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3. Performance of crisis standards of care guidelines in a cohort of critically ill COVID-19 patients in the United States.

Author

Jezmir, Julia L, Bharadwaj, Maheetha, Chaitoff, Alexander, Diephuis, Bradford, Crowley, Conor P, Kishore, Sandeep P, Goralnick, Eric, Merriam, Louis T, Milliken, Aimee, Rhee, Chanu, Sadovnikoff, Nicholas, Shah, Sejal B, Gupta, Shruti, Leaf, David E, Feldman, William B, Kim, Edy Y, and STOP-COVID Investigators

Subjects
STOP-COVID Investigators, Humans, Critical Illness, Critical Care, Hospital Mortality, Retrospective Studies, Cohort Studies, Comorbidity, Algorithms, Adult, Aged, Middle Aged, United States, Female, Male, Practice Guidelines as Topic, Pandemics, Standard of Care, Organ Dysfunction Scores, Crew Resource Management, Healthcare, COVID-19, SARS-CoV-2, ARDS, acute respiratory distress syndrome, crisis standards of care, critical care, intensive care, medical ethics, triage, Clinical Research, Good Health and Well Being
Abstract

Many US states published crisis standards of care (CSC) guidelines for allocating scarce critical care resources during the COVID-19 pandemic. However, the performance of these guidelines in maximizing their population benefit has not been well tested. In 2,272 adults with COVID-19 requiring mechanical ventilation drawn from the Study of the Treatment and Outcomes in Critically Ill Patients with COVID-19 (STOP-COVID) multicenter cohort, we test the following three approaches to CSC algorithms: Sequential Organ Failure Assessment (SOFA) scores grouped into ranges, SOFA score ranges plus comorbidities, and a hypothetical approach using raw SOFA scores not grouped into ranges. We find that area under receiver operating characteristic (AUROC) curves for all three algorithms demonstrate only modest discrimination for 28-day mortality. Adding comorbidity scoring modestly improves algorithm performance over SOFA scores alone. The algorithm incorporating comorbidities has modestly worse predictive performance for Black compared to white patients. CSC algorithms should be empirically examined to refine approaches to the allocation of scarce resources during pandemics and to avoid potential exacerbation of racial inequities.

Published
2021

4. Single-cell transcriptomics reveal a hyperacute cytokine and immune checkpoint axis after cardiac arrest in patients with poor neurological outcome

Author

Tamura, Tomoyoshi, Cheng, Changde, Chen, Wenan, Merriam, Louis T., Athar, Humra, Kim, Yaunghyun H., Manandhar, Reshmi, Amir Sheikh, Muhammad Dawood, Pinilla-Vera, Mayra, Varon, Jack, Hou, Peter C., Lawler, Patrick R., Oldham, William M., Seethala, Raghu R., Tesfaigzi, Yohannes, Weissman, Alexandra J., Baron, Rebecca M., Ichinose, Fumito, Berg, Katherine M., Bohula, Erin A., Morrow, David A., Chen, Xiang, and Kim, Edy Y.

Published
2023
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5. Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases

Author

Korsunsky, Ilya, Wei, Kevin, Pohin, Mathilde, Kim, Edy Y., Barone, Francesca, Major, Triin, Taylor, Emily, Ravindran, Rahul, Kemble, Samuel, Watts, Gerald F.M., Jonsson, A. Helena, Jeong, Yunju, Athar, Humra, Windell, Dylan, Kang, Joyce B., Friedrich, Matthias, Turner, Jason, Nayar, Saba, Fisher, Benjamin A., Raza, Karim, Marshall, Jennifer L., Croft, Adam P., Tamura, Tomoyoshi, Sholl, Lynette M., Vivero, Marina, Rosas, Ivan O., Bowman, Simon J., Coles, Mark, Frei, Andreas P., Lassen, Kara, Filer, Andrew, Powrie, Fiona, Buckley, Christopher D., Brenner, Michael B., and Raychaudhuri, Soumya

Published
2022
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9. Leukemia inhibitory factor (LIF) receptor amplifies pathogenic activation of fibroblasts in lung fibrosis

Author

Nguyen, Hung N., primary, Jeong, Yunju, additional, Kim, Yunhye, additional, Kim, Yaunghyun H., additional, Athar, Humra, additional, Castaldi, Peter J., additional, Hersh, Craig P., additional, Padera, Robert F., additional, Sholl, Lynette M., additional, Vivero, Marina, additional, Sharma, Nirmal S., additional, Yun, Jeong, additional, Merriam, Louis T., additional, Yuan, Ke, additional, Kim, Edy Y., additional, and Brenner, Michael B., additional

Published
2024
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10. Lactate transport inhibition therapeutically reprograms fibroblast metabolism in experimental pulmonary fibrosis

Author

Ziehr, David R., primary, Li, Fei, additional, Parnell, K. Mark, additional, Krah, Nathan M., additional, Leahy, Kevin J., additional, Guillermier, Christelle, additional, Varon, Jack, additional, Baron, Rebecca M., additional, Maron, Bradley A., additional, Philp, Nancy J., additional, Hariri, Lida P., additional, Kim, Edy Yong, additional, Steinhauser, Matthew L., additional, Knipe, Rachel S., additional, Rutter, Jared, additional, and Oldham, William, additional

