Readings

WEEK # TOPICS READINGS
1

Class introduction

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 No readings

2

Development of immune cells

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Kondo, M., Weissman, I.L., and Akashi, K. (1997). Identification of clonogenic common lymphoid progenitors in mouse bone marrow. Cell 91, 661-672.

Schulz, C., Gomez Perdiguero, E., Chorro, L., Szabo-Rogers, H., Cagnard, N., Kierdorf, K., Prinz, M., Wu, B., Jacobsen, S.E., Pollard, J.W., Frampton, J., Liu, K.J., and Geissmann, F. (2012). A lineage of myeloid cells independent of Myb and hematopoietic stem cells. Science 336, 86-90.

3

DNA rearrangements in adaptive immune cells

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Schatz, D.G., Oettinger, M.A., and Baltimore, D. (1989). The V(D)J recombination activating gene, RAG-1. Cell 59, 1035-1048.

Jain, S., Ba, Z., Zhang, Y., Dai, H.Q., and Alt, F.W. (2018). CTCF-binding elements mediate accessibility of RAG substrates during chromatin scanning. Cell 174, 102-116 e114.

4

T cells: Th2 and cytotoxic T cells

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Zheng, W., and Flavell, R.A. (1997). The transcription factor GATA-3 is necessary and sufficient for Th2 cytokine gene expression in CD4 T cells. Cell 89, 587-596.

Trautmann, L., Janbazian, L., Chomont, N., Said, E.A., Gimmig, S., Bessette, B., Boulassel, M.R., Delwart, E., Sepulveda, H., Balderas, R.S., Routy, J.P., Haddad, E.K., and Sekaly, R.P. (2006). Upregulation of PD-1 expression on HIV-specific CD8+ T cells leads to reversible immune dysfunction. Nature Medicine 12, 1198-1202.

5

Cell death and immune processes

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Yuan, J., Shaham, S., Ledoux, S., Ellis, H.M., and Horvitz, H.R. (1993). The C. elegans cell death gene ced-3 encodes a protein similar to mammalian interleukin-1 beta-converting enzyme. Cell 75, 641-652.

Kayagaki, N., Stowe, I.B., Lee, B.L., O’Rourke, K., Anderson, K., Warming, S., Cuellar, T., Haley, B., Roose-Girma, M., Phung, Q.T., Liu, P.S., Lill, J.R., Li, H., Wu, J., Kummerfeld, S., Zhang, J., Lee, W.P., Snipas, S.J., Salvesen, G.S., Morris, L.X., Fitzgerald, L., Zhang, Y., Bertram, E.M., Goodnow, C.C., and Dixit, V.M. (2015). Caspase-11 cleaves gasdermin D for non-canonical inflammasome signalling. Nature 526, 666-671.

6

Lymphocytes in disease

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Erikson, J., ar-Rushdi, A., Drwinga, H.L., Nowell, P.C., and Croce, C.M. (1983). Transcriptional activation of the translocated c-myc oncogene in burkitt lymphoma. Proceedings of the National Academy of Sciences of the United States of America 80, 820-824.

Doitsh, G., Galloway, N.L., Geng, X., Yang, Z., Monroe, K.M., Zepeda, O., Hunt, P.W., Hatano, H., Sowinski, S., Munoz-Arias, I., and Greene, W.C. (2014). Cell death by pyroptosis drives CD4 T cell depletion in HIV-1 infection. Nature 505, 509-514.

7

Th17 cells

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Ivanov, II, McKenzie, B.S., Zhou, L., Tadokoro, C.E., Lepelley, A., Lafaille, J.J., Cua, D.J., and Littman, D.R. (2006). The orphan nuclear receptor RORgt directs the differentiation program of proinflammatory IL-17+ T helper cells. Cell 126, 1121-1133.

McAllister, F., Bailey, J.M., Alsina, J., Nirschl, C.J., Sharma, R., Fan, H., Rattigan, Y., Roeser, J.C., Lankapalli, R.H., Zhang, H., Jaffee, E.M., Drake, C.G., Housseau, F., Maitra, A., Kolls, J.K., Sears, C.L., Pardoll, D.M., and Leach, S.D. (2014). Oncogenic Kras activates a hematopoietic-to-epithelial IL-17 signaling axis in preinvasive pancreatic neoplasia. Cancer Cell 25, 621-637.

