Erratum: A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells (Cell (2016) 166(6) (1500–1511) (S0092867416311497) (10.1016/j.cell.2016.08.052));A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

Cell

Volumn 166, Issue 6, 2016, Pages 1500-1511.e9

  Singer, Meromit ^a   Wang, Chao ^b   Cong, Le ^a   Marjanovic, Nemanja D ^a,c   Kowalczyk, Monika S ^a   Zhang, Huiyuan ^b   Nyman, Jackson ^a   Sakuishi, Kaori ^b   Kurtulus, Sema ^b   Gennert, David ^a   Xia, Junrong ^b   Kwon, John Y H ^a   Nevin, James ^b   Herbst, Rebecca H ^a   Yanai, Itai ^d   Rozenblatt Rosen, Orit ^a   Kuchroo, Vijay K ^b   Regev, Aviv ^a,c,e   Anderson, Ana C ^b  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

cancer; CD8; CRISPR Cas9; dysfunction; exhaustion; Gata 3; metallothioneins; single cell; T cell; TILs; tumor; zinc

Indexed keywords

GAMMA INTERFERON; GRANZYME B; INTERLEUKIN 2; METALLOTHIONEIN; PROGRAMMED DEATH 1 RECEPTOR; T LYMPHOCYTE RECEPTOR; TRANSCRIPTION FACTOR GATA 3; TUMOR NECROSIS FACTOR; TUMOR NECROSIS FACTOR RECEPTOR;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CD8+ T LYMPHOCYTE; CONTROLLED STUDY; CRISPR CAS SYSTEM; CYTOKINE PRODUCTION; FEMALE; GENE ACTIVATION; LYMPHOCYTE PROLIFERATION; MELANOMA; MELANOMA CELL; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; REGULATORY T LYMPHOCYTE; RNA SEQUENCE; SINGLE CELL ANALYSIS; T LYMPHOCYTE ACTIVATION; TRANSCRIPTION INITIATION; TUMOR ASSOCIATED LEUKOCYTE; TUMOR GROWTH; ANIMAL; BAGG ALBINO MOUSE; C57BL MOUSE; CARCINOGENESIS; DEFICIENCY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HUMAN; IMMUNOLOGY; LYMPHOCYTE ACTIVATION; METABOLISM; PATHOLOGY; PATHOPHYSIOLOGY;

ANIMALS; CARCINOGENESIS; CD8-POSITIVE T-LYMPHOCYTES; CRISPR-CAS SYSTEMS; FEMALE; GATA3 TRANSCRIPTION FACTOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LYMPHOCYTE ACTIVATION; LYMPHOCYTES, TUMOR-INFILTRATING; MELANOMA; METALLOTHIONEIN; MICE; MICE, INBRED BALB C; MICE, INBRED C57BL;

EID: 84986285632     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2017.11.006     Document Type: Erratum

References (38)

