Albini A, Sporn MB. The tumour microenvironment as a target for chemoprevention. Nat Rev Cancer. 2007;7(2):139–47. https://doi.org/10.1038/nrc2067.
Article
CAS
PubMed
Google Scholar
Vaupel P, Kallinowski F, Okunieff P. Blood flow, oxygen and nutrient supply, and metabolic microenvironment of human tumors: a review. Cancer Res. 1989;49(23):6449–65.
CAS
PubMed
Google Scholar
Fridman WH, Zitvogel L, Sautes-Fridman C, Kroemer G. The immune contexture in cancer prognosis and treatment. Nat Rev Clin Oncol. 2017;14(12):717–34. https://doi.org/10.1038/nrclinonc.2017.101.
Article
CAS
PubMed
Google Scholar
Taube JM, Galon J, Sholl LM, Rodig SJ, Cottrell TR, Giraldo NA, et al. Implications of the tumor immune microenvironment for staging and therapeutics. Mod Pathol. 2018;31(2):214–34. https://doi.org/10.1038/modpathol.2017.156.
Article
CAS
PubMed
Google Scholar
Littman DR. Releasing the brakes on cancer immunotherapy. Cell. 2015;162(6):1186–90. https://doi.org/10.1016/j.cell.2015.08.038.
Article
CAS
PubMed
Google Scholar
Spitzer MH, Nolan GP. Mass cytometry: single cells, many features. Cell. 2016;165(4):780–91. https://doi.org/10.1016/j.cell.2016.04.019.
Article
CAS
PubMed
PubMed Central
Google Scholar
Newell EW, Cheng Y. Mass cytometry: blessed with the curse of dimensionality. Nat Immunol. 2016;17(8):890–5. https://doi.org/10.1038/ni.3485.
Article
CAS
PubMed
Google Scholar
Wagner A, Regev A, Yosef N. Revealing the vectors of cellular identity with single-cell genomics. Nat Biotechnol. 2016;34(11):1145–60. https://doi.org/10.1038/nbt.3711.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kargl J, Busch SE, Yang GH, Kim KH, Hanke ML, Metz HE, et al. Neutrophils dominate the immune cell composition in non-small cell lung cancer. Nat Commun. 2017;8:14381. https://doi.org/10.1038/ncomms14381.
Article
CAS
PubMed
PubMed Central
Google Scholar
Travis WD, Brambilla E, Noguchi M, Nicholson AG, Geisinger K, Yatabe Y, et al. International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society: international multidisciplinary classification of lung adenocarcinoma: executive summary. Proc Am Thorac Soc. 2011;8(5):381–5. https://doi.org/10.1513/pats.201107-042ST.
Article
PubMed
Google Scholar
Bremnes RM, Busund LT, Kilvaer TL, Andersen S, Richardsen E, Paulsen EE, et al. The role of tumor-infiltrating lymphocytes in development, progression, and prognosis of non-small cell lung cancer. J Thorac Oncol. 2016;11(6):789–800. https://doi.org/10.1016/j.jtho.2016.01.015.
Article
PubMed
Google Scholar
Bindea G, Mlecnik B, Tosolini M, Kirilovsky A, Waldner M, Obenauf AC, et al. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity. 2013;39(4):782–95. https://doi.org/10.1016/j.immuni.2013.10.003.
Article
CAS
PubMed
Google Scholar
Iglesia MD, Parker JS, Hoadley KA, Serody JS, Perou CM, Vincent BG. Genomic analysis of immune cell infiltrates across 11 tumor types. J Natl Cancer Inst. 2016. https://doi.org/10.1093/jnci/djw144.
Article
PubMed
PubMed Central
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(1–2):48–61. https://doi.org/10.1016/j.cell.2014.12.033.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bremnes RM, Al-Shibli K, Donnem T, Sirera R, Al-Saad S, Andersen S, et al. The role of tumor-infiltrating immune cells and chronic inflammation at the tumor site on cancer development, progression, and prognosis: emphasis on non-small cell lung cancer. J Thorac Oncol. 2011;6(4):824–33. https://doi.org/10.1097/JTO.0b013e3182037b76.
Article
PubMed
Google Scholar
Ishibashi Y, Tanaka S, Tajima K, Yoshida T, Kuwano H. Expression of Foxp3 in non-small cell lung cancer patients is significantly higher in tumor tissues than in normal tissues, especially in tumors smaller than 30 mm. Oncol Rep. 2006;15(5):1315–9.
