Perou CM, Sùrlie T, Eisen MB, Van De Rijn M, Jeffrey SS, Rees CA, et al. Molecular portraits of human breast tumours. Nature. 2000;533:747–52. https://www.stanford.edu/molecularportraits/
Article
Google Scholar
Prat A, Ellis MJ, Perou CM. Practical implications of gene-expression-based assays for breast oncologists. Nat Rev Clin Oncol. 2012;9:48–57.
Article
CAS
Google Scholar
Bernard PS, Parker JS, Mullins M, Cheung MCU, Leung S, Voduc D, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol. 2009;27:1160–7.
Article
Google Scholar
Abe O, Abe R, Enomoto K, Kikuchi K, Koyama H, Masuda H, et al. Relevance of breast cancer hormone receptors and other factors to the efficacy of adjuvant tamoxifen: patient-level meta-analysis of randomised trials. Lancet. 2011;378:771–84. https://doi.org/10.1016/S0140-6736(11)60993-8.
Article
CAS
Google Scholar
Viale G, Regan MM, Maiorano E, Mastropasqua MG, Dell’Orto P, Rasmussen BB, et al. Prognostic and predictive value of centrally reviewed expression of estrogen and progesterone receptors in a randomized trial comparing letrozole and tamoxifen adjuvant therapy for postmenopausal early breast cancer: BIG 1–98. J Clin Oncol. 2007;25:3846–52.
Article
Google Scholar
Paik S, Tang G, Shak S, Kim C, Baker J, Kim W, et al. Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. J Clin Oncol. 2006;24:3726–34.
Article
CAS
Google Scholar
Prat A, Cheang MCU, Martín M, Parker JS, Carrasco E, Caballero R, et al. Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined luminal a breast cancer. J Clin Oncol. 2013;31:203–9.
Article
CAS
Google Scholar
Bae SY, Kim S, Lee JH, Hyun-chul L, Se Kyung L, Kil WH, et al. Poor prognosis of single hormone receptor-positive breast cancer: similar outcome as triple-negative breast cancer. BMC Cancer. 2015;15:1–9.
Article
CAS
Google Scholar
Purdie CA, Quinlan P, Jordan LB, Ashfield A, Ogston S, Dewar JA, et al. Progesterone receptor expression is an independent prognostic variable in early breast cancer: a population-based study. Br J Cancer. 2014;110:565–72.
Article
CAS
Google Scholar
Cui X, Schiff R, Arpino G, Osborne CK, Lee AV. Biology of progesterone receptor loss in breast cancer and its implications for endocrine therapy. J Clin Oncol. 2005;23:7721–35.
Article
CAS
Google Scholar
Dowsett M, Allred C, Knox J, Quinn E, Salter J, Wale C, et al. Relationship between quantitative estrogen and progesterone receptor expression and human epidermal growth factor receptor 2 (HER-2) status with recurrence in the arimidex, tamoxifen, alone or in combination trial. J Clin Oncol. 2008;26:1059–65.
Article
CAS
Google Scholar
Shou J, Massarweh S, Osborne CK, Wakeling AE, Ali S, Weiss H, et al. Mechanisms of tamoxifen resistance: increased estrogen receptor-HER2/neu cross-talk in ER/HER2-positive breast cancer. J Natl Cancer Inst. 2004;96:926–35.
Article
CAS
Google Scholar
Nicholson RI, Gee JMW. Oestrogen and growth factor cross-talk and endocrine insensitivity and acquired resistance in breast cancer. Br J Cancer. 2000;82:501–13.
Article
CAS
Google Scholar
Loibl S, Gianni L. HER2-positive breast cancer. Lancet. 2017;389:2415–29. https://doi.org/10.1016/S0140-6736(16)32417-5.
Article
CAS
PubMed
Google Scholar
Brahmer JR, Tykodi SS, Chow LQM, Hwu WJ, Topalian SL, Hwu P, et al. Safety and activity of anti-PD-L1 antibody in patients with advanced cancer. N Engl J Med. 2012;366:2455–65.
Article
CAS
Google Scholar
Schmid P, Rugo HS, Adams S, Schneeweiss A, Barrios CH, Iwata H, et al. Atezolizumab plus nab-paclitaxel as first-line treatment for unresectable, locally advanced or metastatic triple-negative breast cancer (IMpassion130): updated efficacy results from a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Oncol. 2020;21:44–59.