Published
2024
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11. Protocol for immunophenotyping out-of-hospital cardiac arrest patients

Author

Yamada, Kohei, primary, Menon, Jaivardhan A., additional, Kim, Yaunghyun, additional, Cheng, Changde, additional, Chen, Wenan, additional, Shih, Jenny A., additional, Villasenor-Altamirano, Ana B., additional, Chen, Xiang, additional, Tamura, Tomoyoshi, additional, Merriam, Louis T., additional, Kim, Edy Y., additional, and Weissman, Alexandra J., additional

Published
2024
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12. Post-sepsis immunosuppression depends on NKT cell regulation of mTOR/IFN-[gamma] in NK cells

Author

Kim, Edy Y., Ner-Gaon, Hadas, Varon, Jack, Cullen, Aidan M., Guo, Jingyu, Choi, Jiyoung, Barragan-Bradford, Diana, Higuera, Angelica, Pinilla-Vera, Mayra, Short, Samuel A.P., Arciniegas-Rubio, Antonio, Tamura, Tomoyoshi, Leaf, David E., Baron, Rebecca M., Shay, Tal, and Brenner, Michael B.

Subjects
Thermo Fisher Scientific Inc., Analysis, Development and progression, Health aspects, Antigens -- Health aspects -- Analysis, Killer cells -- Analysis -- Health aspects, Macrophages -- Analysis -- Health aspects, Diseases -- Development and progression -- United States -- Massachusetts, Immunotherapy -- Analysis -- Health aspects, Scientific equipment industry -- Analysis -- Health aspects
Abstract

Introduction In sepsis, an excessive inflammatory response to infection leads to end organ damage (1). After surviving the early, inflammatory phase of sepsis, previously healthy patients can develop post-sepsis immunosuppression [...], As treatment of the early, inflammatory phase of sepsis improves, post-sepsis immunosuppression and secondary infection have increased in importance. How early inflammation drives immunosuppression remains unclear. Although IFN-[gamma] typically helps microbial clearance, we found that increased plasma IFN-[gamma] in early clinical sepsis was associated with the later development of secondary Candida infection. Consistent with this observation, we found that exogenous IFN-[gamma] suppressed macrophage phagocytosis of zymosan in vivo, and antibody blockade of IFN-[gamma] after endotoxemia improved survival of secondary candidemia. Transcriptomic analysis of innate lymphocytes during endotoxemia suggested that NKT cells drove IFN-[gamma] production by NK cells via mTORC1. Activation of invariant NKT (iNKT) cells with glycolipid antigen drove immunosuppression. Deletion of iNKT cells in [Cd1d.sup.-/-] mice or inhibition of mTOR by rapamycin reduced immunosuppression and susceptibility to secondary Candida infection. Thus, although rapamycin is typically an immunosuppressive medication, in the context of sepsis, rapamycin has the opposite effect. These results implicated an NKT cell/mTOR/IFN-[gamma] axis in immunosuppression following endotoxemia or sepsis. In summary, in vivo iNKT cells activated mTORC1 in NK cells to produce IFN-[gamma], which worsened macrophage phagocytosis, clearance of secondary Candida infection, and mortality.

Published
2020
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14. The cis-Regulatory Atlas of the Mouse Immune System

Author

Yoshida, Hideyuki, Lareau, Caleb A., Ramirez, Ricardo N., Rose, Samuel A., Maier, Barbara, Wroblewska, Aleksandra, Desland, Fiona, Chudnovskiy, Aleksey, Mortha, Arthur, Dominguez, Claudia, Tellier, Julie, Kim, Edy, Dwyer, Dan, Shinton, Susan, Nabekura, Tsukasa, Qi, YiLin, Yu, Bingfei, Robinette, Michelle, Kim, Ki-Wook, Wagers, Amy, Rhoads, Andrew, Nutt, Stephen L., Brown, Brian D., Mostafavi, Sara, Buenrostro, Jason D., and Benoist, Christophe

Published
2019
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16. Activation of CD8+ T Cells in Chronic Obstructive Pulmonary Disease Lung

