High-resolution comparative genomic hybridization of Inflammatory breast cancer and identification of candidate genes

PLoS ONE

Volumn 6, Issue 2, 2011, Pages

  Bekhouche, Ismahane ^a   Finetti, Pascal ^a   Adelaïde, José ^a   Ferrari, Anthony ^a   Tarpin, Carole ^a   Charafe Jauffret, Emmanuelle ^a,b   Charpin, Colette ^b,c   Houvenaeghel, Gilles ^a   Jacquemier, Jocelyne ^a   Bidaut, Ghislain ^d   Birnbaum, Daniel ^a   Viens, Patrice ^a,b   Chaffanet, Max ^a   Bertucci, François ^a,b  

^a INSTITUT PAOLI CALMETTES   (France)

^b AIX MARSEILLE UNIVERSITY   (France)

^c HÔPITAL NORD   (France)

^d AIX MARSEILLE UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MESSENGER RNA;

ABCC3 GENE; ACCURACY; ADULT; AGED; ARID2 GENE; ARTICLE; ATAD2 GENE; CANCER TISSUE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DCC1 GENE; DNA MICROARRAY; EPN3 GENE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ANALYSIS; HUMAN; HUMAN GENOME; HUMAN TISSUE; INFLAMMATORY BREAST CANCER; INST2 GENE; INST8 GENE; KIAA1429 GENE; LRRC59 GENE; MAJOR CLINICAL STUDY; MRPL27 GENE; MTBP GENE; MTSS1 GENE; NUCLEOTIDE SEQUENCE; PABPC1 GENE; PROGNOSIS; PTPN2 GENE; RAD21 GENE; RAD54B GENE; RBM13 GENE; SQLE GENE; ST3GAL1 GENE; TAF2 GENE; TUMOR GENE; UTP23 GENE; VALIDATION PROCESS; VPS13B GENE; WDR67 GENE; ADENOCARCINOMA; CHROMOSOME ABERRATION; FEMALE; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION; GENETICS; METHODOLOGY; MICROARRAY ANALYSIS; MIDDLE AGED; VALIDATION STUDY;

ADENOCARCINOMA; ADULT; AGED; AGED, 80 AND OVER; CHROMOSOME ABERRATIONS; COMPARATIVE GENOMIC HYBRIDIZATION; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC ASSOCIATION STUDIES; HUMANS; INFLAMMATORY BREAST NEOPLASMS; MICROARRAY ANALYSIS; MIDDLE AGED; YOUNG ADULT;

EID: 79951784545     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016950     Document Type: Article

References (85)

