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2. A biology-driven deep generative model for cell-type annotation in cytometry

Author

Blampey, Quentin, Bercovici, Nadège, Dutertre, Charles-Antoine, Pic, Isabelle, André, Fabrice, Ribeiro, Joana Mourato, and Cournède, Paul-Henry

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning
Abstract

Cytometry enables precise single-cell phenotyping within heterogeneous populations. These cell types are traditionally annotated via manual gating, but this method suffers from a lack of reproducibility and sensitivity to batch-effect. Also, the most recent cytometers - spectral flow or mass cytometers - create rich and high-dimensional data whose analysis via manual gating becomes challenging and time-consuming. To tackle these limitations, we introduce Scyan (https://github.com/MICS-Lab/scyan), a Single-cell Cytometry Annotation Network that automatically annotates cell types using only prior expert knowledge about the cytometry panel. We demonstrate that Scyan significantly outperforms the related state-of-the-art models on multiple public datasets while being faster and interpretable. In addition, Scyan overcomes several complementary tasks such as batch-effect removal, debarcoding, and population discovery. Overall, this model accelerates and eases cell population characterisation, quantification, and discovery in cytometry.

Published
2022
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3. iPS-cell-derived microglia promote brain organoid maturation via cholesterol transfer

Author

Park, Dong Shin, Kozaki, Tatsuya, Tiwari, Satish Kumar, Moreira, Marco, Khalilnezhad, Ahad, Torta, Federico, Olivié, Nicolas, Thiam, Chung Hwee, Liani, Oniko, Silvin, Aymeric, Phoo, Wint Wint, Gao, Liang, Triebl, Alexander, Tham, Wai Kin, Gonçalves, Leticia, Kong, Wan Ting, Raman, Sethi, Zhang, Xiao Meng, Dunsmore, Garett, Dutertre, Charles Antoine, Lee, Salanne, Ong, Jia Min, Balachander, Akhila, Khalilnezhad, Shabnam, Lum, Josephine, Duan, Kaibo, Lim, Ze Ming, Tan, Leonard, Low, Ivy, Utami, Kagistia Hana, Yeo, Xin Yi, Di Tommaso, Sylvaine, Dupuy, Jean-William, Varga, Balazs, Karadottir, Ragnhildur Thora, Madathummal, Mufeeda Changaramvally, Bonne, Isabelle, Malleret, Benoit, Binte, Zainab Yasin, Wei Da, Ngan, Tan, Yingrou, Wong, Wei Jie, Zhang, Jinqiu, Chen, Jinmiao, Sobota, Radoslaw M., Howland, Shanshan W., Ng, Lai Guan, Saltel, Frédéric, Castel, David, Grill, Jacques, Minard, Veronique, Albani, Salvatore, Chan, Jerry K. Y., Thion, Morgane Sonia, Jung, Sang Yong, Wenk, Markus R., Pouladi, Mahmoud A., Pasqualini, Claudia, Angeli, Veronique, Cexus, Olivier N. F., and Ginhoux, Florent

Published
2023
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5. Dendritic cell type 3 arises from Ly6C+ monocyte-dendritic cell progenitors

Author

Liu, Zhaoyuan, Wang, Haiting, Li, Ziyi, Dress, Regine J., Zhu, Yiwen, Zhang, Shuangyan, De Feo, Donatella, Kong, Wan Ting, Cai, Peiliang, Shin, Amanda, Piot, Cécile, Yu, Jiangyan, Gu, Yaqi, Zhang, Mingnan, Gao, Caixia, Chen, Lei, Wang, Honglin, Vétillard, Mathias, Guermonprez, Pierre, Kwok, Immanuel, Ng, Lai Guan, Chakarov, Svetoslav, Schlitzer, Andreas, Becher, Burkhard, Dutertre, Charles-Antoine, Su, Bing, and Ginhoux, Florent

Published
2023
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6. Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

Author

Cossarizza, Andrea, Chang, Hyun-Dong, Radbruch, Andreas, Acs, Andreas, Adam, Dieter, Adam-Klages, Sabine, Agace, William W, Aghaeepour, Nima, Akdis, Mübeccel, Allez, Matthieu, Almeida, Larissa Nogueira, Alvisi, Giorgia, Anderson, Graham, Andrä, Immanuel, Annunziato, Francesco, Anselmo, Achille, Bacher, Petra, Baldari, Cosima T, Bari, Sudipto, Barnaba, Vincenzo, Barros-Martins, Joana, Battistini, Luca, Bauer, Wolfgang, Baumgart, Sabine, Baumgarth, Nicole, Baumjohann, Dirk, Baying, Bianka, Bebawy, Mary, Becher, Burkhard, Beisker, Wolfgang, Benes, Vladimir, Beyaert, Rudi, Blanco, Alfonso, Boardman, Dominic A, Bogdan, Christian, Borger, Jessica G, Borsellino, Giovanna, Boulais, Philip E, Bradford, Jolene A, Brenner, Dirk, Brinkman, Ryan R, Brooks, Anna ES, Busch, Dirk H, Büscher, Martin, Bushnell, Timothy P, Calzetti, Federica, Cameron, Garth, Cammarata, Ilenia, Cao, Xuetao, Cardell, Susanna L, Casola, Stefano, Cassatella, Marco A, Cavani, Andrea, Celada, Antonio, Chatenoud, Lucienne, Chattopadhyay, Pratip K, Chow, Sue, Christakou, Eleni, Čičin-Šain, Luka, Clerici, Mario, Colombo, Federico S, Cook, Laura, Cooke, Anne, Cooper, Andrea M, Corbett, Alexandra J, Cosma, Antonio, Cosmi, Lorenzo, Coulie, Pierre G, Cumano, Ana, Cvetkovic, Ljiljana, Dang, Van Duc, Dang-Heine, Chantip, Davey, Martin S, Davies, Derek, De Biasi, Sara, Del Zotto, Genny, Dela Cruz, Gelo Victoriano, Delacher, Michael, Della Bella, Silvia, Dellabona, Paolo, Deniz, Günnur, Dessing, Mark, Di Santo, James P, Diefenbach, Andreas, Dieli, Francesco, Dolf, Andreas, Dörner, Thomas, Dress, Regine J, Dudziak, Diana, Dustin, Michael, Dutertre, Charles-Antoine, Ebner, Friederike, Eckle, Sidonia BG, Edinger, Matthias, Eede, Pascale, Ehrhardt, Götz RA, Eich, Marcus, Engel, Pablo, Engelhardt, Britta, and Erdei, Anna

Subjects
1.1 Normal biological development and functioning, Underpinning research, Inflammatory and immune system, Allergy and Immunology, Cell Separation, Consensus, Flow Cytometry, Humans, Phenotype, Immunology
Abstract

These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.

