Transcriptomic and epigenetic analysis of breast cancer stem cells.

AIM Cancer stem cells (CSCs) drive triple-negative breast cancer recurrence via their properties of self-renewal, invasiveness and radio/chemotherapy resistance. This study examined how CSCs might sustain these properties. MATERIALS & METHODS Transcriptomes, DNA methylomes and histone modifications were compared between CSCs and non CSCs. RESULTS Transcriptome analysis revealed several pathways that were activated in CSCs, whereas cell cycle regulation pathways were inhibited. Cell development and signaling genes were differentially methylated, with histone methylation analysis suggesting distinct H3K4me2 and H3K27me3 enrichment profiles. An integrated analysis revealed several tumor suppressor genes downregulated in CSCs. CONCLUSION Differential activation of various signaling pathways and genes contributes to the tumor-promoting properties of CSCs. Therapeutic targets identified in the analysis may contribute to improving treatment options for patients.

[1]  King-Jen Chang,et al.  Activation of Robo1 signaling of breast cancer cells by Slit2 from stromal fibroblast restrains tumorigenesis via blocking PI3K/Akt/β-catenin pathway. , 2012, Cancer research.

[2]  J. Knoblich,et al.  Mammary Stem Cell Self-Renewal Is Regulated by Slit2/Robo1 Signaling through SNAI1 and mINSC. , 2015, Cell reports.

[3]  David J Harrison,et al.  GnRH receptor activation competes at a low level with growth signaling in stably transfected human breast cell lines , 2011, BMC Cancer.

[4]  Yuwen Li,et al.  Histone signature of metanephric mesenchyme cell lines , 2013, Epigenetics.

[5]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[6]  M. Ji,et al.  KIBRA Regulates Hippo Signaling Activity via Interactions with Large Tumor Suppressor Kinases* , 2011, The Journal of Biological Chemistry.

[7]  B. Karlan,et al.  YAP modifies cancer cell sensitivity to EGFR and survivin inhibitors and is negatively regulated by the non-receptor type protein tyrosine phosphatase 14 , 2012, Oncogene.

[8]  Huikun Zhang,et al.  Low Expression of Slit2 and Robo1 is Associated with Poor Prognosis and Brain-specific Metastasis of Breast Cancer Patients , 2015, Scientific Reports.

[9]  Michael F. Clarke,et al.  Phenotypic characterization of human colorectal cancer stem cells , 2007, Proceedings of the National Academy of Sciences.

[10]  Peter A. Jones,et al.  A decade of exploring the cancer epigenome — biological and translational implications , 2011, Nature Reviews Cancer.

[11]  A. Feinberg,et al.  The history of cancer epigenetics , 2004, Nature Reviews Cancer.

[12]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[13]  C. Cooper,et al.  Concepts of epigenetics in prostate cancer development , 2008, British Journal of Cancer.

[14]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[15]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[16]  A. Elias.  Triple-Negative Breast Cancer: A Short Review , 2010, American journal of clinical oncology.

[17]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[18]  C. Allis,et al.  Epigenetics: A Landscape Takes Shape , 2007, Cell.

[19]  Chun Zhang,et al.  Histone methyltransferase G9a and H3K9 dimethylation inhibit the self-renewal of glioma cancer stem cells , 2014, Molecular and Cellular Biochemistry.

[20]  S. Baylin,et al.  DNA methylation and gene silencing in cancer , 2005, Nature Clinical Practice Oncology.

[21]  A. De Benedetti,et al.  Clinical outcome in stage I to III breast carcinoma and eIF4E overexpression. , 1998, Annals of Surgery.

[22]  A. Komar,et al.  The eIF2A knockout mouse , 2016, Cell cycle.

[23]  Q. Ye,et al.  Downregulation and antiproliferative role of fhl3 in breast cancer , 2011, IUBMB life.

[24]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[25]  Ji Young Kim,et al.  Salinomycin Promotes Anoikis and Decreases the CD44+/CD24- Stem-Like Population via Inhibition of STAT3 Activation in MDA-MB-231 Cells , 2015, PloS one.

[26]  K. Robertson.  DNA methylation and human disease , 2005, Nature Reviews Genetics.

[27]  B. Woda,et al.  Expression of the translation initiation factors eIF-4E and eIF-2* is frequently increased in neoplastic cells of Hodgkin lymphoma. , 2008, Human pathology.

[28]  S. Lowe,et al.  Survival signalling by Akt and eIF4E in oncogenesis and cancer therapy , 2004, Nature.

[29]  D. Noh,et al.  Brain-metastatic triple-negative breast cancer cells regain growth ability by altering gene expression patterns. , 2013, Cancer genomics & proteomics.

[30]  Yan Zhang,et al.  Transgenerational analysis of H3K4me3 and H3K27me3 by ChIP-Seq links epigenetic inheritance to metabolism. , 2017, Journal of genetics and genomics = Yi chuan xue bao.

[31]  Heidi Dvinge,et al.  PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci , 2010, BMC Bioinformatics.

[32]  Danila Coradini,et al.  Isolation and in vitro propagation of tumorigenic breast cancer cells with stem/progenitor cell properties. , 2005, Cancer research.

[33]  André F. Vieira,et al.  Breast cancer stem cell markers CD44, CD24 and ALDH1: expression distribution within intrinsic molecular subtype , 2011, Journal of Clinical Pathology.

[34]  Tao Ye,et al.  seqMINER: an integrated ChIP-seq data interpretation platform , 2010, Nucleic acids research.

[35]  Naveid A Ali,et al.  The tyrosine phosphatase PTPN14 (Pez) inhibits metastasis by altering protein trafficking , 2015, Science Signaling.