Author

Villaseñor-Altamirano, Ana B., primary, Jain, Dhawal, additional, Jeong, Yunju, additional, Menon, Jaivardhan A., additional, Kamiya, Mari, additional, Haider, Hibah, additional, Manandhar, Reshmi, additional, Sheikh, Muhammad Dawood Amir, additional, Athar, Humra, additional, Merriam, Louis T., additional, Ryu, Min Hyung, additional, Sasaki, Takanori, additional, Castaldi, Peter J., additional, Rao, Deepak A., additional, Sholl, Lynette M., additional, Vivero, Marina, additional, Hersh, Craig P., additional, Zhou, Xiaobo, additional, Veerkamp, Justus, additional, Yun, Jeong H., additional, Kim, Edy Y., additional, Koch, Markus, additional, Arduini, Alessandro, additional, Cernecka, Hana, additional, Schmidt, Nicole, additional, Laux-Biehlmann, Alexis, additional, Brockschnieder, Damian, additional, Cong, Xiaofei, additional, Engler, Anna, additional, Ibrahim, Mahmoud, additional, Kryukov, Ivan, additional, Kumawat, Kuldeep, additional, Lang, T., additional, Leathurby, Yelena, additional, Lin, Xin, additional, Meding, Joerg, additional, Neideck, Carlos, additional, Obraztsova, Kseniya, additional, Pavuluri, C., additional, Platzk, Magdalena, additional, Smith, Patrick, additional, Sohler, Florian, additional, Srivastava, Salil, additional, Srinivasa, P., additional, Strunz, Tobias, additional, Sylvia, Jody, additional, Vaas, Lea, additional, Zink, Alex, additional, Zhang, Lingyao, additional, Zeng, L., additional, Silverman, Edwin, additional, Carey, Vincent, additional, Castaldi, Peter, additional, Cho, Michael, additional, DeMeo, Dawn, additional, Hersh, Craig, additional, Hobbs, Brian, additional, Moll, Matthew, additional, Rijhwani, Heena, additional, Yun, Jeong, additional, Levy, Bruce D., additional, Tesfaigzi, Yohannes, additional, Bai, Yan, additional, Baron, Rebecca, additional, Doyle, Tracy, additional, El-Chemaly, Souheil, additional, Fredenburgh, Laura, additional, Hunninghake, G. Matt, additional, Krishnamoorthy, Nandini, additional, Mebratu, Yohannes, additional, Perrella, Mark, additional, Quintero, Joselyn Rojas, additional, Negasi, Zerihun, additional, Rahman, Mizanur, additional, Tassew, Dereje, additional, Sharma, Nirmal, additional, Tamura, Tomoyoshi, additional, Villaseñor-Altamirano, Ana B., additional, Medoff, Benjamin, additional, Abe, Elizabeth, additional, Black, Katherine, additional, Hardin, Corey, additional, Knipe, Rachel, additional, Shea, Barry, additional, Spiney, Jill, additional, Albsuharif, Mahaa, additional, Giacona, Francesca, additional, Jayaswai, Armin, additional, Keras, Greg, additional, Lee, Sool, additional, Liu, Jianyuan, additional, Pavuluri, Chandan, additional, Pham, Betty, additional, Saliba, Samuel, additional, Srivastava, Pooja, additional, Wang, Yichao, additional, and Xu, Shuang, additional

Published
2023
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17. P2Y6 signaling in alveolar macrophages prevents leukotriene-dependent type 2 allergic lung inflammation

Author

Nagai, Jun, Balestrieri, Barbara, Fanning, Laura B., Kyin, Timothy, Cirka, Haley, Lin, Junrui, Idzko, Marco, Zech, Andreas, Kim, Edy Y., Brennan, Patrick J., and Boyce, Joshua A.

Subjects
Thermo Fisher Scientific Inc., R and D Systems, Prevention, Killer cells, Macrophages, Cytokines, Inflammation -- Prevention, Software industry, Asthma -- Prevention, Allergens, Scientific equipment industry, Immune response, Rhinitis
Abstract

Introduction Type 2 immunity (T2I) mediates host defense against helminthic parasites (1) and facilitates epithelial barrier repair (2). If dysregulated or directed against innocuous antigens (allergens), T2I can also promote [...], Antagonists of the type 1 cysteinyl leukotriene receptor ([CysLT.sub.1]R) are widely used to treat asthma and allergic rhinitis, with variable response rates. Alveolar macrophages express UDP-specific [P2Y.sub.6] receptors that can be blocked by off- target effects of [CysLT.sub.1]R antagonists. Sensitizing intranasal doses of an extract from the house dust mite Dermatophagoides farinae (Df) sharply increased the levels of UDP detected in bronchoalveolar lavage fluid of mice. Conditional deletion of [P2Y.sub.6] receptors before sensitization exacerbated eosinophilic lung inflammation and type 2 cytokine production in response to subsequent Df challenge. [P2Y.sub.6] receptor signaling was necessary for dectin-2-dependent production of protective IL-12p40 and Th1 chemokines by alveolar macrophages, leading to activation of NK cells to generate IFN-[gamma]. Administration of [CysLT.sub.1]R antagonists during sensitization blocked UDP-elicited potentiation of IL-12p40 production by macrophages in vitro, suppressed the Df-induced production of IL-12p40 and IFN-[gamma] in vivo, and suppressed type 2 inflammation only in [P2Y.sub.6]-deficient mice. Thus, [P2Y.sub.6] receptor signaling drives an innate macrophage/IL-12/NK cell/IFN-[gamma] axis that prevents inappropriate allergic type 2 immune responses on respiratory allergen exposure and counteracts the Th2 priming effect of [CysLT.sub.1]R signaling at sensitization. Targeting [P2Y.sub.6] signaling might prove to be a potential additional treatment strategy for allergy.