Published
2019

7. Twin study reveals non-heritable immune perturbations in multiple sclerosis

Author

Ingelfinger, Florian, Gerdes, Lisa Ann, Kavaka, Vladyslav, Krishnarajah, Sinduya, Friebel, Ekaterina, Galli, Edoardo, Zwicky, Pascale, Furrer, Reinhard, Peukert, Christian, Dutertre, Charles-Antoine, Eglseer, Klara Magdalena, Ginhoux, Florent, Flierl-Hecht, Andrea, Kümpfel, Tania, De Feo, Donatella, Schreiner, Bettina, Mundt, Sarah, Kerschensteiner, Martin, Hohlfeld, Reinhard, Beltrán, Eduardo, and Becher, Burkhard

Published
2022
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8. Prevalence and functional profile of SARS-CoV-2 T cells in asymptomatic Kenyan adults

Author

Samandari, Taraz, Ongalo, Joshua B., McCarthy, Kimberly D., Biegon, Richard K., Madiega, Philister A., Mithika, Anne, Orinda, Joseph, Mboya, Grace M., Mwaura, Patrick, Anzala, Omu, Onyango, Clayton, Oluoch, Fredrick O., Osoro, Eric, Dutertre, Charles-Antoine, Tan, Nicole, Hang, Shou Kit, Hariharaputran, Smrithi, Lye, David C., Herman-Roloff, Amy, Le Ber, Nina, and Bertoletti, Antonio

Subjects
T cells -- Physiological aspects -- Health aspects, Immune response -- Physiological aspects -- Health aspects, Immunity -- Health aspects, Health care industry
Abstract

BACKGROUND. SARS-CoV-2 infection in Africa has been characterized by a less severe disease profile than what has been observed elsewhere, but the profile of SARS-CoV-2-specific adaptive immunity in these mainly asymptomatic patients has not, to our knowledge, been analyzed. METHODS. We collected blood samples from residents of rural Kenya (n = 80), who had not experienced any respiratory symptoms or had contact with individuals with COVID-19 and had not received COVID-19 vaccines. We analyzed spike- specific antibodies and T cells specific for SARS-CoV-2 structural (membrane, nucleocapsid, and spike) and accessory (ORF3a, ORF7, ORF8) proteins. Pre-pandemic blood samples collected in Nairobi (n = 13) and blood samples from mild-to-moderately symptomatic COVID-19 convalescent patients (n = 36) living in the urban environment of Singapore were also studied. RESULTS. Among asymptomatic Africans, we detected anti-spike antibodies in 41.0% of the samples and T cell responses against 2 or more SARS-CoV-2 proteins in 82.5% of samples examined. Such a pattern was absent in the pre-pandemic samples. Furthermore, distinct from cellular immunity in European and Asian COVID-19 convalescents, we observed strong T cell immunogenicity against viral accessory proteins (ORF3a, ORF8) but not structural proteins, as well as a higher IL-10/ IFN-[gamma] cytokine ratio profile. CONCLUSIONS. The high incidence of T cell responses against different SARS-CoV-2 proteins in seronegative participants suggests that serosurveys underestimate SARS-CoV-2 prevalence in settings where asymptomatic infections prevail. The functional and antigen-specific profile of SARS-CoV-2-specific T cells in African individuals suggests that environmental factors can play a role in the development of protective antiviral immunity. FUNDING. US Centers for Disease Control and Prevention, Division of Global Health Protection; the Singapore Ministry of Health's National Medical Research Council (COVID19RF3-0060, COVID19RF-001, COVID19RF-008, MOH-StaR17Nov-0001)., Introduction SARS-CoV-2 infection in Africa is characterized by a low number of mild and severe cases of disease (1, 2). The incidence of severe COVID-19 has been particularly low in [...]

Published
2023
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9. A single-cell and spatially resolved atlas of human breast cancers

Author

Wu, Sunny Z., Al-Eryani, Ghamdan, Roden, Daniel Lee, Junankar, Simon, Harvey, Kate, Andersson, Alma, Thennavan, Aatish, Wang, Chenfei, Torpy, James R., Bartonicek, Nenad, Wang, Taopeng, Larsson, Ludvig, Kaczorowski, Dominik, Weisenfeld, Neil I., Uytingco, Cedric R., Chew, Jennifer G., Bent, Zachary W., Chan, Chia-Ling, Gnanasambandapillai, Vikkitharan, Dutertre, Charles-Antoine, Gluch, Laurence, Hui, Mun N., Beith, Jane, Parker, Andrew, Robbins, Elizabeth, Segara, Davendra, Cooper, Caroline, Mak, Cindy, Chan, Belinda, Warrier, Sanjay, Ginhoux, Florent, Millar, Ewan, Powell, Joseph E., Williams, Stephen R., Liu, X. Shirley, O’Toole, Sandra, Lim, Elgene, Lundeberg, Joakim, Perou, Charles M., and Swarbrick, Alexander

Published
2021
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10. Timing and location dictate monocyte fate and their transition to tumor-associated macrophages.

