S. C. Bendall, E. F. Simonds, P. Qiu, A. D. Amir-el, P. O. Krutzik et al., Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum, Science, vol.332, pp.687-696, 2011.

S. C. Bendall and G. P. Nolan, From single cells to deep phenotypes in cancer, Nat Biotechnol, vol.30, pp.639-647, 2012.

G. K. Behbehani, S. C. Bendall, M. R. Clutter, W. J. Fantl, and G. P. Nolan, Singlecell mass cytometry adapted to measurements of the cell cycle, Cytometry Part A, vol.81, pp.552-566, 2012.

S. Z. Ben-sasson, R. Gerstel, J. Hu-li, and W. E. Paul, Cell division is not a "clock" measuring acquisition of competence to produce IFN-or IL

, J Immunol, vol.166, pp.112-120, 2001.

J. J. Bird, D. R. Brown, A. C. Mullen, N. H. Moskowitz, M. A. Mahowald et al., Helper T-cell differentiation is controlled by the cell cycle, Immunity, vol.9, pp.229-237, 1998.
DOI : 10.1016/s1074-7613(00)80605-6

URL : https://doi.org/10.1016/s1074-7613(00)80605-6

B. Combadière, B. Combadiere, C. Blanc, T. Li, G. Carcelain et al., CD41Ki671 lymphocytes in HIV-infected patients are effector T cells accumulated in the G1 phase of the cell cycle, Eur J Immunol, vol.30, pp.3598-3603, 2000.

A. De-masson, A. Kirilovsky, R. Zoorob, V. Avettand-fenoel, V. Morin et al., Blimp-1 overexpression is associated with low HIV-1 reservoir and transcription levels in central memory CD41 T cells from elite controllers, AIDS, vol.28, issue.11, pp.1567-77, 2014.

M. Pogliaghi, S. Lambert, L. Assoumou, R. Zoorob, L. Papagno et al., and the Eramune-01 study group. HIV reservoir changes in resting CD4 subsets in the IL7 plus ART intensification Eramune 01 study, Conference on Retroviruses and Opportunistic infections, p.977, 2014.

K. E. Pauken and E. J. Wherry, Overcoming T cell exhaustion in infection and cancer, Trends Immunol, vol.36, pp.265-276, 2015.

J. Attanasio and E. J. Wherry, Costimulatory and Coinhibitory Receptor Pathways in Infectious Disease, Immunity, vol.44, pp.1052-1068, 2016.

G. M. Chew, T. Fujita, G. M. Webb, B. J. Burwitz, H. L. Wu et al., TIGIT Marks Exhausted T Cells, Correlates with Disease Progression, and Serves as a Target for Immune Restoration in HIV and SIV Infection, PLoS Pathog, vol.12, p.1005349, 2016.

A. C. Anderson, N. Joller, and V. K. Kuchroo, Lag-3, Tim-3, and TIGIT: Coinhibitory Receptors with Specialized Functions in Immune Regulation, Immunity, vol.44, pp.989-1004, 2016.

J. P. Moorman, J. M. Wang, Y. Zhang, X. J. Ji, C. J. Ma et al., Tim-3 Pathway Controls Regulatory and Effector T Cell Balance during Hepatitis C Virus Infection, J Immunol, vol.189, pp.755-766, 2012.

Z. Darzynkiewicz, J. Gong, G. Juan, B. Ardelt, and F. Traganos, Cytometry of cyclin proteins, Cytometry, vol.25, pp.1-13, 1996.

J. W. Jacobberger, R. M. Sramkoski, and T. Stefan, Multiparameter cell cycle analysis, Methods Mol Biol, vol.699, pp.229-249, 2011.

Z. Darzynkiewicz, H. Crissman, and J. W. Jacobberger, Cytometry of the cell cycle: Cycling through history, Cytometry Part A, vol.58, pp.21-32, 2004.

D. D. Richman, D. M. Margolis, M. Delaney, W. C. Greene, D. Hazuda et al., The challenge of finding a cure for HIV infection, Science, vol.323, pp.1304-1307, 2009.

S. G. Deeks, B. Autran, B. Berkhout, M. Benkirane, S. Cairns et al., Towards an HIV cure: a global scientific strategy, International AIDS Society Scientific Working Group on HIV Cure, vol.12, pp.607-614, 2012.

C. Katlama, S. G. Deeks, B. Autran, J. Martinez-picado, J. Van-lunzen et al., Barriers to a cure for HIV: New ways to target and eradicate HIV-1 reservoirs, Lancet, vol.381, pp.2109-2117, 2013.

F. Maldarelli, X. Wu, L. Su, F. R. Simonetti, W. Shao et al., HIV latency Specific HIV integration sites are linked to clonal expansion and persistence of infected cells, Science, vol.345, pp.179-183, 2014.

N. Chomont, M. El-far, P. Ancuta, L. Trautmann, F. A. Procopio et al., HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation, Nat Med, vol.15, pp.893-900, 2009.

R. F. Siliciano, W. C. Greene, and . Hiv, Cold Spring Harb Perspect Med, vol.1, p.7096, 2011.

B. Descours, V. Avettand-fenoel, C. Blanc, A. Samri, V. Supervie et al., Immune responses driven by protective human leukocyte antigen alleles from long-term nonprogressors are associated with low HIV reservoir in central memory CD4 T cells, Clin Infect Dis, vol.54, pp.1495-1503, 2012.

A. S-aez-ciri-on, C. Bacchus, L. Hocqueloux, V. Avettand-fenoel, I. Girault et al., Post-treatment HIV-1 controllers with a long-term virological remission after the interruption of early initiated antiretroviral therapy ANRS VISCONTI Study, PLoS Pathog, vol.9, p.1003211, 2013.

C. Bacchus, A. Cheret, A. El, V. Nembot, G. Blanc et al., A single HIV-1 cluster and a skewed immune homeostasis drive the early spread of HIV among resting CD41 cell subsets within one month post-infection, PLoS One, vol.8, p.64219, 2013.

E. Lugli, L. Gattinoni, A. Roberto, D. Mavilio, D. A. Price et al., Identification, isolation and in vitro expansion of human and nonhuman primate T stem cell memory cells, Nat Protoc, vol.8, pp.33-42, 2012.

M. J. Buzon, H. Sun, C. Li, A. Shaw, K. Seiss et al., HIV-1 persistence in CD41 T cells with stem cell-like properties, Nat Med, vol.20, pp.139-142, 2014.

M. Perreau, A. L. Savoye, D. Crignis, E. Corpataux, J. M. Cubas et al., Follicular helper T cells serve as the major CD4 T cell compartment for HIV-1 infection, replication, and production, J Exp Med, vol.210, pp.143-156, 2013.

B. Autran, R. Murphy, D. Costagliola, R. Tubiana, B. Clotet et al., Greater viral rebound & reduced time to resume antretroviral therapy after therapeutic immunization with the ALVAC-HIV vaccine (vCP1452), AIDS, vol.22, pp.1313-1322, 2008.

A. Cosma, G. Nolan, and B. Gaudilliere, Mass Cytometry: the time to settle down, Cytometry A, vol.91, pp.12-13, 2017.

D. Strauss-albee, E. Liang, T. Ranganath, N. Aziz, and C. Blish, The newborn human NK cell repertoire is phenotypically formed but functionally reduced, Cytometry B Clin Cytom, vol.92, pp.33-41, 2017.

Y. Abraham, B. Gerrits, M. Rebhan, M. Ludwig, G. Keller et al., Exploring glucocorticoid receptor agonists mechanism of action through mass cytometry and radial visualizations, Cytometry B Clin Cytom, vol.92, pp.42-56, 2017.

E. Vendrame, J. Fukuyama, D. Strauss-albee, S. Holmes, and C. Blish, Mass cytometry analytical approaches reveal cytokine-induced changes in natural killer cells, Cytometry B Clin Cytom, vol.92, pp.57-67, 2017.

N. Leelatian, D. B. Doxie, A. R. Greenplate, B. C. Mobley, J. M. Lehman et al., Single cell analysis of human tissues and solid tumors with mass cytometry, Cytometry B Clin Cytom, vol.92, pp.68-78, 2017.

R. Banga, R. Procopio, F. A. Noto, A. Pollakis, G. Cavassini et al.,

L. Leval, G. Pantaleo, and M. Perreau, PD-1(+) and follicular helper T cells are responsible for persistent HIV-1 transcription in treated aviremic individuals, Nat Med, vol.22, pp.754-61, 2016.

M. J. Buzon, H. Sun, C. Li, A. Shaw, K. Seiss et al.,

L. J. Tj, F. Pereyra, R. Zurakowski, B. D. Walker, E. S. Rosenberg et al., , 2014.

, HIV-1 persistence in CD4+ T cells with stem cell-like properties, Nat Med, vol.20, pp.139-181

A. Corneau, A. Cosma, S. Even, C. Katlama, R. Le-grand et al., Comprehensive Mass Cytometry Analysis of Cell Cycle, Activation, and Coinhibitory Receptors Expression in CD4 T Cells from Healthy and HIV Infected Individuals, Cytometry Part B: Clinical Cytometry, vol.92, issue.1, pp.21-32, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01515290

B. ;. Descours, . Petitjean, ;. Gaël, and J. López-zaragoza,

T. Bruel,

R. ;. Raffel, C. ;. Psomas, J. ;. Reynes, C. ;. Lacabaratz, and Y. Levy,

. Schwartz, . Olivier;-;-r, W. Bakeman, M. B. Lawani, G. Khoury et al., CD32a is a marker of a CD4 T-cell HIV reservoir harbouring replication-competent proviruses, Nature, vol.543, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01503531

S. Dafonseca, .. .. Hecht, F. M. Gosselin, A. , W. Salinas et al., CD4+ T cells expressing PD-1, TIGIT and LAG-3 contribute to HIV persistence during ART, PLoS pathogens, vol.12, issue.7, pp.35-48, 2016.

H. , O. N. Lwanga, J. Ramjee, G. Kaleebu, P. Porter et al., CD32-Expressing CD4 T Cells Are Phenotypically Diverse and Can Contain Proviral HIV DNA. Frontiers in Immunology 9, vol.34, p.2018, 2018.

S. C. Bendall, E. F. Simonds, and P. Qiu, Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum, Science, vol.332, pp.687-96, 2011.

S. C. Bendall and G. P. Nolan, From single cells to deep phenotypes in cancer, Nat Biotechnol, vol.30, pp.639-686, 2012.

A. Cosma, L. Grand, and R. , La couleur du métal, brève introduction à la cytométrie de masse, Med Sci (Paris), vol.27, pp.1072-1076, 2011.