Article
CAS
Google Scholar
Rugo HS, Delord JP, Im SA, Ott PA, Piha-Paul SA, Bedard PL, et al. Safety and antitumor activity of pembrolizumab in patients with estrogen receptor-positive/human epidermal growth factor receptor 2-negative advanced breast cancer. Clin Cancer Res. 2018;24:2804–11.
Article
CAS
Google Scholar
Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, et al. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 2017;18:248–62. https://doi.org/10.1016/j.celrep.2016.12.019.
Article
CAS
PubMed
Google Scholar
Becht E, Giraldo NA, Lacroix L, Buttard B, Elarouci N, Petitprez F, et al. Erratum to estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 2016;17:1–20. https://doi.org/10.1186/s13059-016-1070-5.
Article
CAS
Google Scholar
Bhattacharya S, Dunn P, Thomas CG, Smith B, Schaefer H, Chen J, et al. ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. Sci Data. 2018;5:1–9.
Article
CAS
Google Scholar
Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10:1523. https://doi.org/10.1038/s41467-019-09234-6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miao YR, Zhang Q, Lei Q, Luo M, Xie GY, Wang H, et al. ImmuCellAI: a unique method for comprehensive T-cell subsets abundance prediction and its application in cancer immunotherapy. Adv Sci. 2020;7:1902880.
Article
CAS
Google Scholar
Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612.
Article
Google Scholar
Beck AH, Espinosa I, Edris B, Li R, Montgomery K, Zhu S, et al. The macrophage colony-stimulating factor 1 response signature in breast carcinoma. Clin Cancer Res. 2009;15:778–87.
Article
CAS
Google Scholar
Calabrò A, Beissbarth T, Kuner R, Stojanov M, Benner A, Asslaber M, et al. Effects of infiltrating lymphocytes and estrogen receptor on gene expression and prognosis in breast cancer. Breast Cancer Res Treat. 2009;116:69–77.
Article
Google Scholar
Wolf DM, Lenburg ME, Yau C, Boudreau A, Van’t Veer LJ. Gene co-expression modules as clinically relevant hallmarks of breast cancer diversity. PLoS ONE. 2014;9:e88309.
Article
Google Scholar
Teschendorff AE, Gomez S, Arenas A, El-Ashry D, Schmidt M, Gehrmann M et al. Improved prognostic classification of breast cancer defined by antagonistic activation patterns of immune response pathway modules. BMC Cancer. 2010;10:604. http://www.biomedcentral.com/1471-2407/10/604.
Ayers M, Lunceford J, Nebozhyn M, Murphy E, Loboda A, Kaufman DR, et al. IFN-γ-related mRNA profile predicts clinical response to PD-1 blockade. J Clin Invest. 2017;127:2930–40.
Article
Google Scholar
Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. 2015;160:48–61. https://doi.org/10.1016/j.cell.2014.12.033.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu J, Zhao W, Zhou B, Su Z, Gu X, Zhou Z, et al. TSNAdb: a database for tumor-specific neoantigens from immunogenomics data analysis. Genomics, Proteomics Bioinforma. 2018;16:276–82. https://doi.org/10.1016/j.gpb.2018.06.003.
Article
Google Scholar
Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, et al. Oncogenic signaling pathways in the cancer genome atlas. Cell. 2018;173:321-337.e10.
Article
CAS
Google Scholar
Dangaj D, Bruand M, Grimm AJ, Ronet C, Barras D, Duttagupta PA, et al. Cooperation between constitutive and inducible chemokines enables T cell engraftment and immune attack in solid tumors. Cancer Cell. 2019;35:885-900.e10.
Article
CAS
Google Scholar
Barrow AD, Edeling MA, Trifonov V, Luo J, Goyal P, Bohl B, et al. Natural killer cells control tumor growth by sensing a growth factor. Cell. 2018;172:534-548.e19. https://doi.org/10.1016/j.cell.2017.11.037.
Article
CAS
PubMed
Google Scholar
Batlle E, Massagué J. Transforming growth factor-β signaling in immunity and cancer. Immunity. 2019;50:924–40.
