The prognostic landscape of genes and infiltrating immune cells across human cancers (original) (raw)

• Coussens, L.M. & Werb, Z. Inflammation and cancer. Nature 420, 860–867 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, L. et al. Intratumoral T cells, recurrence, and survival in epithelial ovarian cancer. N. Engl. J. Med. 348, 203–213 (2003).
  Article CAS PubMed Google Scholar
• Topalian, S.L. et al. Safety, activity, and immune correlates of anti-PD-1 antibody in cancer. N. Engl. J. Med. 366, 2443–2454 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Fan, J.B., Chee, M. & Gunderson, K. Highly parallel genomic assays. Nat. Rev. Genet. 7, 632–644 (2006).
  Article CAS PubMed Google Scholar
• Koscielny, S. Why most gene expression signatures of tumors have not been useful in the clinic. Sci. Transl. Med. 2, ps2 (2010).
  Article Google Scholar
• Dupuy, A. & Simon, R.M. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J. Natl. Cancer Inst. 99, 147–157 (2007).
  Article PubMed Google Scholar
• Subramanian, J. & Simon, R. Gene expression–based prognostic signatures in lung cancer: ready for clinical use? J. Natl. Cancer Inst. 102, 464–474 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Dalton, W.S. & Friend, S.H. Cancer biomarkers: an invitation to the table. Science 312, 1165–1168 (2006).
  Article CAS PubMed Google Scholar
• Ein-Dor, L., Zuk, O. & Domany, E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc. Natl. Acad. Sci. USA 103, 5923–5928 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Ransohoff, D.F. Rules of evidence for cancer molecular-marker discovery and validation. Nat. Rev. Cancer 4, 309–314 (2004).
  Article CAS PubMed Google Scholar
• Varmus, H. Ten years on: the human genome and medicine. N. Engl. J. Med. 362, 2028–2029 (2010).
  Article CAS PubMed Google Scholar
• Lee, H.K., Hsu, A.K., Sajdak, J., Qin, J. & Pavlidis, P. Coexpression analysis of human genes across many microarray data sets. Genome Res. 14, 1085–1094 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Mizuno, H., Kitada, K., Nakai, K. & Sarai, A. PrognoScan: a new database for meta-analysis of the prognostic value of genes. BMC Med. Genomics 2, 18 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Hebestreit, K. et al. Leukemia Gene Atlas: a public platform for integrative exploration of genome-wide molecular data. PLoS ONE 7, e39148 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Yuan, Y. et al. Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Nat. Biotechnol. 32, 644–652 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Newman, A.M. et al. Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 12, 453–457 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Hanahan, D. & Weinberg, R.A. Hallmarks of cancer: the next generation. Cell 144, 646–674 (2011).
  Article CAS PubMed Google Scholar
• Mantovani, A. et al. Chemokines in the recruitment and shaping of the leukocyte infiltrate of tumors. Semin. Cancer Biol. 14, 155–160 (2004).
  Article CAS PubMed Google Scholar
• Coussens, L.M., Zitvogel, L. & Palucka, A.K. Neutralizing tumor-promoting chronic inflammation: a magic bullet? Science 339, 286–291 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Gerstein, M.B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91–100 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Leek, J.T. et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet. 11, 733–739 (2010).
  Article CAS PubMed Google Scholar
• Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Newman, A.M. & Cooper, J.B. AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. BMC Bioinformatics 11, 117 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Gentles, A.J., Plevritis, S.K., Majeti, R. & Alizadeh, A.A. Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia. J. Am. Med. Assoc. 304, 2706–2715 (2010).
  Article CAS Google Scholar
• Zeuner, A., Todaro, M., Stassi, G. & De Maria, R. Colorectal cancer stem cells: from the crypt to the clinic. Cell Stem Cell 15, 692–705 (2014).
  Article CAS PubMed Google Scholar
• Myatt, S.S. & Lam, E.W.-F. The emerging roles of forkhead box (Fox) proteins in cancer. Nat. Rev. Cancer 7, 847–859 (2007).
  Article CAS PubMed Google Scholar
• Scholzen, T. & Gerdes, J. The Ki-67 protein: from the known and the unknown. J. Cell. Physiol. 182, 311–322 (2000).