CAS
PubMed
Google Scholar
Kataki A, Scheid P, Piet M, Marie B, Martinet N, Martinet Y, et al. Tumor infiltrating lymphocytes and macrophages have a potential dual role in lung cancer by supporting both host-defense and tumor progression. J Lab Clin Med. 2002;140(5):320–8. https://doi.org/10.1067/mlc.2002.128317.
Article
PubMed
Google Scholar
Anichini A, Tassi E, Grazia G, Mortarini R. The non-small cell lung cancer immune landscape: emerging complexity, prognostic relevance and prospective significance in the context of immunotherapy. Cancer Immunol Immunother. 2018;67(6):1011–22. https://doi.org/10.1007/s00262-018-2147-7.
Article
CAS
PubMed
Google Scholar
Lavin Y, Kobayashi S, Leader A, Amir ED, Elefant N, Bigenwald C, et al. Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses. Cell. 2017;169(4):750.e17–765.e17. https://doi.org/10.1016/j.cell.2017.04.014.
Article
CAS
Google Scholar
Engblom C, Pfirschke C, Pittet MJ. The role of myeloid cells in cancer therapies. Nat Rev Cancer. 2016;16(7):447–62. https://doi.org/10.1038/nrc.2016.54.
Article
CAS
PubMed
Google Scholar
Gabrilovich DI, Ostrand-Rosenberg S, Bronte V. Coordinated regulation of myeloid cells by tumours. Nat Rev Immunol. 2012;12(4):253–68. https://doi.org/10.1038/nri3175.
Article
CAS
PubMed
PubMed Central
Google Scholar
Merad M, Sathe P, Helft J, Miller J, Mortha A. The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting. Annu Rev Immunol. 2013;31:563–604. https://doi.org/10.1146/annurev-immunol-020711-074950.
Article
CAS
PubMed
Google Scholar
Broz ML, Binnewies M, Boldajipour B, Nelson AE, Pollack JL, Erle DJ, et al. Dissecting the tumor myeloid compartment reveals rare activating antigen-presenting cells critical for T cell immunity. Cancer Cell. 2014;26(6):938. https://doi.org/10.1016/j.ccell.2014.11.010.
Article
CAS
PubMed
Google Scholar
Hildner K, Edelson BT, Purtha WE, Diamond M, Matsushita H, Kohyama M, et al. Batf3 deficiency reveals a critical role for CD8alpha+ dendritic cells in cytotoxic T cell immunity. Science. 2008;322(5904):1097–100. https://doi.org/10.1126/science.1164206.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salmon H, Idoyaga J, Rahman A, Leboeuf M, Remark R, Jordan S, et al. Expansion and activation of CD103(+) dendritic cell progenitors at the tumor site enhances tumor responses to therapeutic PD-L1 and BRAF inhibition. Immunity. 2016;44(4):924–38. https://doi.org/10.1016/j.immuni.2016.03.012.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanchez-Paulete AR, Cueto FJ, Martinez-Lopez M, Labiano S, Morales-Kastresana A, Rodriguez-Ruiz ME, et al. Cancer immunotherapy with immunomodulatory anti-CD137 and anti-PD-1 monoclonal antibodies requires BATF3-dependent dendritic cells. Cancer Discov. 2016;6(1):71–9. https://doi.org/10.1158/2159-8290.CD-15-0510.
Article
CAS
PubMed
Google Scholar
Becht E, Goc J, Germain C, Giraldo NA, Dieu-Nosjean MC, Sautes-Fridman C, et al. Shaping of an effective immune microenvironment to and by cancer cells. Cancer Immunol Immunother. 2014;63(10):991–7. https://doi.org/10.1007/s00262-014-1590-3.
Article
CAS
PubMed
Google Scholar
Wendel M, Galani IE, Suri-Payer E, Cerwenka A. Natural killer cell accumulation in tumors is dependent on IFN-gamma and CXCR28 ligands. Cancer Res. 2008;68(20):8437–45. https://doi.org/10.1158/0008-5472.CAN-08-1440.
Article
CAS
PubMed
Google Scholar
Geukes Foppen MH, Donia M, Svane IM, Haanen JB. Tumor-infiltrating lymphocytes for the treatment of metastatic cancer. Mol Oncol. 2015;9(10):1918–35. https://doi.org/10.1016/j.molonc.2015.10.018.