1. Hance KW, Anderson WF, Devesa SS, Young HA, Levine PH, (2005) Trends in inflammatory breast carcinoma incidence and survival: the surveillance, epidemiology, and end results program at the National Cancer Institute. J Natl Cancer Inst 97: 966-975.
2. Singletary SE, Cristofanilli M, (2008) Defining the clinical diagnosis of inflammatory breast cancer. Semin Oncol 35: 7-10.
3. Resetkova E, (2008) Pathologic aspects of inflammatory breast carcinoma: part 1. Histomorphology and differential diagnosis. Semin Oncol 35: 25-32.
4. Alpaugh ML, Tomlinson JS, Kasraeian S, Barsky SH, (2002) Cooperative role of E-cadherin and sialyl-Lewis X/A-deficient MUC1 in the passive dissemination of tumor emboli in inflammatory breast carcinoma. Oncogene 21: 3631-3643.
5. Dawood S, Ueno NT, Cristofanilli M, (2008) The medical treatment of inflammatory breast cancer. Semin Oncol 35: 64-71.
6. Woodward WA, Cristofanilli M, (2009) Inflammatory breast cancer. Semin Radiat Oncol 19: 256-265.
7. Charafe-Jauffret E, Tarpin C, Viens P, Bertucci F, (2008) Defining the molecular biology of inflammatory breast cancer. Semin Oncol 35: 41-50.
8. Houchens NW, Merajver SD, (2008) Molecular determinants of the inflammatory breast cancer phenotype. Oncology 22: 1556-1561.
9. van Golen KL, Davies S, Wu ZF, Wang Y, Bucana CD, et al. (1999) A novel putative low-affinity insulin-like growth factor-binding protein, LIBC (lost in inflammatory breast cancer), and RhoC GTPase correlate with the inflammatory breast cancer phenotype. Clin Cancer Res 5: 2511-2519.
10. van Golen KL, Wu ZF, Qiao XT, Bao L, Merajver SD, (2000) RhoC GTPase overexpression modulates induction of angiogenic factors in breast cells. Neoplasia 2: 418-425.
11. van Golen KL, Wu ZF, Qiao XT, Bao LW, Merajver SD, (2000) RhoC GTPase, a novel transforming oncogene for human mammary epithelial cells that partially recapitulates the inflammatory breast cancer phenotype. Cancer Res 60: 5832-5838.
12. Kleer CG, Zhang Y, Pan Q, van Golen KL, Wu ZF, et al. (2002) WISP3 is a novel tumor suppressor gene of inflammatory breast cancer. Oncogene 21: 3172-3180.
13. Kleer CG, Zhang Y, Pan Q, Merajver SD, (2004) WISP3 (CCN6) is a secreted tumor-suppressor protein that modulates IGF signaling in inflammatory breast cancer. Neoplasia 6: 179-185.
14. Huang W, Zhang Y, Varambally S, Chinnaiyan AM, Banerjee S, et al. (2008) Inhibition of CCN6 (Wnt-1-induced signaling protein 3) down-regulates E-cadherin in the breast epithelium through induction of snail and ZEB1. Am J Pathol 172: 893-904.
15. Zhang Y, Pan Q, Zhong H, Merajver SD, Kleer CG, (2005) Inhibition of CCN6 (WISP3) expression promotes neoplastic progression and enhances the effects of insulin-like growth factor-1 on breast epithelial cells. Breast Cancer Res 7: R1080-1089.
16. Vermeulen PB, van Golen KL, Dirix LY, (2010) Angiogenesis, lymphangiogenesis, growth pattern, and tumor emboli in inflammatory breast cancer: a review of the current knowledge. Cancer 116: 2748-2754.
17. Kleer CG, Zhang Y, Pan Q, Gallagher G, Wu M, et al. (2004) WISP3 and RhoC guanosine triphosphatase cooperate in the development of inflammatory breast cancer. Breast Cancer Res 6: R110-115.
18. van Golen KL, Bao L, DiVito MM, Wu Z, Prendergast GC, et al. (2002) Reversion of RhoC GTPase-induced inflammatory breast cancer phenotype by treatment with a farnesyl transferase inhibitor. Mol Cancer Ther 1: 575-583.
19. van Golen KL, Bao LW, Pan Q, Miller FR, Wu ZF, et al. (2002) Mitogen activated protein kinase pathway is involved in RhoC GTPase induced motility, invasion and angiogenesis in inflammatory breast cancer. Clin Exp Metastasis 19: 301-311.
20. Wu M, Wu ZF, Kumar-Sinha C, Chinnaiyan A, Merajver SD, (2004) RhoC induces differential expression of genes involved in invasion and metastasis in MCF10A breast cells. Breast Cancer Res Treat 84: 3-12.
21. Kleer CG, van Golen KL, Braun T, Merajver SD, (2001) Persistent E-cadherin expression in inflammatory breast cancer. Mod Pathol 14: 458-464.
22. Van den Eynden GG, Van der Auwera I, Van Laere S, Colpaert CG, van Dam P, et al. (2004) Validation of a tissue microarray to study differential protein expression in inflammatory and non-inflammatory breast cancer. Breast Cancer Res Treat 85: 13-22.
23. Van Laere SJ, Van der Auwera I, Van den Eynden GG, Elst HJ, Weyler J, et al. (2006) Nuclear factor-kappaB signature of inflammatory breast cancer by cDNA microarray validated by quantitative real-time reverse transcription-PCR, immunohistochemistry, and nuclear factor-kappaB DNA-binding. Clin Cancer Res 12: 3249-3256.
24. Lerebours F, Vacher S, Andrieu C, Espie M, Marty M, et al. (2008) NF-kappa B genes have a major role in inflammatory breast cancer. BMC Cancer 8: 41.
25. Silvera D, Arju R, Darvishian F, Levine PH, Zolfaghari L, et al. (2009) Essential role for eIF4GI overexpression in the pathogenesis of inflammatory breast cancer. Nat Cell Biol 11: 903-908.
26. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, et al. (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 98: 10869-10874.
27. Bertucci F, Finetti P, Rougemont J, Charafe-Jauffret E, Cervera N, et al. (2005) Gene expression profiling identifies molecular subtypes of inflammatory breast cancer. Cancer Res 65: 2170-2178.
28. Bertucci F, Finetti P, Rougemont J, Charafe-Jauffret E, Nasser V, et al. (2004) Gene expression profiling for molecular characterization of inflammatory breast cancer and prediction of response to chemotherapy. Cancer Res 64: 8558-8565.
29. Boersma BJ, Reimers M, Yi M, Ludwig JA, Luke BT, et al. (2008) A stromal gene signature associated with inflammatory breast cancer. Int J Cancer 122: 1324-1332.
30. Dressman HK, Hans C, Bild A, Olson JA, Rosen E, et al. (2006) Gene expression profiles of multiple breast cancer phenotypes and response to neoadjuvant chemotherapy. Clin Cancer Res 12: 819-826.
31. Nguyen DM, Sam K, Tsimelzon A, Li X, Wong H, et al. (2006) Molecular heterogeneity of inflammatory breast cancer: a hyperproliferative phenotype. Clin Cancer Res 12: 5047-5054.
32. Van Laere S, Van der Auwera I, Van den Eynden G, Van Hummelen P, van Dam P, et al. (2007) Distinct molecular phenotype of inflammatory breast cancer compared to non-inflammatory breast cancer using Affymetrix-based genome-wide gene-expression analysis. Br J Cancer 97: 1165-1174.
33. Van Laere S, Van der Auwera I, Van den Eynden GG, Fox SB, Bianchi F, et al. (2005) Distinct molecular signature of inflammatory breast cancer by cDNA microarray analysis. Breast Cancer Res Treat 93: 237-246.
34. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, et al. (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A 99: 12963-12968.
35. Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, et al. (2006) Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 6: 96.
36. Loo LW, Grove DI, Williams EM, Neal CL, Cousens LA, et al. (2004) Array comparative genomic hybridization analysis of genomic alterations in breast cancer subtypes. Cancer Res 64: 8541-8549.
37. van Beers EH, Nederlof PM, (2006) Array-CGH and breast cancer. Breast Cancer Res 8: 210.
38. Bergamaschi A, Kim YH, Wang P, Sorlie T, Hernandez-Boussard T, et al. (2006) Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 45: 1033-1040.
39. Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, et al. (2006) Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10: 529-541.
40. Ahomadegbe JC, Tourpin S, Kaghad M, Zelek L, Vayssade M, et al. (2000) Loss of heterozygosity, allele silencing and decreased expression of p73 gene in breast cancers: prevalence of alterations in inflammatory breast cancers. Oncogene 19: 5413-5418.
41. Lerebours F, Bertheau P, Bieche I, Driouch K, De The H, et al. (2002) Evidence of chromosome regions and gene involvement in inflammatory breast cancer. Int J Cancer 102: 618-622.
42. Lerebours F, Bertheau P, Bieche I, Plassa LF, Champeme MH, et al. (2003) Two prognostic groups of inflammatory breast cancer have distinct genotypes. Clin Cancer Res 9: 4184-4189.
43. Adelaide J, Finetti P, Bekhouche I, Repellini L, Geneix J, et al. (2007) Integrated profiling of basal and luminal breast cancers. Cancer Res 67: 11565-11575.
44. 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.
45. Olshen AB, Venkatraman ES, Lucito R, Wigler M, (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572.
46. Geyer FC, Marchio C, Reis-Filho JS, (2009) The role of molecular analysis in breast cancer. Pathology 41: 77-88.
47. Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, et al. (2006) Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 16: 1465-1479.
48. Eisen MB, Spellman PT, Brown PO, Botstein D, (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
49. Suzuki R, Shimodaira H, (2006) Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22: 1540-1542.
50. Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, et al. (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A 104: 20007-20012.
51. Hochberg Y, Benjamini Y, (1990) More powerful procedures for multiple significance testing. Stat Med 9: 811-818.
52. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
53. Hu Z, Fan C, Oh DS, Marron JS, He X, et al. (2006) The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 7: 96.
54. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531-537.
55. Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, et al. (2007) Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol 25: 1239-1246.
56. Miller LD, Smeds J, George J, Vega VB, Vergara L, et al. (2005) An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A 102: 13550-13555.
57. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347: 1999-2009.
58. 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.
59. Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, et al. (2005) Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 365: 671-679.