Published
2019
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19. Integrated Immunopeptidomic and Proteomic Analysis of COVID-19 lung biopsies

Author

Yin, Shanye, primary, Klaeger, Susan, additional, Chea, Vipheaviny A., additional, Carulli, Isabel P., additional, Rachimi, Suzanna, additional, Black, Katharine E., additional, Filbin, Michael, additional, Hariri, Lida P., additional, Knipe, Rachel S., additional, Padera, Robert F., additional, Stevens, Jonathan D., additional, Lane, William J., additional, Carr, Steven A., additional, Wu, Catherine J., additional, Kim, Edy Yong, additional, and Keskin, Derin B., additional

Published
2023
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22. Effect of Angiotensin-Converting Enzyme Inhibitor and Angiotensin Receptor Blocker Initiation on Organ Support-Free Days in Patients Hospitalized With COVID-19: A Randomized Clinical Trial

Author

Writing Committee for the REMAP-CAP Investigators, Lawler, Patrick R, Derde, Lennie PG, van de Veerdonk, Frank L, McVerry, Bryan J, Huang, David T, Berry, Lindsay R, Lorenzi, Elizabeth, van Kimmenade, Roland, Gommans, Frank, Vaduganathan, Muthiah, Leaf, David E, Baron, Rebecca M, Kim, Edy Y, Frankfurter, Claudia, Epelman, Slava, Kwan, Yvonne, Grieve, Richard, O'Neill, Stephen, Sadique, Zia, Puskarich, Michael, Marshall, John C, Higgins, Alisa M, Mouncey, Paul R, Rowan, Kathryn M, Al-Beidh, Farah, Annane, Djillali, Arabi, Yaseen M, Au, Carly, Beane, Abi, van Bentum-Puijk, Wilma, Bonten, Marc JM, Bradbury, Charlotte A, Brunkhorst, Frank M, Burrell, Aidan, Buzgau, Adrian, Buxton, Meredith, Cecconi, Maurizio, Cheng, Allen C, Cove, Matthew, Detry, Michelle A, Estcourt, Lise J, Ezekowitz, Justin, Fitzgerald, Mark, Gattas, David, Godoy, Lucas C, Goossens, Herman, Haniffa, Rashan, Harrison, David A, Hills, Thomas, Horvat, Christopher M, Ichihara, Nao, Lamontagne, Francois, Linstrum, Kelsey M, McAuley, Daniel F, McGlothlin, Anna, McGuinness, Shay P, McQuilten, Zoe, Murthy, Srinivas, Nichol, Alistair D, Owen, David RJ, Parke, Rachael L, Parker, Jane C, Pollock, Katrina M, Reyes, Luis Felipe, Saito, Hiroki, Santos, Marlene S, Saunders, Christina T, Seymour, Christopher W, Shankar-Hari, Manu, Singh, Vanessa, Turgeon, Alexis F, Turner, Anne M, Zarychanski, Ryan, Green, Cameron, Lewis, Roger J, Angus, Derek C, Berry, Scott, Gordon, Anthony C, McArthur, Colin J, Webb, Steve A, and Apollo - University of Cambridge Repository

Subjects
Male, Renin-Angiotensin System, Hospitalization, Angiotensin Receptor Antagonists, Critical Illness, Humans, COVID-19, Female, Angiotensin-Converting Enzyme Inhibitors, Bayes Theorem, Receptors, Chemokine, Middle Aged, COVID-19 Drug Treatment
Abstract

IMPORTANCE: Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. OBJECTIVE: To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS: In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non-critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS: Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES: The primary outcome was organ support-free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS: On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support-free days among critically ill patients was 10 (-1 to 16) in the ACE inhibitor group (n = 231), 8 (-1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support-free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE: In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02735707.

Published
2023

25. Anticoagulation and Antiplatelet Therapy for Prevention of Venous and Arterial Thrombotic Events in Critically Ill Patients With COVID-19: COVID-PACT

