Dual roles for immune metagenes in breast cancer prognosis and therapy prediction

Genome Medicine

Volumn 6, Issue 10, 2014, Pages

  Alistar, Angela ^a,d   Chou, Jeff W ^a   Nagalla, Srikanth ^b   Black, Michael A ^c   D'Agostino, Ralph ^a,d   Miller, Lance D ^a,d  

^a WAKE FOREST SCHOOL OF MEDICINE   (United States)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

^c UNIVERSITY OF OTAGO   (New Zealand)

^d WAKE FOREST BAPTIST HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; ARTICLE; BREAST CANCER; CANCER ADJUVANT THERAPY; CANCER IMMUNOLOGY; CANCER PROGNOSIS; DENDRITIC CELL; DISTANT METASTASIS FREE SURVIVAL; GENE EXPRESSION; HUMAN; HUMAN TISSUE; METAGENOME; MICROARRAY ANALYSIS; MONOCYTE; NATURAL KILLER CELL; PRIORITY JOURNAL; TREATMENT OUTCOME; TUMOR ASSOCIATED LEUKOCYTE;

EID: 84927914705     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-014-0080-8     Document Type: Article

References (78)

1. Jemal A, Siegel R, Xu J, Ward E. Cancer statistics, 2010. CA Cancer J Clin 2010, 60:277-300. doi:10.3322/caac.20073, 10.3322/caac.20073, 20610543.
2. Fisher B, Bryant J, Wolmark N, Mamounas E, Brown A, Fisher ER, Wickerham DL, Begovic M, DeCillis A, Robidoux A, Margolese RG, Cruz AB, Hoehn JL, Lees AW, Dimitrov NV, Bear HD. Effect of preoperative chemotherapy on the outcome of women with operable breast cancer. J Clin Oncol 1998, 16:2672-2685. 9704717.
3. van der Hage JA, van de Velde CJ, Julien JP, Tubiana-Hulin M, Vandervelden C, Duchateau L. Preoperative chemotherapy in primary operable breast cancer: results from the European Organization for Research and Treatment of Cancer trial 10902. J Clin Oncol 2001, 19:4224-4237. 11709566.
4. Rastogi P, Anderson SJ, Bear HD, Geyer CE, Kahlenberg MS, Robidoux A, Margolese RG, Hoehn JL, Vogel VG, Dakhil SR, Tamkus D, King KM, Pajon ER, Wright MJ, Robert J, Paik S, Mamounas EP, Wolmark N. Preoperative chemotherapy: updates of National Surgical Adjuvant Breast and Bowel Project Protocols B-18 and B-27. J Clin Oncol 2008, 26:778-785. doi:10.1200/JCO.2007.15.0235, 10.1200/JCO.2007.15.0235, 18258986.
5. Schott AF, Hayes DF. Defining the benefits of neoadjuvant chemotherapy for breast cancer. J Clin Oncol 2012, 30:1747-1749. doi:10.1200/JCO.2011.41.3161, 10.1200/JCO.2011.41.3161, 22508810.
6. Smith IC, Heys SD, Hutcheon AW, Miller ID, Payne S, Gilbert FJ, Ah-See AK, Eremin O, Walker LG, Sarkar TK, Eggleton SP, Ogston KN. Neoadjuvant chemotherapy in breast cancer: significantly enhanced response with docetaxel. J Clin Oncol 2002, 20:1456-1466. 10.1200/JCO.20.6.1456, 11896092.
7. Ellis MJ, Tao Y, Luo J, A'Hern R, Evans DB, Bhatnagar AS, Chaudri Ross HA, von Kameke A, Miller WR, Smith I, Eiermann W, Dowsett M. Outcome prediction for estrogen receptor-positive breast cancer based on postneoadjuvant endocrine therapy tumor characteristics. J Natl Cancer Inst 2008, 100:1380-1388. doi:10.1093/jnci/djn309, 10.1093/jnci/djn309, 18812550.
