Y. Okabe and R. Medzhitov, Tissue biology perspective on macrophages, Nature Immunology, vol.195, issue.1, pp.9-17, 2016.
DOI : 10.1084/jem.20001858

T. A. Wynn, A. Chawla, and J. W. Pollard, Macrophage biology in development, homeostasis and disease, Nature, vol.6, issue.7446, pp.445-455, 2013.
DOI : 10.1038/nprot.2011.376
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3725458

A. Sica and A. Mantovani, Macrophage plasticity and polarization: in vivo veritas, Journal of Clinical Investigation, vol.122, issue.3, pp.787-795, 2012.
DOI : 10.1172/JCI59643DS1
URL : http://www.jci.org/articles/view/59643/files/pdf

P. J. Murray, Macrophage Polarization, Annual Review of Physiology, vol.79, issue.1, pp.541-566, 2017.
DOI : 10.1146/annurev-physiol-022516-034339

M. Stein, S. Keshav, N. Harris, G. , and S. , Interleukin 4 potently enhances murine macrophage mannose receptor activity: a marker of alternative immunologic macrophage activation, Journal of Experimental Medicine, vol.176, issue.1, pp.287-292, 1992.
DOI : 10.1084/jem.176.1.287

F. O. Martinez, G. , and S. , The M1 and M2 paradigm of macrophage activation: time for reassessment. F1000prime Rep, p.13, 2014.

M. Sironi, F. O. Martinez, D. D-'ambrosio, M. Gattorno, N. Polentarutti et al., Differential regulation of chemokine production by Fc?? receptor engagement in human monocytes: association of CCL1 with a distinct form of M2 monocyte activation (M2b, Type 2), Journal of Leukocyte Biology, vol.80, issue.2, pp.342-349, 2006.
DOI : 10.1189/jlb.1005586

G. Chinetti-gbaguidi and B. Staels, Macrophage polarization in metabolic disorders, Current Opinion in Lipidology, vol.22, issue.5, pp.365-372, 2011.
DOI : 10.1097/MOL.0b013e32834a77b4
URL : https://hal.archives-ouvertes.fr/inserm-00618280

A. Chow, B. D. Brown, and M. Merad, Studying the mononuclear phagocyte system in the molecular age, Nature Reviews Immunology, vol.83, issue.11, pp.788-798, 2011.
DOI : 10.4049/jimmunol.176.4.2465

D. M. Mosser and J. P. Edwards, Exploring the full spectrum of macrophage activation, Nature Reviews Immunology, vol.117, issue.12, pp.958-969, 2008.
DOI : 10.4049/jimmunol.171.7.3550

P. J. Murray, W. , and T. A. , Protective and pathogenic functions of macrophage subsets, Nature Reviews Immunology, vol.332, issue.11, pp.723-737, 2011.
DOI : 10.1126/science.1201475

F. Ginhoux, J. L. Schultze, P. J. Murray, J. Ochando, and S. K. Biswas, New insights into the multidimensional concept of macrophage ontogeny, activation and function, Nature Immunology, vol.332, issue.1, pp.34-40, 2015.
DOI : 10.1126/science.1198704

J. Xue, S. V. Schmidt, J. Sander, A. Draffehn, W. Krebs et al., Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation, Immunity, vol.40, issue.2, pp.274-288, 2014.
DOI : 10.1016/j.immuni.2014.01.006

M. Csete, Oxygen in the Cultivation of Stem Cells, Annals of the New York Academy of Sciences, vol.22, issue.1, pp.1-8, 2005.
DOI : 10.1038/nbt922

A. Johansson, M. Lundborg, C. M. Sköld, J. Lundahl, G. Tornling et al., Functional, morphological, and phenotypical differences between rat alveolar and interstitial macrophages., American Journal of Respiratory Cell and Molecular Biology, vol.16, issue.5, pp.582-588, 1997.
DOI : 10.1165/ajrcmb.16.5.9160840

J. C. Pfau, J. C. Schneider, A. J. Archer, J. Sentissi, F. J. Leyva et al., Environmental oxygen tension affects phenotype in cultured bone marrow-derived macrophages, AJP: Lung Cellular and Molecular Physiology, vol.286, issue.2, pp.354-362, 2004.
DOI : 10.1152/ajplung.00380.2002
URL : http://ajplung.physiology.org/content/ajplung/286/2/L354.full.pdf

A. C. Grodzki, C. Giulivi, and P. J. Lein, Oxygen Tension Modulates Differentiation and Primary Macrophage Functions in the Human Monocytic THP-1 Cell Line, PLoS ONE, vol.20, issue.1, p.54926, 2013.
DOI : 10.1371/journal.pone.0054926.t001

