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2. Integrated analysis of whole blood oxylipin and cytokine responses after bacterial, viral, and T cell stimulation reveals new immune networks

Author

Abel, Laurent, Alcover, Andres, Aschard, Hugues, Bousso, Philippe, Bourke, Nollaig, Brodin, Petter, Bruhns, Pierre, Cerf-Bensussan, Nadine, Cumano, Ana, D’Enfert, Christophe, Deriano, Ludovic, Dillies, Marie-Agnès, Di Santo, James, Eberl, Gérard, Enninga, Jost, Fellay, Jacques, Gomperts-Boneca, Ivo, Hasan, Milena, Hedestam, Gunilla Karlsson, Hercberg, Serge, Ingersoll, Molly A., Lantz, Olivier, Kenny, Rose Anne, Ménager, Mickaël, Mouquet, Hugo, O'Farrelly, Cliona, Patin, Etienne, Pellegrini, Sandra, Rausell, Antonio, Rieux-Laucat, Frédéric, Rogge, Lars, Fontes, Magnus, Sakuntabhai, Anavaj, Schwartz, Olivier, Schwikowski, Benno, Shorte, Spencer, Tangy, Frédéric, Toubert, Antoine, Touvier, Mathilde, Ungeheuer, Marie-Noëlle, Zimmer, Christophe, Albert, Matthew L., Duffy, Darragh, Quintana-Murci, Lluis, Villain, Etienne, Chanson, Aurélie, Mainka, Malwina, Kampschulte, Nadja, Le Faouder, Pauline, Bertrand-Michel, Justine, Brandolini-Bunlon, Marion, Charbit, Bruno, Musvosvi, Munyaradzi, Bilek, Nicole, Scriba, Thomas J., Schebb, Nils Helge, and Gladine, Cécile

Published
2023
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3. Associations of autozygosity with a broad range of human phenotypes.

Author

Clark, David W, Okada, Yukinori, Moore, Kristjan HS, Mason, Dan, Pirastu, Nicola, Gandin, Ilaria, Mattsson, Hannele, Barnes, Catriona LK, Lin, Kuang, Zhao, Jing Hua, Deelen, Patrick, Rohde, Rebecca, Schurmann, Claudia, Guo, Xiuqing, Giulianini, Franco, Zhang, Weihua, Medina-Gomez, Carolina, Karlsson, Robert, Bao, Yanchun, Bartz, Traci M, Baumbach, Clemens, Biino, Ginevra, Bixley, Matthew J, Brumat, Marco, Chai, Jin-Fang, Corre, Tanguy, Cousminer, Diana L, Dekker, Annelot M, Eccles, David A, van Eijk, Kristel R, Fuchsberger, Christian, Gao, He, Germain, Marine, Gordon, Scott D, de Haan, Hugoline G, Harris, Sarah E, Hofer, Edith, Huerta-Chagoya, Alicia, Igartua, Catherine, Jansen, Iris E, Jia, Yucheng, Kacprowski, Tim, Karlsson, Torgny, Kleber, Marcus E, Li, Shengchao Alfred, Li-Gao, Ruifang, Mahajan, Anubha, Matsuda, Koichi, Meidtner, Karina, Meng, Weihua, Montasser, May E, van der Most, Peter J, Munz, Matthias, Nutile, Teresa, Palviainen, Teemu, Prasad, Gauri, Prasad, Rashmi B, Priyanka, Tallapragada Divya Sri, Rizzi, Federica, Salvi, Erika, Sapkota, Bishwa R, Shriner, Daniel, Skotte, Line, Smart, Melissa C, Smith, Albert Vernon, van der Spek, Ashley, Spracklen, Cassandra N, Strawbridge, Rona J, Tajuddin, Salman M, Trompet, Stella, Turman, Constance, Verweij, Niek, Viberti, Clara, Wang, Lihua, Warren, Helen R, Wootton, Robyn E, Yanek, Lisa R, Yao, Jie, Yousri, Noha A, Zhao, Wei, Adeyemo, Adebowale A, Afaq, Saima, Aguilar-Salinas, Carlos Alberto, Akiyama, Masato, Albert, Matthew L, Allison, Matthew A, Alver, Maris, Aung, Tin, Azizi, Fereidoun, Bentley, Amy R, Boeing, Heiner, Boerwinkle, Eric, Borja, Judith B, de Borst, Gert J, Bottinger, Erwin P, Broer, Linda, Campbell, Harry, Chanock, Stephen, Chee, Miao-Li, and Chen, Guanjie

Subjects
Humans, Body Size, Risk-Taking, Cognition, Health Status, Consanguinity, Fertility, Haplotypes, Homozygote, Alleles, Inbreeding Depression
Abstract

