Breast cancer subtype dictates DNA methylation and ALDH1A3-mediated expression of tumor suppressor RARRES1

Oncotarget

Volumn 7, Issue 28, 2016, Pages 44096-44112

  Coyle, Krysta M ^a   Murphy, J Patrick ^a   Vidovic, Dejan ^a   Vaghar Kashani, Ahmad ^a,b   Dean, Cheryl A ^a   Sultan, Mohammad ^a   Clements, Derek ^a   Wallace, Melissa ^a   Thomas, Margaret L ^a   Hundert, Amos ^a   Giacomantonio, Carman A ^a   Helyer, Lucy ^a   Gujar, Shashi A ^a,c   Lee, Patrick W K ^a   Weaver, Ian C G ^a   Marcato, Paola ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

^b UPPSALA UNIVERSITY   (Sweden)

^c IWK HEALTH CENTRE   (Canada)

Author keywords

ALDH1A3; Breast cancer; DNA methylation; RARRES1; Retinoic acid

Indexed keywords

ALDEHYDE DEHYDROGENASE 1A3; ALDEHYDE DEHYDROGENASE ISOENZYME 1; RETINOIC ACID RECEPTOR; RETINOIC ACID RECEPTOR RESPONDER 1; UNCLASSIFIED DRUG; ALDEHYDE DEHYDROGENASE; ALDEHYDE DEHYDROGENASE (NAD(P)+); MEMBRANE PROTEIN; RARRES1 PROTEIN, HUMAN;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CANCER INHIBITION; CELL PROLIFERATION; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA METHYLATION; FEMALE; HUMAN; HUMAN CELL; HUMAN TISSUE; LIMIT OF QUANTITATION; MAJOR CLINICAL STUDY; MOUSE; NONHUMAN; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; TRIPLE NEGATIVE BREAST CANCER; ANIMAL; BREAST TUMOR; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MIDDLE AGED; NONOBESE DIABETIC MOUSE; PATHOLOGY; PROGNOSIS; RNA INTERFERENCE; SCID MOUSE; TUMOR CELL LINE; TUMOR VOLUME; XENOGRAFT;

ALDEHYDE OXIDOREDUCTASES; ANIMALS; BREAST NEOPLASMS; CELL LINE, TUMOR; DNA METHYLATION; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MEMBRANE PROTEINS; MICE, INBRED NOD; MICE, SCID; MIDDLE AGED; PROGNOSIS; PROTEIN INTERACTION MAPS; RNA INTERFERENCE; TRANSPLANTATION, HETEROLOGOUS; TRIPLE NEGATIVE BREAST NEOPLASMS; TUMOR BURDEN;

EID: 84978712015     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.9858     Document Type: Article

References (50)