Article
CAS
PubMed
PubMed Central
Google Scholar
Man YG, Stojadinovic A, Mason J, Avital I, Bilchik A, Bruecher B, et al. Tumor-infiltrating immune cells promoting tumor invasion and metastasis: existing theories. J Cancer. 2013;4(1):84–95. https://doi.org/10.7150/jca.5482.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hendry S, Salgado R, Gevaert T, Russell PA, John T, Thapa B, et al. Assessing tumor-infiltrating lymphocytes in solid tumors: a practical review for pathologists and proposal for a standardized method from the international immuno-oncology biomarkers working group: Part 2: TILs in melanoma, gastrointestinal tract carcinomas, non-small cell lung carcinoma and mesothelioma, endometrial and ovarian carcinomas, squamous cell carcinoma of the head and neck, genitourinary carcinomas, and primary brain tumors. Adv Anat Pathol. 2017;24(6):311–35. https://doi.org/10.1097/PAP.0000000000000161.
Article
PubMed
PubMed Central
Google Scholar
Schreiber RD, Old LJ, Smyth MJ. Cancer immunoediting: integrating immunity’s roles in cancer suppression and promotion. Science. 2011;331(6024):1565–70. https://doi.org/10.1126/science.1203486.
Article
CAS
PubMed
Google Scholar
Fridman WH, Pages F, Sautes-Fridman C, Galon J. The immune contexture in human tumours: impact on clinical outcome. Nat Rev Cancer. 2012;12(4):298–306. https://doi.org/10.1038/nrc3245.
Article
CAS
PubMed
Google Scholar
Angell H, Galon J. From the immune contexture to the Immunoscore: the role of prognostic and predictive immune markers in cancer. Curr Opin Immunol. 2013;25(2):261–7. https://doi.org/10.1016/j.coi.2013.03.004.
Article
CAS
PubMed
Google Scholar
Galon J, Mlecnik B, Bindea G, Angell HK, Berger A, Lagorce C, et al. Towards the introduction of the ‘Immunoscore’ in the classification of malignant tumours. J Pathol. 2014;232(2):199–209. https://doi.org/10.1002/path.4287.
Article
CAS
PubMed
Google Scholar
Yan X, Jiao SC, Zhang GQ, Guan Y, Wang JL. Tumor-associated immune factors are associated with recurrence and metastasis in non-small cell lung cancer. Cancer Gene Ther. 2017;24(2):57–63. https://doi.org/10.1038/cgt.2016.40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Al-Shibli KI, Donnem T, Al-Saad S, Persson M, Bremnes RM, Busund LT. Prognostic effect of epithelial and stromal lymphocyte infiltration in non-small cell lung cancer. Clin Cancer Res. 2008;14(16):5220–7. https://doi.org/10.1158/1078-0432.CCR-08-0133.
Article
CAS
PubMed
Google Scholar
Lin Y, Liu L, Zhang T, Liu J. Functional investigation of Fas ligand expressions in human non-small cell lung cancer cells and its clinical implications. Ann Thorac Surg. 2013;95(2):412–8. https://doi.org/10.1016/j.athoracsur.2012.08.012.
Article
PubMed
Google Scholar
Rutkowski J, Cyman M, Slebioda T, Bemben K, Rutkowska A, Gruchala M, et al. Evaluation of peripheral blood T lymphocyte surface activation markers and transcription factors in patients with early stage non-small cell lung cancer. Cell Immunol. 2017;322:26–33. https://doi.org/10.1016/j.cellimm.2017.09.007.
Article
CAS
PubMed
Google Scholar
Liu H, Zhang T, Ye J, Li H, Huang J, Li X, et al. Tumor-infiltrating lymphocytes predict response to chemotherapy in patients with advance non-small cell lung cancer. Cancer Immunol Immunother. 2012;61(10):1849–56. https://doi.org/10.1007/s00262-012-1231-7.
Article
CAS
PubMed
Google Scholar
Masucci GV, Cesano A, Hawtin R, Janetzki S, Zhang J, Kirsch I, et al. Validation of biomarkers to predict response to immunotherapy in cancer: volume I—pre-analytical and analytical validation. J Immunother Cancer. 2016;4:76. https://doi.org/10.1186/s40425-016-0178-1.
Article
PubMed
PubMed Central
Google Scholar
Brody R, Zhang Y, Ballas M, Siddiqui MK, Gupta P, Barker C, et al. PD-L1 expression in advanced NSCLC: insights into risk stratification and treatment selection from a systematic literature review. Lung Cancer. 2017;112:200–15. https://doi.org/10.1016/j.lungcan.2017.08.005.