In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p

Published
2019

4. Loss of the intracellular enzyme QPCTL limits chemokine function and reshapes myeloid infiltration to augment tumor immunity

Author

Barreira da Silva, Rosa, Leitao, Ricardo M., Pechuan-Jorge, Ximo, Werneke, Scott, Oeh, Jason, Javinal, Vincent, Wang, Yingyun, Phung, Wilson, Everett, Christine, Nonomiya, Jim, Arnott, David, Lu, Cheng, Hsiao, Yi-Chun, Koerber, James T., Hötzel, Isidro, Ziai, James, Modrusan, Zora, Pillow, Thomas H., Roose-Girma, Merone, Schartner, Jill M., Merchant, Mark, Rutz, Sascha, Eidenschenk, Céline, Mellman, Ira, and Albert, Matthew L.

Published
2022
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5. Early IFNβ secretion determines variable downstream IL-12p70 responses upon TLR4 activation

Author

Abel, Laurent, Alcover, Andres, Aschard, Hugues, Bousso, Philippe, Bourke, Nollaig, Brodin, Petter, Bruhns, Pierre, Cerf-Bensussan, Nadine, Cumano, Ana, Demangel, Caroline, Christophe d’Enfert, Deriano, Ludovic, Dillies, Marie-Agnès, Di Santo, James, Dromer, Françoise, Eberl, Gérard, Enninga, Jost, Fellay, Jacques, Gomperts-Boneca, Ivo, Hasan, Milena, Fontes, Magnus, Hedestam, Gunilla Karlsson, Hercberg, Serge, Ingersoll, Molly A., Kenny, Rose Anne, Lantz, Olivier, Ménager, Mickael, Michel, Frédérique, Mouquet, Hugo, O'Farrelly, Cliona, Patin, Etienne, Pellegrini, Sandra, Pol, Stanislas, Rausell, Antonio, Rieux-Laucat, Frédéric, Rogge, Lars, Sakuntabhai, Anavaj, Schwartz, Olivier, Schwikowski, Benno, Shorte, Spencer, Tangy, Frédéric, Toubert, Antoine, Touvier, Mathilde, Ungeheuer, Marie-Noëlle, Zimmer, Christophe, Albert, Matthew L., Duffy, Darragh, Quintana-Murci, Lluis, Posseme, Celine, Llibre, Alba, Charbit, Bruno, Bondet, Vincent, Rouilly, Vincent, Saint-André, Violaine, Boussier, Jeremy, Bergstedt, Jacob, Smith, Nikaïa, Townsend, Liam, Sugrue, Jamie A., Ní Cheallaigh, Clíona, Conlon, Niall, Rotival, Maxime, Kobor, Michael S., and Mottez, Estelle

Published
2022
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10. Associations between consumption of dietary fibers and the risk of cardiovascular diseases, cancers, type 2 diabetes, and mortality in the prospective NutriNet-Santé cohort

Author

Partula, Valentin, Deschasaux, Mélanie, Druesne-Pecollo, Nathalie, Latino-Martel, Paule, Desmetz, Elisa, Chazelas, Eloi, Kesse-Guyot, Emmanuelle, Julia, Chantal, Fezeu, Léopold K, Galan, Pilar, Hercberg, Serge, Mondot, Stanislas, Lantz, Olivier, Quintana-Murci, Lluis, Albert, Matthew L, Duffy, Darragh, Srour, Bernard, and Touvier, Mathilde

Published
2020
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12. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Author