S. Tricot, M. Meyrand, and C. Sammicheli, Evaluating the efficiency of isotope transmission for improved panel design and a comparison of the detection sensitivities of mass cytometer instruments, Cytometry A, vol.87, pp.357-68, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01515301

B. Anchang, T. D. Hart, and S. C. Bendall, Visualization and cellular hierarchy inference of single-cell data using SPADE, Nat Protoc, vol.11, pp.1264-79, 2016.

M. Masaeli, D. Gupta, and S. O'byrne, Multiparameter mechanical and morphometric screening of cells, Sci Rep, vol.6, p.37863, 2016.

L. A. Kamentsky, M. R. Melamed, and H. Derman, Spectrophotometer: new instrument for ultrarapid cell analysis, Science, vol.150, pp.630-631, 1965.

L. A. Kamentsky and M. R. Melamed, Spectrophotometric cell sorter, Science, vol.156, pp.1364-1369, 1967.

W. A. Bonner, H. R. Hulett, R. G. Sweet, and L. A. Herzenberg, Fluorescence activated cell sorting, Rev Sci Instrum, vol.43, pp.404-413, 1972.

G. Köhler and C. Milstein, Continuous cultures of fused cells secreting antibody of predefined specificity, Nature, vol.256, pp.495-502, 1975.

A. H. Coons and M. H. Kaplan, Localization of antigen in tissue cells; improvements in a method for the detection of antigen by means of fluorescent antibody, J Exp Med, vol.91, pp.1-13, 1950.

, The molecular probes handbook. A guide to fluorescent probes and labeling technologies, 11 th ed. Life Technologies Corporation, 2010.

G. Grégori, V. Patsekin, and B. Rajwa, Hyperspectral cytometry at the single-cell level using a 32-channel photodetector, Cytometry, vol.81, pp.35-44, 2012.

D. Novo, G. Grégori, and B. Rajwa, Generalized unmixing model for multispectral flow cytometry utilizing nonsquare compensation matrices, Cytometry, vol.83, pp.508-528, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00807657

J. L. Pauly, E. M. Allison, and E. L. Hurley, Fluorescent human lung macrophages analyzed by spectral confocal laser scanning microscopy and multispectral cytometry, Microsc Res Tech, vol.67, pp.79-89, 2005.
DOI : 10.1002/jemt.20191

S. Schmutz, M. Valente, A. Cumano, and S. Novault, Spectral cytometry has unique properties allowing multicolor analysis of cell suspensions isolated from solid tissue, PLoS One, vol.8, p.11, 2016.

K. Futamura, M. Sekino, and A. Hata, Novel full-spectral flow cytometry with multiple spectrallyadjacent fluorescent proteins and fluorochromes and visualization of in vivo cellular movement, Cytometry, vol.87, pp.830-872, 2015.

Z. B. Bjornson, G. P. Nolan, and W. J. Fantl, Single-cell mass cytometry for analysis of immune system functional states, Curr Opin Immunol, vol.25, issue.4, p.23999316, 2013.

S. C. Bendall, E. F. Simonds, P. Qiu, . Amir-el-a, P. O. Krutzik et al., Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum, Science, vol.332, issue.6030, p.21551058, 2011.

E. R. Zunder, R. Finck, G. K. Behbehani, E. Amir, S. Krishnaswamy et al., Palladiumbased mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm, Nat Protoc, vol.10, issue.2, p.25612231, 2015.

S. Baumgart, A. Peddinghaus, U. Schulte-wrede, H. E. Mei, and A. Grützkau, OMIP-034: Comprehensive immune phenotyping of human peripheral leukocytes by mass cytometry for monitoring immunomodulatory therapies, vol.91, pp.34-42, 2017.

P. O. Krutzik, M. R. Clutter, and G. P. Nolan, Coordinate analysis of murine immune cell surface markers and intracellular phosphoproteins by flow cytometry, J Immunol Baltim Md, vol.175, issue.4, pp.2357-65, 1950.

Y. Yao, R. Liu, M. S. Shin, M. Trentalange, H. Allore et al., CyTOF supports efficient detection of immune cell subsets from small samples, J Immunol Methods, vol.415, p.25450003, 2014.

A. F. Nassar, A. V. Wisnewski, and K. Raddassi, Automation of sample preparation for mass cytometry barcoding in support of clinical research: protocol optimization, Anal Bioanal Chem, 2017.

G. K. Behbehani, C. Thom, E. R. Zunder, R. Finck, B. Gaudilliere et al., Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining, Cytom Part J Int Soc Anal Cytol, vol.85, issue.12, pp.1011-1020, 2014.

B. Bodenmiller, E. R. Zunder, R. Finck, T. J. Chen, E. S. Savig et al., Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators, Nat Biotechnol, vol.30, issue.9, p.22902532, 2012.

L. Han, P. Qiu, Z. Zeng, J. L. Jorgensen, D. H. Mak et al., Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells. Cytom A, vol.87, pp.346-56, 2015.

A. Corneau, A. Cosma, S. Even, C. Katlama, L. Grand et al., Comprehensive Mass Cytometry Analysis of Cell Cycle, Activation, and Coinhibitory Receptors Expression in CD4 T Cells from Healthy and HIV-Infected Individuals, vol.92, pp.21-32, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01515290

A. F. Nassar, A. V. Wisnewski, and K. Raddassi, Mass cytometry moving forward in support of clinical research: advantages and considerations, Bioanalysis, vol.8, issue.4, p.26847541, 2016.

A. F. Nassar, H. Ogura, and A. V. Wisnewski, Impact of recent innovations in the use of mass cytometry in support of drug development, Drug Discov Today, vol.20, issue.10, p.26092491, 2015.

H. W. Lim, P. Hillsamer, A. H. Banham, and C. H. Kim, Cutting edge: direct suppression of B cells by CD4+ CD25 + regulatory T cells, J Immunol Baltim Md, vol.175, issue.7, pp.4180-4183, 1950.

W. Lin, J. L. Chen, H. Wu, Q. Fei, Y. Zheng et al., B cell subsets and dysfunction of regulatory B cells in IgG4-related diseases and primary Sjögren's syndrome: the similarities and differences, Arthritis Res Ther, vol.16, issue.3, p.24887143, 2014.

P. Schaerli, K. Willimann, A. B. Lang, M. Lipp, P. Loetscher et al., CXC chemokine receptor 5 expression defines follicular homing T cells with B cell helper function, J Exp Med, vol.192, issue.11, pp.1553-62, 2000.

H. Morbach, E. M. Eichhorn, J. G. Liese, and H. J. Girschick, Reference values for B cell subpopulations from infancy to adulthood, Clin Exp Immunol, vol.162, issue.2, p.20854328, 2010.

U. Ateba-ngoa, G. Mombo-ngoma, E. Zettlmeissl, L. Van-der-vlugt, S. E. De-jong et al., CD4+CD25hiFOXP3+ cells in cord blood of neonates born from filaria infected mother are negatively associated with CD4+Tbet+ and CD4+ROR?t+ T cells, PloS One, vol.9, issue.12, p.25531674, 2014.

T. Sayg?l?, S. C. Ak?nc?lar, B. Akgül, and A. Nalbant, Aggregatibacter actinomycetemcomitans GroEL protein promotes conversion of human CD4+ T cells into IFN? IL10 producing Tbet+ Th1 cells, PloS One, vol.7, issue.11, p.23152883, 2012.

H. Shen, J. C. Goodall, H. Gaston, and J. S. , Frequency and phenotype of peripheral blood Th17 cells in ankylosing spondylitis and rheumatoid arthritis, Arthritis Rheum, vol.60, issue.6, p.19479869, 2009.

H. E. Mei, M. D. Leipold, A. R. Schulz, C. Chester, and H. T. Maecker, Barcoding of live human peripheral blood mononuclear cells for multiplexed mass cytometry, J Immunol Baltim Md, vol.194, issue.4, pp.2022-2053, 1950.

L. Lai, R. Ong, J. Li, and S. Albani, A CD45-based barcoding approach to multiplex mass-cytometry (CyTOF), Cytom Part J Int Soc Anal Cytol, vol.87, issue.4, pp.369-74, 2015.

, , vol.13, 2018.

D. R. Bandura, V. I. Baranov, O. I. Ornatsky, A. Antonov, R. Kinach et al., Mass cytometry: Technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry, Anal Chem, vol.81, pp.6813-6822, 2009.

S. C. Bendall, E. F. Simonds, P. Qiu, E. D. Amir, P. O. Krutzik et al., Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum, Science, vol.332, pp.687-696, 2011.

B. Bodenmiller, E. R. Zunder, R. Finck, T. J. Chen, E. S. Savig et al., Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators, Nat Biotechnol, vol.30, pp.858-867, 2012.

E. W. Newell, N. Sigal, S. C. Bendall, G. P. Nolan, and M. M. Davis, Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD81 T cell phenotypes, Immunity, vol.36, pp.142-152, 2012.

G. K. Behbehani, S. C. Bendall, M. R. Clutter, W. J. Fantl, and G. P. Nolan, Single-cell mass cytometry adapted to measurements of the cell cycle, Cytometry A, vol.81, pp.552-566, 2012.

S. C. Bendall, G. P. Nolan, M. Roederer, and P. K. Chattopadhyay, A deep profiler's guide to cytometry, Trends Immunol, vol.33, pp.323-332, 2012.

H. T. Maecker, T. Frey, L. E. Nomura, and J. Trotter, Selecting fluorochrome conjugates for maximum sensitivity, Cytometry A, vol.62, pp.169-173, 2004.

Y. D. Mahnke and M. Roederer, Optimizing a multicolor immunophenotyping assay, Clin Lab Med, vol.27, pp.469-485, 2007.

L. Wang, F. Abbasi, O. Ornatsky, K. D. Cole, M. Misakian et al., Human CD41 lymphocytes for antigen quantification: Characterization using conventional flow cytometry and mass cytometry, Cytometry A, vol.81, pp.567-575, 2012.

M. D. Leipold and H. T. Maecker, Mass cytometry: Protocol for daily tuning and running cell samples on a CyTOF mass cytometer, J Vis Exp, vol.69, p.4398, 2012.

S. Guenounou, N. Bosquet, C. J. Dembek, L. Grand, R. Cosma et al., OMIP-016: Characterization of antigen-responsive macaque and human T-cells, Cytometry A, 2013.

H. Niu and R. S. Houk, Fundamental aspects of ion extraction in inductively coupled plasma mass spectrometry, Spectrochim Acta B Atomic Spectrosc, vol.51, pp.779-815, 1996.