M. R. Elliott and K. S. And-ravichandran, The Dynamics of Apoptotic Cell Clearance, Developmental Cell, vol.38, issue.2, pp.147-160, 2016.
DOI : 10.1016/j.devcel.2016.06.029

P. J. Murray, J. E. Allen, S. K. Biswas, E. A. Fisher, D. W. Gilroy et al., Macrophage Activation and Polarization: Nomenclature and Experimental Guidelines, Immunity, vol.41, issue.1, pp.14-20, 2014.
DOI : 10.1016/j.immuni.2014.06.008
URL : http://doi.org/10.1016/j.immuni.2014.07.009

A. Kraut, M. Marcellin, A. Adrait, L. Kuhn, M. Louwagie et al., Peptide Storage: Are You Getting the Best Return on Your Investment? Defining Optimal Storage Conditions for Proteomics Samples, Journal of Proteome Research, vol.8, issue.7, pp.3778-3785, 2009.
DOI : 10.1021/pr900095u

J. Cox, N. Neuhauser, A. Michalski, R. A. Scheltema, J. V. Olsen et al., Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment, Journal of Proteome Research, vol.10, issue.4, pp.1794-1805, 2011.
DOI : 10.1021/pr101065j
URL : http://doi.org/10.1021/pr101065j

J. Cox, M. Y. Hein, C. A. Luber, I. Paron, N. Nagaraj et al., Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ, Molecular & Cellular Proteomics, vol.10, issue.9, pp.2513-2526, 2014.
DOI : 10.1074/mcp.M111.011015
URL : http://www.mcponline.org/content/13/9/2513.full.pdf

M. Pathan, S. Keerthikumar, C. Ang, L. Gangoda, C. Y. Quek et al., FunRich: An open access standalone functional enrichment and interaction network analysis tool, PROTEOMICS, vol.35, issue.10 Suppl, pp.2597-2601, 2015.
DOI : 10.1093/nar/gkm327

D. W. Huang, B. T. Sherman, and R. A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nature Protocols, vol.99, issue.1, pp.44-57, 2009.
DOI : 10.6026/97320630002428

D. Y. Vogel, J. E. Glim, A. W. Stavenuiter, M. Breur, P. Heijnen et al., Human macrophage polarization in vitro: Maturation and activation methods compared, Immunobiology, vol.219, issue.9, pp.695-703, 2014.
DOI : 10.1016/j.imbio.2014.05.002

S. J. Wuest, M. Crucet, C. Gemperle, C. Loretz, and M. Hersberger, Expression and regulation of 12/15-lipoxygenases in human primary macrophages, Atherosclerosis, vol.225, issue.1, pp.121-127, 2012.
DOI : 10.1016/j.atherosclerosis.2012.07.022

C. Lee, E. Song, C. Yoo, Y. Kwak, and M. Han, Lipopolysaccharide induces CD38 expression and solubilization in J774 macrophage cells, Molecules and Cells, vol.74, issue.6, pp.573-576, 2012.
DOI : 10.1016/j.lfs.2003.08.033
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3887823

O. Shea, J. J. Gadina, M. Schreiber, and R. D. , Cytokine Signaling in 2002, Cell, vol.109, issue.2, pp.121-131, 2002.
DOI : 10.1016/S0092-8674(02)00701-8

A. Lehtonen, S. Matikainen, and I. Julkunen, Interferons up-regulate STAT1, STAT2, and IRF family transcription factor gene expression in human peripheral blood mononuclear cells and macrophages, J. Immunol. Baltim. Md, vol.159, pp.794-803, 1950.

L. C. Platanias, Mechanisms of type-I- and type-II-interferon-mediated signalling, Nature Reviews Immunology, vol.132, issue.5, pp.375-386, 2005.
DOI : 10.1001/jama.290.24.3222

P. Newsholme, R. Curi, S. Gordon, and E. A. Newsholme, Metabolism of glucose, glutamine, long-chain fatty acids and ketone bodies by murine macrophages, Biochemical Journal, vol.239, issue.1, pp.121-125, 1986.
DOI : 10.1042/bj2390121

B. Kelly, O. Neill, and L. A. , Metabolic reprogramming in macrophages and dendritic cells in innate immunity, Cell Research, vol.131, issue.7, pp.771-784, 2015.
DOI : 10.1016/j.cmet.2014.03.014

