcriptomic and Epigenetic Analysis of Breast Cancer Stem Cells

, , , , , , , , , , , , , , & show all
Pages 765-783 | Received 13 Jan 2018, Accepted 13 Feb 2018, Published online: 26 Feb 2018

References

  • Siegel RL , MillerKD , JemalA . Cancer statistics, 2018 . CA Cancer J. Clin.68 ( 1 ), 7 – 30 ( 2018 ).
  • Dent R , TrudeauM , PritchardKIet al. Triple-negative breast cancer: clinical features and patterns of recurrence . Clin. Cancer Res.13 , 4429 – 4434 ( 2007 ).
  • Schneider BP , WinerEP , FoulkesWDet al. Triple-negative breast cancer: risk factors to potential targets . Clin. Cancer Res.14 , 8010 – 8018 ( 2008 ).
  • Elias AD . Triple-negative breast cancer: a short review . Am. J. Clin. Oncol.33 , 637 – 645 ( 2010 ).
  • Anders CK , CareyLA . Biology metastatic patterns, and treatment of patients with triple-negative breast cancer . Clin. Breast Cancer9 ( 2 ), S73 – S81 ( 2009 ).
  • Gansler T , GanzPA , GrantMet al. Sixty years of CA: a cancer journal for clinicians . CA Cancer J. Clin.60 , 345 – 350 ( 2010 ).
  • Hudis CA , GianniL . Triple-negative breast cancer: an unmet medical need . Oncologist16 ( 1 ), 1 – 11 ( 2011 ).
  • Chacon RD , CostanzoMV . Triple-negative breast cancer . Breast Cancer Res.12 ( 2 ), S3 ( 2010 ).
  • De Laurentiis M , CiannielloD , CaputoRet al. Treatment of triple negative breast cancer (TNBC): current options and future perspectives . Cancer Treat. Rev.36 ( 3 ), S80 – S86 ( 2010 ).
  • Newman LA , Reis-FilhoJS , MorrowM , CareyLA , KingTA . The 2014 Society of Surgical Oncology Susan G. Komen for the Cure Symposium: triple-negative breast cancer . Ann. Surg. Oncol.22 , 874 – 882 ( 2015 ).
  • Al-Hajj M , WichaMS , Benito-HernandezA , MorrisonSJ , ClarkeMF . Prospective identification of tumorigenic breast cancer cells . Proc. Natl Acad. Sci. USA100 , 3983 – 3988 ( 2003 ).
  • Ginestier C , HurMH , Charafe-JauffretEet al. ALDH1 is a marker of normal and malignant human mammary stem cells and a predictor of poor clinical outcome . Cell Stem Cell1 , 555 – 567 ( 2007 ).
  • Dalerba P , DyllaSJ , ParkIKet al. Phenotypic characterization of human colorectal cancer stem cells . Proc. Natl Acad. Sci. USA104 , 10158 – 10163 ( 2007 ).
  • Feinberg AP , TyckoB . Timeline – the history of cancer epigenetics . Nat. Rev. Cancer4 , 143 – 153 ( 2004 ).
  • Bernstein BE , MeissnerA , LanderES . The mammalian epigenome . Cell128 , 669 – 681 ( 2007 ).
  • Goldberg AD , AllisCD , BernsteinE . Epigenetics: a landscape takes shape . Cell128 , 635 – 638 ( 2007 ).
  • Esteller M . CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future . Oncogene21 , 5427 – 5440 ( 2002 ).
  • Baylin SB . DNA methylation and gene silencing in cancer . Nat. Clin. Pract. Oncol.2 ( 1 ), S4 – S11 ( 2005 ).
  • Baylin SB , JonesPA . A decade of exploring the cancer epigenome – biological and translational implications . Nat. Rev. Cancer11 , 726 – 734 ( 2011 ).
  • Tao H , LiHY , SuYHet al. Histone methyltransferase G9a and H3K9 dimethylation inhibit the self-renewal of glioma cancer stem cells . Mol. Cell Biochem.394 , 23 – 30 ( 2014 ).