Klionsky, Daniel J, Abdelmohsen, Kotb, Abe, Akihisa, Abedin, Md Joynal, Abeliovich, Hagai, Acevedo Arozena, Abraham, Adachi, Hiroaki, Adams, Christopher M, Adams, Peter D, Adeli, Khosrow, Adhihetty, Peter J, Adler, Sharon G, Agam, Galila, Agarwal, Rajesh, Aghi, Manish K, Agnello, Maria, Agostinis, Patrizia, Aguilar, Patricia V, Aguirre-Ghiso, Julio, Airoldi, Edoardo M, Ait-Si-Ali, Slimane, Akematsu, Takahiko, Akporiaye, Emmanuel T, Al-Rubeai, Mohamed, Albaiceta, Guillermo M, Albanese, Chris, Albani, Diego, Albert, Matthew L, Aldudo, Jesus, Algül, Hana, Alirezaei, Mehrdad, Alloza, Iraide, Almasan, Alexandru, Almonte-Beceril, Maylin, Alnemri, Emad S, Alonso, Covadonga, Altan-Bonnet, Nihal, Altieri, Dario C, Alvarez, Silvia, Alvarez-Erviti, Lydia, Alves, Sandro, Amadoro, Giuseppina, Amano, Atsuo, Amantini, Consuelo, Ambrosio, Santiago, Amelio, Ivano, Amer, Amal O, Amessou, Mohamed, Amon, Angelika, An, Zhenyi, Anania, Frank A, Andersen, Stig U, Andley, Usha P, Andreadi, Catherine K, Andrieu-Abadie, Nathalie, Anel, Alberto, Ann, David K, Anoopkumar-Dukie, Shailendra, Antonioli, Manuela, Aoki, Hiroshi, Apostolova, Nadezda, Aquila, Saveria, Aquilano, Katia, Araki, Koichi, Arama, Eli, Aranda, Agustin, Araya, Jun, Arcaro, Alexandre, Arias, Esperanza, Arimoto, Hirokazu, Ariosa, Aileen R, Armstrong, Jane L, Arnould, Thierry, Arsov, Ivica, Asanuma, Katsuhiko, Askanas, Valerie, Asselin, Eric, Atarashi, Ryuichiro, Atherton, Sally S, Atkin, Julie D, Attardi, Laura D, Auberger, Patrick, Auburger, Georg, Aurelian, Laure, Autelli, Riccardo, Avagliano, Laura, Avantaggiati, Maria Laura, Avrahami, Limor, Awale, Suresh, Azad, Neelam, Bachetti, Tiziana, Backer, Jonathan M, Bae, Dong-Hun, Bae, Jae-Sung, Bae, Ok-Nam, Bae, Soo Han, Baehrecke, Eric H, Baek, Seung-Hoon, Baghdiguian, Stephen, and Bagniewska-Zadworna, Agnieszka

Subjects
Biochemistry and Cell Biology, Biological Sciences, Animals, Autophagy, Biological Assay, Computer Simulation, Humans, autolysosome, autophagosome, chaperone-mediated autophagy, flux, LC3, lysosome, macroautophagy, phagophore, stress, vacuole, Biochemistry & Molecular Biology, Biochemistry and cell biology
Published
2016

14. Associations between usual diet and gut microbiota composition: results from the Milieu Intérieur cross-sectional study

Author

Partula, Valentin, Mondot, Stanislas, Torres, Marion J, Kesse-Guyot, Emmanuelle, Deschasaux, Mélanie, Assmann, Karen, Latino-Martel, Paule, Buscail, Camille, Julia, Chantal, Galan, Pilar, Hercberg, Serge, Rouilly, Vincent, Thomas, Stéphanie, Quintana-Murci, Lluis, Albert, Matthew L, Duffy, Darragh, Lantz, Olivier, and Touvier, Mathilde

Published
2019
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19. Guidelines for the use and interpretation of assays for monitoring autophagy.

Author

Klionsky, Daniel J, Abdalla, Fabio C, Abeliovich, Hagai, Abraham, Robert T, Acevedo-Arozena, Abraham, Adeli, Khosrow, Agholme, Lotta, Agnello, Maria, Agostinis, Patrizia, Aguirre-Ghiso, Julio A, Ahn, Hyung Jun, Ait-Mohamed, Ouardia, Ait-Si-Ali, Slimane, Akematsu, Takahiko, Akira, Shizuo, Al-Younes, Hesham M, Al-Zeer, Munir A, Albert, Matthew L, Albin, Roger L, Alegre-Abarrategui, Javier, Aleo, Maria Francesca, Alirezaei, Mehrdad, Almasan, Alexandru, Almonte-Becerril, Maylin, Amano, Atsuo, Amaravadi, Ravi, Amarnath, Shoba, Amer, Amal O, Andrieu-Abadie, Nathalie, Anantharam, Vellareddy, Ann, David K, Anoopkumar-Dukie, Shailendra, Aoki, Hiroshi, Apostolova, Nadezda, Arancia, Giuseppe, Aris, John P, Asanuma, Katsuhiko, Asare, Nana YO, Ashida, Hisashi, Askanas, Valerie, Askew, David S, Auberger, Patrick, Baba, Misuzu, Backues, Steven K, Baehrecke, Eric H, Bahr, Ben A, Bai, Xue-Yuan, Bailly, Yannick, Baiocchi, Robert, Baldini, Giulia, Balduini, Walter, Ballabio, Andrea, Bamber, Bruce A, Bampton, Edward TW, Bánhegyi, Gábor, Bartholomew, Clinton R, Bassham, Diane C, Bast, Robert C, Batoko, Henri, Bay, Boon-Huat, Beau, Isabelle, Béchet, Daniel M, Begley, Thomas J, Behl, Christian, Behrends, Christian, Bekri, Soumeya, Bellaire, Bryan, Bendall, Linda J, Benetti, Luca, Berliocchi, Laura, Bernardi, Henri, Bernassola, Francesca, Besteiro, Sébastien, Bhatia-Kissova, Ingrid, Bi, Xiaoning, Biard-Piechaczyk, Martine, Blum, Janice S, Boise, Lawrence H, Bonaldo, Paolo, Boone, David L, Bornhauser, Beat C, Bortoluci, Karina R, Bossis, Ioannis, Bost, Frédéric, Bourquin, Jean-Pierre, Boya, Patricia, Boyer-Guittaut, Michaël, Bozhkov, Peter V, Brady, Nathan R, Brancolini, Claudio, Brech, Andreas, Brenman, Jay E, Brennand, Ana, Bresnick, Emery H, Brest, Patrick, Bridges, Dave, Bristol, Molly L, Brookes, Paul S, Brown, Eric J, and Brumell, John H