Author

Bohula, Erin A., primary, Berg, David D., additional, Lopes, Mathew S., additional, Connors, Jean M., additional, Babar, Ijlal, additional, Barnett, Christopher F., additional, Chaudhry, Sunit-Preet, additional, Chopra, Amit, additional, Ginete, Wilson, additional, Ieong, Michael H., additional, Katz, Jason N., additional, Kim, Edy Y., additional, Kuder, Julia F., additional, Mazza, Emilio, additional, McLean, Dalton, additional, Mosier, Jarrod M., additional, Moskowitz, Ari, additional, Murphy, Sabina A., additional, O’Donoghue, Michelle L., additional, Park, Jeong-Gun, additional, Prasad, Rajnish, additional, Ruff, Christian T., additional, Shahrour, Mohamad N., additional, Sinha, Shashank S., additional, Wiviott, Stephen D., additional, Van Diepen, Sean, additional, Zainea, Mark, additional, Baird-Zars, Vivian, additional, Sabatine, Marc S., additional, Morrow, David A., additional, Im, Kyung Ah, additional, Saxena, Retu, additional, Wiley, Brandon, additional, Benson, Carina, additional, Delamed, Roman, additional, Skeik, Nedaa, additional, Chopra, Ami, additional, Judson, Marc, additional, Beegle, Scott, additional, Shkolnik, Boris, additional, Tiwari, Anupama, additional, Wu, Gregory, additional, Raval, Abhijit, additional, Branch, Emerald, additional, Rischard, Franz, additional, Hypes, Cameron, additional, Bixby, Billie, additional, Bime, Christian, additional, Sundaram, Madhan, additional, Sweitzer, Nancy, additional, Sandoval, Alfredo Vazquez, additional, White, Heath, additional, Berg, Katherine, additional, Shaefi, Shahzad, additional, Donnino, Michael, additional, Carroll, Brett, additional, Ieong, Michael, additional, Ackerbauer, Kimberly, additional, Murphy, Jaime, additional, Bhatt, Ankeet, additional, Blood, Alexander, additional, Patel, Siddharth, additional, Luu, Victor, additional, Narechania, Shraddha, additional, Lorganger, Austin, additional, Plambeck, Robert, additional, Nayfeh, Ali, additional, Sanley, Michael, additional, Del Cor, Michel, additional, Hegg, AJ, additional, Nara, Winston, additional, Snyder, Michael, additional, Khan, Faisal, additional, Shawa, Imad, additional, Larned, Joshua, additional, Collado, Elias, additional, Al Faiyumi, Mohammed, additional, Mehta, Rajeev, additional, Komanapalli, Sudarshan, additional, Muppidi, Vijayadershan, additional, Desai, Mehul, additional, Flanagan, Casey, additional, Genovese, Leonard, additional, Haddad, Tariq, additional, King, Christopher, additional, Peterson, Amber, additional, Htun, Thane, additional, Pionk, Elizabeth, additional, Mouawad, Nicolas, additional, Kumar, Chintalapudi, additional, Nguyen, Kevin, additional, Mughal, Majid, additional, Malek, Ryan, additional, Parekh, Akarsh, additional, Provenzano, Christopher, additional, Ianitelli, Melissa, additional, Prentice-Gaytan, Nicole, additional, Bykowski, Adam, additional, Tait, Don, additional, Schendel, Shelley, additional, Yalamanchili, Varun, additional, Lala, Vasim, additional, Hunyadi, Victor, additional, Papolos, Alexander, additional, Kenigsberg, Benjamin, additional, Shenoy, Aarthi, additional, Stuckey, Thomas, additional, McQuaid, Douglas, additional, Mannam, Praveen, additional, McClung, Jeffrey, additional, Nilsson, Kent, additional, McKown, Andrew, additional, Wells, Jason, additional, Hotchkin, David, additional, Jacobs, Marc, additional, Strauss, Wayne, additional, Balestra, Rick, additional, Sahni, Vikram, additional, Snell, R. Jeffrey, additional, Suradi, Hussam, additional, Sungurlu, Sarah, additional, Kuppy, Jessica, additional, Gajo, Eileen, additional, Adams, Foster, additional, Shehadeh, Abbas, additional, Suleiman, Addi, additional, Nandigam, Harish, additional, Slim, Jihad, additional, Babar, Sardar Ijlal, additional, Baral, Dipti, additional, Nawaz, Talha, additional, Waheed, Syed Abdullah, additional, Roth, Randy, additional, Sitaula, Subhas, additional, Hayat, Shahid, additional, Babu, Jooby, additional, Caberto, Jason, additional, Hsu, Victor, additional, Chang, Robert, additional, Bochan, Markian, additional, Garcia-Cortes, Rafael, additional, Skopicki, Hal, additional, Chen, On, additional, Pilato, Lauren, additional, Richman, Paul, additional, Adler, Alexander, additional, Sudhindra, Praveen, additional, Beversdorf, Jamie, additional, Kashyap, Ravindra, additional, Mehta, Parth, additional, Mehrad, Borna, additional, Ataya, Ali, additional, Lascano, Jorge, additional, Brantly, Mark, additional, Austin, Adam, additional, Koman, Eduard, additional, Galski, Thomas, additional, Kumar, Vijaya, additional, Soubani, Ayman, additional, Harrison, Nicolas, additional, Reddy, Vineet, additional, and Fonkam, Audrey, additional

Published
2022
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26. Serum proteomic profiling of rheumatoid arthritis–interstitial lung disease with a comparison to idiopathic pulmonary fibrosis

Author

Wu, Xiaoping, primary, Jeong, Yunju, additional, Poli de Frías, Sergio, additional, Easthausen, Imaani, additional, Hoffman, Katherine, additional, Oromendia, Clara, additional, Taheri, Shahrad, additional, Esposito, Anthony J, additional, Quesada Arias, Luisa, additional, Ayaub, Ehab A, additional, Maurer, Rie, additional, Gill, Ritu R, additional, Hatabu, Hiroto, additional, Nishino, Mizuki, additional, Frits, Michelle L, additional, Iannaccone, Christine K, additional, Weinblatt, Michael E, additional, Shadick, Nancy A, additional, Dellaripa, Paul F, additional, Choi, Augustine M K, additional, Kim, Edy Y, additional, Rosas, Ivan O, additional, Martinez, Fernando J, additional, and Doyle, Tracy J, additional