8. Mathieu MC, Mazouni C, Kesty NC, Zhang Y, Scott V, Passeron J, Arnedos M, Schnabel CA, Delaloge S, Erlander MG, Andre F. Breast Cancer Index predicts pathological complete response and eligibility for breast conserving surgery in breast cancer patients treated with neoadjuvant chemotherapy. Ann Oncol 2012, 23:2046-2052. doi:10.1093/annonc/mdr550, 10.1093/annonc/mdr550, 22112967.
9. Symmans WF, Peintinger F, Hatzis C, Rajan R, Kuerer H, Valero V, Assad L, Poniecka A, Hennessy B, Green M, Buzdar AU, Singletary SE, Hortobagyi GN, Pusztai L. Measurement of residual breast cancer burden to predict survival after neoadjuvant chemotherapy. J Clin Oncol 2007, 25:4414-4422. doi:10.1200/JCO.2007.10.6823, 10.1200/JCO.2007.10.6823, 17785706.
10. Nishimura R, Osako T, Okumura Y, Hayashi M, Arima N. Clinical significance of Ki-67 in neoadjuvant chemotherapy for primary breast cancer as a predictor for chemosensitivity and for prognosis. Breast Cancer 2010, 17:269-275. doi:10.1007/s12282-009-0161-5, 10.1007/s12282-009-0161-5, 19730975.
11. Petit T, Wilt M, Velten M, Millon R, Rodier JF, Borel C, Mors R, Haegele P, Eber M, Ghnassia JP. Comparative value of tumour grade, hormonal receptors, Ki-67, HER-2 and topoisomerase II alpha status as predictive markers in breast cancer patients treated with neoadjuvant anthracycline-based chemotherapy. Eur J Cancer 2004, 40:205-211. 10.1016/S0959-8049(03)00675-0, 14728934.
12. Andre F, Mazouni C, Liedtke C, Kau SW, Frye D, Green M, Gonzalez-Angulo AM, Symmans WF, Hortobagyi GN, Pusztai L. HER2 expression and efficacy of preoperative paclitaxel/FAC chemotherapy in breast cancer. Breast Cancer Res Treat 2008, 108:183-190. doi:10.1007/s10549-007-9594-8, 10.1007/s10549-007-9594-8, 17468948.
13. Dowsett M, Smith IE, Ebbs SR, Dixon JM, Skene A, Griffith C, Boeddinghaus I, Salter J, Detre S, Hills M, Ashley S, Francis S, Walsh G, A'Hern R. Proliferation and apoptosis as markers of benefit in neoadjuvant endocrine therapy of breast cancer. Clin Cancer Res 2006, 12:1024s-1030s. doi:10.1158/1078-0432.CCR-05-2127, 10.1158/1078-0432.CCR-05-2127, 16467120.
14. Burcombe RJ, Makris A, Richman PI, Daley FM, Noble S, Pittam M, Wright D, Allen SA, Dove J, Wilson GD. Evaluation of ER, PgR, HER-2 and Ki-67 as predictors of response to neoadjuvant anthracycline chemotherapy for operable breast cancer. Br J Cancer 2005, 92:147-155. doi:10.1038/sj.bjc.6602256, 10.1038/sj.bjc.6602256, 15611798.
15. Apetoh L, Ghiringhelli F, Tesniere A, Obeid M, Ortiz C, Criollo A, Mignot G, Maiuri MC, Ullrich E, Saulnier P, Yang H, Amigorena S, Ryffel B, Barrat FJ, Saftig P, Levi F, Lidereau R, Nogues C, Mira JP, Chompret A, Joulin V, Clavel-Chapelon F, Bourhis J, Andre F, Delaloge S, Tursz T, Kroemer G, Zitvogel L. Toll-like receptor 4-dependent contribution of the immune system to anticancer chemotherapy and radiotherapy. Nat Med 2007, 13:1050-1059. doi:10.1038/nm1622, 10.1038/nm1622, 17704786.
16. Casares N, Pequignot MO, Tesniere A, Ghiringhelli F, Roux S, Chaput N, Schmitt E, Hamai A, Hervas-Stubbs S, Obeid M, Coutant F, Metivier D, Pichard E, Aucouturier P, Pierron G, Garrido C, Zitvogel L, Kroemer G. Caspase-dependent immunogenicity of doxorubicin-induced tumor cell death. J Exp Med 2005, 202:1691-1701. doi:10.1084/jem.20050915, 10.1084/jem.20050915, 16365148.