  • UCSC genome annotation database for the Feb. 2009 . Assembly of the human genome (hg19, GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)) . http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ .
  • Langmead B , SalzbergSL . Fast gapped-read alignment with Bowtie 2 . Nat. Methods9 , U357 – U354 ( 2012 ).
  • Kim D , PerteaG , TrapnellC , PimentelH , KelleyR , SalzbergSL . TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions . Genome Biol.14 , R36 ( 2013 ).
  • Gentleman RC , CareyVJ , BatesDMet al. Bioconductor: open software development for computational biology and bioinformatics . Genome Biol.5 , R80 ( 2004 ).
  • Anders S , PylPT , HuberW . HTSeq-a Python framework to work with high-throughput sequencing data . Bioinformatics31 ( 2 ), 166 – 169 ( 2015 ).
  • Li H , HandsakerB , WysokerAet al. The sequence alignment/map format and SAMtools . Bioinformatics25 ( 16 ), 2078 – 2079 ( 2009 ).
  • Wang L , FengZ , WangX , WangX , ZhangX . DEGseq: identify differentially expressed genes from RNA-seq data . Bioinformatics26 ( 1 ), 136 – 138 ( 2017 ).
  • McLean CY , BristorD , HillerMet al. GREAT improves functional interpretation of cis-regulatory regions . Nat. Biotechnol.28 , U495 – U155 ( 2010 ).
  • Falcon S , GentlemanR . Using GOstats to test gene lists for GO term association . Bioinformatics23 ( 2 ), 257 – 258 ( 2007 ).
  • Luo W , BrouwerC . Pathview: an R/Bioconductor package for pathway-based data integration and visualization . Bioinformatics29 ( 14 ), 1830 – 1831 ( 2013 ).
  • Krueger F , AndrewsSR . Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications . Bioinformatics27 ( 11 ), 1571 – 1572 ( 2011 ).
  • Akalin A , KormakssonM , LiSet al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles . Genome Biol.13 , R87 ( 2012 ).
  • Salmon-Divon M , DvingeH , TammojaK , BertoneP . PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci . BMC Bioinformatics11 ( 1 ), 415 ( 2010 ).
  • An K , DuF , MengHet al. Transgenerational analysis of H3K4me3 and H3K27me3 by ChIP-seq links epigenetic inheritance to metabolism . J. Genet. Genomics doi:10.1016/j.jgg.2017.11.004 ( 2017 ) ( Epub ahead of print ).
  • Li H , DurbinR . Fast and accurate short read alignment with Burrows–Wheeler transform . Bioinformatics25 , 1754 – 1760 ( 2009 ).
  • Zhang Y , TaoL , MeyerCAet al. Model-based analysis of ChIP-seq (MACS) . Genome Biol.9 ( 9 ), R137 ( 2008 ).
  • Ye T , KrebsAR , ChoukrallahMAet al. seqMINER: an integrated ChIP-seq data interpretation platform . Nucleic Acids Res.39 ( 6 ), e35 – e35 ( 2010 ).
  • Genome sequence archive . http://gsa.big.ac.cn .
  • Ni F , QuCK . A metabolic stress-induced cell cycle checkpoint in stem cells . Cell Cycle15 , 2539 – 2540 ( 2016 ).
  • Wimmer-Kleikamp SH , LackmannM . Eph-modulated cell morphology, adhesion and motility in carcinogenesis . IUBMB Life57 , 421 – 431 ( 2005 ).
  • Chen MS , WoodwardWA , BehbodFet al. Wnt/beta-catenin mediates radiation resistance of Sca1(+) progenitors in an immortalized mammary gland cell line . J. Cell. Sci.120 , 468 – 477 ( 2007 ).
  • Pinto D , GregorieffA , BegthelH , CleversH . Canonical Wnt signals are essential for homeostasis of the intestinal epithelium . Genes Dev.17 , 1709 – 1713 ( 2003 ).
  • Kuhnert F , DavisCR , WangHTet al. Essential requirement for Wnt signaling in proliferation of adult small intestine and colon revealed by adenoviral expression of Dickkopf-1 . Proc. Natl Acad. Sci. USA101 , 266 – 271 ( 2004 ).