D. Gerlich, Inhomogeneous RF-fields-A versatile tool for the study of processes with slow ions, Adv Chem Phys, vol.82, pp.1-176, 1992.

R. Finck, E. F. Simonds, A. Jager, S. Krishnaswamy, K. Sachs et al., Normalization of mass cytometry data with bead standards, Cytometry A, vol.83, pp.483-494, 2013.

M. Abdel-mohsen, L. Kuri-cervantes, J. Grau-exposito, A. M. Spivak, R. A. Nell et al., CD32 is expressed on cells with transcriptionally active HIV but does not enrich for HIV DNA in resting T cells, vol.10, 2018.

. Acosta-rodriguez, V. Eva, L. ;. Rivino, J. ;. Geginat, . Jarrossay et al., Surface phenotype and antigenic specificity of human interleukin 17-producing T helper memory cells, Nature immunology, 2007.

Z. ;. Ahmed, . Kawamura, ;. Tatsuyoshi, . Shimada, ;. Shinji et al., The role of human dendritic cells in HIV-1 infection, Journal of Investigative Dermatology, vol.135, pp.1225-1233, 2015.

B. Ajami and J. L. Bennett,

C. ;. Krieger, . Mcnagny, and M. Kelly,

F. Rossi and . Mv, Infiltrating monocytes trigger EAE progression, but do not contribute to the resident microglia pool, Nature neuroscience, vol.14, 1142.

I. Albrecht, U. Niesner, M. Janke, A. Radbruch, and H. Chang, The pro-inflammatory immunological memory: twist1 as a marker for chronically activated T lymphocytes, Zeitschrift fur Rheumatologie, vol.67, p.6, 2008.

J. Allen, . Wong, . Hl;-guyre, . Pm;-simon, and S. M. Gl;-wahl, Association of circulating receptor Fc gamma RIII-positive monocytes in AIDS patients with elevated levels of transforming growth factor-beta, The Journal of clinical investigation, vol.87, pp.1773-1779, 1991.

. Álvarez-errico, ;. Damiana, . Vento-tormo, ;. Roser, . Sieweke et al., Epigenetic control of myeloid cell differentiation, identity and function, Nature Reviews Immunology, vol.15, 2015.

K. ;. Anbazhagan, I. ;. Duroux-richard, and C. Jorgensen,

F. ;. Apparailly, Transcriptomic network support distinct roles of classical and non-classical monocytes in human, International reviews of immunology, vol.33, pp.470-489, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01845071

P. ;. Ancuta, R. ;. Rao, A. ;. Moses, A. ;. Mehle, . Shaw et al.,

. Luscinskas, ;. William, . Gabuzda, and ;. Dana, Fractalkine preferentially mediates arrest and migration of CD16+ monocytes, Journal of Experimental Medicine, vol.197, pp.1701-1707, 2003.

R. ;. Andargachew, R. Martinez, E. M. Kolawole, . Evavold, and D. Brian,

, Cell Affinity Diversity Is Equally Maintained during Acute and Chronic Infection, The Journal of Immunology, p.11, 2018.

V. Appay and D. Sauce, Immune activation and inflammation in HIV-1 infection: causes and consequences, The Journal of Pathology: A Journal of the Pathological Society of Great Britain and Ireland, vol.214, p.12, 2008.

N. J. Arhel, S. Souquere-besse, S. Munier, P. Souque, S. Guadagnini et al.,

P. Charneau, HIV-1 DNA Flap formation promotes uncoating of the preintegration complex at the nuclear pore, The EMBO journal, vol.26, issue.12, pp.3025-3037, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00167661

K. T. Arrildt, S. B. Joseph, and R. Swanstrom, The HIV-1 env protein: a coat of many colors, Current HIV/AIDS Reports, vol.9, issue.1, pp.52-63, 2012.

C. ;. Auffray, . Sieweke, H. Michael, and F. ;. Geissmann, Blood monocytes: development, heterogeneity, and relationship with dendritic cells, Annual review of immunology, vol.27, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00407757

B. Autran, G. Carcelain, T. S. Li, C. Blanc, D. Mathez et al., Positive effects of combined antiretroviral therapy on CD4+ T cell homeostasis and function in advanced HIV disease, Science, vol.277, issue.5322, pp.112-116, 1997.

B. ;. Autran, . Murphy, and L. Robert,

D. ;. Costagliola, R. ;. Tubiana, . Clotet, ;. Bonaventura, J. ;. Gatell et al., Greater viral rebound and reduced time to resume antiretroviral therapy after therapeutic immunization with the ALVAC-HIV vaccine (vCP1452), vol.22, pp.1313-1322, 2008.

D. Bandura, V. I. Baranov, O. I. Ornatsky, A. ;. Antonov, . Kinach et al.,

S. D. Tanner, Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry, Analytical chemistry, vol.81, pp.6813-6822, 2009.

R. Banga, F. A. Procopio, A. Noto, G. Pollakis, M. Cavassini et al., PD-1(+) and follicular helper T cells are responsible for persistent HIV-1 transcription in treated aviremic individuals, Nat Med, vol.22, pp.754-61, 2016.

D. H. Barouch, . Ghneim, ;. Khader, . Bosche, and J. William,

Y. Li and B. Berkemeier,

M. ;. Hull, . Bhattacharyya, ;. Sanghamitra, . Cameron, ;. Mark et al., Rapid inflammasome activation following mucosal SIV infection of rhesus monkeys, Viruses, vol.165, pp.1715-1758, 2014.

B. ;. Becher, A. ;. Schlitzer, . Chen, ;. Jinmiao, F. ;. Mair et al.,

K. W. Teng, ;. Weng, . Low, ;. Donovan, C. ;. Ruedl et al., High-dimensional analysis of the murine myeloid cell system, Nature immunology, vol.15, 1181.

G. K. Behbehani,

S. C. Bendall, . Clutter, R. Matthew, W. J. Fantl, . Nolan et al., Single-cell mass cytometry adapted to measurements of the cell cycle, Cytometry Part A, vol.81, pp.552-566, 2012.

R. Bellman, A Markovian decision process, Journal of Mathematics and Mechanics, pp.679-684, 1957.

S. C. Bendall, . Nolan, P. Garry, M. ;. Roederer, . Chattopadhyay et al., A deep profiler's guide to cytometry, Trends in immunology, vol.33, pp.323-332, 2012.

S. C. Bendall, E. F. Simonds, . Qiu, ;. Peng, . El-ad et al.,

R. ;. Melamed, A. ;. Trejo, and O. I. Ornatsky,

, Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum, Science, vol.332, pp.687-696, 2011.

A. ;. Biancotto, . Iglehart, J. Sarah, C. ;. Vanpouille, . Condack et al.,

A. ;. Lisco, E. ;. Ruecker, . Hirsch, ;. Ivan, L. B. Margolis et al.,

, HIV-1-induced activation of CD4+ T cells creates new targets for HIV-1 infection in human lymphoid tissue ex vivo, Blood, vol.111, p.27, 2008.

D. L. Birx, . Redfield, R. Robert, K. ;. Tencer, A. ;. Fowler et al., Induction of interleukin-6 during human immunodeficiency virus infection, Blood, vol.76, 1990.

Z. B. Bjornson, . Nolan, P. Garry, and W. J. Fantl, Single-cell mass cytometry for analysis of immune system functional states, Current opinion in immunology, vol.25, pp.484-494, 2013.

B. ;. Bodenmiller, E. R. Zunder, R. ;. Finck, T. J. Chen, and E. S. Savig,

R. Bruggner, E. F. Simonds, . Bendall, and C. Sean,

K. ;. Sachs, . Krutzik, and O. Peter,

, Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators, Nature biotechnology, vol.30, 2012.

W. Bonner, . Hulett, . Hr;-sweet, and L. A. Rg;-herzenberg, Fluorescence activated cell sorting, vol.43, pp.404-409, 1972.

O. Bourry, A. Mannioui, P. Sellier, C. Roucairol, L. Durand-gasselin et al., Effect of a short-term HAART on SIV load in macaque tissues is dependent on time of initiation and antiviral diffusion, Retrovirology, vol.7, issue.1, p.78, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00668445

J. M. Brenchley, T. W. Schacker, L. E. Ruff, . Price, A. David et al.,

A. T. Haase, CD4+ T cell depletion during all stages of HIV disease occurs predominantly in the gastrointestinal tract, Journal of Experimental Medicine, vol.6, pp.749-759, 2004.

M. J. Buzón, M. ;. Massanella, . Llibre, M. Josep, A. ;. Esteve et al.,

M. C. Puertas,

J. Gatell, . Domingo, ;. Pere, . Paredes, ;. Roger et al.,

, HIV-1 replication and immune dynamics are affected by raltegravir intensification of HAART-suppressed subjects, Nature medicine, vol.16, issue.4, 2010.

M. J. Buzon, H. Sun, C. Li, A. Shaw, K. Seiss et al., HIV-1 persistence in CD4+ T cells with stem cell-like properties, Nat Med, vol.20, pp.139-181, 2014.

J. F. Camargo,

. Kulkarni, . Hemant;-agan, and K. Brian,

A. Gaitan and L. A. Beachy,

. Srinivas, . Sowmya;-he, ;. Weijing, S. ;. Anderson, . Marconi et al., Responsiveness of T Cells to Interleukin-7 Is Associated with Higher CD4+ T Cell Counts in HIV-1-Positive Individuals with Highly Active Antiretroviral Therapy-Induced Viral Load Suppression, vol.12, pp.1872-1882, 2009.

A. Caruso, S. Licenziati, M. Corulli, A. D. Canaris, M. A. De-francesco et al., Flow cytometric analysis of activation markers on stimulated T cells and their correlation with cell proliferation, Cytometry: The Journal of the International Society for Analytical Cytology, vol.27, issue.1, pp.71-76, 1997.

M. Catalfamo, M. Di-mascio, Z. Hu, S. Srinivasula, V. Thaker et al., HIV infection associated immune activation occurs by two distinct pathways that differentially affect CD4 and CD8 T cells, Proceedings of the National Academy of Sciences, p.810032105, 2008.

M. ;. Cavrois and T. Banerjee,

G. ;. Mukherjee and N. Raman,

R. ;. Hussien, B. Rodriguez, and . Aguilar,

J. ;. Vasquez, . Spitzer, and H. Matthew,

N. H. Lazarus, J. J. Jones, ;. Valentina, . Tryniszewska, ;. Elzbieta et al., Mass cytometric analysis of HIV entry, replication, and remodeling in tissue CD4+ T cells, Cell reports, vol.20, pp.984-998, 2017.