Article
PubMed
Google Scholar
Doroshow DB, Sanmamed MF, Hastings K, Politi K, Rimm DL, Chen L, et al. Immunotherapy in non-small cell lung cancer: facts and hopes. Clin Cancer Res. 2019. https://doi.org/10.1158/1078-0432.ccr-18-1538.
Article
PubMed
PubMed Central
Google Scholar
Wang VE, Urisman A, Albacker L, Ali S, Miller V, Aggarwal R, et al. Checkpoint inhibitor is active against large cell neuroendocrine carcinoma with high tumor mutation burden. J Immunother Cancer. 2017;5(1):75. https://doi.org/10.1186/s40425-017-0281-y.
Article
PubMed
PubMed Central
Google Scholar
Cristescu R, Mogg R, Ayers M, Albright A, Murphy E, Yearley J, et al. Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy. Science. 2018;362(6411):eaar3593. https://doi.org/10.1126/science.aar3593.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fruh M, Peters S. Genomic features of response to combination immunotherapy in lung cancer. Cancer Cell. 2018;33(5):791–3. https://doi.org/10.1016/j.ccell.2018.04.005.
Article
CAS
PubMed
Google Scholar
Rolfo C, Caglevic C, Santarpia M, Araujo A, Giovannetti E, Gallardo CD, et al. Immunotherapy in NSCLC: a promising and revolutionary weapon. Adv Exp Med Biol. 2017;995:97–125. https://doi.org/10.1007/978-3-319-53156-4_5.
Article
CAS
PubMed
Google Scholar
Zheng C, Zheng L, Yoo JK, Guo H, Zhang Y, Guo X, et al. Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing. Cell. 2017;169(7):1342.e16–1356.e16. https://doi.org/10.1016/j.cell.2017.05.035.
Article
CAS
Google Scholar
Jiang Y, Li Y, Zhu B. T-cell exhaustion in the tumor microenvironment. Cell Death Dis. 2015;6:e1792. https://doi.org/10.1038/cddis.2015.162.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xiao X, Lao XM, Chen MM, Liu RX, Wei Y, Ouyang FZ, et al. PD-1hi identifies a novel regulatory B-cell population in human hepatoma that promotes disease progression. Cancer Discov. 2016;6(5):546–59. https://doi.org/10.1158/2159-8290.CD-15-1408.
Article
CAS
PubMed
Google Scholar
Van Cutsem E, Sagaert X, Topal B, Haustermans K, Prenen H. Gastric cancer. Lancet. 2016;388(10060):2654–64. https://doi.org/10.1016/S0140-6736(16)30354-3.
Article
CAS
PubMed
Google Scholar
Wang B, Xu D, Yu X, Ding T, Rao H, Zhan Y, et al. Association of intra-tumoral infiltrating macrophages and regulatory T cells is an independent prognostic factor in gastric cancer after radical resection. Ann Surg Oncol. 2011;18(9):2585–93. https://doi.org/10.1245/s10434-011-1609-3.
Article
PubMed
Google Scholar
Feichtenbeiner A, Haas M, Buttner M, Grabenbauer GG, Fietkau R, Distel LV. Critical role of spatial interaction between CD8(+) and Foxp3(+) cells in human gastric cancer: the distance matters. Cancer Immunol Immunother. 2014;63(2):111–9. https://doi.org/10.1007/s00262-013-1491-x.
Article
CAS
PubMed
Google Scholar
Okita Y, Ohira M, Tanaka H, Tokumoto M, Go Y, Sakurai K, et al. Alteration of CD4 T cell subsets in metastatic lymph nodes of human gastric cancer. Oncol Rep. 2015;34(2):639–47. https://doi.org/10.3892/or.2015.4064.
Article
CAS
PubMed
Google Scholar
Gao Q, Qiu SJ, Fan J, Zhou J, Wang XY, Xiao YS, et al. Intratumoral balance of regulatory and cytotoxic T cells is associated with prognosis of hepatocellular carcinoma after resection. J Clin Oncol. 2007;25(18):2586–93. https://doi.org/10.1200/JCO.2006.09.4565.
Article
PubMed
Google Scholar
Greten TF, Sangro B. Targets for immunotherapy of liver cancer. J Hepatol. 2017. https://doi.org/10.1016/j.jhep.2017.09.007.
