References

Works cited in the project

Review papers

  • Mansour, M. K., Tam, J. M., & Vyas, J. M. (2012). The Cell Biology of the Innate Immune Response to Aspergillus Fumigatus. Annals of the New York Academy of Sciences, 1273(1), 78–84. https://doi.org/10.1111/j.1749-6632.2012.06837.x
  • Margalit, A., & Kavanagh, K. (2015). The Innate Immune Response to Aspergillus Fumigatus at the Alveolar Surface. FEMS Microbiology Reviews, 39(5), 670–687. https://doi.org/10.1093/femsre/fuv018
  • Park, S. J., & Mehrad, B. (2009). Innate Immunity to Aspergillus Species. Clinical Microbiology Reviews, 22(4), 535–551. https://doi.org/10.1128/CMR.00014-09
  • Gazendam, R. P., van de Geer, A., Roos, D., van den Berg, T. K., & Kuijpers, T. W. (2016). How Neutrophils Kill Fungi. Immunological Reviews, 273(1), 299–311. https://doi.org/10.1111/imr.12454

    Bioinformatic tools

    Statistical tools

      Preprocessing tools used in comparison between DCs and Macrophages response to A. fumigatus

      • Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A Flexible Trimmer for Illumina Sequence Data. Bioinformatics, 30(15), 2114–2120. https://doi.org/10.1093/bioinformatics/btu170
      • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report. Bioinformatics, 32(19), 3047–3048. https://doi.org/10.1093/bioinformatics/btw354
      • García-Alcalde, F., Okonechnikov, K., Carbonell, J., Cruz, L. M., Götz, S., Tarazona, S., Dopazo, J., Meyer, T. F., & Conesa, A. (2012). Qualimap: Evaluating next-Generation Sequencing Alignment Data. Bioinformatics, 28(20), 2678–2679. https://doi.org/10.1093/bioinformatics/bts503
      • Tommaso, P. D., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow Enables Reproducible Computational Workflows. Nature Biotechnology, 35(4), 316–319. https://doi.org/10.1038/nbt.3820

      Postprocessing tools used in comparison between DCs and Macrophages response to A. fumigatus

      • Love, M. I., Huber, W., & Anders, S. (2014). Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2. Genome Biology, 15(12). https://doi.org/10.1186/s13059-014-0550-8

      Papers about interactions of cells with A. fumigatus

      Epithelial cells

        Dendritic cells

        Specific to Aspergillus fumigatus

        • Bozza, S., Gaziano, R., Spreca, A., Bacci, A., Montagnoli, C., di Francesco, P., & Romani, L. (2002). Dendritic Cells Transport Conidia and Hyphae of Aspergillus Fumigatus from the Airways to the Draining Lymph Nodes and Initiate Disparate Th Responses to the Fungus. The Journal of Immunology, 168(3), 1362–1371. https://doi.org/10.4049/jimmunol.168.3.1362
        • Czakai, K., Leonhardt, I., Dix, A., Bonin, M., Linde, J., Einsele, H., Kurzai, O., & Loeffler, J. (2016). Krüppel-like Factor 4 Modulates Interleukin-6 Release in Human Dendritic Cells after in Vitro Stimulation with Aspergillus Fumigatus and Candida Albicans. Scientific Reports, 6, 27990. https://doi.org/10.1038/srep27990
        • Gafa, V., Lande, R., Gagliardi, M. C., Severa, M., Giacomini, E., Remoli, M. E., Nisini, R., Ramoni, C., Di Francesco, P., Aldebert, D., Grillot, R., & Coccia, E. M. (2006). Human Dendritic Cells Following Aspergillus Fumigatus Infection Express the CCR7 Receptor and a Differential Pattern of Interleukin-12 (IL-12), IL-23, and IL-27 Cytokines, Which Lead to a Th1 Response. Infection and Immunity, 74(3), 1480–1489. https://doi.org/10.1128/IAI.74.3.1480-1489.2006
        • Gafa, V., Remoli, M. E., Giacomini, E., Gagliardi, M. C., Lande, R., Severa, M., Grillot, R., & Coccia, E. M. (2007). In Vitro Infection of Human Dendritic Cells by Aspergillus Fumigatus Conidia Triggers the Secretion of Chemokines for Neutrophil and Th1 Lymphocyte Recruitment. Microbes and Infection, 9(8), 971–980. https://doi.org/10.1016/j.micinf.2007.03.015
        • Mezger, M., Kneitz, S., Wozniok, I., Kurzai, O., Einsele, H., & Loeffler, J. (2008). Proinflammatory Response of Immature Human Dendritic Cells Is Mediated by Dectin-1 after Exposure to Aspergillus Fumigatus Germ Tubes. The Journal of Infectious Diseases, 197(6), 924–931. https://doi.org/10.1086/528694
        • Park, S. J., Burdick, M. D., Brix, W. K., Stoler, M. H., Askew, D. S., Strieter, R. M., & Mehrad, B. (2010). Neutropenia Enhances Lung Dendritic Cell Recruitment in Response to Aspergillus via a Cytokine-to-Chemokine Amplification Loop. The Journal of Immunology, 185(10), 6190–6197. https://doi.org/10.4049/jimmunol.1002064
        • Park, S. J., Burdick, M. D., & Mehrad, B. (2012). Neutrophils Mediate Maturation and Efflux of Lung Dendritic Cells in Response to Aspergillus Fumigatus Germ Tubes. Infection and Immunity, 80(5), 1759–1765. https://doi.org/10.1128/IAI.00097-12
        • Stephen-Victor, E., Karnam, A., Fontaine, T., Beauvais, A., Das, M., Hegde, P., Prakhar, P., Holla, S., Balaji, K. N., Kaveri, S. V., Latgé, J.-P., Aimanianda, V., & Bayry, J. (2017). Aspergillus Fumigatus Cell Wall α-(1,3)-Glucan Stimulates Regulatory T-Cell Polarization by Inducing PD-L1 Expression on Human Dendritic Cells. The Journal of Infectious Diseases, 216(10), 1281–1294. https://doi.org/10.1093/infdis/jix469