A. ;. Boasso, . Tsai, and . Wen-po,

C. ;. Petrovas, . Fuchs, ;. Dietmar, and J. Heraud,

D. ;. Venzon, Immune activation driven by CTLA-4 blockade augments viral replication at mucosal sites in simian immunodeficiency virus infection, The Journal of Immunology, vol.180, p.40, 2008.

H. Chang,

C. ;. Helbig, L. ;. Tykocinski, S. ;. Kreher, J. ;. Koeck, . Niesner et al., Expression of IL-10 in Th memory lymphocytes is conditional on IL-12 or IL-4, unless the IL-10 gene is imprinted by GATA-3, European journal of immunology, vol.37, p.41, 2007.

M. P. Chao, J. Seita, . ;-weissman, and . Il;, Establishment of a normal hematopoietic and leukemia stem cell hierarchy, Cold Spring Harbor symposia on quantitative biology, vol.42, 2008.

R. G. Cheng, . Nixon, and F. Douglas, Herpes simplex virus and HIV-1: deciphering viral synergy,The Lancet Infectious Diseases, vol.9, 2009.

Y. ;. Cheng, . Wong, T. Michael, and . Van-der-maaten,

, Categorical analysis of human T cell heterogeneity with one-dimensional soliexpression by nonlinear stochastic embedding, The Journal of Immunology, 2015.

G. M. Chew, . Fujita, ;. Tsuyoshi, G. M. Webb, . Burwitz et al.,

J. S. Reed, K. B. Hammond, K. Clayton, . Ishii, ;. Naoto et al., TIGIT marks exhausted T cells, correlates with disease progression, and serves as a target for immune restoration in HIV and SIV infection, PLoS pathogens, vol.12, 2016.

N. ;. Chomont, M. ;. El-far, . Ancuta, L. ;. Petronela;-trautmann, . Procopio et al.,

G. ;. Ghattas and J. M. Brenchley, HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation, Nature medicine, vol.15, 2009.

T. Chun,

L. ;. Stuyver, S. B. Mizell, L. A. Ehler, J. Mican, M. Ann et al., Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy, Proceedings of the National Academy of Sciences, vol.94, pp.13193-13197, 1997.

Y. ;. Chung, . Tanaka, ;. Shinya, . Chu, ;. Fuliang et al.,

S. ;. Rawal and Y. Wang,

H. Lim, J. Reynolds, and X. Zhou,

, Follicular regulatory T cells expressing Foxp3 and Bcl-6 suppress germinal center reactions, Nature medicine, vol.17, 2011.

. Cieri, B. ;. Nicoletta;-camisa, . Cocchiarella, ;. Fabienne, . Forcato et al.,

F. Ciceri, IL-7 and IL-15 instruct the generation of human memory stem T cells from naive precursors, Blood, p.49, 2012.

A. Cillo, . Vagratian, ;. David, M. ;. Bedison, E. ;. Anderson et al.,

E. ;. Fyne, D. ;. Koontz, . Coffin, M. John, . Piatak et al., Improved single copy assays for quantification of persistent HIV-1 viremia in patients on suppressive antiretroviral therapy, Journal of clinical microbiology, 2014.

K. L. Clayton, . Douglas-vail, B. Matthew, A. Rahman, and . Nur-ur,

K. E. Medcalf,

I. Y. Xie, . Chew, M. Glen, R. ;. Tandon, . Lanteri et al., Soluble T cell immunoglobulin mucin domain 3 is shed from CD8+ T cells by the sheddase ADAM10, is increased in plasma during untreated HIV infection, and correlates with HIV disease progression, Journal of virology, vol.89, pp.3723-3736, 2015.

L. Cockerham and J. D. Siliciano,

E. ;. Sinclair, U. ;. O'doherty, S. ;. Palmer, . Yukl, A. Steven et al.,

R. F. Siliciano, CD4+ and CD8+ T cell activation are associated with HIV DNA in resting CD4+ T cells, PloS one, vol.9, 2014.

C. Coleman, . Wu, and ;. Li, HIV interactions with monocytes and dendritic cells: viral latency and reservoirs, BioMed Central, p.53, 2009.

M. Colonna, G. Trinchieri, and Y. J. Liu, Plasmacytoid dendritic cells in immunity, Nature immunology, vol.5, issue.12, p.1219, 2004.

A. Coons, . Kaplan, and H. Melvin, Localization of antigen in tissue cells: II. Improvements in a method for the detection of antigen by means of fluorescent antibody, Journal of Experimental Medicine, vol.91, pp.1-13, 1950.

A. ;. Cooper, M. ;. García, C. ;. Petrovas, . Yamamoto, ;. Takuya et al., HIV-1 causes CD4 cell death through DNA-dependent protein kinase during viral integration, Nature, vol.498, 2013.

L. ;. Cosmi, R. ;. Cimaz, L. ;. Maggi, V. ;. Santarlasci, M. ;. Capone et al., Evidence of the transient nature of the Th17 phenotype of CD4+ CD161+ T cells in the synovial fluid of patients with juvenile idiopathic arthritis, Arthritis & Rheumatism, vol.63, 2011.

S. ;. Crotty, T follicular helper cell differentiation, function, and roles in disease, Immunity, vol.41, pp.529-542, 2014.

S. ;. Crotty, Follicular helper CD4 T cells (Tfh), Annual Reviews, vol.29, pp.621-663, 2011.

S. ;. Crotty, . Ahmed, and ;. Rafi, Immunological memory in humans, Seminars in immunology, vol.16, 2004.

R. Cubas, . Mudd, C. Joseph, and A. Savoye,

M. ;. Perreau, . Van-grevenynghe, ;. Julien, . Metcalf, ;. Talibah et al., Inadequate T follicular cell help impairs B cell immunity during HIV infection, Nature medicine, p.61, 2013.

D. Danilovic and . Mendes-correa,

É. Lima, . Zambrini, ;. K. Heverton, . Barros, ;. Raffaelle et al., Correlations of CTLA-4 gene polymorphisms and hepatitis C chronic infection, Liver International, vol.32, p.62, 2012.

L. Davies, . Jenkins, and J. Stephen,

J. E. Allen,

P. R. Taylor, Tissue-resident macrophages, Nature immunology, vol.14, 2013.

D. Boer and J. Rob, Time scales of CD4+ T cell depletion in HIV infection, PLoS medicine, 2007.

S. Deeks, . Walker, and D. Bruce, The immune response to AIDS virus infection: good, bad, or both?, The Journal of clinical investigation, vol.113, pp.808-810, 2004.

B. Descours, A. Cribier, C. Chable-bessia, D. Ayinde, G. Rice et al., SAMHD1 restricts HIV-1 reverse transcription in quiescent CD4+ T-cells, vol.9, p.87, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00750251

B. ;. Descours, . Petitjean, ;. Gaël, and J. López-zaragoza,

T. Bruel,

R. ;. Raffel, C. ;. Psomas, J. ;. Reynes, C. ;. Lacabaratz, and Y. Levy,

O. ;. Schwartz, CD32a is a marker of a CD4 T-cell HIV reservoir harbouring replication-competent proviruses, Nature, vol.543, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01503531

D. Nunzio, F. Danckaert, A. Fricke, T. Perez, P. Fernandez et al., Human nucleoporins promote HIV-1 docking at the nuclear pore, nuclear import and integration, PloS one, vol.7, issue.9, p.46037, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01536163

D. Pucchio, ;. Tiziana, . Chatterjee, ;. Bithi, and . Smed-sörensen,

A. ;. Palazzo, M. ;. Montes, . Xue, . Yaming;-mellman, ;. Ira et al.,

J. E. Connolly, Direct proteasome-independent cross-presentation of viral antigen by plasmacytoid dendritic cells on major histocompatibility complex class I, Nature immunology, vol.9, issue.5, 2008.

S. M. Dillon, E. J. Lee, A. M. Donovan, K. Guo, M. S. Harper et al., Enhancement of HIV-1 infection and intestinal CD4+ T cell depletion ex vivo by gut microbes altered during chronic HIV-1 infection, Retrovirology, vol.13, issue.1, p.5, 2016.

K. E. Diggins,

. Ferrell, ;. Brent, and J. M. Irish, Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data, Methods, vol.82, pp.55-63, 2015.

G. ;. Doitsh, M. ;. Cavrois, . Lassen, G. Kara, . Zepeda et al.,

M. L. Santiago,

A. M. Hebbeler,

W. C. Greene, Abortive HIV infection mediates CD4 T cell depletion and inflammation in human lymphoid tissue, Cell, vol.143, pp.789-801, 2010.

G. ;. Doitsh, N. Galloway, . Lk;-geng, ;. Xin, . Yang et al.,

O. ;. Zepeda, . Hunt, W. Peter, . Hatano, ;. Hiroyu et al., Cell death by pyroptosis drives CD4 T-cell depletion in HIV-1 infection, Nature, vol.505, 2014.

M. Dustin, . Choudhuri, and ;. Kaushik, Signaling and polarized communication across the T cell immunological synapse, Annual review of cell and developmental biology, vol.32, pp.303-325, 2016.

C. Dutertre,

S. ;. Amraoui, A. ;. Derosa, and J. Jourdain,

L. ;. Vimeux, M. ;. Goguet, . Degrelle, ;. Séverine, . Feuillet et al.,

M. ;. Müller-trutwin, Pivotal role of M-DC8+ monocytes from viremic HIV-infected patients in TNF? over-production in response to microbial products, Blood, 2012.

M. Eggena, . Barugahare, ;. Banson, N. ;. Jones, . Okello et al., Depletion of regulatory T cells in HIV infection is associated with immune activation, The Journal of Immunology, vol.174, pp.4407-4414, 2005.

G. Paukovics, . Cameron, and U. Paul,

A. ;. Solomon, S. R. Lewin, . Gorry, R. Paul, A. ;. Jaworowski et al., The CD16+ monocyte subset is more permissive to infection and preferentially harbors HIV-1 in vivo, The Journal of Immunology, vol.178, pp.6581-6589, 2007.

L. J. Else, . Taylor, ;. Stephen, . Back, J. David et al., Pharmacokinetics of antiretroviral drugs in anatomical sanctuary sites: the fetal compartment (placenta and amniotic fluid), vol.16, p.78, 2011.

. Epelman, K. J. Slava;-lavine, . Randolph, and J. Gwendalyn, Origin and functions of tissue macrophages, Immunity, vol.41, pp.21-35, 2014.

M. Estébanez-muñoz, N. Stella, and J. I. Bernardino, HIV infection and chronic inflammation: is the bacterial translocation the underlying cause, Medicina clinica, vol.138, issue.15, pp.673-677, 2012.