17. Ghiringhelli F, Apetoh L, Tesniere A, Aymeric L, Ma Y, Ortiz C, Vermaelen K, Panaretakis T, Mignot G, Ullrich E, Perfettini JL, Schlemmer F, Tasdemir E, Uhl M, Genin P, Civas A, Ryffel B, Kanellopoulos J, Tschopp J, Andre F, Lidereau R, McLaughlin NM, Haynes NM, Smyth MJ, Kroemer G, Zitvogel L. Activation of the NLRP3 inflammasome in dendritic cells induces IL-1beta-dependent adaptive immunity against tumors. Nat Med 2009, 15:1170-1178. doi:10.1038/nm.2028, 10.1038/nm.2028, 19767732.
18. Michaud M, Martins I, Sukkurwala AQ, Adjemian S, Ma Y, Pellegatti P, Shen S, Kepp O, Scoazec M, Mignot G, Rello-Varona S, Tailler M, Menger L, Vacchelli E, Galluzzi L, Ghiringhelli F, di Virgilio F, Zitvogel L, Kroemer G. Autophagy-dependent anticancer immune responses induced by chemotherapeutic agents in mice. Science 2011, 334:1573-1577. doi:10.1126/science.1208347, 10.1126/science.1208347, 22174255.
19. Demaria S, Volm MD, Shapiro RL, Yee HT, Oratz R, Formenti SC, Muggia F, Symmans WF. Development of tumor-infiltrating lymphocytes in breast cancer after neoadjuvant paclitaxel chemotherapy. Clin Cancer Res 2001, 7:3025-3030. 11595690.
20. Ladoire S, Arnould L, Apetoh L, Coudert B, Martin F, Chauffert B, Fumoleau P, Ghiringhelli F. Pathologic complete response to neoadjuvant chemotherapy of breast carcinoma is associated with the disappearance of tumor-infiltrating foxp3+ regulatory T cells. Clin Cancer Res 2008, 14:2413-2420. doi:10.1158/1078-0432.CCR-07-4491, 10.1158/1078-0432.CCR-07-4491, 18413832.
21. Ladoire S, Mignot G, Dabakuyo S, Arnould L, Apetoh L, Rebe C, Coudert B, Martin F, Bizollon MH, Vanoli A, Coutant C, Fumoleau P, Bonnetain F, Ghiringhelli F. In situ immune response after neoadjuvant chemotherapy for breast cancer predicts survival. J Pathol 2011, 224:389-400. doi:10.1002/path.2866, 10.1002/path.2866, 21437909.
22. Denkert C, Loibl S, Noske A, Roller M, Muller BM, Komor M, Budczies J, Darb-Esfahani S, Kronenwett R, Hanusch C, von Torne C, Weichert W, Engels K, Solbach C, Schrader I, Dietel M, von Minckwitz G. Tumor-associated lymphocytes as an independent predictor of response to neoadjuvant chemotherapy in breast cancer. J Clin Oncol 2010, 28:105-113. doi:10.1200/JCO.2009.23.7370, 10.1200/JCO.2009.23.7370, 19917869.
23. Hornychova H, Melichar B, Tomsova M, Mergancova J, Urminska H, Ryska A. Tumor-infiltrating lymphocytes predict response to neoadjuvant chemotherapy in patients with breast carcinoma. Cancer Invest 2008, 26:1024-1031. doi:10.1080/07357900802098165, 10.1080/07357900802098165, 19093260.
24. Loi S, Sirtaine N, Piette F, Salgado R, Viale G, Van Eenoo F, Rouas G, Francis P, Crown JP, Hitre E, de Azambuja E, Quinaux E, Di Leo A, Michiels S, Piccart MJ, Sotiriou C. Prognostic and predictive value of tumor-infiltrating lymphocytes in a phase III randomized adjuvant breast cancer trial in node-positive breast cancer comparing the addition of docetaxel to doxorubicin with doxorubicin-based chemotherapy: BIG 02-98. J Clin Oncol 2013, 31:860-867. doi:10.1200/JCO.2011.41.0902, 10.1200/JCO.2011.41.0902, 23341518.