1. DeSantis CE, Fedewa SA, Goding Sauer A, Kramer JL, Smith RA, Jemal A. Breast cancer statistics, 2015: Convergence of incidence rates between black and white women. CA Cancer J Clin. 2016;66:31-42.
2. Van Poznak C, Somerfield MR, Bast RC, Cristofanilli M, Goetz MP, Gonzalez-Angulo AM, Hicks DG, Hill EG, Liu MC, Lucas W, Mayer IA, Mennel RG, Symmans WF, et al. Use of Biomarkers to Guide Decisions on Systemic Therapy for Women With Metastatic Breast Cancer: American Society of Clinical Oncology Clinical Practice Guideline. J Clin Oncol OffJ Am Soc Clin Oncol. 2015;33:2695-704.
3. Osborne CK. Tamoxifen in the Treatment of Breast Cancer. N Engl J Med. 1998;339:1609-18.
4. Sabatier R, Finetti P, Guille A, Adelaide J, Chaffanet M, Viens P, Birnbaum D, Bertucci F. Claudin-low breast cancers: clinical, pathological, molecular and prognostic characterization. Mol Cancer. 2014;13:228.
5. Bernardino J, Roux C, Almeida A, Vogt N, Gibaud A, Gerbault-Seureau M, Magdelenat H, Bourgeois CA, Malfoy B, Dutrillaux B. DNA hypomethylation in breast cancer: an independent parameter of tumor progression? Cancer Genet Cytogenet. 1997;97:83-9.
6. Soares J, Pinto AE, Cunha CV, André S, Barão I, Sousa JM, Cravo M. Global DNA hypomethylation in breast carcinoma: correlation with prognostic factors and tumor progression. Cancer. 1999;85:112-8.
7. Roll JD, Rivenbark AG, Sandhu R, Parker JS, Jones WD, Carey LA, Livasy CA, Coleman WB. Dysregulation of the epigenome in triple-negative breast cancers: Basallike and claudin-low breast cancers express aberrant DNA hypermethylation. Exp Mol Pathol. 2013;95:276-87.
8. Park SY, Kwon HJ, Choi Y, Lee HE, Kim S-W, Kim JH, Kim IA, Jung N, Cho N-Y, Kang GH. Distinct patterns of promoter CpG island methylation of breast cancer subtypes are associated with stem cell phenotypes. Mod Pathol OffJ U S Can Acad Pathol Inc. 2012;25:185-96.
9. Sproul D, Nestor C, Culley J, Dickson JH, Dixon JM, Harrison DJ, Meehan RR, Sims AH, Ramsahoye BH. Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer. Proc Natl Acad Sci U S A. 2011;108:4364-9.
10. Stefansson OA, Moran S, Gomez A, Sayols S, Arribas-Jorba C, Sandoval J, Hilmarsdottir H, Olafsdottir E, Tryggvadottir L, Jonasson JG, Eyfjord J, Esteller M. A DNA methylation-based definition of biologically distinct breast cancer subtypes. Mol Oncol. 2015;9:555-68.
11. Grigoriadis A, Mackay A, Noel E, Wu PJ, Natrajan R, Frankum J, Reis-Filho JS, Tutt A. Molecular characterisation of cell line models for triple-negative breast cancers. BMC Genomics. 2012;13:619.
12. Li N, Li S. Epigenetic inactivation of SOX1 promotes cell migration in lung cancer. Tumor Biol. 2015;36:4603-10.
13. Bediaga NG, Acha-Sagredo A, Guerra I, Viguri A, Albaina C, Diaz IR, Rezola R, Alberdi MJ, Dopazo J, Montaner D, Renobales M de, Fernández AF, Field JK, et al. DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res. 2010;12:R77.
14. Hickey TE, Robinson JLL, Carroll JS, Tilley WD. Minireview: The androgen receptor in breast tissues: growth inhibitor, tumor suppressor, oncogene? Mol Endocrinol Baltim Md. 2012;26:1252-67.
15. Marcato P, Dean CA, Liu R-Z, Coyle KM, Bydoun M, Wallace M, Clements D, Turner C, Mathenge EG, Gujar SA, Giacomantonio CA, Mackey JR, Godbout R, et al. Aldehyde dehydrogenase 1A3 influences breast cancer progression via differential retinoic acid signaling. Mol Oncol. 2015;9:17-31.
16. Wang X, Saso H, Iwamoto T, Xia W, Gong Y, Pusztai L, Woodward WA, Reuben JM, Warner SL, Bearss DJ, Hortobagyi GN, Hung M-C, Ueno NT. TIG1 promotes the development and progression of inflammatory breast cancer through activation of Axl kinase. Cancer Res. 2013;73:6516-25.
17. Peng Z, Shen R, Li Y-W, Teng K-Y, Shapiro CL, Lin H-JL. Epigenetic repression of RARRES1 is mediated by methylation of a proximal promoter and a loss of CTCF binding. PloS One. 2012;7:e36891.
18. Network TCGA. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61-70.
19. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6:pl1.
20. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2:401-4.
21. Prat A, Perou CM. Deconstructing the molecular portraits of breast cancer. Mol Oncol. 2011;5:5-23.
22. Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, Kok CY, Jia M, De T, et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015;43:D805-11.
23. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012;483:603-7.
