Proper genomic profiling of (BRCA1-mutated) basal-like breast carcinomas requires prior removal of tumor infiltrating lymphocytes

Molecular Oncology

Volumn 9, Issue 4, 2015, Pages 877-888

  Massink, Maarten P G ^a   Kooi, Irsan E ^a   van Mil, Saskia E ^a   Jordanova, Ekaterina S ^a   Ameziane, Najim ^a   Dorsman, Josephine C ^a   van Beek, Daphne M ^a   van der Voorn, J Patrick ^a   Sie, Daoud ^a   Ylstra, Bauke ^a   van Deurzen, Carolien H M ^b   Martens, John W ^b   Smid, Marcel ^b   Sieuwerts, Anieta M ^b   de Weerd, Vanja ^b   Foekens, John A ^b   van den Ouweland, Ans M W ^b   van Dyk, Ewald ^c   Nederlof, Petra M ^c   Waisfisz, Quinten ^a   Meijers Heijboer, Hanne ^a   more..

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^b ERASMUS MC CANCER INSTITUTE   (Netherlands)

^c NETHERLANDS CANCER INSTITUTE   (Netherlands)

Author keywords

BRCA1; Copy number; FACS analysis; Gene expression; Genomic profiling; Tumor infiltrating lymphocytes

Indexed keywords

BRCA1 PROTEIN; PARAFFIN;

ADULT; ALLELIC IMBALANCE; ARTICLE; CANCER CELL; CARCINOGENESIS; CELL ISOLATION; CLINICAL ARTICLE; FAMILIAL DISEASE; FEMALE; FLOW CYTOMETRY; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; LYMPHOCYTIC INFILTRATION; PATHOGENICITY; PRIORITY JOURNAL; TRIPLE NEGATIVE BREAST CANCER; TUMOR ASSOCIATED LEUKOCYTE; VALIDATION STUDY; BREAST TUMOR; CLUSTER ANALYSIS; COPY NUMBER VARIATION; DNA SEQUENCE; GENE DOSAGE; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; IMMUNOLOGY; MUTATION; REPRODUCIBILITY;

BRCA1 PROTEIN; BREAST NEOPLASMS; CLUSTER ANALYSIS; DNA COPY NUMBER VARIATIONS; FEMALE; FLOW CYTOMETRY; GENE DOSAGE; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; HUMANS; LYMPHOCYTES, TUMOR-INFILTRATING; MUTATION; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 84926419171     PISSN: 15747891     EISSN: 18780261     Source Type: Journal    
DOI: 10.1016/j.molonc.2014.12.012     Document Type: Article

References (48)