J. Estes, C. ;. Kityo, . Ssali, ;. Francis, L. ;. Swainson et al.,

D. Prete and Q. Gregory,

S. Deeks, . Luciw, A. Paul, . Chipman, and G. Jeffrey,

G. J. Beilman, Defining total-body AIDS-virus burden with implications for curative strategies, Nature medicine, vol.23, 1271.

J. D. Estes, Q. Li, M. R. Reynolds, S. Wietgrefe, L. Duan et al., Premature induction of an immunosuppressive regulatory T cell response during acute simian immunodeficiency virus infection, The Journal of infectious diseases, vol.193, issue.5, pp.703-712, 2006.

L. M. Fahey, E. B. Wilson, H. ;. Elsaesser, C. D. Fistonich, D. B. Mcgavern et al., Viral persistence redirects CD4 T cell differentiation toward T follicular helper cells, Journal of Experimental Medicine, vol.208, pp.987-999, 2011.

L. ;. Fantuzzi, P. ;. Borghi, . Ciolli, ;. Veniero, . Pavlakis et al.,

S. Gessani, Loss of CCR2 expression and functional response to monocyte chemotactic protein (MCP-1) during the differentiation of human monocytes: role of secreted MCP-1 in the regulation of the chemotactic response, Blood, vol.94, pp.875-883, 1999.

D. L. Farber, N. A. Yudanin, . Restifo, and P. Nicholas, Human memory T cells: generation, compartmentalization and homeostasis, Nature Reviews Immunology, 2014.

S. ;. Farkona, . Diamandis, P. Eleftherios, . Blasutig, and M. Ivan, Cancer immunotherapy: the beginning of the end of cancer?, BioMed Central, vol.86, 2016.

N. ;. Fazilleau, L. Mcheyzer-williams, H. ;. Rosen, . Mcheyzer-williams, and G. Michael, The function of follicular helper T cells is regulated by the strength of T cell antigen receptor binding, Nature immunology, 2009.

M. ;. Ferreira, E. ;. Pichon, D. ;. Carmier, E. ;. Bouquet, and C. Pageot,

T. ;. Bejan-angoulvant, M. ;. Campana, . Vermes, ;. Emmanuelle, . Marchandadam et al., Coronary Toxicities of Anti-PD-1 and Anti-PD-L1 Immunotherapies: a Case Report and Review of the Literature and International Registries, Targeted oncology, pp.1-7, 2018.

M. ;. Février, . Dorgham, ;. Karim, and A. ;. Rebollo, CD4+ T cell depletion in human immunodeficiency virus (HIV) infection: role of apoptosis, Molecular Diversity Preservation International, vol.3, pp.586-612, 2011.

R. ;. Finck and E. F. Simonds,

A. ;. Jager, . Krishnaswamy, ;. Smita, and K. Sachs,

W. ;. Fantl, . Pe'er, ;. Dana, . Nolan, and P. Garry,

S. C. Bendall, Normalization of mass cytometry data with bead standards, Cytometry Part A, vol.83, pp.483-494, 2013.

D. ;. Finzi, M. ;. Hermankova, T. ;. Pierson, L. M. Carruth, . Buck et al., Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy, Science, vol.278, 1295.

C. Fletcher, K. ;. Staskus, . Wietgrefe, W. Stephen, M. ;. Rothenberger et al.,

A. ;. Thorkelson, . Schmidt, and E. Thomas, Persistent HIV-1 replication is associated with lower antiretroviral drug concentrations in lymphatic tissues, Proceedings of the National Academy of Sciences, vol.111, pp.2307-2312, 2014.

S. Fleury, . Rizzardi, A. Gp;-chapuis, G. Tambussi, C. Knabenhans et al.,

J. Corpataux,

A. Lazzarin and F. Miedema, Long-term kinetics of T cell production in HIV-infected subjects treated with highly active antiretroviral therapy, Proceedings of the National Academy of Sciences, vol.97, pp.5393-5398, 2000.

R. B. Foxall,

A. S. Albuquerque, . Soares, S. Rui, . Baptista, and P. António,

R. ;. Cavaleiro, R. ;. Tendeiro, . Gomes, ;. Perpétua, . Victorino et al.,

A. E. Sousa,

, Memory and naive-like regulatory CD4+ T cells expand during HIV-2 infection in direct association with CD4+ T-cell depletion irrespectively of viremia, Aids, vol.25, 1961.

L. ;. Franken, . Schiwon, ;. Marzena, . Kurts, and ;. Christian, Macrophages: sentinels and regulators of the immune system, Cellular microbiology, vol.18, p.95, 2016.

A. P. Frei, F. A. Bava, E. R. Zunder, E. W. Hsieh, S. Y. Chen et al., Highly multiplexed simultaneous detection of RNAs and proteins in single cells, Nature methods, vol.13, issue.3, p.269, 2016.

R. ;. Fromentin, W. ;. Bakeman, M. Lawani, and G. Khoury,

W. ;. Hartogensis, . Dafonseca, ;. Sandrina, M. ;. Killian, L. ;. Epling et al., CD4+ T cells expressing PD-1, TIGIT and LAG-3 contribute to HIV persistence during ART, PLoS pathogens, vol.12, 2016.

G. ;. Galicia and J. L. Gommerman, Plasmacytoid dendritic cells and autoimmune inflammation, vol.395, p.98, 2014.

L. ;. Gama and E. N. Shirk,

J. N. Russell,

K. I. Carvalho, M. ;. Li, and S. E. Queen,

J. Kalil, M. Zink, J. E. Clements, . Kallas, G. Esper et al., Expansion of a subset of CD14highCD16negCCR2low/neg monocytes functionally similar to myeloid-derived suppressor cells during SIV and HIV infection, Journal of leukocyte biology, vol.91, pp.803-816, 2012.

O. ;. Schwartz, R. Koup, . Nabel, and J. Gary, Infection of specific dendritic cells by CCR5-tropic human immunodeficiency virus type 1 promotes cell-mediated transmission of virus resistant to broadly neutralizing antibodies, Journal of virology, vol.78, pp.11980-11987, 2004.

L. ;. Gattinoni, E. ;. Lugli, Y. ;. Ji, . Pos, ;. Zoltan et al.,

M. F. Quigley,

J. R. Almeida, E. ;. Gostick, . Yu, ;. Zhiya, and C. ;. Carpenito, A human memory T cell subset with stem cell-like properties, Nature medicine, vol.17, 1290.

K. D. Gerold,

P. ;. Zheng, . Rainbow, B. Daniel, A. ;. Zernecke, and L. S. Wicker,

S. ;. Kissler, The soluble CTLA-4 splice variant protects from type 1 diabetes and potentiates regulatory T-cell function, Am Diabetes Assoc, 2011.

F. ;. Ginhoux, . Guilliams, and ;. Martin, Tissue-resident macrophage ontogeny and homeostasis, Immunity, vol.44, pp.439-449, 2016.

F. Ginhoux, . Jung, and ;. Steffen, Monocytes and macrophages: developmental pathways and tissue homeostasis, Nature Reviews Immunology, vol.14, pp.392-404, 2014.

J. V. Giorgi, L. E. Hultin, J. A. Mckeating, T. D. Johnson, B. Owens et al., Shorter survival in advanced human immunodeficiency virus type 1 infection is more closely associated with T lymphocyte activation than with plasma virus burden or virus chemokine coreceptor usage, The Journal of infectious diseases, vol.179, issue.4, pp.859-870, 1999.

G. Silva, ;. Isabel, L. ;. Rüegg, B. F. Gibbs, and M. Bardelli,

A. ;. Fruehwirth, . Varani, ;. Luca, . Berger, M. Steffen et al.,

. Sumbayev and V. Vadim, The immune receptor Tim-3 acts as a trafficker in a Tim-3/galectin-9 autocrine loop in human myeloid leukemia cells, 2016.

F. González-scarano and J. Martín-garcía, The neuropathogenesis of AIDS, Nature reviews immunology, vol.5, issue.1, p.69, 2005.

A. Gosselin, W. Salinas, T. R. Planas, D. Wacleche, V. S. Zhang et al., HIV persists in CCR6+CD4+ T cells from colon and blood during antiretroviral therapy, Aids, vol.31, pp.35-48, 2017.

M. L. Gougeon, H. Lecoeur, F. Boudet, E. Ledru, S. Marzabal et al., Lack of chronic immune activation in HIV-infected chimpanzees correlates with the resistance of T cells to Fas/Apo-1 (CD95)-induced apoptosis and preservation of a T helper 1 phenotype, The Journal of Immunology, vol.158, issue.6, pp.2964-2976, 1997.

G. ;. Grégori, V. ;. Patsekin, . Rajwa, ;. Bartek, J. ;. Jones et al.,

C. ;. Holdman, . Robinson, and . Paul, Hyperspectral cytometry at the single-cell level using a 32-channel photodetector, Cytometry Part A, vol.81, pp.35-44, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00691181

L. ;. Haghverdi, F. ;. Buettner, . Theis, and J. Fabian, Diffusion maps for highdimensional single-cell analysis of differentiation data, Bioinformatics, vol.31, 2015.

A. ;. Harari, F. ;. Vallelian, and G. ;. Pantaleo, Phenotypic heterogeneity of antigen-specific CD4 T cells under different conditions of antigen persistence and antigen load, European journal of immunology, vol.34, pp.3525-3533, 2004.

J. C. Hassel,

L. ;. Heinzerling, J. ;. Aberle, . Bähr, ;. Oliver, . Eigentler et al.,

M. Grimm,

. Grünwald, J. ;. Victor;-leipe, N. ;. Reinmuth, and J. K. Tietze,

, Combined immune checkpoint blockade (anti-PD-1/anti-CTLA-4): evaluation and management of adverse drug reactions, Cancer treatment reviews, vol.57, pp.36-49, 2017.

M. D. Hazenberg,

D. ;. Hamann, . Schuitemaker, ;. Hanneke, . Miedema, and ;. Frank, T cell depletion in HIV-1 infection: how CD4+ T cells go out of stock, Nature immunology, 2000.

M. K. Hellerstein, R. A. Hoh, M. B. Hanley, D. Cesar, D. Lee et al., Subpopulations of long-lived and short-lived T cells in advanced HIV-1 infection, The Journal of clinical investigation, vol.112, issue.6, pp.956-966, 2003.

N. J. Hill, K. ;. Van-gunst, and N. ;. Sarvetnick, Th1 and Th2 pancreatic inflammation differentially affects homing of islet-reactive CD4 cells in nonobese diabetic mice, The Journal of Immunology, vol.170, pp.1649-1658, 2003.