Article
PubMed
PubMed Central
Google Scholar
Finger EC, Giaccia AJ. Hypoxia, inflammation, and the tumor microenvironment in metastatic disease. Cancer Metastasis Rev. 2010;29(2):285–93. https://doi.org/10.1007/s10555-010-9224-5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jimenez-Sanchez A, Memon D, Pourpe S, Veeraraghavan H, Li Y, Vargas HA, et al. Heterogeneous tumor-immune microenvironments among differentially growing metastases in an ovarian cancer patient. Cell. 2017;170(5):927.e20–938.e20. https://doi.org/10.1016/j.cell.2017.07.025.
Article
CAS
Google Scholar
Azizi E, Carr AJ, Plitas G, Cornish AE, Konopacki C, Prabhakaran S, et al. Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. Cell. 2018;174(5):1293.e36–1308.e36. https://doi.org/10.1016/j.cell.2018.05.060.
Article
CAS
Google Scholar
Liu PS, Wang H, Li X, Chao T, Teav T, Christen S, et al. alpha-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming. Nat Immunol. 2017;18(9):985–94. https://doi.org/10.1038/ni.3796.
Article
CAS
PubMed
Google Scholar
Mantovani A, Locati M. Tumor-associated macrophages as a paradigm of macrophage plasticity, diversity, and polarization: lessons and open questions. Arterioscler Thromb Vasc Biol. 2013;33(7):1478–83. https://doi.org/10.1161/ATVBAHA.113.300168.
Article
CAS
PubMed
Google Scholar
Denkert C, Loibl S, Noske A, Roller M, Muller BM, Komor M, et al. Tumor-associated lymphocytes as an independent predictor of response to neoadjuvant chemotherapy in breast cancer. J Clin Oncol. 2010;28(1):105–13. https://doi.org/10.1200/JCO.2009.23.7370.
Article
CAS
PubMed
Google Scholar
Ali HR, Provenzano E, Dawson SJ, Blows FM, Liu B, Shah M, et al. Association between CD8+ T-cell infiltration and breast cancer survival in 12,439 patients. Ann Oncol. 2014;25(8):1536–43. https://doi.org/10.1093/annonc/mdu191.
Article
CAS
PubMed
Google Scholar
Aaltomaa S, Lipponen P, Eskelinen M, Kosma VM, Marin S, Alhava E, et al. Lymphocyte infiltrates as a prognostic variable in female breast cancer. Eur J Cancer. 1992;28A(4–5):859–64.
Article
CAS
PubMed
Google Scholar
Baitsch L, Baumgaertner P, Devevre E, Raghav SK, Legat A, Barba L, et al. Exhaustion of tumor-specific CD8(+) T cells in metastases from melanoma patients. J Clin Invest. 2011;121(6):2350–60. https://doi.org/10.1172/JCI46102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee PP, Yee C, Savage PA, Fong L, Brockstedt D, Weber JS, et al. Characterization of circulating T cells specific for tumor-associated antigens in melanoma patients. Nat Med. 1999;5(6):677–85. https://doi.org/10.1038/9525.
Article
CAS
PubMed
Google Scholar
Liu F, Lang R, Zhao J, Zhang X, Pringle GA, Fan Y, et al. CD8(+) cytotoxic T cell and FOXP3(+) regulatory T cell infiltration in relation to breast cancer survival and molecular subtypes. Breast Cancer Res Treat. 2011;130(2):645–55. https://doi.org/10.1007/s10549-011-1647-3.
Article
CAS
PubMed
Google Scholar
West NR, Kost SE, Martin SD, Milne K, Deleeuw RJ, Nelson BH, et al. Tumour-infiltrating FOXP3(+) lymphocytes are associated with cytotoxic immune responses and good clinical outcome in oestrogen receptor-negative breast cancer. Br J Cancer. 2013;108(1):155–62. https://doi.org/10.1038/bjc.2012.524.
Article
CAS
PubMed
Google Scholar
Ott PA, Bang YJ, Piha-Paul SA, Razak ARA, Bennouna J, Soria JC, et al. T-Cell-Inflamed gene-expression profile, programmed death ligand 1 expression, and tumor mutational burden predict efficacy in patients treated with pembrolizumab across 20 cancers: KEYNOTE-028. J Clin Oncol. 2019;37(4):318–27. https://doi.org/10.1200/JCO.2018.78.2276.
Article
PubMed
Google Scholar
Heimes AS, Schmidt M. Atezolizumab for the treatment of triple-negative breast cancer. Expert Opin Investig Drugs. 2019;28(1):1–5. https://doi.org/10.1080/13543784.2019.1552255.