  Article CAS PubMed Google Scholar
• Fergusson, J.R. et al. CD161 defines a transcriptional and functional phenotype across distinct human T cell lineages. Cell Rep. 9, 1075–1088 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Lachmann, A. et al. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 26, 2438–2444 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Liberzon, A. et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics 27, 1739–1740 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Chen, X. et al. The forkhead transcription factor FOXM1 controls cell cycle-dependent gene expression through an atypical chromatin binding mechanism. Mol. Cell. Biol. 33, 227–236 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Galon, J. et al. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science 313, 1960–1964 (2006).
  Article CAS PubMed Google Scholar
• Fridman, W.H., Pagès, F., Sautès-Fridman, C. & Galon, J. The immune contexture in human tumours: impact on clinical outcome. Nat. Rev. Cancer 12, 298–306 (2012).
  Article CAS PubMed Google Scholar
• Lewis, C.E. & Pollard, J.W. Distinct role of macrophages in different tumor microenvironments. Cancer Res. 66, 605–612 (2006).
  Article CAS PubMed Google Scholar
• de Visser, K.E., Eichten, A. & Coussens, L.M. Paradoxical roles of the immune system during cancer development. Nat. Rev. Cancer 6, 24–37 (2006).
  Article CAS PubMed Google Scholar
• Beyer, M. & Schultze, J.L. Regulatory T cells in cancer. Blood 108, 804–811 (2006).
  Article CAS PubMed Google Scholar
• Girardi, M. et al. Regulation of cutaneous malignancy by γδ T cells. Science 294, 605 (2001).
  Article CAS PubMed Google Scholar
• Haas, W., Pereira, P. & Tonegawa, S. Gamma/delta cells. Annu. Rev. Immunol. 11, 637–685 (1993).
  Article CAS PubMed Google Scholar
• Fridlender, Z.G. & Albelda, S.M. Tumor-associated neutrophils: friend or foe? Carcinogenesis 33, 949–955 (2012).
  Article CAS PubMed Google Scholar
• Di Carlo, E. et al. The intriguing role of polymorphonuclear neutrophils in antitumor reactions. Blood 97, 339–345 (2001).
  Article CAS PubMed Google Scholar
• Vakkila, J. & Lotze, M.T. Inflammation and necrosis promote tumour growth. Nat. Rev. Immunol. 4, 641–648 (2004).
  Article CAS PubMed Google Scholar
• Sica, A., Schioppa, T., Mantovani, A. & Allavena, P. Tumour-associated macrophages are a distinct M2 polarised population promoting tumour progression: potential targets of anti-cancer therapy. Eur. J. Cancer 42, 717–727 (2006).
  Article CAS PubMed Google Scholar
• Teramukai, S. et al. Pretreatment neutrophil count as an independent prognostic factor in advanced non-small-cell lung cancer: an analysis of Japan Multinational Trial Organisation LC00–03. Eur. J. Cancer 45, 1950–1958 (2009).
  Article PubMed Google Scholar
• de Visser, K.E., Korets, L.V. & Coussens, L.M. De novo carcinogenesis promoted by chronic inflammation is B lymphocyte dependent. Cancer Cell 7, 411–423 (2005).
  Article CAS PubMed Google Scholar
• Liyanage, U.K. et al. Prevalence of regulatory T cells is increased in peripheral blood and tumor microenvironment of patients with pancreas or breast adenocarcinoma. J. Immunol. 169, 2756–2761 (2002).
  Article CAS PubMed Google Scholar
• Minárik, I. et al. Regulatory T cells, dendritic cells and neutrophils in patients with renal cell carcinoma. Immunol. Lett. 152, 144–150 (2013).
  Article CAS PubMed Google Scholar
• Yamanaka, T. et al. The baseline ratio of neutrophils to lymphocytes is associated with patient prognosis in advanced gastric cancer. Oncology 73, 215–220 (2007).
  Article PubMed Google Scholar
• Paik, S. et al. A multigene assay to predict recurrence of Tamoxifen-treated, node-negative breast cancer. N. Engl. J. Med. 351, 2817–2826 (2004).