1. Anderson, A.C., Joller, N., Kuchroo, V.K., Lag-3, Tim-3, and TIGIT: Co-inhibitory Receptors with Specialized Functions in Immune Regulation. Immunity 44 (2016), 989–1004.
2. + T cells in metastases from melanoma patients. J. Clin. Invest. 121 (2011), 2350–2360.
3. Baitsch, L., Fuertes-Marraco, S.A., Legat, A., Meyer, C., Speiser, D.E., The three main stumbling blocks for anticancer T cells. Trends Immunol. 33 (2012), 364–372.
4. Blackburn, S.D., Shin, H., Haining, W.N., Zou, T., Workman, C.J., Polley, A., Betts, M.R., Freeman, G.J., Vignali, D.A., Wherry, E.J., Coregulation of CD8+ T cell exhaustion by multiple inhibitory receptors during chronic viral infection. Nat. Immunol. 10 (2009), 29–37.
5. Bonaventura, P., Benedetti, G., Albarède, F., Miossec, P., Zinc and its role in immunity and inflammation. Autoimmun. Rev. 14 (2015), 277–285.
6. Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A., Zhang, F., Multiplex genome engineering using CRISPR/Cas systems. Science 339 (2013), 819–823.
7. Doering, T.A., Crawford, A., Angelosanto, J.M., Paley, M.A., Ziegler, C.G., Wherry, E.J., Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory. Immunity 37 (2012), 1130–1144.
8. Eden, E., Lipson, D., Yogev, S., Yakhini, Z., Discovering motifs in ranked lists of DNA sequences. PLoS Comput. Biol., 3, 2007, e39.
9. Fourcade, J., Sun, Z., Benallaoua, M., Guillaume, P., Luescher, I.F., Sander, C., Kirkwood, J.M., Kuchroo, V., Zarour, H.M., Upregulation of Tim-3 and PD-1 expression is associated with tumor antigen-specific CD8+ T cell dysfunction in melanoma patients. J. Exp. Med. 207 (2010), 2175–2186.
10. Fuertes Marraco, S.A., Neubert, N.J., Verdeil, G., Speiser, D.E., Inhibitory Receptors Beyond T Cell Exhaustion. Front. Immunol., 6, 2015, 310.
11. Gaublomme, J.T., Yosef, N., Lee, Y., Gertner, R.S., Yang, L.V., Wu, C., Pandolfi, P.P., Mak, T., Satija, R., Shalek, A.K., et al. Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity. Cell 163 (2015), 1400–1412.
12. Giordano, M., Henin, C., Maurizio, J., Imbratta, C., Bourdely, P., Buferne, M., Baitsch, L., Vanhille, L., Sieweke, M.H., Speiser, D.E., et al. Molecular profiling of CD8 T cells in autochthonous melanoma identifies Maf as driver of exhaustion. EMBO J. 34 (2015), 2042–2058.
13. Hamer, D.H., Metallothionein. Annu. Rev. Biochem. 55 (1986), 913–951.
14. Johnson, W.E., Li, C., Rabinovic, A., Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8 (2007), 118–127.
15. Kim, P.S., Ahmed, R., Features of responding T cells in cancer and chronic infection. Curr. Opin. Immunol. 22 (2010), 223–230.
16. Kim, H.J., Barnitz, R.A., Kreslavsky, T., Brown, F.D., Moffett, H., Lemieux, M.E., Kaygusuz, Y., Meissner, T., Holderried, T.A., Chan, S., et al. Stable inhibitory activity of regulatory T cells requires the transcription factor Helios. Science 350 (2015), 334–339.
17. Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, 2009, R25.
18. Li, B., Dewey, C.N., RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 2011, 323.
19. Matsuzaki, J., Gnjatic, S., Mhawech-Fauceglia, P., Beck, A., Miller, A., Tsuji, T., Eppolito, C., Qian, F., Lele, S., Shrikant, P., et al. Tumor-infiltrating NY-ESO-1-specific CD8+ T cells are negatively regulated by LAG-3 and PD-1 in human ovarian cancer. Proc. Natl. Acad. Sci. USA 107 (2010), 7875–7880.
20. Picelli, S., Björklund, A.K., Faridani, O.R., Sagasser, S., Winberg, G., Sandberg, R., Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat. Methods 10 (2013), 1096–1098.
21. Ran, F.A., Cong, L., Yan, W.X., Scott, D.A., Gootenberg, J.S., Kriz, A.J., Zetsche, B., Shalem, O., Wu, X., Makarova, K.S., et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520 (2015), 186–191.
22. Reich, M., Liefeld, T., Gould, J., Lerner, J., Tamayo, P., Mesirov, J.P., GenePattern 2.0. Nat. Genet. 38 (2006), 500–501.
23. Restifo, N.P., Smyth, M.J., Snyder, A., Acquired resistance to immunotherapy and future challenges. Nat. Rev. Cancer 16 (2016), 121–126.
24. Rosvall, M., Bergstrom, C.T., Maps of random walks on complex networks reveal community structure. Proc. Natl. Acad. Sci. USA 105 (2008), 1118–1123.
25. Sakuishi, K., Apetoh, L., Sullivan, J.M., Blazar, B.R., Kuchroo, V.K., Anderson, A.C., Targeting Tim-3 and PD-1 pathways to reverse T cell exhaustion and restore anti-tumor immunity. J. Exp. Med. 207 (2010), 2187–2194.
26. Sarkar, S., Kalia, V., Haining, W.N., Konieczny, B.T., Subramaniam, S., Ahmed, R., Functional and genomic profiling of effector CD8 T cell subsets with distinct memory fates. J. Exp. Med. 205 (2008), 625–640.
27. Shalek, A.K., Satija, R., Adiconis, X., Gertner, R.S., Gaublomme, J.T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D., et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498 (2013), 236–240.
28. Shalem, O., Sanjana, N.E., Hartenian, E., Shi, X., Scott, D.A., Mikkelsen, T.S., Heckl, D., Ebert, B.L., Root, D.E., Doench, J.G., Zhang, F., Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343 (2014), 84–87.
29. Shekhar, K., Lapan, S.W., Whitney, I.E., Tran, N.M., Macosko, E.Z., Kowalczyk, M., Adiconis, X., Levin, J.Z., Nemesh, J., Goldman, M., et al. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics. Cell 166 (2016), 1308–1323.
30. Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., Mesirov, J.P., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102 (2005), 15545–15550.
31. Tindemans, I., Serafini, N., Di Santo, J.P., Hendriks, R.W., GATA-3 function in innate and adaptive immunity. Immunity 41 (2014), 191–206.
32. Tirosh, I., Izar, B., Prakadan, S.M., Wadsworth, M.H. 2nd, Treacy, D., Trombetta, J.J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352 (2016), 189–196.
33. van der Maaten, L., Hinton, G., Visualizing data using t-SNE. J. Mach. Learn. Res., 9, 2008, 26.
34. Wagner, F., GO-PCA: an unsupervised method to explore gene expression data using prior knowledge. PLoS ONE, 10, 2015, e0143196.
35. Wherry, E.J., Kurachi, M., Molecular and cellular insights into T cell exhaustion. Nat. Rev. Immunol. 15 (2015), 486–499.
36. Wherry, E.J., Ha, S.J., Kaech, S.M., Haining, W.N., Sarkar, S., Kalia, V., Subramaniam, S., Blattman, J.N., Barber, D.L., Ahmed, R., Molecular signature of CD8+ T cell exhaustion during chronic viral infection. Immunity 27 (2007), 670–684.
37. Zhou, Q., Munger, M.E., Veenstra, R.G., Weigel, B.J., Hirashima, M., Munn, D.H., Murphy, W.J., Azuma, M., Anderson, A.C., Kuchroo, V.K., Blazar, B.R., Coexpression of Tim-3 and PD-1 identifies a CD8+ T-cell exhaustion phenotype in mice with disseminated acute myelogenous leukemia. Blood 117 (2011), 4501–4510.
38. Zuniga, E.I., Macal, M., Lewis, G.M., Harker, J.A., Innate and adaptive immune regulation during chronic viral infections. Annu. Rev. Virol. 2 (2015), 573–597.