Subjects
Animals, Humans, Biological Assay, Models, Biological, Autophagy, Generic health relevance, autolysosome, autophagosome, flux, LC3, lysosome, phagophore, stress, vacuole, Biochemistry and Cell Biology, Biochemistry & Molecular Biology
Abstract

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Published
2012

20. Standardized whole blood stimulation improves immunomonitoring of induced immune responses in multi-center study

Author

Duffy, Darragh, Rouilly, Vincent, Braudeau, Cecile, Corbière, Véronique, Djebali, Raouf, Ungeheuer, Marie-Noelle, Josien, Regis, LaBrie, Samuel T., Lantz, Olivier, Louis, Delphine, Martinez-Caceres, Eva, Mascart, Francoise, Ruiz de Morales, Jose G., Ottone, Catherine, Redjah, Lydia, Guen, Nina Salabert-Le, Savenay, Alain, Schmolz, Manfred, Toubert, Antoine, and Albert, Matthew L.

Published
2017
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21. Multimarker risk stratification approach at multiple sclerosis onset

Author

Fernández-Paredes, Lidia, Casrouge, Armanda, Decalf, Jérémie, de Andrés, Clara, Villar, Luisa Maria, Pérez de Diego, Rebeca, Alonso, Bárbara, Álvarez Cermeño, José Carlos, Arroyo, Rafael, Tejera-Alhambra, Marta, Navarro, Joaquín, Oreja-Guevara, Celia, López Trascasa, Margarita, Seyfferth, Ansgar, García Martínez, Maria Angel, Álvarez Lafuente, Roberto, Albert, Matthew L., and Sánchez-Ramón, Silvia

Published
2017
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22. Systemic DPP4 activity is reduced during primary HIV-1 infection and is associated with intestinal [RORC.sup.+][CD4.sup.+] cell levels: a surrogate marker candidate of HIV-induced intestinal damage

Author

Ploquin, Mickael J., Casrouge, Armanda, Madec, Yoann, Noel, Nicolas, Jacquelin, Beatrice, Huot, Nicolas, Duffy, Darragh, Jochems, Simon P., Micci, Luca, Lecuroux, Camille, Boufassa, Faroudy, Booima, Thijs, Garcia-Tellez, Thalia, Ghislain, Mathilde, Grand, Roger Le, Lambotte, Olivier, Kootstra, Neeltje, Meyer, Laurence, Goujard, Cecile, Paiardini, Mirko, Albert, Matthew L., and Muller-Trutwin, Michaela

Subjects
HIV infections -- Risk factors -- Drug therapy, Proteases -- Research, Antiretroviral agents -- Dosage and administration, Quality of life -- Health aspects, Health
Abstract

Introduction: Combined anti-retroviral therapy (cART) transformed HIV-1 from a deadly disease into a chronic infection, but does not cure HIV infection. It also does not fully restore HIV-induced gut damage unless administered extremely early after infection. Additional biomarkers are needed to evaluate the capacity of therapies aimed at HIV remission/cure to restore HIV-induced intestinal immune damage and limit chronic inflammation. Herein, we aimed to identify a systemic surrogate marker whose levels would reflect gut immune damage such as intestinal Th17 cell loss starting from primary HIV-1 infection. Methods: Biomarker discovery approaches were performed in four independent cohorts, covering HIV-1 primary and chronic infection in 496 naive or cART-treated patients (Amsterdam cohort (ACS), ANRS PRIMO, COPANA and CODEX cohorts). The concentration and activity of soluble Dipeptidylpeptidase 4 (sDPP4) were quantified in the blood from these patients, including pre- and post-infection samples in the ACS cohort. For quantification of DPP4 in the gut, we utilized two non-human primate models, representing pathogenic (macaque) and non-pathogenic (African green monkey) SIV infection. Four gut compartments were analysed in each animal model (ileum, jejunum, colon and rectum) for quantification of DPP4, RORC and TBX21 gene expression in sorted [CD4.sup.+] cells. To analyse if sDPP4 levels increase when Th17 cells were restored, we quantified sDPP4 in plasma from SIV-infected macaques treated with IL-21. Results: We showed that sDPP4 levels were strongly decreased in primary HIV-1 infection. Strikingly, sDPP4 levels in primary HIV-1 infection predicted time to AIDS. They were not increased by cART in chronic HIV-1 infection (median 36 months on cART). In the gut of SIV-infected non-human primates, DPP4 mRNA was higher in [CD4.sup.+] than [CD4.sup.-] leucocytes. DPP4 specifically correlated with RORC expression, a Th17 marker, in [CD4.sup.+] cells from the intestine. We further demonstrated that sDPP4 activity levels were increased in animals treated with IL-21 and that this increase was associated with restoration of the Th17 compartment and reduced inflammation. Furthermore, DPP4 mRNA levels in small intestine [CD4.sup.+] cells positively correlated with circulating DPP4 activity. Conclusion: These data provide evidence that blood sDPP4 levels could be useful as a correlate for HIV-induced intestinal damage. Keywords: HIV; SIV; inflammation; intestine; dipeptidylpeptidase; biomarker; Th17, 1 | INTRODUCTION Combined anti-retroviral treatment (cART) drastically improves life expectancy and quality of life of HIV-infected individuals [1,2] but does not result in viral cure. Despite sustained undetectable viraemia [...]