1. Abecasis G.R., Auton A., Brooks L.D., DePristo M.A., Durbin R.M., Handsaker R.E., Kang H.M., et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491:56-65.
2. Bergamaschi A., Kim Y.H., Wang P., Sorlie T., Hernandez-Boussard T., Lonning P.E., Tibshirani R., et al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 2006, 45:1033-1040.
3. Bernstein B.E., Birney E., Dunham I., Green E.D., Gunter C., Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
4. Birgisdottir V., Stefansson O.A., Bodvarsdottir S.K., Hilmarsdottir H., Jonasson J.G., Eyfjord J.E. Epigenetic silencing and deletion of the BRCA1 gene in sporadic breast cancer. Breast Cancer Res. 2006, 8:R38.
5. Bouwman P., Aly A., Escandell J.M., Pieterse M., Bartkova J., van der Gulden H., Hiddingh S., et al. 53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers. Nat. Struct. Mol. Biol. 2010, 17:688-695.
6. Corver W.E., Ter Haar N.T., Dreef E.J., Miranda N.F., Prins F.A., Jordanova E.S., Cornelisse C.J., et al. High-resolution multi-parameter DNA flow cytometry enables detection of tumor and stromal cell subpopulations in paraffin-embedded tissues. J.Pathol. 2005, 206:233-241.
7. Corver W.E., ter Haar N.T. High-resolution multiparameter DNA flow cytometry for the detection and sorting of tumor and stromal subpopulations from paraffin-embedded tissues. Curr. Protoc. Cytom 2011, (Chapter 7):Unit 7.37.
8. Curtis C., Shah S.P., Chin S.F., Turashvili G., Rueda O.M., Dunning M.J., Speed D., et al. The genomic and transcriptomic architecture of 2,000 breast tumors reveals novel subgroups. Nature 2012, 486:346-352.
9. Foulkes W.D., Stefansson I.M., Chappuis P.O., Begin L.R., Goffin J.R., Wong N., Trudel M., et al. Germline BRCA1 mutations and a basal epithelial phenotype in breast cancer. J.Natl. Cancer Inst. 2003, 95:1482-1485.
10. Futreal P.A., Liu Q., Shattuck-Eidens D., Cochran C., Harshman K., Tavtigian S., Bennett L.M., et al. BRCA1 mutations in primary breast and ovarian carcinomas. Science 1994, 266:120-122.
11. Gonzalez-Angulo A.M., Timms K.M., Liu S., Chen H., Litton J.K., Potter J., Lanchbury J.S., et al. Incidence and outcome of BRCA mutations in unselected patients with triple receptor-negative breast cancer. Clin. Cancer Res. 2011, 17:1082-1089.
12. Honrado E., Osorio A., Palacios J., Milne R.L., Sanchez L., Diez O., Cazorla A., et al. Immunohistochemical expression of DNA repair proteins in familial breast cancer differentiate BRCA2-associated tumors. J.Clin. Oncol. 2005, 23:7503-7511.
13. Huang d.W., Sherman B.T., Lempicki R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37:1-13.
14. Huang D.W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
15. Jonsson G., Naylor T.L., Vallon-Christersson J., Staaf J., Huang J., Ward M.R., Greshock J.D., et al. Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization. Cancer Res. 2005, 65:7612-7621.
16. Jonsson G., Staaf J., Vallon-Christersson J., Ringner M., Holm K., Hegardt C., Gunnarsson H., et al. Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics. Breast Cancer Res. 2010, 12:R42.
17. Joosse S.A., van Beers E.H., Tielen I.H., Horlings H., Peterse J.L., Hoogerbrugge N., Ligtenberg M.J., et al. Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res. Treat 2009, 116:479-489.
18. Lakhani S.R., van de Vijver M.J., Acquemier J., Anderson T.J., Osin P.P., McGuffog L., Easton D.F. The pathology of familial breast cancer: predictive value of immunohistochemical markers estrogen receptor, progesterone receptor, HER-2, and p53 in patients with mutations in BRCA1 and BRCA2. J.Clin. Oncol. 2002, 20:2310-2318.
19. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
20. Lips E.H., Mulder L., Hannemann J., Laddach N., Vrancken Peeters M.T., van de Vijver M.J., Wesseling J., et al. Indicators of homologous recombination deficiency in breast cancer and association with response to neoadjuvant chemotherapy. Ann. Oncol. 2011, 22:870-876.
21. Lips E.H., Laddach N., Savola S.P., Vollebergh M.A., Oonk A.M., Imholz A.L., Wessels L.F., Wesseling J., Nederlof P.M., Rodenhuis S. Quantitative copy number analysis by Multiplex Ligation-dependent Probe Amplification (MLPA) of BRCA1-associated breast cancer regions identifies BRCAness. Breast Cancer Res. 2011, 13:R107.
22. Mehta A.M., Jordanova E.S., Corver W.E., van Wezel T., Uh H.W., Kenter G.G., Jan Fleuren G. Single nucleotide polymorphisms in antigen processing machinery component ERAP1 significantly associate with clinical outcome in cervical carcinoma. Genes Chromosomes Cancer 2009, 48:410-418.
23. Middeldorp A., van Puijenbroek M., Nielsen M., Corver W.E., Jordanova E.S., ter Haar N., et al. High frequency of copy-neutral LOH in MUTYH-associated polyposis carcinomas. J.Pathol. 2008, 216:25-31.