G. Hoeffel and F. Ginhoux, Ontogeny of tissue-resident macrophages, Frontiers in immunology, vol.6, p.486, 2015.

L. ;. Hu, . Liu, ;. Jibin, . Chen, ;. Xiaojun et al.,

H. ;. Shen, . Qiang, ;. Fulin, . Hu, and ;. Zhibin, CTLA-4 gene polymorphism+ 49 A/G contributes to genetic susceptibility to two infection-related cancershepatocellular carcinoma and cervical cancer, Human immunology, vol.71, pp.888-891, 2010.

R. Johnston, L. ;. Comps-agrar, J. ;. Hackney, . Yu, ;. Xin et al.,

Y. Yang, . Park, ;. Summer, . Javinal, ;. Vincent et al., The immunoreceptor TIGIT regulates antitumor and antiviral CD8+ T cell effector function, Cancer cell, vol.26, pp.923-937, 2014.

L. Josefsson, S. ;. Stockenstrom, . Faria, and R. Nuno,

P. ;. Bacchetti, . Killian, ;. Maudi, L. ;. Epling, A. ;. Tan et al., The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time, Proceedings of the National Academy of Sciences, vol.110, pp.4987-4996, 2013.

L. Kamentsky, . Melamed, R. Myron, . Spectrophotometric, and . Sorter, Science, vol.156, pp.1364-1365, 1967.

L. Kamentsky and M. R. Melamed,

H. ;. Derman, Spectrophotometer: new instrument for ultrarapid cell analysis, Science, vol.150, pp.630-631, 1965.

A. ;. Kaufmann, R. ;. Salentin, . Gemsa, ;. Diethard, . Sprenger et al., Increase of CCR1 and CCR5 expression and enhanced functional response to MIP-1? during differentiation of human monocytes to macrophages, Journal of leukocyte biology, vol.69, pp.248-252, 2001.

D. E. Kaufmann,

D. Kavanagh, F. ;. Pereyra, and J. J. Zaunders,

E. W. Mackey, . Miura, ;. Toshiyuki, S. ;. Palmer, . Brockman et al., Upregulation of CTLA-4 by HIV-specific CD4+ T cells correlates with disease progression and defines a reversible immune dysfunction, Nature immunology, 1246.

D. E. Kaufmann, . Walker, and D. Bruce, PD-1 and CTLA-4 inhibitory cosignaling pathways in HIV infection and the potential for therapeutic intervention, The Journal of Immunology, vol.182, pp.5891-5897, 2009.

P. S. Kim,

R. ;. Ahmed, Features of responding T cells in cancer and chronic infection, Current opinion in immunology, vol.22, pp.223-230, 2010.

R. Kim, . Fromm, and F. Martin,

C. ;. Wandel, B. ;. Leake, and A. J. Wood,

D. M. Roden, . Wilkinson, and R. Grant, The drug transporter P-glycoprotein limits oral absorption and brain entry of HIV-1 protease inhibitors, The Journal of clinical investigation, vol.101, pp.289-294, 1998.

N. R. Klatt,

N. T. Funderburg,

J. M. Brenchley, Microbial translocation, immune activation, and HIV disease, Trends in microbiology, vol.21, pp.6-13, 2013.

N. R. Klatt, E. Shudo, A. M. Ortiz, J. C. Engram, M. Paiardini et al., CD8+ lymphocytes control viral replication in SIVmac239-infected rhesus macaques without decreasing the lifespan of productively infected cells, PLoS pathogens, vol.6, issue.1, p.1000747, 2010.

G. ;. Köhler and C. ;. Milstein, Continuous cultures of fused cells secreting antibody of predefined specificity, Nature, vol.256, 1975.

D. S. Kwon,

G. ;. Gregorio, N. ;. Bitton, W. Hendrickson, . Littman, R. Dan et al., SIGN-mediated internalization of HIV is required for trans-enhancement of T cell infection, Immunity, vol.16, pp.135-144, 2002.

M. A. Linterman, . Pierson, ;. Wim, . Lee, and K. Sau,

A. ;. Kallies and S. Kawamoto,

T. F. Rayner, M. ;. Srivastava, D. Divekar, L. ;. Beaton, and J. J. Hogan, Foxp3+ follicular regulatory T cells control the germinal center response, vol.17, 2011.

R. ;. Lorenzo-redondo and H. R. Fryer,

T. ;. Bedford and E. Kim,

J. ;. Archer, S. L. Pond, and . Kosakovsky,

Y. Chung and S. Penugonda,

J. Chipman, . Fletcher, and V. Courtney, Persistent HIV-1 replication maintains the tissue reservoir during therapy, Nature, vol.530, 2016.

X. ;. Lou, . Zhang, ;. Guohua, . Herrera, ;. Isaac et al.,

V. ;. Baranov, . Nitz, ;. Mark, . Winnik, and A. Mitchell, Polymer-based elemental tags for sensitive bioassays, Angewandte Chemie International Edition, vol.46, pp.6111-6114, 2007.

. Maaten, Laurens van der

G. ;. Hinton, Visualizing data using t-SNE, Journal of machine learning research, vol.9, 2008.

L. K. Mackay, E. Wynne-jones, D. Freestone, D. G. Pellicci, L. A. Mielke et al., T-box transcription factors combine with the cytokines TGF-? and IL-15 to control tissue-resident memory T cell fate, Immunity, vol.43, issue.6, pp.1101-1111, 2015.

G. ;. Magiorkinis, . Angelis, ;. Konstantinos, and I. Mamais,

A. Hatzakis, J. ;. Albert, . Lawyer, ;. Glenn, . Hamouda et al.,

J. ;. Vercauteren, The global spread of HIV-1 subtype B epidemic, vol.46, pp.169-179, 2016.

D. ;. Majonis, . Herrera, ;. Isaac, O. ;. Ornatsky, M. ;. Schulze et al.,

M. ;. Soleimani, . Nitz, ;. Mark, . Winnik, and A. Mitchell, Synthesis of a functional metalchelating polymer and steps toward quantitative mass cytometry bioassays, Analytical chemistry, vol.82, pp.8961-8969, 2010.

F. ;. Maldarelli, X. Wu, L. Su, . Simonetti, and . Fr;,

W. Shao, S. Hill, J. Spindler, and A. ;. Ferris,

J. Mellors and M. F. Kearney, Specific HIV integration sites are linked to clonal expansion and persistence of infected cells, Science, vol.345, pp.179-183, 2014.

O. ;. Manches, . Frleta, ;. Davor, and N. ;. Bhardwaj, Dendritic cells in progression and pathology of HIV infection, Trends in immunology, vol.35, pp.114-122, 2014.

N. ;. Manel, . Unutmaz, . Derya;-littman, and R. Dan, The differentiation of human T H-17 cells requires transforming growth factor-? and induction of the nuclear receptor ROR?t, Nature immunology, vol.9, issue.6, 2008.

J. A. Manuzak and S. M. Dillon,

E. J. Lee,

Z. M. Dong,

D. K. Hecht,

C. C. Wilson, Increased Escherichia coli-induced interleukin-23 production by CD16+ monocytes correlates with systemic immune activation in untreated HIV-1-infected individuals, Journal of virology, vol.87, pp.13252-13262, 2013.

G. E. Martin, M. Pace, J. P. Thornhill, C. Phetsouphanh, J. Meyerowitz et al., CD32-Expressing CD4 T Cells Are Phenotypically Diverse and Can Contain Proviral HIV DNA, Frontiers in Immunology, vol.9, 2018.
DOI : 10.3389/fimmu.2018.00928

URL : https://www.frontiersin.org/articles/10.3389/fimmu.2018.00928/pdf

M. ;. Massanella, E. ;. Gómez-mora, J. ;. Carrillo, and M. Curriu,

D. Ouchi,

J. ;. Puig, . Negredo, ;. Eugènia, C. ;. Cabrera, . Clotet et al., Increased ex vivo cell death of central memory CD4 T cells in treated HIV infected individuals with unsatisfactory immune recovery, Journal of translational medicine, vol.13, 2015.

D. Masopust, V. Vezys, A. L. Marzo, and L. Lefrançois, Preferential localization of effector memory cells in nonlymphoid tissue, Science, vol.291, issue.5512, pp.2413-2417, 2001.

J. J. Mattapallil,

D. C. Douek,

B. ;. Hill, . Nishimura, ;. Yoshiaki, . Martin, ;. Malcolm et al., Massive infection and loss of memory CD4+ T cells in multiple tissues during acute SIV infection, Nature, vol.434, 1093.

B. J. Masten, G. K. Olson, C. A. Tarleton, C. Rund, M. Schuyler et al., Characterization of myeloid and plasmacytoid dendritic cells in human lung, The Journal of Immunology, vol.177, issue.11, pp.7784-7793, 2006.

M. ;. Mäurer, . Loserth, ;. Silke, A. ;. Kolb-mäurer, . Ponath et al.,

N. ;. Kruse, . Rieckmann, and ;. Peter, A polymorphism in the human cytotoxic Tlymphocyte antigen 4 (CTLA4) gene (exon 1+ 49) alters T-cell activation, Immunogenetics, vol.54, 2002.

D. ;. Mcdonald, L. ;. Wu, . Bohks, and M. Stacy,

. Kewalramani and N. Vineet,

D. Unutmaz,

T. J. Hope, Recruitment of HIV and its receptors to dendritic cell-T cell junctions, Science, vol.300, pp.1295-1297, 2003.

M. ;. Merad, . Sathe, ;. Priyanka, J. ;. Helft, J. ;. Miller et al., The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting, Annual review of immunology, vol.31, pp.563-604, 2013.

M. Merad and M. G. Manz, Dendritic cell homeostasis, Blood, vol.113, issue.15, pp.3418-3427, 2009.

L. ;. Micci, . Alvarez, ;. Xavier, and . Iriele,

A. M. Ortiz,

E. S. Ryan,

C. S. Mcgary,

C. ;. Deleage, B. B. Mcatee, . He, ;. Tianyu, . Apetrei et al., CD4 depletion in SIV-infected macaques results in macrophage and microglia infection with rapid turnover of infected cells, PLoS pathogens, 2014.

M. ;. Miyara, . Yoshioka, ;. Yumiko, . Kitoh, ;. Akihiko et al.,

A. ;. Niwa, C. ;. Parizot, . Taflin, ;. Cécile, . Heike et al., Functional delineation and differentiation dynamics of human CD4+ T cells expressing the FoxP3 transcription factor, Immunity, vol.30, pp.899-911, 2009.

S. ;. Moir and A. S. Fauci, B cells in HIV infection and disease, Nature Reviews Immunology, vol.9, 2009.

P. ;. Muranski, Z. A. Borman, and S. P. Kerkar,

C. A. Klebanoff, Y. ;. Ji, L. ;. Sanchez-perez, . Sukumar, ;. Madhusudhanan et al.,

S. J. Kern, Th17 cells are long lived and retain a stem cell-like molecular signature, Immunity, vol.35, pp.972-985, 2011.