Published
2018
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24. Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

Author

Patin, Etienne, Hasan, Milena, Bergstedt, Jacob, Rouilly, Vincent, Libri, Valentina, Urrutia, Alejandra, Alanio, Cécile, Scepanovic, Petar, Hammer, Christian, Jönsson, Friederike, Beitz, Benoît, Quach, Hélène, Lim, Yoong Wearn, Hunkapiller, Julie, Zepeda, Magge, Green, Cherie, Piasecka, Barbara, Leloup, Claire, Rogge, Lars, Huetz, François, Peguillet, Isabelle, Lantz, Olivier, Fontes, Magnus, Di Santo, James P., Thomas, Stéphanie, Fellay, Jacques, Duffy, Darragh, Quintana-Murci, Lluís, Albert, Matthew L., and The Milieu Intérieur Consortium

Published
2018
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25. Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

Author

Quach, Hélène, Rotival, Maxime, Pothlichet, Julien, Loh, Yong-Hwee Eddie, Dannemann, Michael, Zidane, Nora, Laval, Guillaume, Patin, Etienne, Harmant, Christine, Lopez, Marie, Deschamps, Matthieu, Naffakh, Nadia, Duffy, Darragh, Coen, Anja, Leroux-Roels, Geert, Clément, Frederic, Boland, Anne, Deleuze, Jean-François, Kelso, Janet, Albert, Matthew L., and Quintana-Murci, Lluis

Published
2016
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27. A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals

Author

Scepanovic, Petar, Hodel, Flavia, Mondot, Stanislas, Partula, Valentin, Byrd, Allyson, Hammer, Christian, Alanio, Cécile, Bergstedt, Jacob, Patin, Etienne, Touvier, Mathilde, Lantz, Olivier, Albert, Matthew L., Duffy, Darragh, Quintana-Murci, Lluis, Fellay, Jacques, and The Milieu Intérieur Consortium

Published
2019
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31. The Milieu Intérieur study — An integrative approach for study of human immunological variance

Author

Abel, Laurent, Alcover, Andres, Bousso, Philippe, Bruhns, Pierre, Cumano, Ana, Daëron, Marc, Delval, Cécile, Demangel, Caroline, Deriano, Ludovic, Di Santo, James, Dromer, Françoise, Eberl, Gérard, Enninga, Jost, Freitas, Antonio, Gelpi, Odile, Gomperts-Boneca, Ivo, Hercberg, Serge, Lantz, Olivier, Leclerc, Claude, Mouquet, Hugo, Pellegrini, Sandra, Pol, Stanislas, Rogge, Lars, Sakuntabhai, Anavaj, Schwartz, Olivier, Schwikowski, Benno, Shorte, Spencer, Soumelis, Vassili, Tangy, Frédéric, Tartour, Eric, Toubert, Antoine, Ungeheuer, Marie-Noëlle, Quintana-Murci, Lluis, Albert, Matthew L., Thomas, Stéphanie, Rouilly, Vincent, Patin, Etienne, Alanio, Cécile, Dubois, Annick, Marquier, Louis-Guillaume, Fauchoux, Nicolas, Sayegrih, Seloua, Vray, Muriel, and Duffy, Darragh

Published
2015
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33. Summary of the 8th Annual Bladder Cancer Think Tank: Collaborating to move research forward

Author

Apolo, Andrea B., Hoffman, Vanessa, Kaag, Matthew G., Latini, David M., Lee, Cheryl T., Rosenberg, Jonathan E., Knowles, Margaret, Theodorescu, Dan, Czerniak, Bogdan A., Efstathiou, Jason A., Albert, Matthew L., Sridhar, Srikala S., Margulis, Vitaly, Matin, Surena F., Galsky, Matthew D., Hansel, Donna, Kamat, Ashish M., Flaig, Thomas W., Smith, Angela B., Messing, Edward, Zipursky Quale, Diane, and Lotan, Yair