Article
CAS
PubMed
Google Scholar
Zhou X, Li B, Zhang Y, Gu Y, Chen B, Shi T, et al. A relative ordering-based predictor for tamoxifen-treated estrogen receptor-positive breast cancer patients: multi-laboratory cohort validation. Breast Cancer Res Treat. 2013;142(3):505–14. https://doi.org/10.1007/s10549-013-2767-8.
Article
CAS
PubMed
Google Scholar
Chevrier S, Levine JH, Zanotelli VRT, Silina K, Schulz D, Bacac M, et al. An immune atlas of clear cell renal cell carcinoma. Cell. 2017;169(4):736.e18–749.e18. https://doi.org/10.1016/j.cell.2017.04.016.
Article
CAS
Google Scholar
Shin DS, Ribas A. The evolution of checkpoint blockade as a cancer therapy: what’s here, what’s next? Curr Opin Immunol. 2015;33:23–35. https://doi.org/10.1016/j.coi.2015.01.006.
Article
CAS
PubMed
Google Scholar
Maus MV, June CH. Making better chimeric antigen receptors for adoptive T-cell therapy. Clin Cancer Res. 2016;22(8):1875–84. https://doi.org/10.1158/1078-0432.CCR-15-1433.
Article
CAS
PubMed
PubMed Central
Google Scholar
Komohara Y, Niino D, Saito Y, Ohnishi K, Horlad H, Ohshima K, et al. Clinical significance of CD163+ tumor-associated macrophages in patients with adult T-cell leukemia/lymphoma. Cancer Sci. 2013;104(7):945–51. https://doi.org/10.1111/cas.12167.
Article
CAS
PubMed
PubMed Central
Google Scholar
Behnes CL, Bremmer F, Hemmerlein B, Strauss A, Strobel P, Radzun HJ. Tumor-associated macrophages are involved in tumor progression in papillary renal cell carcinoma. Virchows Arch. 2014;464(2):191–6. https://doi.org/10.1007/s00428-013-1523-0.
Article
CAS
PubMed
Google Scholar
Dannenmann SR, Thielicke J, Stockli M, Matter C, von Boehmer L, Cecconi V, et al. Tumor-associated macrophages subvert T-cell function and correlate with reduced survival in clear cell renal cell carcinoma. Oncoimmunology. 2013;2(3):e23562. https://doi.org/10.4161/onci.23562.
Article
PubMed
PubMed Central
Google Scholar
Daurkin I, Eruslanov E, Stoffs T, Perrin GQ, Algood C, Gilbert SM, et al. Tumor-associated macrophages mediate immunosuppression in the renal cancer microenvironment by activating the 15-lipoxygenase-2 pathway. Cancer Res. 2011;71(20):6400–9. https://doi.org/10.1158/0008-5472.CAN-11-1261.
Article
CAS
PubMed
Google Scholar
Steidl C, Connors JM, Gascoyne RD. Molecular pathogenesis of Hodgkin’s lymphoma: increasing evidence of the importance of the microenvironment. J Clin Oncol. 2011;29(14):1812–26. https://doi.org/10.1200/JCO.2010.32.8401.
Article
CAS
PubMed
Google Scholar
Roemer MGM, Redd RA, Cader FZ, Pak CJ, Abdelrahman S, Ouyang J, et al. Major histocompatibility complex class II and programmed death ligand 1 expression predict outcome after programmed death 1 blockade in classic hodgkin lymphoma. J Clin Oncol. 2018;36(10):942–50. https://doi.org/10.1200/JCO.2017.77.3994.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tumeh PC, Harview CL, Yearley JH, Shintaku IP, Taylor EJ, Robert L, et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature. 2014;515(7528):568–71. https://doi.org/10.1038/nature13954.
Article
CAS
PubMed
PubMed Central
Google Scholar
Im SJ, Hashimoto M, Gerner MY, Lee J, Kissick HT, Burger MC, et al. Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy. Nature. 2016;537(7620):417–21. https://doi.org/10.1038/nature19330.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kamphorst AO, Wieland A, Nasti T, Yang S, Zhang R, Barber DL, et al. Rescue of exhausted CD8 T cells by PD-1-targeted therapies is CD28-dependent. Science. 2017;355(6332):1423–7. https://doi.org/10.1126/science.aaf0683.
Article
CAS
PubMed
PubMed Central
Google Scholar
Juneja VR, McGuire KA, Manguso RT, LaFleur MW, Collins N, Haining WN, et al. PD-L1 on tumor cells is sufficient for immune evasion in immunogenic tumors and inhibits CD8 T cell cytotoxicity. J Exp Med. 2017;214(4):895–904. https://doi.org/10.1084/jem.20160801.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, et al. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015;125(7):1061–72. https://doi.org/10.1182/blood-2014-11-610436.