25. Ono M, Tsuda H, Shimizu C, Yamamoto S, Shibata T, Yamamoto H, Hirata T, Yonemori K, Ando M, Tamura K, Katsumata N, Kinoshita T, Takiguchi Y, Tanzawa H, Fujiwara Y. Tumor-infiltrating lymphocytes are correlated with response to neoadjuvant chemotherapy in triple-negative breast cancer. Breast Cancer Res Treat 2012, 132:793-805. doi:10.1007/s10549-011-1554-7, 10.1007/s10549-011-1554-7, 21562709.
26. Aaltomaa S, Lipponen P, Eskelinen M, Kosma VM, Marin S, Alhava E, Syrjanen K. Lymphocyte infiltrates as a prognostic variable in female breast cancer. Eur J Cancer 1992, 28A:859-864. 10.1016/0959-8049(92)90134-N, 1524909.
27. Andre F, Dieci MV, Dubsky P, Sotiriou C, Curigliano G, Denkert C, Loi S. Molecular pathways: involvement of immune pathways in the therapeutic response and outcome in breast cancer. Clin Cancer Res 2013, 19:28-33. doi:10.1158/1078-0432.CCR-11-2701, 10.1158/1078-0432.CCR-11-2701, 23258741.
28. Lee AH, Gillett CE, Ryder K, Fentiman IS, Miles DW, Millis RR. Different patterns of inflammation and prognosis in invasive carcinoma of the breast. Histopathology 2006, 48:692-701. doi:10.1111/j.1365-2559.2006.02410.x, 10.1111/j.1365-2559.2006.02410.x, 16681685.
29. Mahmoud SM, Paish EC, Powe DG, Macmillan RD, Grainge MJ, Lee AH, Ellis IO, Green AR. Tumor-infiltrating CD8+ lymphocytes predict clinical outcome in breast cancer. J Clin Oncol 2011, 29:1949-1955. doi:10.1200/JCO.2010.30.5037, 10.1200/JCO.2010.30.5037, 21483002.
30. Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, DeLisi C, Harris L, Barnard N, Martel M, Levine AJ, Ganesan S, Bhanot G. High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Cancer Res 2007, 67:10669-10676. doi:10.1158/0008-5472.CAN-07-0539, 10.1158/0008-5472.CAN-07-0539, 18006808.
31. Broet P, Kuznetsov VA, Bergh J, Liu ET, Miller LD. Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients. Bioinformatics 2006, 22:1477-1485. doi:10.1093/bioinformatics/btl110, 10.1093/bioinformatics/btl110, 16551658.
32. Dave SS, Wright G, Tan B, Rosenwald A, Gascoyne RD, Chan WC, Fisher RI, Braziel RM, Rimsza LM, Grogan TM, Miller TP, LeBlanc M, Greiner TC, Weisenburger DD, Lynch JC, Vose J, Armitage JO, Smeland EB, Kvaloy S, Holte H, Delabie J, Connors JM, Lansdorp PM, Ouyang Q, Lister TA, Davies AJ, Norton AJ, Muller-Hermelink HK, Ott G, Campo E, et al. Prediction of survival in follicular lymphoma based on molecular features of tumor-infiltrating immune cells. N Engl J Med 2004, 351:2159-2169. doi:10.1056/NEJMoa041869, 10.1056/NEJMoa041869, 15548776.
33. Donson AM, Birks DK, Barton VN, Wei Q, Kleinschmidt-Demasters BK, Handler MH, Waziri AE, Wang M, Foreman NK. Immune gene and cell enrichment is associated with a good prognosis in ependymoma. J Immunol 2009, 183:7428-7440. doi:10.4049/jimmunol.0902811, 10.4049/jimmunol.0902811, 19917695.
34. Donson AM, Birks DK, Schittone SA, Kleinschmidt-DeMasters BK, Sun DY, Hemenway MF, Handler MH, Waziri AE, Wang M, Foreman NK. Increased immune gene expression and immune cell infiltration in high-grade astrocytoma distinguish long-term from short-term survivors. J Immunol 2012, 189:1920-1927. doi:10.4049/jimmunol.1103373, 10.4049/jimmunol.1103373, 22802421.