24. Metzger-Filho O, Tutt A, de Azambuja E, Saini KS, Viale G, Loi S, Bradbury I, Bliss JM, Azim HA, Ellis P, Di Leo A, Baselga J, Sotiriou C, et al. Dissecting the heterogeneity of triple-negative breast cancer. J Clin Oncol OffJ Am Soc Clin Oncol. 2012;30:1879-87.
25. Jing C, El-Ghany MA, Beesley C, Foster CS, Rudland PS, Smith P, Ke Y. Tazarotene-induced gene 1 (TIG1) expression in prostate carcinomas and its relationship to tumorigenicity. J Natl Cancer Inst. 2002;94:482-90.
26. Sahab ZJ, Hall MD, Me Sung Y, Dakshanamurthy S, Ji Y, Kumar D, Byers SW. Tumor suppressor RARRES1 interacts with cytoplasmic carboxypeptidase AGBL2 to regulate the a-tubulin tyrosination cycle. Cancer Res. 2011;71:1219-28.
27. Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015;43:D447-52.
28. Wu C-C, Tsai F-M, Shyu R-Y, Tsai Y-M, Wang C-H, Jiang S-Y. G protein-coupled receptor kinase 5 mediates Tazarotene-induced gene 1-induced growth suppression of human colon cancer cells. BMC Cancer. 2011;11:175.
29. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44-57.
30. Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37:1-13.
31. Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, et al. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015;163:506-19.
32. Stresemann C, Lyko F. Modes of action of the DNA methyltransferase inhibitors azacytidine and decitabine. Int J Cancer J Int Cancer. 2008;123:8-13.
33. Chambon P. A decade of molecular biology of retinoic acid receptors. FASEB J. 1996;10:940-54.
34. Torchia J, Glass C, Rosenfeld MG. Co-activators and co-repressors in the integration of transcriptional responses. Curr Opin Cell Biol. 1998;10:373-83.
35. Holwerda SJB, Laat W de. CTCF: the protein, the binding partners, the binding sites and their chromatin loops. Phil Trans R Soc B. 2013;368:20120369.
36. Nagpal S, Patel S, Asano AT, Johnson AT, Duvic M, Chandraratna RA. Tazarotene-induced gene 1 (TIG1), a novel retinoic acid receptor-responsive gene in skin. J Invest Dermatol. 1996;106:269-74.
37. Chen X-H, Wu W-G, Ding J. Aberrant TIG1 methylation associated with its decreased expression and clinicopathological significance in hepatocellular carcinoma. Tumour Biol J Int Soc Oncodevelopmental Biol Med. 2014;35:967-71.
38. Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, et al. Molecular portraits of human breast tumours. Nature. 2000;406:747-52.
39. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AAM, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002;415:530-6.
40. Parker JS, Mullins M, Cheang MCU, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol OffJ Am Soc Clin Oncol. 2009;27:1160-7.
41. Sellers WR. A Blueprint for Advancing Genetics-Based Cancer Therapy. Cell. 2011;147:26-31.
42. Hua S, Kittler R, White KP. Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell. 2009;137:1259-71.
43. Ross-Innes CS, Stark R, Holmes KA, Schmidt D, Spyrou C, Russell R, Massie CE, Vowler SL, Eldridge M, Carroll JS. Cooperative interaction between retinoic acid receptoralpha and estrogen receptor in breast cancer. Genes Dev. 2010;24:171-82.
44. Jiménez-Lara AM, Aranda A, Gronemeyer H. Retinoic acid protects human breast cancer cells against etoposideinduced apoptosis by NF-kappaB-dependent but cIAP2-independent mechanisms. Mol Cancer. 2010;9:15.
45. Marcato P, Dean CA, Pan D, Araslanova R, Gillis M, Joshi M, Helyer L, Pan L, Leidal A, Gujar S, Giacomantonio CA, Lee PWK. Aldehyde dehydrogenase activity of breast cancer stem cells is primarily due to isoform ALDH1A3 and its expression is predictive of metastasis. Stem Cells Dayt Ohio. 2011;29:32-45.
46. Crane-Robinson C, Myers FA, Hebbes TR, Clayton AL, Thorne AW. Chromatin immunoprecipitation assays in acetylation mapping of higher eukaryotes. Methods Enzymol. 1999;304:533-47.
47. Weaver ICG, Hellstrom IC, Brown SE, Andrews SD, Dymov S, Diorio J, Zhang T-Y, Szyf M, Meaney MJ. The methylated-DNA binding protein MBD2 enhances NGFI-A (egr-1)-mediated transcriptional activation of the glucocorticoid receptor. Philos Trans R Soc Lond B Biol Sci. 2014;369.
48. Erickson BK, Jedrychowski MP, McAlister GC, Everley RA, Kunz R, Gygi SP. Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer. Anal Chem. 2015;87:1241-9.
49. Ting L, Rad R, Gygi SP, Haas W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods. 2011;8:937-40.
50. Murphy JP, Everley RA, ColoffJL, Gygi SP. Combining Amine Metabolomics and Quantitative Proteomics of Cancer Cells Using Derivatization with Isobaric Tags. Anal Chem. 2014;86:3585-93.