Author

Dunsmore, Garett, Guo, Wei, Li, Ziyi, Bejarano, David Alejandro, Pai, Rhea, Yang, Katharine, Kwok, Immanuel, Tan, Leonard, Ng, Melissa, De La Calle Fabregat, Carlos, Yatim, Aline, Bougouin, Antoine, Mulder, Kevin, Thomas, Jake, Villar, Javiera, Bied, Mathilde, Kloeckner, Benoit, Dutertre, Charles-Antoine, Gessain, Grégoire, and Chakarov, Svetoslav

Subjects
TRANSCRIPTION factors, CELL populations, PANCREATIC duct, GENE expression profiling, TUMOR growth
Abstract

Tumor-associated macrophages (TAMs) are a heterogeneous population of cells whose phenotypes and functions are shaped by factors that are incompletely understood. Herein, we asked when and where TAMs arise from blood monocytes and how they evolve during tumor development. We initiated pancreatic ductal adenocarcinoma (PDAC) in inducible monocyte fate-mapping mice and combined single-cell transcriptomics and high-dimensional flow cytometry to profile the monocyte-to-TAM transition. We revealed that monocytes differentiate first into a transient intermediate population of TAMs that generates two longer-lived lineages of terminally differentiated TAMs with distinct gene expression profiles, phenotypes, and intratumoral localization. Transcriptome datasets and tumor samples from patients with PDAC evidenced parallel TAM populations in humans and their prognostic associations. These insights will support the design of new therapeutic strategies targeting TAMs in PDAC. Editor's summary: Tumor-associated macrophages (TAMs) promote tumor growth and immune suppression, but how TAMs develop from circulating monocytes and local tissue-resident macrophages remains incompletely understood. Using a model of pancreatic ductal adenocarcinoma (PDAC) in monocyte fate-mapping mice, Dunsmore et al. examined the dynamics of the monocyte-to-macrophage transition in tumors. A population of "intermediate" TAMs gave rise to two more differentiated TAM subsets, distinguishable by their distinct surface marker phenotype, dependence on the transcription factor Maf, migratory behavior, and localization in tumors. These findings provide a time- and space-resolved picture of TAM heterogeneity and development in PDAC, which could guide the future development of TAM-targeted therapeutic strategies. —Claire Olingy [ABSTRACT FROM AUTHOR]

Published
2024
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11. Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor

Author

Kwok, Immanuel, Becht, Etienne, Xia, Yu, Ng, Melissa, Teh, Ye Chean, Tan, Leonard, Evrard, Maximilien, Li, Jackson L.Y., Tran, Hoa T.N., Tan, Yingrou, Liu, Dehua, Mishra, Archita, Liong, Ka Hang, Leong, Keith, Zhang, Yuning, Olsson, Andre, Mantri, Chinmay Kumar, Shyamsunder, Pavithra, Liu, Zhaoyuan, Piot, Cecile, Dutertre, Charles-Antoine, Cheng, Hui, Bari, Sudipto, Ang, Nicholas, Biswas, Subhra K., Koeffler, H. Philip, Tey, Hong Liang, Larbi, Anis, Su, I-Hsin, Lee, Bernett, St. John, Ashley, Chan, Jerry K.Y., Hwang, William Y.K., Chen, Jinmiao, Salomonis, Nathan, Chong, Shu Zhen, Grimes, H. Leighton, Liu, Bing, Hidalgo, Andrés, Newell, Evan W., Cheng, Tao, Ginhoux, Florent, and Ng, Lai Guan

Published
2020
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12. Liver fibrosis and CD206+ macrophage accumulation are suppressed by anti-GM-CSF therapy

Author

Tan-Garcia, Alfonso, Lai, Fritz, Yeong, Joe Poh Sheng, Irac, Sergio E., Ng, Pei Y., Msallam, Rasha, Lim, Jeffrey Chun Tatt, Wai, Lu-En, Tham, Christine Y.L., Choo, Su P., Lim, Tony, Young, Dan Y., D'Ambrosio, Roberta, Degasperi, Elisabetta, Perbellini, Riccardo, Newell, Evan, Le Bert, Nina, Ginhoux, Florent, Bertoletti, Antonio, Chen, Qingfeng, and Dutertre, Charles-Antoine

Published
2020
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15. Intravenous nanoparticle vaccination generates stem-like TCF1+ neoantigen-specific CD8+ T cells

Author

Baharom, Faezzah, Ramirez-Valdez, Ramiro A., Tobin, Kennedy K. S., Yamane, Hidehiro, Dutertre, Charles-Antoine, Khalilnezhad, Ahad, Reynoso, Glennys V., Coble, Vincent L., Lynn, Geoffrey M., Mulè, Matthew P., Martins, Andrew J., Finnigan, John P., Zhang, Xiao Meng, Hamerman, Jessica A., Bhardwaj, Nina, Tsang, John S., Hickman, Heather D., Ginhoux, Florent, Ishizuka, Andrew S., and Seder, Robert A.

Published
2021
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18. TIM4 expression by dendritic cells mediates uptake of tumor-associated antigens and anti-tumor responses

Author

Caronni, Nicoletta, Piperno, Giulia Maria, Simoncello, Francesca, Romano, Oriana, Vodret, Simone, Yanagihashi, Yuichi, Dress, Regine, Dutertre, Charles-Antoine, Bugatti, Mattia, Bourdeley, Pierre, Del Prete, Annalisa, Schioppa, Tiziana, Mazza, Emilia Maria Cristina, Collavin, Licio, Zacchigna, Serena, Ostuni, Renato, Guermonprez, Pierre, Vermi, William, Ginhoux, Florent, Bicciato, Silvio, Nagata, Shigekatzu, and Benvenuti, Federica

Published
2021
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19. Supplementary Figure S3 from BCL2 Inhibition Reveals a Dendritic Cell–Specific Immune Checkpoint That Controls Tumor Immunosurveillance

Author

Zhao, Liwei, primary, Liu, Peng, primary, Mao, Misha, primary, Zhang, Shuai, primary, Bigenwald, Camille, primary, Dutertre, Charles-Antoine, primary, Lehmann, Christian H.K., primary, Pan, Hui, primary, Paulhan, Nicolas, primary, Amon, Lukas, primary, Buqué, Aitziber, primary, Yamazaki, Takahiro, primary, Galluzzi, Lorenzo, primary, Kloeckner, Benoit, primary, Silvin, Aymeric, primary, Pan, Yuhong, primary, Chen, Hui, primary, Tian, Ai-Ling, primary, Ly, Pierre, primary, Dudziak, Diana, primary, Zitvogel, Laurence, primary, Kepp, Oliver, primary, and Kroemer, Guido, primary