T. T. Murooka,

M. ;. Deruaz, F. ;. Marangoni, . Vrbanac, and D. Vladimir,

E. Seung, . Andrian, H. Ulrich, . Tager, M. Andrew et al.,

T. R. Mempel, HIV-infected T cells are migratory vehicles for viral dissemination, Nature, vol.490, 2012.

P. Murray and M. Polarization, Annual review of physiology, vol.79, pp.541-566, 2017.

E. W. Newell,

N. ;. Sigal, . Bendall, C. Sean, . Nolan, and P. Garry,

M. M. Davis, Cytometry by time-of-flight shows combinatorial cytokine expression and virusspecific cell niches within a continuum of CD8+ T cell phenotypes, Immunity, vol.36, issue.1, pp.142-152, 2012.

K. J. Nicholas,

E. K. Zern,

L. ;. Barnett and R. M. Smith,

S. L. Lorey,

C. Copeland, . Sadagopal, ;. Shanmugalakshmi, . Kalams, and A. Spyros, B cell responses to HIV antigen are a potent correlate of viremia in HIV-1 infection and improve with PD-1 blockade, PloS one, 2013.

U. Niesner, . Albrecht, ;. Inka, . Janke, ;. Marko et al.,

R. Baumgrass, Autoregulation of Th1-mediated inflammation by twist1, Journal of Experimental Medicine, vol.205, 1889.

Y. ;. Nishimura, . Brown, and R. Charles,

J. Mattapallil and T. Igarashi,

A. ;. Buckler-white, . Lafont, A. Bernard, . Hirsch, M. Vanessa et al.,

M. A. Martin, Resting naive CD4+ T cells are massively infected and eliminated by X4-tropic simian-human immunodeficiency viruses in macaques, Proceedings of the National Academy of Sciences, vol.102, pp.8000-8005, 2005.

M. Nowak, . Lloyd, and L. Alun,

G. M. Vasquez, T. Wiltrout, L. M. Wahl, N. ;. Bischofberger, J. ;. Williams et al.,

V. M. Hirsch, Viral dynamics of primary viremia and antiretroviral therapy in simian immunodeficiency virus infection, Journal of virology, vol.71, pp.7518-7525, 1997.

R. I. Nurieva,

Y. ;. Chung, G. J. Martinez, . Yang, O. Xuexian, . Tanaka et al.,

Y. Wang,

C. ;. Dong, Bcl6 mediates the development of T follicular helper cells, Science, vol.325, 1001.

J. J. O'shea,

W. E. Paul, Mechanisms underlying lineage commitment and plasticity of helper CD4+ T cells, Science, vol.327, 1098.

A. Okoye, . Picker, J. Louis, and C. D. 4+, HIV infection: mechanisms of immunological failure, vol.254, pp.54-64, 2013.

O. I. Ornatsky, R. ;. Kinach, . Bandura, and R. Dmitry,

X. Lou, . Tanner, and D. Scott,

V. I. Baranov, . Nitz, ;. Mark, . Winnik, and A. Mitchell, Development of analytical methods for multiplex bio-assay with inductively coupled plasma mass spectrometry, Journal of analytical atomic spectrometry, vol.23, pp.463-469, 2008.

G. Panos and D. C. Watson, Effect of HIV-1 subtype and tropism on treatment with chemokine coreceptor entry inhibitors; overview of viral entry inhibition, Critical reviews in microbiology, vol.41, issue.4, pp.473-487, 2015.

A. Patel, Y. ;. Zhang, and J. N. Fullerton,

L. ;. Boelen and A. Rongvaux,

A. Maini, . Bigley, ;. Venetia, R. Flavell, D. W. Gilroy et al., The fate and lifespan of human monocyte subsets in steady state and systemic inflammation, Journal of Experimental Medicine, vol.214, 1913.

P. ;. Patel, . Borkowf, B. Craig, . Brooks, T. John et al.,

J. ;. Mermin, Estimating per-act HIV transmission risk: a systematic review, Aids, vol.28, pp.1509-1519, 2014.

J. ;. Pieper, S. ;. Johansson, . Snir, ;. Omri, L. ;. Linton et al., Peripheral and Site-Specific CD 4+ CD 28null T Cells from Rheumatoid Arthritis Patients Show Distinct Characteristics, Scandinavian journal of immunology, vol.79, pp.149-155, 2014.
DOI : 10.1111/sji.12139

URL : https://onlinelibrary.wiley.com/doi/pdf/10.1111/sji.12139

V. ;. Piguet, . Steinman, and M. Ralph, The interaction of HIV with dendritic cells: outcomes and pathways, Trends in immunology, vol.28, pp.503-510, 2007.

S. ;. Popov and A. Chenine,

A. ;. Gruber and P. Li,

R. M. Ruprecht, Long-term productive human immunodeficiency virus infection of CD1a-sorted myeloid dendritic cells, Journal of virology, vol.79, pp.602-608, 2005.

F. ;. Porichis, . Kwon, and S. Douglas,

J. ;. Zupkosky, . Tighe, and P. Daniel,

A. ;. Mcmullen, . Brockman, A. Mark, . Pavlik, F. David et al., Responsiveness of HIV-specific CD4 T cells to PD-1 blockade, 2011.

T. ;. Prezzemolo, G. Guggino, M. Manna, and . Pio,

D. Liberto, ;. Diana, F. ;. Dieli, and N. ;. Caccamo, Functional signatures of human CD4 and CD8 T cell responses to Mycobacterium tuberculosis, Frontiers in immunology, vol.5, 2014.

M. ;. Rangachari, C. ;. Zhu, . Sakuishi, ;. Kaori, . Xiao et al.,

E. Greenfield and R. A. Sobel, Bat3 promotes T cell responses and autoimmunity by repressing Tim-3-mediated cell death and exhaustion, Nature medicine, vol.18, 1394.

R. A. Raposo and . Saraiva,

. De-mulder-rougvie,

P. Brailey, . Cabido, D. Vinicius, . Zdinak, M. Paul et al.,

S. Huang,

G. A. Beckerle and R. B. Jones, IFITM1 targets HIV-1 latently infected cells for antibody-dependent cytolysis, vol.2, 2017.

S. Ren, . Rollins, J. Barrett, and C. Cyclin, Cell, vol.117, pp.239-251, 2004.

N. P. Restifo,

L. ;. Gattinoni, Lineage relationship of effector and memory T cells, Current opinion in immunology, vol.25, pp.556-563, 2013.

S. Rhee,

W. Fessel and . Jeffrey,

T. F. Liu,

N. M. Marlowe, C. Rowland, . Rode, A. Richard, A. Vandamme et al., Predictive value of HIV-1 genotypic resistance test interpretation algorithms, Journal of Infectious Diseases, vol.3, pp.453-463, 2009.

K. Richards, . Aasa-chapman, and M. I. Marlén,

Á. ;. Mcknight, . Clapham, and R. Paul, Modulation of HIV-1 macrophage-tropism among R5 envelopes occurs before detection of neutralizing antibodies, Retrovirology, 2010.

L. V. Riella,

A. M. Paterson,

A. H. Sharpe, . Chandraker, and ;. Anil, Role of the PD-1 Pathway in the Immune Response, American Journal of Transplantation, vol.12, 2012.

B. Rodríguez,

A. K. Sethi,

. Cheruvu and K. Vinay,

W. ;. Mackay, R. Bosch, M. ;. Kitahata, . Boswell, and L. Stephen,

W. Mathews and . Christopher,

J. ;. Martin, Predictive value of plasma HIV RNA level on rate of CD4 T-cell decline in untreated HIV infection, Jama, vol.296, 1498.

M. K. Rothenberger,

B. F. Keele,

S. W. Wietgrefe,

C. Fletcher, . Beilman, J. Gregory, J. Chipman, A. ;. Khoruts et al.,

J. ;. Anderson, . Callisto, and P. Samuel, Large number of rebounding/founder HIV variants emerge from multifocal infection in lymphatic tissues after treatment interruption, Proceedings of the National Academy of Sciences, 2015.

I. ;. Sada-ovalle, . Ocaña-guzman, ;. Ranferi, . Pérez-patrigeón, ;. Santiago et al., Tim-3 blocking rescue macrophage and T cell function against Mycobacterium tuberculosis infection in HIV+ patients, Journal of the International AIDS Society, 2015.

F. ;. Sallusto, J. ;. Geginat, and A. ;. Lanzavecchia, Central memory and effector memory T cell subsets: function, generation, and maintenance, Annu. Rev. Immunol, vol.22, pp.745-763, 2004.

P. Sampath, K. Moideen, U. D. Ranganathan, and R. Bethunaickan, Monocyte subsets: Phenotypes and Function in tuberculosis infection, Frontiers in immunology, p.9, 2018.

N. Sandler, . Douek, and C. Daniel, Microbial translocation in HIV infection: causes, consequences and treatment opportunities, Nature Reviews Microbiology, vol.10, 2012.

M. ;. Santa-marta, P. ;. Brito, A. ;. Godinho-santos, and J. ;. Goncalves, Host factors and HIV-1 replication: clinical evidence and potential therapeutic approaches, Frontiers in immunology, vol.4, 2013.

A. ;. Schlitzer, N. ;. Mcgovern, . Ginhoux, and ;. Florent, Dendritic cells and monocyte-derived cells: Two complementary and integrated functional systems, Seminars in cell & developmental biology, vol.41, pp.9-22, 2015.

N. Schmitt,

J. ;. Bustamante, L. ;. Bourdery, S. Bentebibel, and . Eddine,

S. ;. Boisson-dupuis, . Hamlin, ;. Fran, . Tran, V. Mau et al., IL-12 receptor ?1 deficiency alters in vivo T follicular helper cell response in humans, Blood, 2013.

N. ;. Schmitt, Y. ;. Liu, . Bentebibel, and . Salah-eddine,

I. ;. Munagala, L. ;. Bourdery, K. Venuprasad, J. ;. Banchereau, . Ueno et al., The cytokine TGF-? coopts signaling via STAT3-STAT4 to promote the differentiation of human T FH cells, Nature immunology, vol.15, 2014.

J. Schwartz and . Ari,

K. L. Clayton,

S. ;. Mujib, . Zhang, A. Hongliang;-rahman, and . Nur-ur,

J. ;. Liu, F. Yue, ;. Yun, E. ;. Benko, C. ;. Kovacs et al., Tim-3 is a Marker of Plasmacytoid Dendritic Cell Dysfunction during HIV Infection and Is Associated with the Recruitment of IRF7 and p85 into Lysosomes and with the Submembrane Displacement of TLR9, The Journal of Immunology, 2017.