Published
2015
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35. Tuberculosis alters immune-metabolic pathways resulting in perturbed IL-1 responses

Author

Llibre, Alba, primary, Smith, Nikaïa, additional, Rouilly, Vincent, additional, Musvosvi, Munyaradzi, additional, Nemes, Elisa, additional, Posseme, Céline, additional, Mabwe, Simbarashe, additional, Charbit, Bruno, additional, Mbandi, Stanley Kimbung, additional, Filander, Elizabeth, additional, Africa, Hadn, additional, Saint-André, Violaine, additional, Bondet, Vincent, additional, Bost, Pierre, additional, Mulenga, Humphrey, additional, Bilek, Nicole, additional, Albert, Matthew L., additional, Scriba, Thomas J., additional, and Duffy, Darragh, additional

Published
2022
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36. Natural killer cell educating KIR/HLA combinations impact survival in anti-PD-L1 treated cancer patients

Author

Roe, David, primary, Rosoff, Howard, additional, Ruan, Dan Fu, additional, Khan, Zia, additional, Dogra, Pranay, additional, Carroll, Jonathan, additional, Hunkapiller, Julie, additional, Mohindra, Rajat, additional, Srivastava, Minu K., additional, Nabet, Barzin Y., additional, Chandler, G. Scott, additional, Albert, Matthew L., additional, McCarthy, Mark I., additional, Mellman, Ira, additional, Horowitz, Amir, additional, and Hammer, Christian, additional

Published
2022
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37. Apolipoprotein H expression is associated with IL28B genotype and viral clearance in hepatitis C virus infection

Author

Laird, Melissa E., Mohsen, Amira, Duffy, Darragh, Mamdouh, Rasha, LeFouler, Lenaig, Casrouge, Armanda, El-Daly, Mai, Rafik, Mona, Abdel-Hamid, Mohamed, Soulier, Alexandre, Pawlotsky, Jean-Michel, Hézode, Christophe, Rosa, Isabelle, Renard, Philippe, Mohamed, Mostafa K., Bonnard, Philippe, Izopet, Jacques, Mallet, Vincent, Pol, Stanislas, Albert, Matthew L., and Fontanet, Arnaud

Published
2014
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38. Functional Analysis via Standardized Whole-Blood Stimulation Systems Defines the Boundaries of a Healthy Immune Response to Complex Stimuli

Author

Abel, Laurent, Alcover, Andres, Bousso, Philippe, Cumano, Ana, Daëron, Marc, Delval, Cécile, Demangel, Caroline, Deriano, Ludovic, Di Santo, James, Dromer, Françoise, Eberl, Gérard, Enninga, Jost, Freitas, Antonio, Gomperts-Boneca, Ivo, Hercberg, Serge, Lantz, Olivier, Leclerc, Claude, Mouquet, Hugo, Pellegrini, Sandra, Pol, Stanislas, Rogge, Lars, Sakuntabhai, Anavaj, Schwartz, Olivier, Schwikowski, Benno, Shorte, Spencer, Soumelis, Vassili, Tangy, Frédéric, Tartour, Eric, Toubert, Antoine, Ungeheuer, Marie-Noëlle, Quintana-Murci, Lluis, Albert, Matthew L., Duffy, Darragh, Rouilly, Vincent, Libri, Valentina, Hasan, Milena, Beitz, Benoit, David, Mikael, Urrutia, Alejandra, Bisiaux, Aurélie, LaBrie, Samuel T., Dubois, Annick, Boneca, Ivo G., Thomas, Stéphanie, and Schmolz, Manfred

Published
2014
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42. In vivo imaging of inflammasome activation reveals a subcapsular macrophage burst response that mobilizes innate and adaptive immunity

Author

Sagoo, Pervinder, Garcia, Zacarias, Breart, Beatrice, Lemaitre, Fabrice, Michonneau, David, Albert, Matthew L., Yves, Levy, and Bousso, Philippe

Subjects
T cells -- Health aspects -- Physiological aspects -- Genetic aspects -- Research, Inflammation -- Development and progression -- Genetic aspects -- Research, Macrophages -- Health aspects -- Physiological aspects -- Genetic aspects -- Research, Biological sciences, Health
Abstract