Article
CAS
Google Scholar
An O, Dall’Olio GM, Mourikis TP, Ciccarelli FD. NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. Nucleic Acids Res. 2016;44:992–9.
Article
Google Scholar
Emens LA. Breast cancer immunotherapy: facts and hopes. Clin Cancer Res. 2018;24:511–20.
Article
CAS
Google Scholar
Bramsen JB, Rasmussen MH, Ongen H, Mattesen TB, Ørntoft MBW, Árnadóttir SS, et al. Molecular-subtype-specific biomarkers improve prediction of prognosis in colorectal cancer. Cell Rep. 2017;19:1268–80.
Article
CAS
Google Scholar
Ott PA, Hodi FS, Kaufman HL, Wigginton JM, Wolchok JD. Combination immunotherapy: a road map. J Immunother Cancer. 2017;5:1–15.
Article
Google Scholar
Mazzaschi G, Madeddu D, Falco A, Bocchialini G, Goldoni M, Sogni F, et al. Low PD-1 expression in cytotoxic CD8 þ tumor-Infiltrating lymphocytes confers an immune-privileged tissue microenvironment in NSCLC with a prognostic and predictive value. Clin Cancer Res. 2018;24:407–19.
Article
CAS
Google Scholar
Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, et al. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348:124–8.
Article
CAS
Google Scholar
Le DT, Durham JN, Smith KN, Wang H, Bartlett BR, Aulakh LK, et al. Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. Science. 2017;357:409–13.
Article
CAS
Google Scholar
Goodwin RG, Din WS, Davis-Smith T, Anderson DM, Gimpel SD, Sato TA, et al. Molecular cloning of a ligand for the inducible T cell gene 4-1BB: a member of an emerging family of cytokines with homology to tumor necrosis factor. Eur J Immunol. 1993;23:2631–41.
Article
CAS
Google Scholar
Bedognetti D, Hendrickx W, Ceccarelli M, Miller LD, Seliger B. Disentangling the relationship between tumor genetic programs and immune responsiveness. Curr Opin Immunol. 2016;39:150–8. https://doi.org/10.1016/j.coi.2016.02.001.
Article
CAS
PubMed
Google Scholar
Biton J, Mansuet-Lupo A, Pécuchet N, Alifano M, Ouakrim H, Arrondeau J, et al. TP53, STK11, and EGFR mutations predict tumor immune profile and the response to anti-PD-1 in lung adenocarcinoma. Clin Cancer Res. 2018;24:5710–23.
Article
CAS
Google Scholar
Dong ZY, Zhong WZ, Zhang XC, Su J, Xie Z, Liu SY, et al. Potential predictive value of TP53 and KRAS mutation status for response to PD-1 blockade immunotherapy in lung adenocarcinoma. Clin Cancer Res. 2017;23:3012–24.
Article
CAS
Google Scholar
Hendrickx W, Simeone I, Anjum S, Mokrab Y, Bertucci F, Finetti P, et al. Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis. Oncoimmunology. 2017;6:1–19. https://doi.org/10.1080/2162402X.2016.1253654.
Article
CAS
Google Scholar
Quigley D, Silwal-Pandit L, Dannenfelser R, Langerød A, Vollan HKM, Vaske C, et al. Lymphocyte invasion in IC10/basal-like breast tumors is associated with wild-type TP53. Mol Cancer Res. 2015;13:493–501.
Article
CAS
Google Scholar
Roelands J, Hendrickx W, Zoppoli G, Mall R, Saad M, Halliwill K, et al. Oncogenic states dictate the prognostic and predictive connotations of intratumoral immune response. J Immunother Cancer. 2020;8:e000617.
Article
Google Scholar
Wellenstein MD, de Visser KE. Cancer-cell-intrinsic mechanisms shaping the tumor immune landscape. Immunity. 2018;48:399–416. https://doi.org/10.1016/j.immuni.2018.03.004.
Article
CAS
PubMed
Google Scholar
Casey SC, Tong L, Li Y, Do R, Walz S, Fitzgerald KN, et al. MYC regulates the antitumor immune response through CD47 and PD-L1. Science. 2016;352(6282):227–31.
Article
CAS
Google Scholar