Published
2023
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20. Supplementary Table S4 from BCL2 Inhibition Reveals a Dendritic Cell–Specific Immune Checkpoint That Controls Tumor Immunosurveillance

Author

Zhao, Liwei, primary, Liu, Peng, primary, Mao, Misha, primary, Zhang, Shuai, primary, Bigenwald, Camille, primary, Dutertre, Charles-Antoine, primary, Lehmann, Christian H.K., primary, Pan, Hui, primary, Paulhan, Nicolas, primary, Amon, Lukas, primary, Buqué, Aitziber, primary, Yamazaki, Takahiro, primary, Galluzzi, Lorenzo, primary, Kloeckner, Benoit, primary, Silvin, Aymeric, primary, Pan, Yuhong, primary, Chen, Hui, primary, Tian, Ai-Ling, primary, Ly, Pierre, primary, Dudziak, Diana, primary, Zitvogel, Laurence, primary, Kepp, Oliver, primary, and Kroemer, Guido, primary

Published
2023
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21. Data from BCL2 Inhibition Reveals a Dendritic Cell–Specific Immune Checkpoint That Controls Tumor Immunosurveillance

Author

Zhao, Liwei, primary, Liu, Peng, primary, Mao, Misha, primary, Zhang, Shuai, primary, Bigenwald, Camille, primary, Dutertre, Charles-Antoine, primary, Lehmann, Christian H.K., primary, Pan, Hui, primary, Paulhan, Nicolas, primary, Amon, Lukas, primary, Buqué, Aitziber, primary, Yamazaki, Takahiro, primary, Galluzzi, Lorenzo, primary, Kloeckner, Benoit, primary, Silvin, Aymeric, primary, Pan, Yuhong, primary, Chen, Hui, primary, Tian, Ai-Ling, primary, Ly, Pierre, primary, Dudziak, Diana, primary, Zitvogel, Laurence, primary, Kepp, Oliver, primary, and Kroemer, Guido, primary

Published
2023
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22. Supplementary Table Legends from BCL2 Inhibition Reveals a Dendritic Cell–Specific Immune Checkpoint That Controls Tumor Immunosurveillance

Author

Zhao, Liwei, primary, Liu, Peng, primary, Mao, Misha, primary, Zhang, Shuai, primary, Bigenwald, Camille, primary, Dutertre, Charles-Antoine, primary, Lehmann, Christian H.K., primary, Pan, Hui, primary, Paulhan, Nicolas, primary, Amon, Lukas, primary, Buqué, Aitziber, primary, Yamazaki, Takahiro, primary, Galluzzi, Lorenzo, primary, Kloeckner, Benoit, primary, Silvin, Aymeric, primary, Pan, Yuhong, primary, Chen, Hui, primary, Tian, Ai-Ling, primary, Ly, Pierre, primary, Dudziak, Diana, primary, Zitvogel, Laurence, primary, Kepp, Oliver, primary, and Kroemer, Guido, primary

Published
2023
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23. 1510 Multiomic functional biomarkers for cancer prediction and early detection

Author

Fidelle, Marine, primary, Suissa, Deborah, additional, Birebent, Roxanne, additional, Ben-Ahmed, Tarek, additional, de la Varende, Anne-Laure Mallard, additional, Costa Silva, Carolina Alves, additional, Blampey, Quentin, additional, Silvin, Aymeric, additional, Dutertre, Charles-Antoine, additional, Durand, Sylvere, additional, Chen, Hui, additional, Caron, Olivier, additional, Mercier, Olaf, additional, Derosa, Lisa, additional, Kroemer, Guido, additional, Renneville, Aline, additional, Drubay, Damien, additional, Delaloge, Suzette, additional, Boulate, David, additional, and Zitvogel, Laurence, additional

Published
2023
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26. HIV-1 reservoirs in urethral macrophages of patients under suppressive antiretroviral therapy

Author

Ganor, Yonatan, Real, Fernando, Sennepin, Alexis, Dutertre, Charles-Antoine, Prevedel, Lisa, Xu, Lin, Tudor, Daniela, Charmeteau, Bénédicte, Couedel-Courteille, Anne, Marion, Sabrina, Zenak, Ali-Redha, Jourdain, Jean-Pierre, Zhou, Zhicheng, Schmitt, Alain, Capron, Claude, Eugenin, Eliseo A, Cheynier, Rémi, Revol, Marc, Cristofari, Sarra, Hosmalin, Anne, and Bomsel, Morgane

Published
2019
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28. Mapping the human DC lineage through the integration of high-dimensional techniques

Author

Dutertre, Charles-Antoine, See, Peter, Chen, Jinmiao, Günther, Patrick, McGovern, Naomi, Irac, Sergio Erdal, Gunawan, Merry, Beyer, Marc, Händler, Kristian, Duan, Kaibo, Sumatoh, Hermi Rizal Bin, Ruffin, Nicolas, Jouve, Mabel, Gea-Mallorquí, Ester, Hennekam, Raoul C. M., Lim, Tony, Yip, Chan Chung, Wen, Ming, Malleret, Benoit, Low, Ivy, Shadan, Nurhidaya Binte, Fen, Charlene Foong Shu, Tay, Alicia, Lum, Josephine, Zolezzi, Francesca, Larbi, Anis, Poidinger, Michael, Chan, Jerry K. Y., Chen, Qingfeng, Rénia, Laurent, Haniffa, Muzlifah, Benaroch, Philippe, Schlitzer, Andreas, Schultze, Joachim L., Newell, Evan W., and Ginhoux, Florent

Published
2017

30. Intrahepatic CD206+ macrophages contribute to inflammation in advanced viral-related liver disease

Author

Tan-Garcia, Alfonso, Wai, Lu-En, Zheng, Dahai, Ceccarello, Erica, Jo, Juandy, Banu, Nasirah, Khakpoor, Atefeh, Chia, Adeline, Tham, Christine Y.L., Tan, Anthony T., Hong, Michelle, Keng, Choong Tat, Rivino, Laura, Tan, Kai Chah, Lee, Kang Hoe, Lim, Seng Gee, Newell, Evan W., Pavelka, Norman, Chen, Jinmiao, Ginhoux, Florent, Chen, Qingfeng, Bertoletti, Antonio, and Dutertre, Charles-Antoine

Published
2017
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33. Guidelines for mouse and human DC functional assays.