Article
CAS
PubMed
Google Scholar
Cader FZ, Schackmann RCJ, Hu X, Wienand K, Redd R, Chapuy B, et al. Mass cytometry of Hodgkin lymphoma reveals a CD4(+) regulatory T-cell-rich and exhausted T-effector microenvironment. Blood. 2018;132(8):825–36. https://doi.org/10.1182/blood-2018-04-843714.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tsirigotis P, Savani BN, Nagler A. Programmed death-1 immune checkpoint blockade in the treatment of hematological malignancies. Ann Med. 2016;48(6):428–39. https://doi.org/10.1080/07853890.2016.1186827.
Article
CAS
PubMed
Google Scholar
Schadendorf D, van Akkooi ACJ, Berking C, Griewank KG, Gutzmer R, Hauschild A, et al. Melanoma. Lancet. 2018;392(10151):971–84. https://doi.org/10.1016/S0140-6736(18)31559-9.
Article
PubMed
Google Scholar
Li H, van der Leun AM, Yofe I, Lubling Y, Gelbard-Solodkin D, van Akkooi ACJ, et al. Dysfunctional CD8 T cells form a proliferative, dynamically regulated compartment within human melanoma. Cell. 2018. https://doi.org/10.1016/j.cell.2018.11.043.
Article
PubMed
PubMed Central
Google Scholar
Hashimoto M, Kamphorst AO, Im SJ, Kissick HT, Pillai RN, Ramalingam SS, et al. CD8 T cell exhaustion in chronic infection and cancer: opportunities for interventions. Annu Rev Med. 2018;69:301–18. https://doi.org/10.1146/annurev-med-012017-043208.
Article
CAS
PubMed
Google Scholar
Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, et al. Defining T cell states associated with response to checkpoint immunotherapy in melanoma. Cell. 2019;176(1–2):404. https://doi.org/10.1016/j.cell.2018.12.034.
Article
CAS
PubMed
PubMed Central
Google Scholar
Landhuis E. Single-cell approaches to immune profiling. Nature. 2018;557(7706):595–7. https://doi.org/10.1038/d41586-018-05214-w.
Article
CAS
PubMed
Google Scholar
Bandura DR, Baranov VI, Ornatsky OI, Antonov A, Kinach R, Lou X, et al. Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem. 2009;81(16):6813–22. https://doi.org/10.1021/ac901049w.
Article
CAS
PubMed
Google Scholar
Ntranos V, Yi L, Melsted P, Pachter L. A discriminative learning approach to differential expression analysis for single-cell RNA-seq. Nat Methods. 2019;16(2):163–6. https://doi.org/10.1038/s41592-018-0303-9.
Article
CAS
PubMed
Google Scholar
Haque A, Engel J, Teichmann SA, Lonnberg T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med. 2017;9(1):75. https://doi.org/10.1186/s13073-017-0467-4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kiselev VY, Andrews TS, Hemberg M. Challenges in unsupervised clustering of single-cell RNA-seq data. Nat Rev Genet. 2019. https://doi.org/10.1038/s41576-018-0088-9.
Article
PubMed
Google Scholar
Restrepo-Perez L, Joo C, Dekker C. Paving the way to single-molecule protein sequencing. Nat Nanotechnol. 2018;13(9):786–96. https://doi.org/10.1038/s41565-018-0236-6.
Article
CAS
PubMed
Google Scholar
Doerr A. Single-cell proteomics. Nat Methods. 2019;16(1):20. https://doi.org/10.1038/s41592-018-0273-y.
Article
PubMed
Google Scholar
Thul PJ, Akesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, et al. A subcellular map of the human proteome. Science. 2017;356(6340):eaal3321. https://doi.org/10.1126/science.aal3321.
Article
CAS
PubMed
Google Scholar
Ho YJ, Anaparthy N, Molik D, Mathew G, Aicher T, Patel A, et al. Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. Genome Res. 2018;28(9):1353–63. https://doi.org/10.1101/gr.234062.117.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gerber T, Willscher E, Loeffler-Wirth H, Hopp L, Schadendorf D, Schartl M, et al. Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq. Oncotarget. 2017;8(1):846–62. https://doi.org/10.18632/oncotarget.13666.