35. Griesinger AM, Birks DK, Donson AM, Amani V, Hoffman LM, Waziri A, Wang M, Handler MH, Foreman NK. Characterization of distinct immunophenotypes across pediatric brain tumor types. J Immunol 2013, 191:4880-4888. doi:10.4049/jimmunol.1301966, 10.4049/jimmunol.1301966, 24078694.
36. Nagalla S, Chou JW, Willingham MC, Ruiz J, Vaughn JP, Dubey P, Lash TL, Hamilton-Dutoit SJ, Bergh J, Sotiriou C, Black MA, Miller LD. Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis. Genome Biol 2013, 14:R34. doi:10.1186/gb-2013-14-4-r34, 10.1186/gb-2013-14-4-r34, 23618380.
37. Rody A, Holtrich U, Pusztai L, Liedtke C, Gaetje R, Ruckhaeberle E, Solbach C, Hanker L, Ahr A, Metzler D, Engels K, Karn T, Kaufmann M. T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers. Breast Cancer Res 2009, 11:R15. doi:10.1186/bcr2234, 10.1186/bcr2234, 19272155.
38. Teschendorff AE, Miremadi A, Pinder SE, Ellis IO, Caldas C. An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer. Genome Biol 2007, 8:R157. doi:gb-2007-8-8-r157, 10.1186/gb-2007-8-8-r157, 17683518.
39. Ascierto ML, Kmieciak M, Idowu MO, Manjili R, Zhao Y, Grimes M, Dumur C, Wang E, Ramakrishnan V, Wang XY, Bear HD, Marincola FM, Manjili MH. A signature of immune function genes associated with recurrence-free survival in breast cancer patients. Breast Cancer Res Treat 2012, 131:871-880. doi:10.1007/s10549-011-1470-x, 10.1007/s10549-011-1470-x, 21479927.
40. Bianchini G, Qi Y, Alvarez RH, Iwamoto T, Coutant C, Ibrahim NK, Valero V, Cristofanilli M, Green MC, Radvanyi L, Hatzis C, Hortobagyi GN, Andre F, Gianni L, Symmans WF, Pusztai L. Molecular anatomy of breast cancer stroma and its prognostic value in estrogen receptor-positive and -negative cancers. J Clin Oncol 2010, 28:4316-4323. doi:10.1200/JCO.2009.27.2419, 10.1200/JCO.2009.27.2419, 20805453.
41. Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G, Delorenzi M, Piccart M, Sotiriou C. Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res 2008, 14:5158-5165. doi:10.1158/1078-0432.CCR-07-4756, 10.1158/1078-0432.CCR-07-4756, 18698033.
42. Iwamoto T, Bianchini G, Booser D, Qi Y, Coutant C, Shiang CY, Santarpia L, Matsuoka J, Hortobagyi GN, Symmans WF, Holmes FA, O'Shaughnessy J, Hellerstedt B, Pippen J, Andre F, Simon R, Pusztai L. Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. J Natl Cancer Inst 2011, 103:264-272. doi:10.1093/jnci/djq524, 10.1093/jnci/djq524, 21191116.
43. Wang E, Miller LD, Ohnmacht GA, Mocellin S, Perez-Diez A, Petersen D, Zhao Y, Simon R, Powell JI, Asaki E, Alexander HR, Duray PH, Herlyn M, Restifo NP, Liu ET, Rosenberg SA, Marincola FM. Prospective molecular profiling of melanoma metastases suggests classifiers of immune responsiveness. Cancer Res 2002, 62:3581-3586. 12097256.
44. Desmedt C, Di Leo A, de Azambuja E, Larsimont D, Haibe-Kains B, Selleslags J, Delaloge S, Duhem C, Kains JP, Carly B, Maerevoet M, Vindevoghel A, Rouas G, Lallemand F, Durbecq V, Cardoso F, Salgado R, Rovere R, Bontempi G, Michiels S, Buyse M, Nogaret JM, Qi Y, Symmans F, Pusztai L, D'Hondt V, Piccart-Gebhart M, Sotiriou C. Multifactorial approach to predicting resistance to anthracyclines. J Clin Oncol 2011, 29:1578-1586. doi:10.1200/JCO.2010.31.2231, 10.1200/JCO.2010.31.2231, 21422418.