        Macrophages

        Specific to Aspergillus fumigatus

        • Toledano, V., Hernández-Jiménez, E., Cubillos-Zapata, C., Flandez, M., Álvarez, E., Varela-Serrano, A., Cantero, R., Valles, G., García-Rio, F., & López-Collazo, E. (2015). Galactomannan Downregulates the Inflammation Responses in Human Macrophages via NFκB2/P100. Mediators of Inflammation, 2015, 942517. https://doi.org/10.1155/2015/942517

        Neutrophils

        Specific to Aspergillus fumigatus

        • Bellocchio, S., Moretti, S., Perruccio, K., Fallarino, F., Bozza, S., Montagnoli, C., Mosci, P., Lipford, G. B., Pitzurra, L., & Romani, L. (2004). TLRs Govern Neutrophil Activity in Aspergillosis. The Journal of Immunology, 173(12), 7406–7415. https://doi.org/10.4049/jimmunol.173.12.7406
        • Bonnett, C. R., Cornish, E. J., Harmsen, A. G., & Burritt, J. B. (2006). Early Neutrophil Recruitment and Aggregation in the Murine Lung Inhibit Germination of Aspergillus Fumigatus Conidia. Infection and Immunity, 74(12), 6528–6539. https://doi.org/10.1128/IAI.00909-06
        • Braem, S. G. E., Rooijakkers, S. H. M., van Kessel, K. P. M., de Cock, H., Wösten, H. A. B., van Strijp, J. A. G., & Haas, P.-J. A. (2015). Effective Neutrophil Phagocytosis of Aspergillus Fumigatus Is Mediated by Classical Pathway Complement Activation. Journal of Innate Immunity, 7(4), 364–374. https://doi.org/10.1159/000369493
        • Garlanda, C., Hirsch, E., Bozza, S., Salustri, A., De Acetis, M., Nota, R., Maccagno, A., Riva, F., Bottazzi, B., Peri, G., Doni, A., Vago, L., Botto, M., De Santis, R., Carminati, P., Siracusa, G., Altruda, F., Vecchi, A., Romani, L., & Mantovani, A. (2002). Non-Redundant Role of the Long Pentraxin PTX3 in Anti-Fungal Innate Immune Response. Nature, 420(6912), 182–186. https://doi.org/10.1038/nature01195
        • Gazendam, R. P., van Hamme, J. L., Tool, A. T. J., Hoogenboezem, M., van den Berg, J. M., Prins, J. M., Vitkov, L., van de Veerdonk, F. L., van den Berg, T. K., Roos, D., & Kuijpers, T. W. (2016). Human Neutrophils Use Different Mechanisms To Kill Aspergillus Fumigatus Conidia and Hyphae: Evidence from Phagocyte Defects. The Journal of Immunology, 196(3), 1272–1283. https://doi.org/10.4049/jimmunol.1501811
        • Levitz, S. M., & Farrell, T. P. (1990). Human Neutrophil Degranulation Stimulated by Aspergillus Fumigatus. Journal of Leukocyte Biology, 47(2), 170–175. https://doi.org/10.1002/jlb.47.2.170
        • van Bruggen, R., Drewniak, A., Jansen, M., van Houdt, M., Roos, D., Chapel, H., Verhoeven, A. J., & Kuijpers, T. W. (2009). Complement Receptor 3, Not Dectin-1, Is the Major Receptor on Human Neutrophils for β-Glucan-Bearing Particles. Molecular Immunology, 47(2), 575–581. https://doi.org/10.1016/j.molimm.2009.09.018
        • Zarember, K. A., Sugui, J. A., Chang, Y. C., Kwon-Chung, K. J., & Gallin, J. I. (2007). Human Polymorphonuclear Leukocytes Inhibit Aspergillus Fumigatus Conidial Growth by Lactoferrin-Mediated Iron Depletion. The Journal of Immunology, 178(10), 6367–6373. https://doi.org/10.4049/jimmunol.178.10.6367