The inflammasome is activated in response to a variety of pathogens and has an important role in shaping adaptive immunity, yet the spatiotemporal orchestration of inflammasome activation in vivo and the mechanisms by which it promotes an effective immune response are not fully understood. Using an in vivo reporter to visualize inflammasome assembly, we establish the distribution, kinetics and propagation of the inflammasome response to a local viral infection. We show that modified vaccinia Ankara virus induces inflammasome activation in subcapsular sinus (SCS) macrophages, which is immediately followed by cell death and release of extracellular ASC specks. This transient inflammasome signaling in the lymph node generates a robust influx of inflammatory cells and mobilizes T cells from the circulation to increase the magnitude of T cell responses. We propose that after infection, SCS macrophages deliver a burst response of inflammasome activity and cell death that translates into the broadening of T cell responses, identifying an important aspect of inflammasome-driven vaccination strategies., Innate immune sensing of pathogens or damage is characterized by activation of membrane and cytosolic pattern-recognition receptors including Toll-like receptors (TLRs), retinoic acid inducible gene I-like helicase receptors, cytosolic DNA [...]

Published
2016
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46. Variability of Primary Sjögren's Syndrome Is Driven by Interferon α and Interferon α Blood Levels Are Associated With the Class II HLA–DQ Locus

Author

Trutschel, Diana, Bost, Pierre, Mariette, Xavier, Bondet, Vincent, Llibre, Alba, Posseme, Celine, Charbit, Bruno, Thorball, Christian W., Jonsson, Roland, Lessard, Christopher J., Felten, Renaud, Ng, Wan Fai, Chatenoud, Lucienne, Dumortier, Hélène, Sibilia, Jean, Fellay, Jacques, Brokstad, Karl A., Appel, Silke, Tarn, Jessica R., Quintana‐Murci, Lluis, Mingueneau, Michael, Meyer, Nicolas, Duffy, Darragh, Schwikowski, Benno, Gottenberg, Jacques Eric, Dernis, Emmanuelle, Devauchelle‐Pensec, Valerie, Dieude, Philippe, Dubost, Jean‐Jacques, Fauchais, Anne‐Laure, Goeb, Vincent, Hachulla, Eric, Hatron, Pierre Yves, Larroche, Claire, Le Guern, Véronique, Morel, Jacques, Perdriger, Aleth, Salliot, Carinne, Rist, Stephanie, Saraux, Alain, Vittecoq, Olivier, Nocturne, Gaétane, Ravaud, Philippe, Seror, Raphaèle, Abel, Laurent, Alcover, Andres, Aschard, Hugues, Astrom, Kalla, Bousso, Philippe, Bruhns, Pierre, Cumano, Ana, Demangel, Caroline, Deriano, Ludovic, Di Santo, James, Dromer, Françoise, Eberl, Gérard, Enninga, Jost, Gelpi, Odile, GompertsBoneca, Ivo, Hasan, Milena, Hercberg, Serge, Lantz, Olivier, Leclerc, Claude, Mouquet, Hugo, Pellegrini, Sandra, Pol, Stanislas, Rausell, Antonio, Rogge, Lars, Sakuntabhai, Anavaj, Schwartz, Olivier, Shorte, Spencer, Soumelis, Vassili, Tangy, Frédéric, Tartour, Eric, Toubert, Antoine, Touvier, Mathilde, Ungeheuer, Marie‐Noëlle, Albert, Matthew L., Biomédecine computationelle des systèmes / Computational systems biomedicine, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Universität Zürich [Zürich] = University of Zurich (UZH), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Service de Rhumatologie [CHU Bicêtre], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Bicêtre, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Projet NECESSITY (PN), Hôpitaux Universitaires Paris Sud [AP-HP] (HUPS)-Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Immunologie Translationnelle - Translational Immunology lab, Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Ecole Polytechnique Fédérale de Lausanne (EPFL), Université de Lausanne = University of Lausanne (UNIL), Lausanne University Hospital, University of Bergen (UiB), Oklahoma Medical Research Foundation (OMRF), University of Oklahoma Health Sciences Center (OUHSC), Université de Strasbourg (UNISTRA), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Newcastle University [Newcastle], Newcastle Upon Tyne Hospitals NHS Foundation Trust, Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Immunologie, Immunopathologie et Chimie Thérapeutique (I2CT), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Biogen Inc. [Cambridge, MA, USA], Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Supported by the Innovative Medicines Initiative 2 Joint Undertaking (JU) (grant 806975). The JU receives support from the European Union’s Horizon 2020 research and innovation program and the European Unionand the European Federation of Pharmaceutical Industries and Associations. This work was also supported by the National Institutes of Health (National Institute of Arthritis and Musculoskeletal Skin Disease grant R01-AR-065953). The Assessment of Systemic Signs and Evolution in Sjögren’s Syndrome(ASSESS) national multicenter prospective cohort was formed in 2006 with aFrench Ministry of Health grant (Programme Hospitalier de Recherche Clinique 2005 P060228). The ASSESS cohort is promoted by the French Society of Rheumatology and receives research grants from the French Society of Rheumatology. Dr. Gottenberg’s work was supported by Bristol Myers Squibbfor transcriptomic analysis of the ASSESS and Norwegian cohorts and by Geneviève Garnier (Association Française du Syndrome de Gougerot-Sjögrenet des syndromes secs). Drs. Trutschel’s and Schwikowski’s work was supported by Geneviève Garnier (Association Française du Syndrome de Gougerot-Sjögren et des syndromes secs)., Milieu Intérieur Consortium, ASSESS study investigators, and NECESSITY Consortium: Emmanuelle Dernis, Valerie Devauchelle-Pensec, Philippe Dieude, Jean-Jacques Dubost, Anne-Laure Fauchais, Vincent Goeb, Eric Hachulla, Pierre Yves Hatron, Claire Larroche, Véronique Le Guern, Jacques Morel, Aleth Perdriger, Carinne Salliot, Stephanie Rist, Alain Saraux, Jean Sibilia, Olivier Vittecoq, Gaétane Nocturne, Philippe Ravaud, Raphaèle Seror, Laurent Abel, Andres Alcover, Hugues Aschard, Kalla Astrom, Philippe Bousso, Pierre Bruhns, Ana Cumano, Caroline Demangel, Ludovic Deriano, James Di Santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Jacques Fellay, Odile Gelpi, Ivo GompertsBoneca, Milena Hasan, Serge Hercberg, Olivier Lantz, Claude Leclerc, Hugo Mouquet, Sandra Pellegrini, Stanislas Pol, Antonio Rausell, Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Vassili Soumelis, Frédéric Tangy, Eric Tartour, Antoine Toubert, Mathilde Touvier, Marie-Noëlle Ungeheuer, Matthew L Albert, Darragh Duffy, Lluis Quintana-Murci., European Project: 806975,NECESSITY, Clauss, Isabelle, and NEw Clinical Endpoints in primary Sjögren’s Syndrome: an Interventional Trial based on stratifYing patients - NECESSITY - 0000-00-00 - 0000-00-00 - 806975 - VALID