45. Ignatiadis M, Singhal SK, Desmedt C, Haibe-Kains B, Criscitiello C, Andre F, Loi S, Piccart M, Michiels S, Sotiriou C. Gene modules and response to neoadjuvant chemotherapy in breast cancer subtypes: a pooled analysis. J Clin Oncol 2012, 30:1996-2004. doi:10.1200/JCO.2011.39.5624, 10.1200/JCO.2011.39.5624, 22508827.
46. Karn T, Pusztai L, Holtrich U, Iwamoto T, Shiang CY, Schmidt M, Muller V, Solbach C, Gaetje R, Hanker L, Ahr A, Liedtke C, Ruckhaberle E, Kaufmann M, Rody A. Homogeneous datasets of triple negative breast cancers enable the identification of novel prognostic and predictive signatures. PLoS One 2011, 6:e28403. doi:10.1371/journal.pone.0028403, 10.1371/journal.pone.0028403, 22220191.
47. Mello-Grand M, Singh V, Ghimenti C, Scatolini M, Regolo L, Grosso E, Zambelli A, Da Prada GA, Villani L, Fregoni V, Baiardi P, Marsoni S, Miller WR, Costa A, Chiorino G. Gene expression profiling and prediction of response to hormonal neoadjuvant treatment with anastrozole in surgically resectable breast cancer. Breast Cancer Res Treat 2010, 121:399-411. doi:10.1007/s10549-010-0887-y, 10.1007/s10549-010-0887-y, 20428938.
48. Hatzis C, Pusztai L, Valero V, Booser DJ, Esserman L, Lluch A, Vidaurre T, Holmes F, Souchon E, Wang H, Martin M, Cotrina J, Gomez H, Hubbard R, Chacon JI, Ferrer-Lozano J, Dyer R, Buxton M, Gong Y, Wu Y, Ibrahim N, Andreopoulou E, Ueno NT, Hunt K, Yang W, Nazario A, DeMichele A, O'Shaughnessy J, Hortobagyi GN, Symmans WF. A genomic predictor of response and survival following taxane-anthracycline chemotherapy for invasive breast cancer. JAMA 2011, 305:1873-1881. doi:10.1001/jama.2011.593, 10.1001/jama.2011.593, 21558518.
49. Popovici V, Chen W, Gallas BG, Hatzis C, Shi W, Samuelson FW, Nikolsky Y, Tsyganova M, Ishkin A, Nikolskaya T, Hess KR, Valero V, Booser D, Delorenzi M, Hortobagyi GN, Shi L, Symmans WF, Pusztai L. Effect of training-sample size and classification difficulty on the accuracy of genomic predictors. Breast Cancer Res 2010, 12:R5. doi:10.1186/bcr2468, 10.1186/bcr2468, 20064235.
50. Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010, 28:827-838. doi:10.1038/nbt.1665, 10.1038/nbt.1665, 20676074.
51. Tabchy A, Valero V, Vidaurre T, Lluch A, Gomez H, Martin M, Qi Y, Barajas-Figueroa LJ, Souchon E, Coutant C, Doimi FD, Ibrahim NK, Gong Y, Hortobagyi GN, Hess KR, Symmans WF, Pusztai L. Evaluation of a 30-gene paclitaxel, fluorouracil, doxorubicin, and cyclophosphamide chemotherapy response predictor in a multicenter randomized trial in breast cancer. Clin Cancer Res 2010, 16:5351-5361. doi:10.1158/1078-0432.CCR-10-1265, 10.1158/1078-0432.CCR-10-1265, 20829329.
52. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31:e15. 10.1093/nar/gng015, 12582260.
53. Bioconductor project []., http://www.bioconductor.org/packages/2.14/bioc/html/affy.html
54. Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8:118-127. doi:10.1093/biostatistics/kxj037, 10.1093/biostatistics/kxj037, 16632515.