I. Zanoni, R. Ostuni, L. R. Marek, S. Barresi, R. Barbalat et al., CD14 Controls the LPS-Induced Endocytosis of Toll-like Receptor 4, Cell, vol.147, issue.4, pp.868-880, 2011.
DOI : 10.1016/j.cell.2011.09.051

C. Abrial, S. Grassin-delyle, H. Salvator, M. Brollo, E. Naline et al., 15-Lipoxygenases regulate the production of chemokines in human lung macrophages, British Journal of Pharmacology, vol.277, issue.Database Issue, pp.4319-4330, 2015.
DOI : 10.1074/jbc.M205738200

D. Mevorach, J. O. Mascarenhas, D. Gershov, and K. B. Elkon, Complement-dependent Clearance of Apoptotic Cells by Human Macrophages, The Journal of Experimental Medicine, vol.9, issue.12, pp.2313-2320, 1998.
DOI : 10.1146/annurev.immunol.15.1.649

G. Zizzo, B. A. Hilliard, M. Monestier, and P. L. Cohen, Efficient Clearance of Early Apoptotic Cells by Human Macrophages Requires M2c Polarization and MerTK Induction, The Journal of Immunology, vol.189, issue.7, pp.3508-3520, 1950.
DOI : 10.4049/jimmunol.1200662

F. O. Martinez, S. Gordon, M. Locati, and A. Mantovani, Transcriptional Profiling of the Human Monocyte-to-Macrophage Differentiation and Polarization: New Molecules and Patterns of Gene Expression, The Journal of Immunology, vol.177, issue.10, pp.7303-7311, 1950.
DOI : 10.4049/jimmunol.177.10.7303

M. Beyer, M. R. Mallmann, J. Xue, A. Staratschek-jox, D. Vorholt et al., High-Resolution Transcriptome of Human Macrophages, PLoS ONE, vol.7, issue.9, p.45466, 2012.
DOI : 10.1371/journal.pone.0045466.s016

F. O. Martinez, L. Helming, R. Milde, A. Varin, B. N. Melgert et al., Genetic programs expressed in resting and IL-4 alternatively activated mouse and human macrophages: similarities and differences, Blood, vol.121, issue.9, pp.57-69, 2013.
DOI : 10.1182/blood-2012-06-436212
URL : http://www.bloodjournal.org/content/bloodjournal/121/9/e57.full.pdf

O. Neill, L. A. , P. , and E. J. , Immunometabolism governs dendritic cell and macrophage function, J. Exp. Med, vol.213, pp.15-23, 2016.

A. Wolf, S. Agnihotri, J. Micallef, J. Mukherjee, N. Sabha et al., Hexokinase 2 is a key mediator of aerobic glycolysis and promotes tumor growth in human glioblastoma multiforme, The Journal of Experimental Medicine, vol.124, issue.2, pp.313-326, 2011.
DOI : 10.1126/science.1170944

M. C. Etienne, S. Chéradame, J. L. Fischel, P. Formento, O. Dassonville et al., Response to fluorouracil therapy in cancer patients: the role of tumoral dihydropyrimidine dehydrogenase activity., Journal of Clinical Oncology, vol.13, issue.7, pp.1663-1670, 1995.
DOI : 10.1200/JCO.1995.13.7.1663

C. A. Janeway, K. Bottomly, J. Babich, P. Conrad, S. Conzen et al., Quantitative variation in la antigen expression plays a central role in immune regulation, Immunology Today, vol.5, issue.4, pp.99-105, 1984.
DOI : 10.1016/0167-5699(84)90043-4

A. Ayala, W. Ertel, and I. H. Chaudry, TRAUMA-INDUCED SUPPRESSION OF ANTIGEN PRESENTATION AND EXPRESSION OF MAJOR HISTOCOMPATIBILITY CLASS II ANTIGEN COMPLEX IN LEUKOCYTES, Shock, vol.5, issue.2, pp.79-90, 1996.
DOI : 10.1097/00024382-199602000-00001

A. Henze and M. Mazzone, The impact of hypoxia on tumor-associated macrophages, Journal of Clinical Investigation, vol.126, issue.10, pp.3672-3679, 2016.
DOI : 10.1172/JCI84427

D. Laoui, E. Van-overmeire, D. Conza, G. Aldeni, C. Keirsse et al., Tumor Hypoxia Does Not Drive Differentiation of Tumor-Associated Macrophages but Rather Fine-Tunes the M2-like Macrophage Population, Cancer Research, vol.74, issue.1, pp.24-30, 2014.
DOI : 10.1158/0008-5472.CAN-13-1196