Author

Clausen, Björn E., Amon, Lukas, Backer, Ronald A., Berod, Luciana, Bopp, Tobias, Brand, Anna, Burgdorf, Sven, Chen, Luxia, Da, Meihong, Distler, Ute, Dress, Regine J., Dudziak, Diana, Dutertre, Charles‐Antoine, Eich, Christina, Gabele, Anna, Geiger, Melanie, Ginhoux, Florent, Giusiano, Lucila, Godoy, Gloria J., and Hamouda, Ahmed E.I.

Subjects
DENDRITIC cells, MICE, IMMUNOLOGISTS, FLUORESCENCE microscopy, LANGERHANS cells
Abstract

This article is part of the Dendritic Cell Guidelines article series, which provides a collection of state‐of‐the‐art protocols for the preparation, phenotype analysis by flow cytometry, generation, fluorescence microscopy, and functional characterization of mouse and human dendritic cells (DC) from lymphoid organs and various non‐lymphoid tissues. Recent studies have provided evidence for an increasing number of phenotypically distinct conventional DC (cDC) subsets that on one hand exhibit a certain functional plasticity, but on the other hand are characterized by their tissue‐ and context‐dependent functional specialization. Here, we describe a selection of assays for the functional characterization of mouse and human cDC. The first two protocols illustrate analysis of cDC endocytosis and metabolism, followed by guidelines for transcriptomic and proteomic characterization of cDC populations. Then, a larger group of assays describes the characterization of cDC migration in vitro, ex vivo, and in vivo. The final guidelines measure cDC inflammasome and antigen (cross)‐presentation activity. While all protocols were written by experienced scientists who routinely use them in their work, this article was also peer‐reviewed by leading experts and approved by all co‐authors, making it an essential resource for basic and clinical DC immunologists. [ABSTRACT FROM AUTHOR]

Published
2023
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34. Table S4 from A TLR3 Ligand Reestablishes Chemotherapeutic Responses in the Context of FPR1 Deficiency

Author

Le Naour, Julie, primary, Liu, Peng, primary, Zhao, Liwei, primary, Adjemian, Sandy, primary, Sztupinszki, Zsofia, primary, Taieb, Julien, primary, Mulot, Claire, primary, Silvin, Aymeric, primary, Dutertre, Charles-Antoine, primary, Ginhoux, Florent, primary, Sauvat, Allan, primary, Cerrato, Giulia, primary, Castoldi, Francesca, primary, Martins, Isabelle, primary, Stoll, Gautier, primary, Paillet, Juliette, primary, Mangane, Khady, primary, Richter, Cornelia, primary, Kepp, Oliver, primary, Maiuri, Maria Chiara, primary, Pietrocola, Federico, primary, Vandenabeele, Peter, primary, André, Fabrice, primary, Delaloge, Suzette, primary, Szallasi, Zoltan, primary, Laurent-Puig, Pierre, primary, Zucman-Rossi, Jessica, primary, Zitvogel, Laurence, primary, Pol, Jonathan G., primary, Vacchelli, Erika, primary, and Kroemer, Guido, primary

Published
2023
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35. Supplementary Figures and Tables from A TLR3 Ligand Reestablishes Chemotherapeutic Responses in the Context of FPR1 Deficiency

Author

Le Naour, Julie, primary, Liu, Peng, primary, Zhao, Liwei, primary, Adjemian, Sandy, primary, Sztupinszki, Zsofia, primary, Taieb, Julien, primary, Mulot, Claire, primary, Silvin, Aymeric, primary, Dutertre, Charles-Antoine, primary, Ginhoux, Florent, primary, Sauvat, Allan, primary, Cerrato, Giulia, primary, Castoldi, Francesca, primary, Martins, Isabelle, primary, Stoll, Gautier, primary, Paillet, Juliette, primary, Mangane, Khady, primary, Richter, Cornelia, primary, Kepp, Oliver, primary, Maiuri, Maria Chiara, primary, Pietrocola, Federico, primary, Vandenabeele, Peter, primary, André, Fabrice, primary, Delaloge, Suzette, primary, Szallasi, Zoltan, primary, Laurent-Puig, Pierre, primary, Zucman-Rossi, Jessica, primary, Zitvogel, Laurence, primary, Pol, Jonathan G., primary, Vacchelli, Erika, primary, and Kroemer, Guido, primary

Published
2023
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36. Data from A TLR3 Ligand Reestablishes Chemotherapeutic Responses in the Context of FPR1 Deficiency

Author

Le Naour, Julie, primary, Liu, Peng, primary, Zhao, Liwei, primary, Adjemian, Sandy, primary, Sztupinszki, Zsofia, primary, Taieb, Julien, primary, Mulot, Claire, primary, Silvin, Aymeric, primary, Dutertre, Charles-Antoine, primary, Ginhoux, Florent, primary, Sauvat, Allan, primary, Cerrato, Giulia, primary, Castoldi, Francesca, primary, Martins, Isabelle, primary, Stoll, Gautier, primary, Paillet, Juliette, primary, Mangane, Khady, primary, Richter, Cornelia, primary, Kepp, Oliver, primary, Maiuri, Maria Chiara, primary, Pietrocola, Federico, primary, Vandenabeele, Peter, primary, André, Fabrice, primary, Delaloge, Suzette, primary, Szallasi, Zoltan, primary, Laurent-Puig, Pierre, primary, Zucman-Rossi, Jessica, primary, Zitvogel, Laurence, primary, Pol, Jonathan G., primary, Vacchelli, Erika, primary, and Kroemer, Guido, primary