Published
2022
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27. Dynamic Monitoring of Systemic Biomarkers with Gastric Sensors

Author

Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Division of Comparative Medicine, Massachusetts Institute of Technology. Department of Mechanical Engineering, Steiger, Christoph, Phan, Nhi V, Huang, Hen-Wei, Sun, Haoying, Chu, Jacqueline N, Reker, Daniel, Gwynne, Declan, Collins, Joy, Tamang, Siddartha, McManus, Rebecca, Lopes, Aaron, Hayward, Alison, Baron, Rebecca M, Kim, Edy Y, Traverso, Giovanni, Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology. Division of Comparative Medicine, Massachusetts Institute of Technology. Department of Mechanical Engineering, Steiger, Christoph, Phan, Nhi V, Huang, Hen-Wei, Sun, Haoying, Chu, Jacqueline N, Reker, Daniel, Gwynne, Declan, Collins, Joy, Tamang, Siddartha, McManus, Rebecca, Lopes, Aaron, Hayward, Alison, Baron, Rebecca M, Kim, Edy Y, and Traverso, Giovanni

Abstract

Continuous monitoring in the intensive care setting has transformed the capacity to rapidly respond with interventions for patients in extremis. Noninvasive monitoring has generally been limited to transdermal or intravascular systems coupled to transducers including oxygen saturation or pressure. Here it is hypothesized that gastric fluid (GF) and gases, accessible through nasogastric (NG) tubes, commonly found in intensive care settings, can provide continuous access to a broad range of biomarkers. A broad characterization of biomarkers in swine GF coupled to time-matched serum is conducted . The relationship and kinetics of GF-derived analyte level dynamics is established by correlating these to serum levels in an acute renal failure and an inducible stress model performed in swine. The ability to monitor ketone levels and an inhaled anaesthetic agent (isoflurane) in vivo is demonstrated with novel NG-compatible sensor systems in swine. Gastric access remains a main stay in the care of the critically ill patient, and here the potential is established to harness this establishes route for analyte evaluation for clinical management.

Published
2022

30. SLAMF7 engagement super-activates macrophages in acute and chronic inflammation

Author

Simmons, Daimon P., Nguyen, Hung N., Gomez-Rivas, Emma, Jeong, Yunju, Jonsson, A. Helena, Chen, Antonia F., Lange, Jeffrey K., Dyer, George S., Blazar, Philip, Earp, Brandon E., Coblyn, Jonathan S., Massarotti, Elena M., Sparks, Jeffrey A., Todd, Derrick J., Rao, Deepak A., Kim, Edy Y., and Brenner, Michael B.

Subjects
Adult, Inflammation, Reverse Transcriptase Polymerase Chain Reaction, SARS-CoV-2, Immunology, Synovial Membrane, COVID-19, General Medicine, Macrophage Activation, Article, Arthritis, Rheumatoid, Crohn Disease, Signaling Lymphocytic Activation Molecule Family, Acute Disease, Chronic Disease, Humans, Female, RNA-Seq, Single-Cell Analysis, Transcriptome, Cells, Cultured
Abstract

Macrophages regulate protective immune responses to infectious microbes, but aberrant macrophage activation frequently drives pathological inflammation. To identify regulators of vigorous macrophage activation, we analyzed RNA-seq data from synovial macrophages and identified SLAMF7 as a receptor associated with a superactivated macrophage state in rheumatoid arthritis. We implicated IFN-γ as a key regulator of SLAMF7 expression and engaging SLAMF7 drove a strong wave of inflammatory cytokine expression. Induction of TNF-α after SLAMF7 engagement amplified inflammation through an autocrine signaling loop. We observed SLAMF7-induced gene programs not only in macrophages from rheumatoid arthritis patients but also in gut macrophages from patients with active Crohn’s disease and in lung macrophages from patients with severe COVID-19. This suggests a central role for SLAMF7 in macrophage superactivation with broad implications in human disease pathology.

Published
2022

32. Effect of Angiotensin-Converting Enzyme Inhibitor and Angiotensin Receptor Blocker Initiation on Organ Support–Free Days in Patients Hospitalized With COVID-19: A Randomized Clinical Trial.

Author

Lawler, Patrick R., Derde, Lennie P. G., van de Veerdonk, Frank L., McVerry, Bryan J., Huang, David T., Berry, Lindsay R., Lorenzi, Elizabeth, van Kimmenade, Roland, Gommans, Frank, Vaduganathan, Muthiah, Leaf, David E., Baron, Rebecca M., Kim, Edy Y., Frankfurter, Claudia, Epelman¸, Slava, Kwan, Yvonne, Grieve, Richard, O'Neill, Stephen, Sadique, Zia, and Puskarich, Michael

Subjects
COVID-19, ANGIOTENSIN-receptor blockers, ACE inhibitors, CLINICAL trials, ANGIOTENSIN converting enzyme
Abstract