P. Conde, M. Rodriguez, W. Van-der-touw, A. Jimenez, M. Burns et al., DC-SIGN+ Macrophages Control the Induction of Transplantation Tolerance, -H., and Ochando, J. (2015) DC-SIGN(+) Macrophages Control the Induction of Transplantation Tolerance, pp.1143-1158
DOI : 10.1016/j.immuni.2015.05.009

T. B. Geijtenbeek and S. I. Gringhuis, Signalling through C-type lectin receptors: shaping immune responses, Nature Reviews Immunology, vol.16, issue.7, pp.465-479, 2009.
DOI : 10.1172/JCI200419655

L. Tailleux, N. Pham-thi, A. Bergeron-lafaurie, J. Herrmann, P. Charles et al., DC-SIGN Induction in Alveolar Macrophages Defines Privileged Target Host Cells for Mycobacteria in Patients with Tuberculosis, PLoS Medicine, vol.32, issue.12, 2005.
DOI : 10.1371/journal.pmed.0020381.t003
URL : https://hal.archives-ouvertes.fr/pasteur-00154028

T. Roszer, M. P. Menéndez-gutiérrez, M. I. Lefterova, D. Alameda, V. Núñez et al., Autoimmune kidney disease and impaired engulfment of apoptotic cells in mice with macrophage peroxisome proliferator-activated receptor gamma or retinoid X receptor alpha deficiency, J. Immunol. Baltim. Md, vol.186, pp.621-631, 1950.

Z. Hu, Q. Zhou, C. Zhang, S. Fan, W. Cheng et al., Structural and biochemical basis for induced self-propagation of NLRC4, Science, vol.16, issue.5, pp.399-404, 2015.
DOI : 10.1016/j.str.2008.03.005

A. Devitt, M. , and L. J. , The innate immune system and the clearance of apoptotic cells, Journal of Leukocyte Biology, vol.90, issue.3, pp.447-457, 2011.
DOI : 10.1189/jlb.0211095

J. N. Fullerton and D. W. Gilroy, Resolution of inflammation: a new therapeutic frontier, Nature Reviews Drug Discovery, vol.182, issue.8, pp.551-567, 2016.
DOI : 10.4049/jimmunol.0801739

A. Devitt, O. D. Moffatt, C. Raykundalia, J. D. Capra, D. L. Simmons et al., Human CD14 mediates recognition and phagocytosis of apoptotic cells, Nature, vol.392, pp.505-509, 1998.

B. Tóth, E. Garabuczi, Z. Sarang, G. Vereb, G. Vámosi et al., Transglutaminase 2 Is Needed for the Formation of an Efficient Phagocyte Portal in Macrophages Engulfing Apoptotic Cells, The Journal of Immunology, vol.182, issue.4, pp.2084-2092, 1950.
DOI : 10.4049/jimmunol.0803444

C. Godson, S. Mitchell, K. Harvey, N. A. Petasis, N. Hogg et al., Cutting Edge: Lipoxins Rapidly Stimulate Nonphlogistic Phagocytosis of Apoptotic Neutrophils by Monocyte-Derived Macrophages, The Journal of Immunology, vol.164, issue.4, pp.1663-1667, 1950.
DOI : 10.4049/jimmunol.164.4.1663

M. Yang, J. Liu, C. Piao, J. Shao, and J. Du, ICAM-1 suppresses tumor metastasis by inhibiting macrophage M2 polarization through blockade of efferocytosis, Cell Death and Disease, vol.2, issue.6, p.1780, 2015.
DOI : 10.4049/jimmunol.1200625

F. Takizawa, S. Tsuji, and S. Nagasawa, Enhancement of macrophage phagocytosis upon iC3b deposition on apoptotic cells, FEBS Letters, vol.373, issue.2-3, pp.269-272, 1996.
DOI : 10.1016/0014-5793(95)01036-E

J. Ehrchen, L. Steinmüller, K. Barczyk, K. Tenbrock, W. Nacken et al., Glucocorticoids induce differentiation of a specifically activated, anti-inflammatory subtype of human monocytes, Blood, vol.109, issue.3, pp.1265-1274, 2007.
DOI : 10.1182/blood-2006-02-001115

S. Eligini, S. Fiorelli, E. Tremoli, C. , and S. , Inhibition of transglutaminase 2 reduces efferocytosis in human macrophages: Role of CD14 and SR-AI receptors, Nutrition, Metabolism and Cardiovascular Diseases, vol.26, issue.10, pp.922-930, 2016.
DOI : 10.1016/j.numecd.2016.05.011