55. Lee YF, Miller LD, Chan XB, Black MA, Pang B, Ong CW, Salto-Tellez M, Liu ET, Desai KV. JMJD6 is a driver of cellular proliferation and motility and a marker of poor prognosis in breast cancer. Breast Cancer Res 2012, 14:R85. doi:10.1186/bcr3200, 10.1186/bcr3200, 22621393.
56. Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PS. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 2009, 27:1160-1167. doi:10.1200/JCO.2008.18.1370, 10.1200/JCO.2008.18.1370, 19204204.
57. Prat A, Parker JS, Karginova O, Fan C, Livasy C, Herschkowitz JI, He X, Perou CM. Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res 2010, 12:R68. doi:10.1186/bcr2635, 10.1186/bcr2635, 20813035.
58. Symmans WF, Ayers M, Clark EA, Stec J, Hess KR, Sneige N, Buchholz TA, Krishnamurthy S, Ibrahim NK, Buzdar AU, Theriault RL, Rosales MF, Thomas ES, Gwyn KM, Green MC, Syed AR, Hortobagyi GN, Pusztai L. Total RNA yield and microarray gene expression profiles from fine-needle aspiration biopsy and core-needle biopsy samples of breast carcinoma. Cancer 2003, 97:2960-2971. doi:10.1002/cncr.11435, 10.1002/cncr.11435, 12784330.
59. Chan OT, Yang LX. The immunological effects of taxanes. Cancer Immunol Immunother 2000, 49:181-185. 10.1007/s002620000122, 10941900.
60. Haynes NM, van der Most RG, Lake RA, Smyth MJ. Immunogenic anti-cancer chemotherapy as an emerging concept. Curr Opin Immunol 2008, 20:545-557. doi: S0952-7915(08)00082-4, 10.1016/j.coi.2008.05.008, 18573339.
61. Mattarollo SR, Loi S, Duret H, Ma Y, Zitvogel L, Smyth MJ. Pivotal role of innate and adaptive immunity in anthracycline chemotherapy of established tumors. Cancer Res 2011, 71:4809-4820. doi:0008-5472.CAN-11-0753, 10.1158/0008-5472.CAN-11-0753, 21646474.
62. Tsavaris N, Kosmas C, Vadiaka M, Kanelopoulos P, Boulamatsis D. Immune changes in patients with advanced breast cancer undergoing chemotherapy with taxanes. Br J Cancer 2002, 87:21-27. doi:10.1038/sj.bjc.6600347, 10.1038/sj.bjc.6600347, 12085250.
63. Maj T, S Awek A, Kaleta-Kuratewicz K, Che Mo Ska-Soyta A. 17beta-Estradiol and interferon tau interact in the regulation of the immune response in a model of experimental autoimmune orchitis. J Interferon Cytokine Res 2011, 31:825-837. doi:10.1089/jir.2010.0147, 10.1089/jir.2010.0147, 21787220.
64. West NR, Milne K, Truong PT, Macpherson N, Nelson BH, Watson PH. Tumor-infiltrating lymphocytes predict response to anthracycline-based chemotherapy in estrogen receptor-negative breast cancer. Breast Cancer Res 2011, 13:R126. doi:10.1186/bcr3072, 10.1186/bcr3072, 22151962.
65. Emens LA, Machiels JP, Reilly RT, Jaffee EM. Chemotherapy: friend or foe to cancer vaccines?. Curr Opin Mol Ther 2001, 3:77-84. 11249735.
66. Zitvogel L, Kepp O, Kroemer G. Decoding cell death signals in inflammation and immunity. Cell 2010, 140:798-804. doi:10.1016/j.cell.2010.02.015, 10.1016/j.cell.2010.02.015, 20303871.
67. Wan S, Pestka S, Jubin RG, Lyu YL, Tsai YC, Liu LF. Chemotherapeutics and radiation stimulate MHC class I expression through elevated interferon-beta signaling in breast cancer cells. PLoS One 2012, 7:e32542. doi:10.1371/journal.pone.0032542, 10.1371/journal.pone.0032542, 22396773.