Key Points: Question: Does initiating an angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) in adult patients hospitalized for COVID-19 improve organ support–free days (a composite of hospital survival and duration of intensive care respiratory or cardiovascular support)? Findings: In this randomized clinical trial that included 779 patients, initiation of an ACE inhibitor or ARB did not improve organ support–free days. Among critically ill patients, there was a 95% probability that treatments worsened this outcome. Meaning: Among critically ill patients, initiation of an ACE inhibitor or ARB as treatment for COVID-19 did not improve, and likely worsened, clinical outcomes. IMPORTANCE: Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective: To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS: In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS: Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES: The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS: On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE: In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02735707 This randomized clinical trial examines the effect of initiation of a renin-angiotensin system inhibitor (ACE inhibitor or an angiotensin receptor blocker) on the composite outcome of hospital survival and organ support through 21 days in hospitalized patients with COVID-19. [ABSTRACT FROM AUTHOR]

Published
2023
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33. Performance of crisis standards of care guidelines in a cohort of critically ill COVID-19 patients in the United States

Author

Walther, Carl P., Anumudu, Samaya J., Arunthamakun, Justin, Kopecky, Kathleen F., Milligan, Gregory P., McCullough, Peter A., Nguyen, Thuy-Duyen, Shaefi, Shahzad, Krajewski, Megan L., Shankar, Sidharth, Pannu, Ameeka, Valencia, Juan D., Waikar, Sushrut S., Kibbelaar, Zoe A., Athavale, Ambarish M., Hart, Peter, Upadhyay, Shristi, Vohra, Ishaan, Oyintayo, Ajiboye, Green, Adam, Rachoin, Jean-Sebastien, Schorr, Christa A., Shea, Lisa, Edmonston, Daniel L., Mosher, Christopher L., Shehata, Alexandre M., Cohen, Zaza, Allusson, Valerie, Bambrick-Santoyo, Gabriela, ul aain Bhatti, Noor, Mehta, Bijal, Williams, Aquino, Brenner, Samantha K., Walters, Patricia, Go, Ronaldo C., Rose, Keith M., Hernán, Miguel A., Zhou, Amy M., Kim, Ethan C., Lisk, Rebecca, Chan, Lili, Mathews, Kusum S., Coca, Steven G., Altman, Deena R., Saha, Aparna, Soh, Howard, Wen, Huei Hsun, Bose, Sonali, Leven, Emily A., Wang, Jing G., Mosoyan, Gohar, Nadkarni, Girish N., Pattharanitima, Pattharawin, Friedman, Allon N., Guirguis, John, Kapoor, Rajat, Meshberger, Christopher, Kelly, Katherine J., Parikh, Chirag R., Garibaldi, Brian T., Corona-Villalobos, Celia P., Wen, Yumeng, Menez, Steven, Malik, Rubab F., Cervantes, Elena, Gautam, Samir, Mallappallil, Mary C., Ouyang, Jie, John, Sabu, Yap, Ernie, Melaku, Yohannes, Mohamed, Ibrahim, Bajracharya, Siddartha, Puri, Isha, Thaxton, Mariah, Bhattacharya, Jyotsna, Wagner, John, Boudourakis, Leon, Nguyen, H. Bryant, Ahoubim, Afshin, Thomas, Leslie F., Sirganagari, Dheeraj Reddy, Guru, Pramod K., Kashani, Kianoush, Zhou, Yan, Bergl, Paul A., Rodriguez, Jesus, Shah, Jatan A., Gupta, Mrigank S., Kumar, Princy N., Lazarous, Deepa G., Kassaye, Seble G., Melamed, Michal L., Johns, Tanya S., Mocerino, Ryan, Prudhvi, Kalyan, Zhu, Denzel, Levy, Rebecca V., Azzi, Yorg, Fisher, Molly, Yunes, Milagros, Sedaliu, Kaltrina, Golestaneh, Ladan, Brogan, Maureen, Kumar, Neelja, Chang, Michael, Raichoudhury, Ritesh, Athreya, Akshay, Farag, Mohamed, Schenck, Edward J., Cho, Soo Jung, Plataki, Maria, Alvarez-Mulett, Sergio L., Gomez-Escobar, Luis G., Pan, Di, Lee, Stefi, Krishnan, Jamuna, Whalen, William, Charytan, David, Macina, Ashley, Chaudhry, Sobaata, Wu, Benjamin, Modersitzki, Frank, Srivastava, Anand, Leidner, Alexander S., Martinez, Carlos, Kruser, Jacqueline M., Wunderink, Richard G., Hodakowski, Alexander J., Velez, Juan Carlos