Published
2023
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37. Anti-inflammatory SARS-CoV-2 T cell immunity in asymptomatic seronegative Kenyan adults

Author

Samandari, Taraz, primary, Ongalo, Joshua, additional, McCarthy, Kim, additional, Biegon, Richard K., additional, Madiega, Philister, additional, Mithika, Anne, additional, Orinda, Joseph, additional, Mboya, Grace M., additional, Mwaura, Patrick, additional, Anzala, Omu, additional, Onyango, Clayton, additional, Oluoch, Fredrick O., additional, Osoro, Eric, additional, Dutertre, Charles-Antoine, additional, Tan, Nicole, additional, Hang, Shou Kit, additional, Hariharaputran, Smrithi, additional, Lye, David C, additional, Herman-Roloff, Amy, additional, Bert, Nina Le, additional, and Bertoletti, Antonio, additional

Published
2023
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38. Notch-dependent cooperativity between myeloid lineages promotes Langerhans cell histiocytosis pathology

Author

Kvedaraite, Egle, primary, Milne, Paul, additional, Khalilnezhad, Ahad, additional, Chevrier, Marion, additional, Sethi, Raman, additional, Lee, Hong Kai, additional, Hagey, Daniel W., additional, von Bahr Greenwood, Tatiana, additional, Mouratidou, Natalia, additional, Jädersten, Martin, additional, Lee, Nicole Yee Shin, additional, Minnerup, Lara, additional, Tan, Yingrou, additional, Dutertre, Charles-Antoine, additional, Benac, Nathan, additional, Hwang, You Yi, additional, Lum, Josephine, additional, Loh, Amos Hong Pheng, additional, Jansson, Jessica, additional, Teng, Karen Wei Weng, additional, Khalilnezhad, Shabnam, additional, Xu, Weili, additional, Resteu, Anastasia, additional, Tey, Hong Liang, additional, Guan, Ng Lai, additional, Larbi, Anis, additional, Howland, Shanshan Wu, additional, Arnell, Henrik, additional, Andaloussi, Samir E. L., additional, Braier, Jorge, additional, Rassidakis, Georgios, additional, Galluzzo, Laura, additional, Dzionek, Andrzej, additional, Henter, Jan-Inge, additional, Chen, Jinmiao, additional, Collin, Matthew, additional, and Ginhoux, Florent, additional

Published
2022
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39. Guidelines for mouse and human DC functional assays

Author

Clausen, Björn E., primary, Amon, Lukas, additional, Backer, Ronald A., additional, Berod, Luciana, additional, Bopp, Tobias, additional, Brand, Anna, additional, Burgdorf, Sven, additional, Chen, Luxia, additional, Da, Meihong, additional, Distler, Ute, additional, Dress, Regine J., additional, Dudziak, Diana, additional, Dutertre, Charles‐Antoine, additional, Eich, Christina, additional, Gabele, Anna, additional, Geiger, Melanie, additional, Ginhoux, Florent, additional, Giusiano, Lucila, additional, Godoy, Gloria J., additional, Hamouda, Ahmed E.I., additional, Hatscher, Lukas, additional, Heger, Lukas, additional, Heidkamp, Gordon F., additional, Hernandez, Lola C., additional, Jacobi, Lukas, additional, Kaszubowski, Tomasz, additional, Kong, Wan Ting, additional, Lehmann, Christian H. K., additional, López‐López, Tamara, additional, Mahnke, Karsten, additional, Nitsche, Dominik, additional, Renkawitz, Jörg, additional, Reza, Rifat A., additional, Sáez, Pablo J., additional, Schlautmann, Laura, additional, Schmitt, Madeleine T., additional, Seichter, Anna, additional, Sielaff, Malte, additional, Sparwasser, Tim, additional, Stoitzner, Patrizia, additional, Tchitashvili, Giorgi, additional, Tenzer, Stefan, additional, Tochoedo, Nounagnon R., additional, Vurnek, Damir, additional, Zink, Fabian, additional, and Hieronymus, Thomas, additional

Published
2022
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40. Publisher Correction: The Extended Polydimensional Immunome Characterization (EPIC) web-based reference and discovery tool for cytometry data

Author

Yeo, Joo Guan, Wasser, Martin, Kumar, Pavanish, Pan, Lu, Poh, Su Li, Ally, Fauziah, Arkachaisri, Thaschawee, Lim, Amanda Jin Mei, Leong, Jing Yao, Lai, Liyun, Yeo, Kee Thai, Lee, Elene Seck Choon, Chua, Camillus Jian Hui, Larbi, Anis, Nyunt, Ma Shwe Zin, Ng, Tze Pin, Chiesa, Sabrina, Gattorno, Marco, Martini, Alberto, Paleja, Bhairav Suryakant, Dutertre, Charles-Antoine, Chen, Jinmiao, Nay Yaung, Katherine, Tang, Swee Ping, Ng, Sue Kheng, Yung, Chee Fu, Tan, Angela Yun June, Lee, Shu Ying, Ginhoux, Florent, and Albani, Salvatore

Published
2020
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41. Single-cell transcriptome analysis of the in vivo response to viral infection in the cave nectar bat Eonycteris spelaea

Author

Gamage, Akshamal M., primary, Chan, Wharton O.Y., additional, Zhu, Feng, additional, Lim, Yan Ting, additional, Long, Sandy, additional, Ahn, Matae, additional, Tan, Chee Wah, additional, Hiang Foo, Randy Jee, additional, Sia, Wan Rong, additional, Lim, Xiao Fang, additional, He, Haopeng, additional, Zhai, Weiwei, additional, Anderson, Danielle E., additional, Sobota, Radoslaw Mikolaj, additional, Dutertre, Charles-Antoine, additional, and Wang, Lin-Fa, additional

Published
2022
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42. Systemic vaccination induces CD8+ T cells and remodels the tumor microenvironment