68. Armeanu S, Bitzer M, Lauer UM, Venturelli S, Pathil A, Krusch M, Kaiser S, Jobst J, Smirnow I, Wagner A, Steinle A, Salih HR. Natural killer cell-mediated lysis of hepatoma cells via specific induction of NKG2D ligands by the histone deacetylase inhibitor sodium valproate. Cancer Res 2005, 65:6321-6329. doi:10.1158/0008-5472.CAN-04-4252, 10.1158/0008-5472.CAN-04-4252, 16024634.
69. Gasser S, Orsulic S, Brown EJ, Raulet DH. The DNA damage pathway regulates innate immune system ligands of the NKG2D receptor. Nature 2005, 436:1186-1190. doi:10.1038/nature03884, 10.1038/nature03884, 15995699.
70. Chakraborty M, Abrams SI, Coleman CN, Camphausen K, Schlom J, Hodge JW. External beam radiation of tumors alters phenotype of tumor cells to render them susceptible to vaccine-mediated T-cell killing. Cancer Res 2004, 64:4328-4337. doi:10.1158/0008-5472.CAN-04-0073, 10.1158/0008-5472.CAN-04-0073, 15205348.
71. Ghiringhelli F, Larmonier N, Schmitt E, Parcellier A, Cathelin D, Garrido C, Chauffert B, Solary E, Bonnotte B, Martin F. CD4 + CD25+ regulatory T cells suppress tumor immunity but are sensitive to cyclophosphamide which allows immunotherapy of established tumors to be curative. Eur J Immunol 2004, 34:336-344. doi:10.1002/eji.200324181, 10.1002/eji.200324181, 14768038.
72. Lutsiak ME, Semnani RT, De Pascalis R, Kashmiri SV, Schlom J, Sabzevari H. Inhibition of CD4(+)25+ T regulatory cell function implicated in enhanced immune response by low-dose cyclophosphamide. Blood 2005, 105:2862-2868. doi:10.1182/blood-2004-06-2410, 10.1182/blood-2004-06-2410, 15591121.
73. MacDonald KP, Rowe V, Bofinger HM, Thomas R, Sasmono T, Hume DA, Hill GR. The colony-stimulating factor 1 receptor is expressed on dendritic cells during differentiation and regulates their expansion. J Immunol 2005, 175:1399-1405. 10.4049/jimmunol.175.3.1399, 16034075.
74. Nace G, Evankovich J, Eid R, Tsung A. Dendritic cells and damage-associated molecular patterns: endogenous danger signals linking innate and adaptive immunity. J Innate Immun 2012, 4:6-15. doi:10.1159/000334245, 10.1159/000334245, 22086146.
75. Obeid M, Tesniere A, Ghiringhelli F, Fimia GM, Apetoh L, Perfettini JL, Castedo M, Mignot G, Panaretakis T, Casares N, Metivier D, Larochette N, van Endert P, Ciccosanti F, Piacentini M, Zitvogel L, Kroemer G. Calreticulin exposure dictates the immunogenicity of cancer cell death. Nat Med 2007, 13:54-61. doi:10.1038/nm1523, 10.1038/nm1523, 17187072.
76. Tesniere A, Apetoh L, Ghiringhelli F, Joza N, Panaretakis T, Kepp O, Schlemmer F, Zitvogel L, Kroemer G. Immunogenic cancer cell death: a key-lock paradigm. Curr Opin Immunol 2008, 20:504-511. doi:10.1016/j.coi.2008.05.007, 10.1016/j.coi.2008.05.007, 18573340.
77. Shurin GV, Tourkova IL, Kaneno R, Shurin MR. Chemotherapeutic agents in noncytotoxic concentrations increase antigen presentation by dendritic cells via an IL-12-dependent mechanism. J Immunol 2009, 183:137-144. doi:10.4049/jimmunol.0900734, 10.4049/jimmunol.0900734, 19535620.
78. Butterfield LH. Dendritic cells in cancer immunotherapy clinical trials: are we making progress?. Frontiers in immunology 2013, 4:454. doi:10.3389/fimmu.2013.00454, 10.3389/fimmu.2013.00454, 24379816.