24. Nagel J.H., Peeters J.K., Smid M., Sieuwerts A.M., Wasielewski M., de Weerd V., Trapman-Jansen A.M., van den Ouweland A., et al. Gene expression profiling assigns CHEK2 1100delC breast cancers to the luminal intrinsic subtypes. Breast Cancer Res. Treat 2012, 132:439-448.
25. Perou C.M., Sorlie T., Eisen M.B., van de Rijn M., Jeffrey S.S., Rees C.A., Pollack J.R., et al. Molecular portraits of human breast tumors. Nature 2000, 406:747-752.
26. Prat A., Cruz C., Hoadley K.A., Diez O., Perou C.M., Balmana J. Molecular features of the basal-like breast cancer subtype based on BRCA1 mutation status. Breast Cancer Res. Treat 2014, 147:185-191.
27. Popova T., Manie E., Stoppa-Lyonnet D., Rigaill G., Barillot E., Stern M.H. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol. 2009, 10:R128.
28. Rasmussen M., Sundstrom M., Goransson K.H., Botling J., Micke P., Birgisson H., Glimelius B., Isaksson A. Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity. Genome Biol. 2011, 12:R108.
29. Roy R., Chun J., Powell S.N. BRCA1 and BRCA2: different roles in a common pathway of genome protection. Nat. Rev. Cancer 2012, 12:68-78.
30. Rubinstein W.S. Hereditary breast cancer: pathobiology, clinical translation, and potential for targeted cancer therapeutics. Fam. Cancer 2008, 7:83-89.
31. Schouten P.C., van Dyk E., Braaf L.M., Mulder L., Lips E.H., de Ronde J.J., Holtman L., et al. Platform comparisons for identification of breast cancers with a BRCA-like copy number profile. Breast Cancer Res. Treat 2013, 139:317-327.
32. Silver D.P., Richardson A.L., Eklund A.C., Wang Z.C., Szallasi Z., Li Q., Juul N., et al. Efficacy of neoadjuvant cisplatin in triple-negative breast cancer. J.Clin. Oncol. 2010, 28:1145-1153.
33. Smeets S.J., Harjes U., van Wieringen W.N., Sie D., Brakenhoff R.H., Meijer G.A., Ylstra B. To DNA or not to DNA? That is the question, when it comes to molecular subtyping for the clinic!. Clin. Cancer Res. 2011, 17:4959-4964.
34. Smid M., Wang Y., Zhang Y., Sieuwerts A.M., Yu J., Klijn J.G., Foekens J.A., et al. Subtypes of breast cancer show preferential site of relapse. Cancer Res. 2008, 68:3108-3114.
35. Smid M., Hoes M., Sieuwerts A.M., Sleijfer S., Zhang Y., Wang Y., Foekens J.A., et al. Patterns and incidence of chromosomal instability and their prognostic relevance in breast cancer subtypes. Breast Cancer Res. Treat 2010, 128:23-30.
36. Sorlie T., Tibshirani R., Parker J., Hastie T., Marron J.S., Nobel A., Deng S., et al. Repeated observation of breast tumor subtypes in independent gene expression datasets. Proc. Natl. Acad. Sci. USA 2003, 100:8418-8423.
37. Staaf J., Lindgren D., Vallon-Christersson J., Isaksson A., Goransson H., Juliusson G., Rosenquist R., et al. Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays. Genome Biol. 2008, 9:R136.
38. Stefansson O.A., Jonasson J.G., Johannsson O.T., Olafsdottir K., Steinarsdottir M., Valgeirsdottir S., Eyfjord J.E. Genomic profiling of breast tumors in relation to BRCA abnormalities and phenotypes. Breast Cancer Res. 2009, 11:R47.
39. Tirkkonen M., Johannsson O., Agnarsson B.A., Olsson H., Ingvarsson S., Karhu R., Tanner M., et al. Distinct somatic genetic changes associated with tumor progression in carriers of BRCA1 and BRCA2 germ-line mutations. Cancer Res. 1997, 57:1222-1227.
40. Turner N., Tutt A., Ashworth A. Hallmarks of 'BRCAness' in sporadic cancers. Nat. Rev. Cancer 2004, 4:814-819.
41. Turner N.C., Reis-Filho J.S. Basal-like breast cancer and the BRCA1 phenotype. Oncogene 2006, 25:5846-5853.
42. van Beers E.H., van Welsem T., Wessels L.F., Li Y., Oldenburg R.A., Devilee P., Cornelisse C.J., et al. Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations. Cancer Res. 2005, 65:822-827.
43. van Thuijl H.F., Ylstra B., Wurdinger T., van Nieuwenhuizen D., Heimans J.J., Wesseling P., Reijneveld J.C. Genetics and pharmacogenomics of diffuse gliomas. Pharmacol. Ther. 2013, 137:78-88.
44. Waddell N., Arnold J., Cocciardi S., da Silva L., Marsh A., Riley J., Johnstone C.N., et al. Subtypes of familial breast tumors revealed by expression and copy number profiling. Breast Cancer Res. Treat 2010, 123:661-677.
45. Wei M., Grushko T.A., Dignam J., Hagos F., Nanda R., Sveen L., Xu J., et al. BRCA1 promoter methylation in sporadic breast cancer is associated with reduced BRCA1 copy number and chromosome 17 aneusomy. Cancer Res. 2005, 65:10692-10699.
46. Wessels L.F., van Welsem T., Hart A.A., van't Veer L.J., Reinders M.J., Nederlof P.M. Molecular classification of breast carcinomas by comparative genomic hybridization: a specific somatic genetic profile for BRCA1 tumors. Cancer Res. 2002, 62:7110-7117.
47. Wickham H. ggplot2: Elegant Graphics for Data Analysis 2009, Springer, New York.
48. Yau C., Mouradov D., Jorissen R.N., Colella S., Mirza G., Steers G., Harris A., et al. A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol. 2010, 11:R92.