Gene expression markers of Tumor Infiltrating Leukocytes

Jochems C, Schlom J. Tumor-infiltrating immune cells and prognosis: the potential link between conventional cancer therapy and immunity. Exp Biol Med. 2011;236(5):567–79.

Galon J, et al. Cancer classification using the Immunoscore: a worldwide task force. J Transl Med. 2012;10:205.

Fridman WH, Pagès F, Sautès-Fridman C, Galon J. The immune contexture in human tumours: impact on clinical outcome. Nat Rev Cancer. 2012;12(4):298–306.

Salgado R, Denkert C, Demaria S, Sirtaine N, Klauschen F, Pruneri G, Wienert S, Van den Eynden G, Baehner FL, Penault-Llorca F, Perez EA. The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014. Ann Oncol. 2015;26(2):259–71.

Gentles AJ, Newman AM, Liu CL, Bratman SV, Feng W, Kim D, Nair VS, Xu Y, Khuong A, Hoang CD, Diehn M. The prognostic landscape of genes and infiltrating immune cells across human cancers. Nat Med. 2015;21(8):938–45.

Topalian SL, et al. Mechanism-driven biomarkers to guide immune checkpoint blockade in cancer therapy. Nat Rev Cancer. 2016;16(5):275–87.

Bindea G, et al. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity. 2013;39(4):782–95.

Angelova M, Charoentong P, Hackl H, Fischer ML, Snajder R, Krogsdam AM, Waldner M, Bindea G, Mlecnik B, Galon J, Trajanoski Z. Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. Genome Biol. 2015;16:64.

Newman AM, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–7.

Senbabaoglu Y, Winer AG, Gejman RS, Liu M, Luna A, Ostrovnaya I, Weinhold N, Lee W, Kaffenberger SD, Chen YB, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Hsieh JJ, Sander C, Hakimi A. The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression. 2015. doi: 10.1101/025908 .

Wherry EJ, Ha SJ, Kaech SM, Haining WN, Sarkar S, Kalia V, Subramaniam S, Blattman JN, Barber DL, Ahmed R. Molecular signature of CD8+ T cell exhaustion during chronic viral infection. Immunity. 2007;27(4):670–84.

Wherry EJ. T cell exhaustion. Nat Immunol. 2011;12(6):492–9.

Gupta PK, Godec J, Wolski D, Adland E, Yates K, Pauken KE, Cosgrove C, Ledderose C, Junger WG, Robson SC, Wherry EJ. CD39 Expression Identifies Terminally Exhausted CD8+ T Cells. PLoS Pathog. 2015;11(10), e1005177.

Zhang M, Yao C, Guo Z, Zou J, Zhang L, Xiao H, Wang D, Yang D, Gong X, Zhu J, Li Y. Apparently low reproducibility of true differential expression discoveries in microarray studies. Bioinformatics. 2008;24(18):2057–63.

Galon J, et al. The continuum of cancer immunosurveillance: prognostic, predictive, and mechanistic signatures. Immunity. 2013;39(1):11–26.

Parmigiani G, Garrett ES, Anbazhagan R, Gabrielson E. A statistical framework for expression-based molecular classification in cancer. J R Stat Soc Ser B (Stat Methodol). 2002;64(4):717–36.

Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res. 2004;14(6):1085–94.

Cheng WY, Yang TH, Anastassiou D. Biomolecular events in cancer revealed by attractor metagenes. PLoS Comput Biol. 2013;9(2):e1002920.

Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC bioinf. 2008;9(1):1.

Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3(7):1–2.

Bonilla FA, Fujita RM, Pivniouk VI, Chan AC, Geha RS. Adapter proteins SLP-76 and BLNK both are expressed by murine macrophages and are linked to signaling via Fcγ receptors I and II/III. Proc Natl Acad Sci. 2000;97(4):1725–30.

Sah NK, Khan Z, Khan GJ, Bisen PS. Structural, functional and therapeutic biology of survivin. Cancer Lett. 2006;244(2):164–71.

Kim JM, Yamada M, Masai H. Functions of mammalian Cdc7 kinase in initiation/monitoring of DNA replication and development. Mutat Res Fundam Mol Mech Mutagen. 2003;532(1):29–40.

Ma L, Zhao X, Zhu X. Mitosin/CENP-F in mitosis, transcriptional control, and differentiation. J Biomed Sci. 2006;13(2):205–13.

Solanilla A, Grosset C, Lemercier C, Dupouy M, Mahon FX, Schweitzer K, Reiffers J, Weksler B, Ripoche J. Expression of Flt3-ligand by the endothelial cell. Leukemia. 2000;14(1):153–62.

Krenacs L, Smyth MJ, Bagdi E, Krenacs T, Kopper L, Rudiger T, Zettl A, Muller-Hermelink HK, Jaffe ES, Raffeld M. The serine protease granzyme M is preferentially expressed in NK-cell, γδ T-cell, and intestinal T-cell lymphomas: evidence of origin from lymphocytes involved in innate immunity. Blood. 2003;101(9):3590–3.

Barnett BE, et al. B Cell-Intrinsic T-bet Expression Is Required To Control Chronic Viral Infection. J Immunol. 2016;197:1017–22. doi: 10.4049/jimmunol.1500368 .

Hagemann AR, Hagemann IS, Cadungog M, Hwang WT, Patel P, Lal P, Hammond R, Gimotty PA, Chu CS, Rubin SC, Birrer MJ. Tissue-based immune monitoring II: multiple tumor sites reveal immunologic homogeneity in serous ovarian carcinoma. Cancer Biol Ther. 2011;12(4):367–77.

Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol. 1995;57:289–300.

Linsley PS, Chaussabel D, Speake C. The Relationship of Immune Cell Signatures to Patient Survival Varies within and between Tumor Types. PLoS ONE. 2015;10(9):e0138726.

Chen PL, Roh W, Reuben A, Cooper ZA, Spencer CN, Prieto PA, Miller JP, Bassett RL, Gopalakrishnan V, Wani K, De Macedo MP. Analysis of immune signatures in longitudinal tumor samples yields insight into biomarkers of response and mechanisms of resistance to immune checkpoint blockade. Cancer Discov. 2016;6(8):827–37.