8

T cells (adoptive immune transfer)

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Iwai, Y., Ishida, M., Tanaka, Y., Okazaki, T., Honjo, T., and Minato, N. (2002). Involvement of PD-L1 on tumor cells in the escape from host immune system and tumor immunotherapy by PD-L1 blockade. Proceedings of the National Academy of Sciences of the United States of America 99, 12293-12297.

Eyquem, J., Mansilla-Soto, J., Giavridis, T., van der Stegen, S.J., Hamieh, M., Cunanan, K.M., Odak, A., Gonen, M., and Sadelain, M. (2017). Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection. Nature 543, 113-117.

9

Autoimmunity

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Fontenot, J.D., Gavin, M.A., and Rudensky, A.Y. (2003). Foxp3 programs the development and function of CD4+CD25+ regulatory T cells. Nature Immunology 4, 330-336.

Wen, L., Ley, R.E., Volchkov, P.Y., Stranges, P.B., Avanesyan, L., Stonebraker, A.C., Hu, C., Wong, F.S., Szot, G.L., Bluestone, J.A., Gordon, J.I., and Chervonsky, A.V. (2008). Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455, 1109- 1113.

10

Innate lymphoid cells (ILC)

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von Moltke, J., Ji, M., Liang, H.E., and Locksley, R.M. (2016). Tuft-cell-derived IL-25 regulates an intestinal ILC2-epithelial response circuit. Nature 529, 221-225.

Sui, P., Wiesner, D.L., Xu, J., Zhang, Y., Lee, J., Van Dyken, S., Lashua, A., Yu, C., Klein, B.S., Locksley, R.M., Deutsch, G., and Sun, X. (2018). Pulmonary neuroendocrine cells amplify allergic asthma responses. Science 360.

11

Macrophages

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Brouard, S., Otterbein, L.E., Anrather, J., Tobiasch, E., Bach, F.H., Choi, A.M., and Soares, M.P. (2000). Carbon monoxide generated by heme oxygenase 1 suppresses endothelial cell apoptosis. The Journal of Experimental Medicine 192, 1015-1026.

Jaiswal, S., Jamieson, C.H., Pang, W.W., Park, C.Y., Chao, M.P., Majeti, R., Traver, D., van Rooijen, N., and Weissman, I.L. (2009). CD47 is upregulated on circulating hematopoietic stem cells and leukemia cells to avoid phagocytosis. Cell 138, 271-285.

12

Trained immunity

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Saeed, S., Quintin, J., Kerstens, H.H., Rao, N.A., Aghajanirefah, A., Matarese, F., Cheng, S.C., Ratter, J., Berentsen, K., van der Ent, M.A., Sharifi, N., Janssen-Megens, E.M., Ter Huurne, M., Mandoli, A., van Schaik, T., Ng, A., Burden, F., Downes, K., Frontini, M., Kumar, V., Giamarellos-Bourboulis, E.J., Ouwehand, W.H., van der Meer, J.W., Joosten, L.A., Wijmenga, C., Martens, J.H., Xavier, R.J., Logie, C., Netea, M.G., and Stunnenberg, H.G. (2014). Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science 345, 1251086.

Kaufmann, E., Sanz, J., Dunn, J.L., Khan, N., Mendonca, L.E., Pacis, A., Tzelepis, F., Pernet, E., Dumaine, A., Grenier, J.C., Mailhot-Leonard, F., Ahmed, E., Belle, J., Besla, R., Mazer, B., King, I.L., Nijnik, A., Robbins, C.S., Barreiro, L.B., and Divangahi, M. (2018). BCG educates hematopoietic stem cells to generate protective innate immunity against tuberculosis. Cell 172, 176-190 e119.

13

Emerging technologies in immunology

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Bendall, S.C., Simonds, E.F., Qiu, P., Amir el, A.D., Krutzik, P.O., Finck, R., Bruggner, R.V., Melamed, R., Trejo, A., Ornatsky, O.I., Balderas, R.S., Plevritis, S.K., Sachs, K., Pe’er, D., Tanner, S.D., and Nolan, G.P. (2011). Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 332, 687-696.

Villani, A.C., Satija, R., Reynolds, G., Sarkizova, S., Shekhar, K., Fletcher, J., Griesbeck, M., Butler, A., Zheng, S., Lazo, S., Jardine, L., Dixon, D., Stephenson, E., Nilsson, E., Grundberg, I., McDonald, D., Filby, A., Li, W., De Jager, P.L., Rozenblatt-Rosen, O., Lane, A.A., Haniffa, M., Regev, A., and Hacohen, N. (2017). Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356.

14 Field trip No readings
15 Oral presentations No readings

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