  Article CAS PubMed Google Scholar
• Chen, X., Sun, X. & Hoshida, Y. Survival analysis tools in genomics research. Hum. Genomics 8, 21 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Alizadeh, A.A. et al. Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironment. Blood 118, 1350–1358 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Bindea, G. et al. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity 39, 782–795 (2013).
  Article CAS PubMed Google Scholar
• Rooney, M.S., Shukla, S.A., Wu, C.J., Getz, G. & Hacohen, N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 160, 48–61 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Gabrilovich, D.I. & Nagaraj, S. Myeloid-derived suppressor cells as regulators of the immune system. Nat. Rev. Immunol. 9, 162–174 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Pardoll, D.M. The blockade of immune checkpoints in cancer immunotherapy. Nat. Rev. Cancer 12, 252–264 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Ribas, A. Tumor immunotherapy directed at PD-1. N. Engl. J. Med. 366, 2517–2519 (2012).
  Article CAS PubMed Google Scholar
• Day, A., Carlson, M.R., Dong, J., O'Connor, B.D. & Nelson, S.F. Celsius: a community resource for Affymetrix microarray data. Genome Biol. 8, R112 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Dai, M. et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 33, e175 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Gautier, L., Cope, L., Bolstad, B.M. & Irizarry, R.A. affy—analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20, 307–315 (2004).
  Article CAS PubMed Google Scholar
• Gentleman, R.C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
  Article PubMed PubMed Central Google Scholar
• Irizarry, R.A. et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Wu, Z., Irizarry, R.A., Gentleman, R., Martinez-Murillo, F. & Spencer, F. A model-based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc. 99, 909–917 (2004).
  Article Google Scholar
• McCall, M.N., Bolstad, B.M. & Irizarry, R.A. Frozen robust multiarray analysis (fRMA). Biostatistics 11, 242–253 (2010).
  Article PubMed PubMed Central Google Scholar
• Piccolo, S.R. et al. A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics 100, 337–344 (2012).
  Article CAS PubMed Google Scholar
• Zhu, Y., Qiu, P. & Ji, Y. TCGA-Assembler: open-source software for retrieving and processing TCGA data. Nat. Methods 11, 599–600 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Lipták, T. On the combination of independent tests. Magyar Tud. Akad. Mat. Kutato Int. Közl 3, 171–196 (1958).
  Google Scholar
• Stouffer, S., DeVinney, L. & Suchmen, E. The American Soldier: Adjustment During Army Life (Princeton University Press, 1949).
• Zaykin, D.V. Optimally weighted _Z_-test is a powerful method for combining probabilities in meta-analysis. J. Evol. Biol. 24, 1836–1841 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Johnson, W.E., Li, C. & Rabinovic, A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118–127 (2007).
  Article PubMed Google Scholar
• Storey, J.D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100, 9440–9445 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Szklarczyk, D. et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39, D561–D568 (2011).
  Article CAS PubMed Google Scholar
• Fiedler, M. Algebraic connectivity of graphs. Czech. Math. J. 23, 298–305 (1973).
  Google Scholar
• Chen, J., Bardes, E.E., Aronow, B.J. & Jegga, A.G. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 37, W305–W311 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Liberzon, A. et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics 27, 1739–1740 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Zhong, Y. & Liu, Z. Gene expression deconvolution in linear space. Nat. Methods 9, 8–9 (2012).
  Article CAS Google Scholar
• Xu, L. et al. Gene expression changes in an animal melanoma model correlate with Aggressiveness of Human Melanoma Metastases. Mol. Cancer Res. 6, 760–769 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Su, L.-J. et al. Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme. BMC Genomics 8, 140 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Landi, M.T. et al. Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival. PLoS ONE 3, e1651 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Brunner, A.L. et al. Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome Biol. 13, R75 (2012).
  Article PubMed PubMed Central Google Scholar
• Holmes, S., Kapelner, A. & Lee, P.P. An interactive java statistical image segmentation system: Gemident. J. Stat. Softw. 30, i10 (2009).
  Article PubMed PubMed Central Google Scholar