Integrated analysis of gene expression, CpG Island methylation, and gene copy number in breast cancer cells by deep sequencing

PLoS ONE

Volumn 6, Issue 2, 2011, Pages

  Sun, Zhifu ^a   Asmann, Yan W ^a   Kalari, Krishna R ^a,b   Bot, Brian ^a   Eckel Passow, Jeanette E ^a   Baker, Tiffany R ^b   Carr, Jennifer M ^b   Khrebtukova, Irina ^c   Luo, Shujun ^c   Zhang, Lu ^c   Schroth, Gary P ^c   Perez, Edith A ^b   Thompson, E Aubrey ^b  

^a Mayo Clinic College of Medicine   (United States)

^b MAYO CLINIC   (United States)

^c ILLUMINA INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN RECEPTOR; MESSENGER RNA;

ARTICLE; BREAST CANCER; CANCER CELL; CHROMOSOME 8; CHROMOSOME DELETION; CONTROLLED STUDY; COPY NUMBER VARIATION; CPG ISLAND; DNA METHYLATION; GENE AMPLIFICATION; GENE DELETION; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; HUMAN; HUMAN CELL; SINGLE NUCLEOTIDE POLYMORPHISM; BREAST TUMOR; CARCINOMA; CELL CULTURE; CLUSTER ANALYSIS; DNA SEQUENCE; FEMALE; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; METHODOLOGY; PATHOLOGY; PHYSIOLOGY; SYSTEM ANALYSIS; TUMOR CELL LINE; VALIDATION STUDY;

BREAST NEOPLASMS; CARCINOMA; CELL LINE, TUMOR; CELLS, CULTURED; CLUSTER ANALYSIS; CPG ISLANDS; DNA METHYLATION; FEMALE; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA; SYSTEMS INTEGRATION;

EID: 79952122331     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0017490     Document Type: Article

References (34)

1. Sotiriou C, Neo SY, McShane LM, Korn EL, Long PM, et al. (2003) Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci U S A 100: 10393-10398.
2. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, et al. (2000) Molecular portraits of human breast tumours. Nature 406: 747-752.
3. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415: 530-536.
4. Gruvberger S, Ringner M, Chen Y, Panavally S, Saal LH, et al. (2001) Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res 61: 5979-5984.
5. Liu ET, Sotiriou C, (2002) Defining the galaxy of gene expression in breast cancer. Breast Cancer Res 4: 141-144.
6. McShane LM, Radmacher MD, Freidlin B, Yu R, Li MC, et al. (2002) Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data. Bioinformatics 18: 1462-1469.
7. Li L, Lee KM, Han W, Choi JY, Lee JY, et al. (2010) Estrogen and progesterone receptor status affect genome-wide DNA methylation profile in breast cancer. Hum Mol Genet 19: 4273-4277.
8. Lu X, Wang ZC, Iglehart JD, Zhang X, Richardson AL, (2008) Predicting features of breast cancer with gene expression patterns. Breast Cancer Res Treat 108: 191-201.
9. Frasor J, Stossi F, Danes JM, Komm B, Lyttle CR, et al. (2004) Selective estrogen receptor modulators: discrimination of agonistic versus antagonistic activities by gene expression profiling in breast cancer cells. Cancer Res 64: 1522-1533.
10. Zheng W, Long J, Gao YT, Li C, Zheng Y, et al. (2009) Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1. Nat Genet 41: 324-328.
11. Stacey SN, Sulem P, Zanon C, Gudjonsson SA, Thorleifsson G, et al. (2010) Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus. PLoS Genet 6: e1001029.
12. Abba MC, Hu Y, Sun H, Drake JA, Gaddis S, et al. (2005) Gene expression signature of estrogen receptor alpha status in breast cancer. BMC Genomics 6: 37.
13. Chou J, Provot S, Werb Z, (2010) GATA3 in development and cancer differentiation: cells GATA have it! J Cell Physiol 222: 42-49.
14. Fang SH, Chen Y, Weigel RJ, (2009) GATA-3 as a marker of hormone response in breast cancer. J Surg Res 157: 290-295.
15. Choi YL, Bocanegra M, Kwon MJ, Shin YK, Nam SJ, et al. (2010) LYN is a mediator of epithelial-mesenchymal transition and a target of dasatinib in breast cancer. Cancer Res 70: 2296-2306.
16. Heinrich C, Keller C, Boulay A, Vecchi M, Bianchi M, et al. (2010) Copine-III interacts with ErbB2 and promotes tumor cell migration. Oncogene 29: 1598-1610.
17. Andre F, Job B, Dessen P, Tordai A, Michiels S, et al. (2009) Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array. Clin Cancer Res 15: 441-451.
18. Hakli M, Lorick KL, Weissman AM, Janne OA, Palvimo JJ, (2004) Transcriptional coregulator SNURF (RNF4) possesses ubiquitin E3 ligase activity. FEBS Lett 560: 56-62.
19. Poukka H, Aarnisalo P, Santti H, Janne OA, Palvimo JJ, (2000) Coregulator small nuclear RING finger protein (SNURF) enhances Sp1- and steroid receptor-mediated transcription by different mechanisms. J Biol Chem 275: 571-579.
20. Gemmill RM, West JD, Boldog F, Tanaka N, Robinson LJ, et al. (1998) The hereditary renal cell carcinoma 3;8 translocation fuses FHIT to a patched-related gene, TRC8. Proc Natl Acad Sci U S A 95: 9572-9577.
21. Salonen J, Butzow R, Palvimo JJ, Heikinheimo M, Heikinheimo O, (2009) Oestrogen receptors and small nuclear ring finger protein 4 (RNF4) in malignant ovarian germ cell tumours. Mol Cell Endocrinol 307: 205-210.
22. Warnat P, Oberthuer A, Fischer M, Westermann F, Eils R, et al. (2007) Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes. BMC Cancer 7: 89.
23. Tam NN, Szeto CY, Sartor MA, Medvedovic M, Ho SM, (2008) Gene expression profiling identifies lobe-specific and common disruptions of multiple gene networks in testosterone-supported, 17beta-estradiol- or diethylstilbestrol-induced prostate dysplasia in Noble rats. Neoplasia 10: 20-40.
24. Song H, Ramus SJ, Kjaer SK, DiCioccio RA, Chenevix-Trench G, et al. (2009) Association between invasive ovarian cancer susceptibility and 11 best candidate SNPs from breast cancer genome-wide association study. Hum Mol Genet 18: 2297-2304.
25. Yoshihara K, Tajima A, Yahata T, Kodama S, Fujiwara H, et al. (2010) Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets. PLoS One 5: e9615.
26. Zhang Q, Zhang L, Wang B, Ou CY, Chien CT, et al. (2006) A hedgehog-induced BTB protein modulates hedgehog signaling by degrading Ci/Gli transcription factor. Dev Cell 10: 719-729.
27. La M, Kim K, Park J, Won J, Lee JH, et al. (2004) Daxx-mediated transcriptional repression of MMP1 gene is reversed by SPOP. Biochem Biophys Res Commun 320: 760-765.
28. Nielsen TO, Parker JS, Leung S, Voduc KD, Ebbert M, et al. (2010) A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor positive breast cancer. Clin Cancer Res.
29. Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, et al. (2009) Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 27: 1160-1167.
30. Smyth GK, (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
31. Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
32. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
33. Xie C, Tammi MT, (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10: 80.
34. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.