Subjects
Proteomics, [SDV.MHEP.RSOA] Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, Sjogren's Syndrome, Rheumatology, [SDV.MHEP.RSOA]Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, HLA-DQ Antigens, Immunology, Humans, Interferon-alpha, Immunology and Allergy, Prospective Studies
Abstract

Objective: Primary Sjögren's syndrome (SS) is the second most frequent systemic autoimmune disease, affecting 0.1% of the general population. To characterize the molecular and clinical variabilities among patients with primary SS, we integrated transcriptomic, proteomic, cellular, and genetic data with clinical phenotypes in a cohort of 351 patients with primary SS. Methods: We analyzed blood transcriptomes and genotypes of 351 patients with primary SS who were participants in a multicenter prospective clinical cohort. We replicated the transcriptome analysis in 3 independent cohorts (n = 462 patients). We determined circulating interferon-α (IFNα) and IFNγ protein concentrations using digital single molecular arrays (Simoa). Results: Transcriptome analysis of the prospective cohort showed a strong IFN gene signature in more than half of the patients; this finding was replicated in the 3 independent cohorts. Because gene expression analysis did not discriminate between type I IFN and type II IFN, we used Simoa to demonstrate that the IFN transcriptomic signature was driven by circulating IFNα and not by IFNγ protein levels. IFNα protein levels, detectable in 75% of patients, were significantly associated with clinical and immunologic features of primary SS disease activity at enrollment and with increased frequency of systemic complications over the 5-year follow-up. Genetic analysis revealed a significant association between IFNα protein levels, a major histocompatibility (MHC) class II haplotype, and anti-SSA antibody. Additional cellular analysis revealed that an MHC class II HLA–DQ locus acts through up-regulation of HLA class II molecules on conventional dendritic cells. Conclusion: We identified the predominance of IFNα as a driver of primary SS variability, with IFNα demonstrating an association with HLA gene polymorphisms., Arthritis & Rheumatology, 74 (12), ISSN:2326-5191, ISSN:2326-5205

Published
2022
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49. Additional file 2 of Integrative genetic and immune cell analysis of plasma proteins in healthy donors identifies novel associations involving primary immune deficiency genes

Author

Caron, Barthelemy, Patin, Etienne, Rotival, Maxime, Charbit, Bruno, Albert, Matthew L., Quintana-Murci, Lluis, Duffy, Darragh, and Rausell, Antonio

Subjects
population characteristics, social sciences
Abstract

Additional file 2: Figure S1. Principal component analysis of age and sex effects. Figure S2. Manhattan plots and allelic expression of levels of cis-pQTLs. Figure S3. Manhattan plots and allelic expression of levels of trans-pQTLs. Figure S4. Impact of blood-cell fractions on associated protein-SNP pairs statistics.

Published
2022
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