  • Aguilar-Rojas A , Perez-SolisMA , Maya-NunezG . The gonadotropin-releasing hormone system: perspectives from reproduction to cancer . Int. J. Oncol.48 , 861 – 868 ( 2016 ).
  • Niu C , YanZF , ChengLet al. Downregulation and antiproliferative role of FHL3 in breast cancer . IUBMB Life63 , 764 – 771 ( 2011 ).
  • Xiao L , ChenY , JiM , DongJ . KIBRA regulates Hippo signaling activity via interactions with large tumor suppressor kinases . J. Biol. Chem.286 , 7788 – 7796 ( 2011 ).
  • Chang PH , Hwang-VersluesWW , ChangYCet al. Activation of Robo1 signaling of breast cancer cells by Slit2 from stromal fibroblast restrains tumorigenesis via blocking PI3K/Akt/beta-catenin pathway . Cancer Res.72 , 4652 – 4661 ( 2012 ).
  • Huang JM , NagatomoI , SuzukiEet al. YAP modifies cancer cell sensitivity to EGFR and survivin inhibitors and is negatively regulated by the nonreceptor type protein tyrosine phosphatase 14 . Oncogene32 , 2220 – 2229 ( 2013 ).
  • Belle L , AliN , LonicAet al. The tyrosine phosphatase PTPN14 (Pez) inhibits metastasis by altering protein trafficking . Sci. Signal.8 ( 264 ), ra18 ( 2015 ).
  • Qin FX , ZhangHK , MaLet al. Low expression of Slit2 and Robo1 is associated with poor prognosis and brain-specific metastasis of breast cancer patients . Sci. Rep.5 , 14430 ( 2015 ).
  • Zhang JM , YaoS , HuQet al. Genetic variations in the Hippo signaling pathway and breast cancer risk in African American women in the AMBER Consortium . Carcinogenesis37 , 951 – 956 ( 2016 ).
  • Choi YK , WooSM , ChoSGet al. Brain-metastatic triple-negative breast cancer cells regain growth ability by altering gene expression patterns . Cancer Genomics Proteomics10 , 265 – 275 ( 2013 ).
  • Marotta LL , AlmendroV , MarusykAet al. The JAK2/STAT3 signaling pathway is required for growth of CD44(+)CD24(-) stem cell-like breast cancer cells in human tumors . J. Clin. Invest.121 , 2723 – 2735 ( 2011 ).
  • Idowu MO , KmieciakM , DumurCet al. CD44(+)/CD24(-/low) cancer stem/progenitor cells are more abundant in triple-negative invasive breast carcinoma phenotype and are associated with poor outcome . Hum. Pathol.43 , 364 – 373 ( 2012 ).
  • Ma F , LiH , WangHet al. Enriched CD44(+)/CD24(-) population drives the aggressive phenotypes presented in triple-negative breast cancer (TNBC) . Cancer Lett.353 , 153 – 159 ( 2014 ).
  • Ricardo S , VieiraAF , GerhardRet al. Breast cancer stem cell markers CD44, CD24 and ALDH1: expression distribution within intrinsic molecular subtype . J. Clin. Pathol.64 , 937 – 946 ( 2011 ).
  • Ponti D , CostaA , ZaffaroniNet al. Isolation and in vitro propagation of tumorigenic breast cancer cells with stem/progenitor cell properties . Cancer Res.65 , 5506 – 5511 ( 2005 ).
  • An H , KimJY , OhEet al. Salinomycin promotes anoikis and decreases the CD44+/CD24- stem-like population via inhibition of STAT3 activation in MDA-MB-231 cells . PLoS ONE10 ( 11 ), e0141919 ( 2015 ).
  • Suling Liu , YangCong , DongWanget al. Breast cancer stem cells transition between epithelial and mesenchymal states reflective of their normal counterparts . Stem Cell Rep.2 , 78 – 91 ( 2014 ).