Author

Baharom, Faezzah, primary, Ramirez-Valdez, Ramiro A., additional, Khalilnezhad, Ahad, additional, Khalilnezhad, Shabnam, additional, Dillon, Marlon, additional, Hermans, Dalton, additional, Fussell, Sloane, additional, Tobin, Kennedy K.S., additional, Dutertre, Charles-Antoine, additional, Lynn, Geoffrey M., additional, Müller, Sören, additional, Ginhoux, Florent, additional, Ishizuka, Andrew S., additional, and Seder, Robert A., additional

Published
2022
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43. Dual ontogeny of disease-associated microglia and disease inflammatory macrophages in aging and neurodegeneration

Author

Silvin, Aymeric, primary, Uderhardt, Stefan, additional, Piot, Cecile, additional, Da Mesquita, Sandro, additional, Yang, Katharine, additional, Geirsdottir, Laufey, additional, Mulder, Kevin, additional, Eyal, David, additional, Liu, Zhaoyuan, additional, Bridlance, Cecile, additional, Thion, Morgane Sonia, additional, Zhang, Xiao Meng, additional, Kong, Wan Ting, additional, Deloger, Marc, additional, Fontes, Vasco, additional, Weiner, Assaf, additional, Ee, Rachel, additional, Dress, Regine, additional, Hang, Jing Wen, additional, Balachander, Akhila, additional, Chakarov, Svetoslav, additional, Malleret, Benoit, additional, Dunsmore, Garett, additional, Cexus, Olivier, additional, Chen, Jinmiao, additional, Garel, Sonia, additional, Dutertre, Charles Antoine, additional, Amit, Ido, additional, Kipnis, Jonathan, additional, and Ginhoux, Florent, additional

Published
2022
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44. Pivotal role of M-DC8+ monocytes from viremic HIV-infected patients in TNFα overproduction in response to microbial products

Author

Dutertre, Charles-Antoine, Amraoui, Sonia, DeRosa, Annalisa, Jourdain, Jean-Pierre, Vimeux, Lene, Goguet, Matthieu, Degrelle, Séverine, Feuillet, Vincent, Liovat, Anne-Sophie, Müller-Trutwin, Michaela, Decroix, Nipa, Deveau, Christiane, Meyer, Laurence, Goujard, Cécile, Loulergue, Pierre, Launay, Odile, Richard, Yolande, and Hosmalin, Anne

Published
2012
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45. Hypoxia‐driven immunosuppression by Treg and type‐2 conventional dendritic cells in HCC

Author

Suthen, Sheena, primary, Lim, Chun Jye, additional, Nguyen, Phuong H. D., additional, Dutertre, Charles‐Antoine, additional, Lai, Hannah L. H., additional, Wasser, Martin, additional, Chua, Camillus, additional, Lim, Tony K. H., additional, Leow, Wei Qiang, additional, Loh, Tracy Jiezhen, additional, Wan, Wei Keat, additional, Pang, Yin Huei, additional, Soon, Gwyneth, additional, Cheow, Peng Chung, additional, Kam, Juinn Huar, additional, Iyer, Shridhar, additional, Kow, Alfred, additional, Tam, Wai Leong, additional, Shuen, Timothy W. H., additional, Toh, Han Chong, additional, Dan, Yock Young, additional, Bonney, Glenn K., additional, Chan, Chung Yip, additional, Chung, Alexander, additional, Goh, Brian K. P., additional, Zhai, Weiwei, additional, Ginhoux, Florent, additional, Chow, Pierce K. H., additional, Albani, Salvatore, additional, and Chew, Valerie, additional

Published
2022
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47. Tissue-resident FOLR2+ macrophages associate with CD8+ T cell infiltration in human breast cancer

Author

Nalio Ramos, Rodrigo, primary, Missolo-Koussou, Yoann, additional, Gerber-Ferder, Yohan, additional, Bromley, Christian P., additional, Bugatti, Mattia, additional, Núñez, Nicolas Gonzalo, additional, Tosello Boari, Jimena, additional, Richer, Wilfrid, additional, Menger, Laurie, additional, Denizeau, Jordan, additional, Sedlik, Christine, additional, Caudana, Pamela, additional, Kotsias, Fiorella, additional, Niborski, Leticia L., additional, Viel, Sophie, additional, Bohec, Mylène, additional, Lameiras, Sonia, additional, Baulande, Sylvain, additional, Lesage, Laëtitia, additional, Nicolas, André, additional, Meseure, Didier, additional, Vincent-Salomon, Anne, additional, Reyal, Fabien, additional, Dutertre, Charles-Antoine, additional, Ginhoux, Florent, additional, Vimeux, Lene, additional, Donnadieu, Emmanuel, additional, Buttard, Bénédicte, additional, Galon, Jérôme, additional, Zelenay, Santiago, additional, Vermi, William, additional, Guermonprez, Pierre, additional, Piaggio, Eliane, additional, and Helft, Julie, additional

Published
2022
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48. Intravenous Vaccination Induces CD8 + T Cells and Type I IFN-Dependent Remodeling of the Tumor Microenvironment

Author

Baharom, Faezzah, primary, Ramirez-Valdez, Ramiro Andrei, additional, Khalilnezhad, Ahad, additional, Khalilnezhad, Shabnam, additional, Dillon, Marlon, additional, Hermans, Dalton, additional, Fussell, Sloane, additional, Tobin, Kennedy K.S., additional, Dutertre, Charles-Antoine, additional, Lynn, Geoffrey M., additional, Ginhoux, Florent, additional, Ishizuka, Andrew, additional, and Seder, Robert A., additional

Published
2022
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49. Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition)