E. ;. Seung and T. E. Dudek,

T. Allen, G. Freeman, A. Luster, . Tager, and M. Andrew, PD-1 blockade in chronically HIV-1-infected humanized mice suppresses viral loads, PloS one, 2013.

A. ;. Sigal and J. T. Kim,

A. B. Balazs,

E. ;. Dekel and A. Mayo,

D. ;. Baltimore, Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy, Nature, vol.477, 2011.

J. D. Siliciano,

J. ;. Kajdas, D. ;. Finzi, . Quinn, and C. Thomas,

K. Chadwick,

J. Margolick, C. ;. Kovacs, . Gange, J. Stephen, . Siliciano et al., Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells, Nature medicine, vol.9, issue.6, 2003.

R. F. Siliciano,

W. Greene, Cold Spring Harbor perspectives in medicine, 2011.

A. Silvin, I. Y. Chun, X. Lahaye, F. Imperatore, J. B. Brault et al., Constitutive resistance to viral infection in human CD141+ dendritic cells, Science immunology, vol.2, issue.13, 2017.
DOI : 10.1126/sciimmunol.aai8071

URL : http://immunology.sciencemag.org/content/immunology/2/13/eaai8071.full.pdf

A. ;. Skapenko, J. ;. Leipe, . Niesner, ;. Uwe, . Devriendt et al.,

H. ;. Schulze-koops, GATA-3 in human T cell helper type 2 development, Journal of Experimental Medicine, vol.199, pp.423-428, 2004.

M. H. Spitzer,

P. Gherardini and . Federico,

G. K. Fragiadakis,

N. ;. Bhattacharya, . Yuan, and T. Robert,

A. Hotson, R. ;. Finck, . Carmi, ;. Yaron, E. R. Zunder et al., An interactive reference framework for modeling a dynamic immune system, Science, vol.349, 2015.

S. J. Szabo,

B. M. Sullivan,

S. Peng and L. H. Glimcher, Annual Reviews 4139 El Camino Way, Molecular mechanisms regulating Th1 immune responses, vol.21, pp.713-758, 2003.

. Tang-huau,

E. ;. Segura, Human in vivo-differentiated monocytederived dendritic cells, Seminars in cell & developmental biology, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02079402

S. D. Tanner,

V. I. Baranov,

O. I. Ornatsky, . Bandura, R. Dmitry, and T. C. George, An introduction to mass cytometry: fundamentals and applications, Cancer Immunology, Immunotherapy, vol.62, pp.955-965, 2013.

D. Tebit and E. J. Arts, Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease,The Lancet infectious diseases, vol.11, pp.45-56, 2011.

N. ;. Thieblemont, L. ;. Weiss, . Sadeghi, M. Hoss, and C. Estcourt,

N. ;. Haeffner-cavaillon, CD14lowCD16high: a cytokine-producing monocyte subset which expands during human immunodeficiency virus infection, European journal of immunology, vol.25, pp.3418-3424, 1995.

J. Thornhill and . Patrick,

S. ;. Fidler, . Klenerman, ;. Paul, J. ;. Frater, . Phetsouphanh et al., The role of CD4+ T follicular helper cells in HIV infection: from the Germinal Center to the Periphery, Frontiers in immunology, vol.8, 2017.

S. ;. Tricot, . Meyrand, ;. Mickael, . Sammicheli, ;. Chiara et al.,

A. ;. Corneau, . Bertholet, M. Sylvie;-malissen, . Grand, ;. Roger et al.,

H. ;. Luche, Evaluating the efficiency of isotope transmission for improved panel design and a comparison of the detection sensitivities of mass cytometer instruments, Cytometry Part A, vol.87, pp.357-368, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01515301

K. ;. Triques and M. ;. Stevenson, Characterization of restrictions to human immunodeficiency virus type 1 infection of monocytes, Journal of virology, vol.78, pp.5523-5527, 2004.

D. ;. Unutmaz, . Pileri, ;. Piero, and S. ;. Abrignani, Antigen-independent activation of naive and memory resting T cells by a cytokine combination, Journal of Experimental Medicine, vol.180, pp.1159-1164, 1994.

,. Van-furth, . R;-cohn, J. Za;-hirsch, J. H. Humphrey, . Spector et al., The mononuclear phagocyte system: a new classification of macrophages, monocytes, and their precursor cells, Bulletin of the World Health Organization, vol.46, 1972.

. Van-wijk, ;. Femke, and H. ;. Cheroutre, Mucosal T cells in gut homeostasis and inflammation, Expert review of clinical immunology, vol.6, pp.559-566, 2010.

C. ;. Vandergeeten, . Fromentin, ;. Rémi, . Dafonseca, ;. Sandrina et al.,

I. ;. Sereti, . Lederman, M. Michael, . Ramgopal, ;. Moti et al.,

R. Sékaly,

N. ;. Chomont, Interleukin-7 promotes HIV persistence during antiretroviral therapy, Blood, 2013.

. Velu, . Vijayakumar;-titanji, ;. Kehmia, . Zhu, ;. Baogong et al.,

L. ;. Lai, . Vanderford, H. Thomas, . Chennareddi, ;. Lakshmi et al., Enhancing SIV-specific immunity in vivo by PD-1 blockade, Nature, 2009.

S. ;. Venzke, . Keppler, and T. Oliver, Role of macrophages in HIV infection and persistence, Expert review of clinical immunology, vol.2, issue.4, pp.613-626, 2006.

C. ;. Vérollet, S. ;. Souriant, E. ;. Bonnaud, P. ;. Jolicoeur, B. ;. Raynaudmessina et al., HIV-1 reprograms the migration of macrophages, 2014.

V. Stockenstrom, ;. Susanne, L. ;. Odevall, . Lee, ;. Eunok et al., Longitudinal genetic characterization reveals that cell proliferation maintains a persistent HIV type 1 DNA pool during effective HIV therapy, The Journal of infectious diseases, vol.212, pp.596-607, 2015.

V. Wacleche and . Sue,

C. L. Tremblay,

J. Routy,

P. ;. Ancuta, The biology of monocytes and dendritic cells: Contribution to HIV pathogenesis, Viruses, 2018.

T. A. Wagner,

S. ;. Mclaughlin, . Garg, ;. Kavita, . Cheung, Y. Charles et al.,

L. M. Frenkel, Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection, Science, vol.345, pp.570-573, 2014.

P. ;. Waterhouse and J. M. Penninger,

E. ;. Timms and A. Wakeham,

A. ;. Shahinian, . Lee, P. Kelvin, C. Thompson, H. ;. Griesser et al.,

, Lymphoproliferative disorders with early lethality in mice deficient in Ctla-4, Science, vol.270, pp.985-988, 1995.

X. ;. Wei, . Ghosh, and K. Sajal,

M. E. Taylor,

V. A. Johnson and E. A. Emini,

P. ;. Deutsch, J. Lifson, . Bonhoeffer, ;. Sebastian, . Nowak et al., Viral dynamics in human immunodeficiency virus type 1 infection, vol.373, 1995.

L. M. Weiner,

W. ;. Li, M. ;. Holmes, R. Catalano, and . Dovnarsky,

K. ;. Padavic, . Alpaugh, and . Katherine, Phase I trial of recombinant macrophage colony-stimulating factor and recombinant ?-interferon: toxicity, monocytosis, and clinical effects, Cancer Research, vol.54, pp.4084-4090, 1994.

F. ;. Wightman, . Solomon, ;. Ajantha, . Kumar, S. Sanjeev et al., Effect of ipilimumab on the HIV reservoir in an HIV-infected individual with metastatic melanoma, AIDS, 2015.

D. W. Williams,

E. A. Eugenin, T. Calderon, and J. W. Berman,

, Monocyte maturation, HIV susceptibility, and transmigration across the blood brain barrier are critical in HIV neuropathogenesis, Journal of leukocyte biology, vol.91, pp.401-415, 2012.

J. P. Williams,

J. ;. Hurst, W. ;. Stöhr, N. ;. Robinson, and . Brown,

M. ;. Fisher, S. ;. Kinloch, D. ;. Cooper, . Schechter, ;. Mauro et al., HIV-1 DNA predicts disease progression and post-treatment virological control, 2014.

E. ;. Wolf, J. T. Herbeck, . Van-rompaey, ;. Stephen, M. ;. Kitahata et al., Phylogenetic evidence of HIV-1 transmission between adult and adolescent men who have sex with men, AIDS research and human retroviruses, vol.33, pp.318-322, 2017.

H. Street,

J. K. Wong,

M. ;. Hezareh, . Günthard, and F. Huldrych,

D. V. Havlir, C. Ignacio, C. Spina, . Richman, and D. Douglas, Recovery of replication-competent HIV despite prolonged suppression of plasma viremia, Science, vol.278, 1291.

M. Wong and . Thomas,

D. E. Ong and . Hui,

F. S. Lim and . Huei,

K. W. Teng, ;. Weng, N. ;. Mcgovern, . Narayanan, ;. Sriram et al.,

R. Anicete, A high-dimensional atlas of human T cell diversity reveals tissue-specific trafficking and cytokine signatures, Immunity, vol.45, pp.442-456, 2016.

L. ;. Wu, . Kewalramani, and N. Vineet, Dendritic-cell interactions with HIV: infection and viral dissemination, Nature reviews immunology, vol.6, issue.859, 2006.

H. ;. Xu, . Zhao, ;. Mingfei, . He, ;. Jiliang et al., Association between cytotoxic Tlymphocyte associated protein 4 gene+ 49 A/G polymorphism and chronic infection with hepatitis B virus: a meta-analysis, Journal of International Medical Research, vol.41, pp.559-567, 2013.

A. ;. Yates, . Stark, ;. Jaroslav, N. ;. Klein, . Antia et al., Understanding the slow depletion of memory CD4+ T cells in HIV infection, PLoS medicine, 2007.

C. ;. Zhu and A. C. Anderson,

A. ;. Schubart, . Xiong, ;. Huabao, J. ;. Imitola, . Khoury et al.,

T. B. Strom,

V. K. Kuchroo, The Tim-3 ligand galectin-9 negatively regulates T helper type 1 immunity, Nature immunology, 1245.

. Ziegler-heitbrock and ;. Loems, Reprint of: Monocyte subsets in man and other species, Cellular immunology, vol.291, 2014.

G. ;. Zyl, . Bale, and J. Michael,

M. F. Kearney, HIV evolution and diversity in ARTtreated patients, vol.15, 2018.