60. Iwamoto T, Bianchini G, Qi Y, Cristofanilli M, Lucci A, et al. (2010) Different gene expressions are associated with the different molecular subtypes of inflammatory breast cancer. Breast Cancer Res Treat [Epub ahead of print].
61. Hwang KT, Han W, Cho J, Lee JW, Ko E, et al. (2008) Genomic copy number alterations as predictive markers of systemic recurrence in breast cancer. Int J Cancer 123: 1807-1815.
62. Yamamoto Y, Chochi Y, Matsuyama H, Eguchi S, Kawauchi S, et al. (2007) Gain of 5p15.33 is associated with progression of bladder cancer. Oncology 72: 132-138.
63. Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, et al. (2002) Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res 62: 6240-6245.
64. Woods AJ, Kantidakis T, Sabe H, Critchley DR, Norman JC, (2005) Interaction of paxillin with poly(A)-binding protein 1 and its role in focal adhesion turnover and cell migration. Mol Cell Biol 25: 3763-3773.
65. Silvera D, Formenti SC, Schneider RJ, (2010) Translational control in cancer. Nat Rev Cancer 10: 254-266.
66. Silvera D, Schneider RJ, (2009) Inflammatory breast cancer cells are constitutively adapted to hypoxia. Cell Cycle 8: 3091-3096.
67. Wickner RB, (1988) Host function of MAK16: G1 arrest by a mak16 mutant of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 85: 6007-6011.
68. Martin J, Halenbeck R, Kaufmann J, (1999) Human transcription factor hTAF(II)150 (CIF150) is involved in transcriptional regulation of cell cycle progression. Mol Cell Biol 19: 5548-5556.
69. Zou JX, Revenko AS, Li LB, Gemo AT, Chen HW, (2007) ANCCA, an estrogen-regulated AAA+ ATPase coactivator for ERalpha, is required for coregulator occupancy and chromatin modification. Proc Natl Acad Sci U S A 104: 18067-18072.
70. Ciro M, Prosperini E, Quarto M, Grazini U, Walfridsson J, et al. (2009) ATAD2 is a novel cofactor for MYC, overexpressed and amplified in aggressive tumors. Cancer Res 69: 8491-8498.
71. Bernstein KA, Baserga SJ, (2004) The small subunit processome is required for cell cycle progression at G1. Mol Biol Cell 15: 5038-5046.
72. Brady M, Vlatkovic N, Boyd MT, (2005) Regulation of p53 and MDM2 activity by MTBP. Mol Cell Biol 25: 545-553.
73. Yan Z, Cui K, Murray DM, Ling C, Xue Y, et al. (2005) PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200, to regulate expression of selective interferon-responsive genes. Genes Dev 19: 1662-1667.
74. Dalziel M, Whitehouse C, McFarlane I, Brockhausen I, Gschmeissner S, et al. (2001) The relative activities of the C2GnT1 and ST3Gal-I glycosyltransferases determine O-glycan structure and expression of a tumor-associated epitope on MUC1. J Biol Chem 276: 11007-11015.
75. Helms MW, Kemming D, Pospisil H, Vogt U, Buerger H, et al. (2008) Squalene epoxidase, located on chromosome 8q24.1, is upregulated in 8q+ breast cancer and indicates poor clinical outcome in stage I and II disease. Br J Cancer 99: 774-780.
76. Atienza JM, Roth RB, Rosette C, Smylie KJ, Kammerer S, et al. (2005) Suppression of RAD21 gene expression decreases cell growth and enhances cytotoxicity of etoposide and bleomycin in human breast cancer cells. Mol Cancer Ther 4: 361-368.
77. Ibarra-Sanchez MJ, Wagner J, Ong MT, Lampron C, Tremblay ML, (2001) Murine embryonic fibroblasts lacking TC-PTP display delayed G1 phase through defective NF-kappaB activation. Oncogene 20: 4728-4739.
78. Blanquart C, Karouri SE, Issad T, (2010) Protein tyrosine phosphatase-1B and T-cell protein tyrosine phosphatase regulate IGF-2-induced MCF-7 cell migration. Biochem Biophys Res Commun 392: 83-88.
79. Callahan CA, Ofstad T, Horng L, Wang JK, Zhen HH, et al. (2004) MIM/BEG4, a Sonic hedgehog-responsive gene that potentiates Gli-dependent transcription. Genes Dev 18: 2724-2729.
80. Parr C, Jiang WG, (2009) Metastasis suppressor 1 (MTSS1) demonstrates prognostic value and anti-metastatic properties in breast cancer. Eur J Cancer 45: 1673-1683.
81. Bompard G, Sharp SJ, Freiss G, Machesky LM, (2005) Involvement of Rac in actin cytoskeleton rearrangements induced by MIM-B. J Cell Sci 118: 5393-5403.
82. Spradling KD, McDaniel AE, Lohi J, Pilcher BK, (2001) Epsin 3 is a novel extracellular matrix-induced transcript specific to wounded epithelia. J Biol Chem 276: 29257-29267.
83. Evans EE, Henn AD, Jonason A, Paris MJ, Schiffhauer LM, et al. (2006) C35 (C17orf37) is a novel tumor biomarker abundantly expressed in breast cancer. Mol Cancer Ther 5: 2919-2930.
84. Dasgupta S, Wasson LM, Rauniyar N, Prokai L, Borejdo J, et al. (2009) Novel gene C17orf37 in 17q12 amplicon promotes migration and invasion of prostate cancer cells. Oncogene 28: 2860-2872.
85. Van der Auwera I, Limane R, van Dam P, Vermeulen PB, Dirix LY, et al. (2010) Integrated miRNA and mRNA expression profiling of the inflammatory breast cancer subtype. Br J Cancer Jul 27 [Epub ahead of print].