Author

Cossarizza, Andrea, primary, Chang, Hyun‐Dong, additional, Radbruch, Andreas, additional, Abrignani, Sergio, additional, Addo, Richard, additional, Akdis, Mübeccel, additional, Andrä, Immanuel, additional, Andreata, Francesco, additional, Annunziato, Francesco, additional, Arranz, Eduardo, additional, Bacher, Petra, additional, Bari, Sudipto, additional, Barnaba, Vincenzo, additional, Barros‐Martins, Joana, additional, Baumjohann, Dirk, additional, Beccaria, Cristian G., additional, Bernardo, David, additional, Boardman, Dominic A., additional, Borger, Jessica, additional, Böttcher, Chotima, additional, Brockmann, Leonie, additional, Burns, Marie, additional, Busch, Dirk H., additional, Cameron, Garth, additional, Cammarata, Ilenia, additional, Cassotta, Antonino, additional, Chang, Yinshui, additional, Chirdo, Fernando Gabriel, additional, Christakou, Eleni, additional, Čičin‐Šain, Luka, additional, Cook, Laura, additional, Corbett, Alexandra J., additional, Cornelis, Rebecca, additional, Cosmi, Lorenzo, additional, Davey, Martin S., additional, De Biasi, Sara, additional, De Simone, Gabriele, additional, del Zotto, Genny, additional, Delacher, Michael, additional, Di Rosa, Francesca, additional, Di Santo, James, additional, Diefenbach, Andreas, additional, Dong, Jun, additional, Dörner, Thomas, additional, Dress, Regine J., additional, Dutertre, Charles‐Antoine, additional, Eckle, Sidonia B. G., additional, Eede, Pascale, additional, Evrard, Maximilien, additional, Falk, Christine S., additional, Feuerer, Markus, additional, Fillatreau, Simon, additional, Fiz‐Lopez, Aida, additional, Follo, Marie, additional, Foulds, Gemma A., additional, Fröbel, Julia, additional, Gagliani, Nicola, additional, Galletti, Giovanni, additional, Gangaev, Anastasia, additional, Garbi, Natalio, additional, Garrote, José Antonio, additional, Geginat, Jens, additional, Gherardin, Nicholas A., additional, Gibellini, Lara, additional, Ginhoux, Florent, additional, Godfrey, Dale I., additional, Gruarin, Paola, additional, Haftmann, Claudia, additional, Hansmann, Leo, additional, Harpur, Christopher M., additional, Hayday, Adrian C., additional, Heine, Guido, additional, Hernández, Daniela Carolina, additional, Herrmann, Martin, additional, Hoelsken, Oliver, additional, Huang, Qing, additional, Huber, Samuel, additional, Huber, Johanna E., additional, Huehn, Jochen, additional, Hundemer, Michael, additional, Hwang, William Y. K., additional, Iannacone, Matteo, additional, Ivison, Sabine M., additional, Jäck, Hans‐Martin, additional, Jani, Peter K., additional, Keller, Baerbel, additional, Kessler, Nina, additional, Ketelaars, Steven, additional, Knop, Laura, additional, Knopf, Jasmin, additional, Koay, Hui‐Fern, additional, Kobow, Katja, additional, Kriegsmann, Katharina, additional, Kristyanto, H., additional, Krueger, Andreas, additional, Kuehne, Jenny F., additional, Kunze‐Schumacher, Heike, additional, Kvistborg, Pia, additional, Kwok, Immanuel, additional, Latorre, Daniela, additional, Lenz, Daniel, additional, Levings, Megan K., additional, Lino, Andreia C., additional, Liotta, Francesco, additional, Long, Heather M., additional, Lugli, Enrico, additional, MacDonald, Katherine N., additional, Maggi, Laura, additional, Maini, Mala K., additional, Mair, Florian, additional, Manta, Calin, additional, Manz, Rudolf Armin, additional, Mashreghi, Mir‐Farzin, additional, Mazzoni, Alessio, additional, McCluskey, James, additional, Mei, Henrik E., additional, Melchers, Fritz, additional, Melzer, Susanne, additional, Mielenz, Dirk, additional, Monin, Leticia, additional, Moretta, Lorenzo, additional, Multhoff, Gabriele, additional, Muñoz, Luis Enrique, additional, Muñoz‐Ruiz, Miguel, additional, Muscate, Franziska, additional, Natalini, Ambra, additional, Neumann, Katrin, additional, Ng, Lai Guan, additional, Niedobitek, Antonia, additional, Niemz, Jana, additional, Almeida, Larissa Nogueira, additional, Notarbartolo, Samuele, additional, Ostendorf, Lennard, additional, Pallett, Laura J., additional, Patel, Amit A., additional, Percin, Gulce Itir, additional, Peruzzi, Giovanna, additional, Pinti, Marcello, additional, Pockley, A. Graham, additional, Pracht, Katharina, additional, Prinz, Immo, additional, Pujol‐Autonell, Irma, additional, Pulvirenti, Nadia, additional, Quatrini, Linda, additional, Quinn, Kylie M., additional, Radbruch, Helena, additional, Rhys, Hefin, additional, Rodrigo, Maria B., additional, Romagnani, Chiara, additional, Saggau, Carina, additional, Sakaguchi, Shimon, additional, Sallusto, Federica, additional, Sanderink, Lieke, additional, Sandrock, Inga, additional, Schauer, Christine, additional, Scheffold, Alexander, additional, Scherer, Hans U., additional, Schiemann, Matthias, additional, Schildberg, Frank A., additional, Schober, Kilian, additional, Schoen, Janina, additional, Schuh, Wolfgang, additional, Schüler, Thomas, additional, Schulz, Axel R., additional, Schulz, Sebastian, additional, Schulze, Julia, additional, Simonetti, Sonia, additional, Singh, Jeeshan, additional, Sitnik, Katarzyna M., additional, Stark, Regina, additional, Starossom, Sarah, additional, Stehle, Christina, additional, Szelinski, Franziska, additional, Tan, Leonard, additional, Tarnok, Attila, additional, Tornack, Julia, additional, Tree, Timothy I. M., additional, van Beek, Jasper J. P., additional, van de Veen, Willem, additional, van Gisbergen, Klaas, additional, Vasco, Chiara, additional, Verheyden, Nikita A., additional, von Borstel, Anouk, additional, Ward‐Hartstonge, Kirsten A., additional, Warnatz, Klaus, additional, Waskow, Claudia, additional, Wiedemann, Annika, additional, Wilharm, Anneke, additional, Wing, James, additional, Wirz, Oliver, additional, Wittner, Jens, additional, Yang, Jennie H. M., additional, and Yang, Juhao, additional

Published
2021
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