  • Ricardo S , VieiraAF , GerhardRet al. Breast cancer stem cell markers CD44, CD24 and ALDH1: expression distribution within intrinsic molecular subtype . J. Clin. Pathol.64 ( 11 ), 937 – 946 ( 2011 ).
  • Golovko A , KojukhovA , GuanBJet al. The eIF2A knockout mouse . Cell Cycle15 , 3115 – 3120 ( 2016 ).
  • Rosenwald IB , KoifmanL , SavasL , ChenJJ , WodaBA , KadinME . Expression of the translation initiation factors eIF-4E and eIF-2 alpha is frequently increased in neoplastic cells of Hodgkin lymphoma . Human Path.39 , 910 – 916 ( 2008 ).
  • Lindqvist L , PelletierJ . Inhibitors of translation initiation as cancer therapeutics . Future Med. Chem.1 , 1709 – 1722 ( 2009 ).
  • Wendel HG , de StanchinaE , FridmanJSet al. Survival signaling by Akt and eIF4E in oncogenesis and cancer therapy . Nature428 , 332 – 337 ( 2004 ).
  • Li BDL , McDonaldJC , NassarR , De BenedettiA . Clinical outcome in stage I to III breast carcinoma and eIF4E overexpression . Ann. Surg.227 , 756 – 763 ( 1998 ).
  • Graff JR , KonicekBW , VincentTMet al. Therapeutic suppression of translation initiation factor eIF4E expression reduces tumor growth without toxicity . J. Clin. Investig.117 , 2638 – 2648 ( 2007 ).
  • Meng E , MitraA , TripathiKet al. ALDH1A1 maintains ovarian cancer stem cell-like properties by altered regulation of cell cycle checkpoint and DNA repair network signaling . PLoS ONE9 ( 9 ), e107142 ( 2014 ).
  • Genander M , FrisenJ . Ephrins and Eph receptors in stem cells and cancer . Curr. Opin. Cell Biol.22 , 611 – 616 ( 2010 ).
  • Noren NK , FoosG , HauserCA , PasqualeEB . The EphB4 receptor suppresses breast cancer cell tumorigenicity through an Abl-Crk pathway . Nat. Cell Biol.8 , U815 – U853 ( 2006 ).
  • Cooper C , FosterC . Concepts of epigenetics in prostate cancer development . Br. J. Cancer100 ( 2 ), 240 – 245 ( 2009 ).
  • Robertson KD . DNA methylation and human disease . Nat. Rev. Genet.6 ( 8 ), 597 – 610 ( 2005 ).
  • Jiang W , WangJ , ZhangY . Histone H3K27me3 demethylases KDM6A and KDM6B modulate definitive endoderm differentiation from human ESCs by regulating WNT signaling pathway . Cell Res.23 , 122 – 130 ( 2013 ).
  • Nusse R . Wnt signaling in disease and in development . Cell Res.15 , 28 – 32 ( 2005 ).
  • McLaughlin N , YaoX , LiY , SaifudeenZ , El-DahrSS . Histone signature of metanephric mesenchyme cell lines . Epigenetics8 , 970 – 978 ( 2013 ).
  • Morgan K , MeyerC , MillerNet al. GnRH receptor activation competes at a low level with growth signaling in stably transfected human breast cell lines . BMC Cancer11 , 476 ( 2011 ).
  • Aguilar-Rojas A , Huerta-ReyesM , Maya-NunezGet al. Gonadotropin-releasing hormone receptor activates GTPase RhoA and inhibits cell invasion in the breast cancer cell line MDA-MB-231 . BMC Cancer12 , 550 ( 2012 ).
  • Naor Z , HuhtaniemiI . Interactions of the GnRH receptor with heterotrimeric G proteins . Front. Neuroendocrinol.34 , 88 – 94 ( 2013 ).
  • Ballard MS , ZhuA , LwaiNet al. Mammary stem cell self-renewal is regulated by Slit2/Robo1 signaling through SNAI1 and mINSC . Cell Rep.13 , 290 – 301 ( 2015 ).
  • Wang X , GudaC . Integrative exploration of genomic profiles for triple negative breast cancer identifies potential drug targets . Medicine95 , e4321 ( 2016 ).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.