[36]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[37]  F. Arechavaleta-Velasco,et al.  Gonadotropin-releasing hormone receptor activates GTPase RhoA and inhibits cell invasion in the breast cancer cell line MDA-MB-231 , 2012, BMC Cancer.

[38]  R. Nusse,et al.  Wnt signaling in disease and in development , 2005, Cell Research.

[39]  C. Guda,et al.  Integrative exploration of genomic profiles for triple negative breast cancer identifies potential drug targets , 2016, Medicine.

[40]  Mithat Gönen,et al.  The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors. , 2011, The Journal of clinical investigation.

[41]  Francine E. Garrett-Bakelman,et al.  methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles , 2012, Genome Biology.

[42]  Charles M. Perou,et al.  Triple-Negative Breast Cancer: Risk Factors to Potential Targets , 2008, Clinical Cancer Research.

[43]  Daniel Birnbaum,et al.  ALDH1 is a marker of normal and malignant human mammary stem cells and a predictor of poor clinical outcome. , 2007, Cell stem cell.

[44]  S. Morrison,et al.  Prospective identification of tumorigenic breast cancer cells , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[45]  G. Arpino,et al.  Treatment of triple negative breast cancer (TNBC): current options and future perspectives. , 2010, Cancer treatment reviews.

[46]  Qiang Hu,et al.  Genetic variations in the Hippo signaling pathway and breast cancer risk in African American women in the AMBER Consortium. , 2016, Carcinogenesis.

[47]  L. Newman,et al.  The 2014 Society of Surgical Oncology Susan G. Komen for the Cure Symposium: Triple-Negative Breast Cancer , 2015, Annals of Surgical Oncology.

[48]  Rebecca L. Siegel Mph,et al.  Cancer statistics, 2018 , 2018 .

[49]  W. Woodward,et al.  Wnt/β-catenin mediates radiation resistance of Sca1+ progenitors in an immortalized mammary gland cell line , 2007, Journal of Cell Science.

[50]  Chen Lin,et al.  Enriched CD44(+)/CD24(-) population drives the aggressive phenotypes presented in triple-negative breast cancer (TNBC). , 2014, Cancer letters.

[51]  Tao Wang,et al.  Therapeutic suppression of translation initiation factor eIF4E expression reduces tumor growth without toxicity. , 2007, The Journal of clinical investigation.

[52]  S. Narod,et al.  Triple-Negative Breast Cancer: Clinical Features and Patterns of Recurrence , 2007, Clinical Cancer Research.

[53]  E. Lander,et al.  The Mammalian Epigenome , 2007, Cell.

[54]  M. Lackmann,et al.  Eph‐modulated Cell Morphology, Adhesion and Motility in Carcinogenesis , 2005, IUBMB life.

[55]  Felix Krueger,et al.  Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..

[56]  I. Huhtaniemi,et al.  Interactions of the GnRH receptor with heterotrimeric G proteins , 2013, Frontiers in Neuroendocrinology.

[57]  C. Hudis,et al.  Triple-negative breast cancer: an unmet medical need. , 2011, The oncologist.

[58]  Robert Gentleman,et al.  Using GOstats to test gene lists for GO term association , 2007, Bioinform..

[59]  Xuegong Zhang,et al.  DEGseq: an R package for identifying differentially expressed genes from RNA-seq data , 2010, Bioinform..

[60]  M. Esteller.  CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future , 2002, Oncogene.

[61]  L. Carey,et al.  Biology, metastatic patterns, and treatment of patients with triple-negative breast cancer. , 2009, Clinical breast cancer.

[62]  E. Reed,et al.  ALDH1A1 Maintains Ovarian Cancer Stem Cell-Like Properties by Altered Regulation of Cell Cycle Checkpoint and DNA Repair Network Signaling , 2014, PloS one.

[63]  Wei Jiang,et al.  Histone H3K27me3 demethylases KDM6A and KDM6B modulate definitive endoderm differentiation from human ESCs by regulating WNT signaling pathway , 2012, Cell Research.

[64]  Weijun Luo,et al.  Pathview: an R/Bioconductor package for pathway-based data integration and visualization , 2013, Bioinform..

[65]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[66]  Pauline Chu,et al.  Essential requirement for Wnt signaling in proliferation of adult small intestine and colon revealed by adenoviral expression of Dickkopf-1 , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[67]  Hans Clevers,et al.  Canonical Wnt signals are essential for homeostasis of the intestinal epithelium. , 2003, Genes & development.

[68]  J. Frisén,et al.  Ephrins and Eph receptors in stem cells and cancer. , 2010, Current opinion in cell biology.

[69]  R. Chacón,et al.  REVIEW Triple-negative , 2022 .

[70]  M. Manjili,et al.  CD44(+)/CD24(-/low) cancer stem/progenitor cells are more abundant in triple-negative invasive breast carcinoma phenotype and are associated with poor outcome. , 2012, Human pathology.

[71]  J. Pelletier,et al.  Inhibitors of translation initiation as cancer therapeutics. , 2009, Future medicinal chemistry.

[72]  Dong Wang,et al.  Breast Cancer Stem Cells Transition between Epithelial and Mesenchymal States Reflective of their Normal Counterparts , 2013, Stem cell reports.

[73]  A. Aguilar-Rojas,et al.  The gonadotropin-releasing hormone system: Perspectives from reproduction to cancer (Review). , 2016, International journal of oncology.

[74]  Charles R. Thomas,et al.  Sixty Years of CA: A Cancer Journal for Clinicians , 2010, CA: a cancer journal for clinicians.

[75]  C. Qu,et al.  A metabolic stress-induced cell cycle checkpoint in stem cells , 2016, Cell cycle.

[76]  Elena B. Pasquale,et al.  The EphB4 receptor suppresses breast cancer cell tumorigenicity through an Abl–Crk pathway , 2006, Nature Cell Biology.