Article
PubMed
Google Scholar
Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016;352(6282):189–96. https://doi.org/10.1126/science.aad0501.
Article
CAS
PubMed
PubMed Central
Google Scholar
Su Y, Wei W, Robert L, Xue M, Tsoi J, Garcia-Diaz A, et al. Single-cell analysis resolves the cell state transition and signaling dynamics associated with melanoma drug-induced resistance. Proc Natl Acad Sci USA. 2017;114(52):13679–84. https://doi.org/10.1073/pnas.1712064115.
Article
CAS
PubMed
PubMed Central
Google Scholar
Povinelli BJ, Rodriguez-Meira A, Mead AJ. Single cell analysis of normal and leukemic hematopoiesis. Mol Aspects Med. 2018;59:85–94. https://doi.org/10.1016/j.mam.2017.08.006.
Article
CAS
PubMed
Google Scholar
Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, et al. Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell. 2012;148(5):873–85. https://doi.org/10.1016/j.cell.2012.02.028.
Article
CAS
PubMed
Google Scholar
Zeng Z, Konopleva M, Andreeff M. Single-cell mass cytometry of acute myeloid leukemia and leukemia stem/progenitor cells. Methods Mol Biol. 2017;1633:75–86. https://doi.org/10.1007/978-1-4939-7142-8_5.
Article
CAS
PubMed
Google Scholar
Kuboki Y, Fischer CG, Beleva Guthrie V, Huang W, Yu J, Chianchiano P, et al. Single-cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions. J Pathol. 2018. https://doi.org/10.1002/path.5194.
Article
Google Scholar
Bernard V, Semaan A, Huang J, San Lucas FA, Mulu FC, Stephens BM, et al. Single cell transcriptomics of pancreatic cancer precursors demonstrates epithelial and microenvironmental heterogeneity as an early event in neoplastic progression. Clin Cancer Res. 2018. https://doi.org/10.1158/1078-0432.ccr-18-1955.
Article
PubMed
PubMed Central
Google Scholar
Santegoets SJ, van Ham VJ, Ehsan I, Charoentong P, Duurland CL, van Unen V, et al. The anatomical location shapes the immune infiltrate in tumors of same etiology and affects survival. Clin Cancer Res. 2018. https://doi.org/10.1158/1078-0432.ccr-18-1749.
Article
PubMed
Google Scholar
Yang D, Zhang W, Liu Y, Liang J, Zhang T, Bai Y, et al. Single-cell whole-genome sequencing identifies human papillomavirus integration in cervical tumour cells prior to and following radiotherapy. Oncol Lett. 2018;15(6):9633–40. https://doi.org/10.3892/ol.2018.8567.
Article
PubMed
PubMed Central
Google Scholar
Wang J, Roy B. Single-cell RNA-seq reveals lincRNA expression differences in Hela-S3 cells. Biotechnol Lett. 2017;39(3):359–66. https://doi.org/10.1007/s10529-016-2260-7.
Article
CAS
PubMed
Google Scholar
Cai YD, Zhang S, Zhang YH, Pan X, Feng K, Chen L, et al. Identification of the gene expression rules that define the subtypes in glioma. J Clin Med. 2018;7(10):350. https://doi.org/10.3390/jcm7100350.
Article
PubMed Central
Google Scholar
Yuan J, Levitin HM, Frattini V, Bush EC, Boyett DM, Samanamud J, et al. Single-cell transcriptome analysis of lineage diversity in high-grade glioma. Genome Med. 2018;10(1):57. https://doi.org/10.1186/s13073-018-0567-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Johnson E, Dickerson KL, Connolly ID, Hayden Gephart M. Single-cell RNA-sequencing in glioma. Curr Oncol Rep. 2018;20(5):42. https://doi.org/10.1007/s11912-018-0673-2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Filbin MG, Tirosh I, Hovestadt V, Shaw ML, Escalante LE, Mathewson ND, et al. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science. 2018;360(6386):331–5. https://doi.org/10.1126/science.aao4750.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jin W, Tang Q, Wan M, Cui K, Zhang Y, Ren G, et al. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature. 2015;528(7580):142–6. https://doi.org/10.1038/nature15740.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lobastova L, Kraus D, Glassmann A, Khan D, Steinhauser C, Wolff C, et al. Collective cell migration of thyroid carcinoma cells: a beneficial ability to override unfavourable substrates. Cell Oncol (Dordr). 2017;40(1):63–76. https://doi.org/10.1007/s13402-016-0305-5.
Article
CAS
Google Scholar