Q., Price-Haywood, Eboni G., Matute-Trochez, Luis A., Hasty, Anna E., Mohamed, Muner MB., Avasare, Rupali S., Zonies, David, Leaf, David E., Gupta, Shruti, Sise, Meghan E., Newman, Erik T., Abu Omar, Samah, Pokharel, Kapil K., Sharma, Shreyak, Singh, Harkarandeep, Correa, Simon, Shaukat, Tanveer, Kamal, Omer, Wang, Wei, Yang, Heather, Boateng, Jeffery O., Lee, Meghan, Strohbehn, Ian A., Li, Jiahua, Mueller, Ariel L., Redfern, Roberta, Cairl, Nicholas S., Naimy, Gabriel, Abu-Saif, Abeer, Hall, Danyell, Bickley, Laura, Rowan, Chris, Madhani-Lovely, Farah, Cruz, Vivian S., Hess, Kristen M., Jacobs, Alanna L., Peev, Vasil, Reiser, Jochen, Byun, John J., Vissing, Andrew, Kapania, Esha M., Post, Zoe, Patel, Nilam P., Hermes, Joy-Marie, Sutherland, Anne K., Patrawalla, Amee, Finkel, Diana G., Danek, Barbara A., Arikapudi, Sowminya, Paer, Jeffrey M., Cangialosi, Peter, Liotta, Mark, Radbel, Jared, Puri, Sonika, Sunderram, Jag, Scharf, Matthew T., Ahmed, Ayesha, Berim, Ilya, Vatson, Jayanth S., Anand, Shuchi, Levitt, Joseph E., Boyle, Suzanne M., Song, Rui, Zhang, Jingjing, Woo, Sang Hoon, Deng, Xiaoying, Katz-Greenberg, Goni, Senter, Katharine, Sharshir, Moh’d A., Rusnak, Vadym V., Ali, Muhammad Imran, Bansal, Anip, Podoll, Amber S., Chonchol, Michel, Sharma, Sunita, Burnham, Ellen L., Rashidi, Arash, Hejal, Rana, Judd, Eric, Latta, Laura, Tolwani, Ashita, Albertson, Timothy E., Adams, Jason Y., Chang, Steven Y., Beutler, Rebecca M., Macedo, Etienne, Rhee, Harin, Liu, Kathleen D., Jotwani, Vasantha K., Koyner, Jay L., Shah, Chintan V., Jaikaransingh, Vishal, Toth-Manikowski, Stephanie M., Joo, Min J., Lash, James P., Neyra, Javier A., Chaaban, Nourhan, Elias, Madona, Ahmad, Yahya, Iardino, Alfredo, Au, Elizabeth H., Sharma, Jill H., Sosa, Marie Anne, Taldone, Sabrina, Contreras, Gabriel, De La Zerda, David, Gershengorn, Hayley B., Shukla, Bhavarth, Fornoni, Alessia, Ferreira, Tanira, Hayek, Salim S., Blakely, Pennelope, Berlin, Hanna, Azam, Tariq U., Shadid, Husam, Pan, Michael, O’ Hayer, Patrick, Meloche, Chelsea, Feroze, Rafey, Kaakati, Rayan, Perry, Danny, Bitar, Abbas, Anderson, Elizabeth, Padalia, Kishan J., Donnelly, John P., Admon, Andrew J., Flythe, Jennifer E., Tugman, Matthew J., Chang, Emily H., Brown, Brent R., Leonberg-Yoo, Amanda K., Spiardi, Ryan C., Miano, Todd A., Roche, Meaghan S., Vasquez, Charles R., Bansal, Amar D., Ernecoff, Natalie C., Kapoor, Sanjana, Verma, Siddharth, Kovesdy, Csaba P., Molnar, Miklos Z., Azhar, Ambreen, Hedayati, S. Susan, Nadamuni, Mridula V., Shastri, Shani, Willett, Duwayne L., Short, Samuel A.P., Renaghan, Amanda D., Enfield, Kyle B., Bhatraju, Pavan K., Malik, A. Bilal, Semler, Matthew W., Vijayan, Anitha, Joy, Christina Mariyam, Li, Tingting, Goldberg, Seth, Kao, Patricia F., Schumaker, Greg L., Goyal, Nitender, Faugno, Anthony J., Hsu, Caroline M., Tariq, Asma, Meyer, Leah, Kshirsagar, Ravi K., Weiner, Daniel E., Jose, Aju, Christov, Marta, Griffiths, Jennifer, Gupta, Sanjeev, Kapoor, Aromma, Wilson, Perry, Arora, Tanima, Ugwuowo, Ugochukwu, Jezmir, Julia L., Bharadwaj, Maheetha, Chaitoff, Alexander, Diephuis, Bradford, Crowley, Conor P., Kishore, Sandeep P., Goralnick, Eric, Merriam, Louis T., Milliken, Aimee, Rhee, Chanu, Sadovnikoff, Nicholas, Shah, Sejal B., Feldman, William B., and Kim, Edy Y.

Published
2021
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38. Dynamic Monitoring of Systemic Biomarkers with Gastric Sensors

Author

Steiger, Christoph, primary, Phan, Nhi V., additional, Huang, Hen‐Wei, additional, Sun, Haoying, additional, Chu, Jacqueline N., additional, Reker, Daniel, additional, Gwynne, Declan, additional, Collins, Joy, additional, Tamang, Siddartha, additional, McManus, Rebecca, additional, Lopes, Aaron, additional, Hayward, Alison, additional, Baron, Rebecca M., additional, Kim, Edy Y., additional, and Traverso, Giovanni, additional

Published
2021
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42. Empirical Assessment of U.S. Coronavirus Disease 2019 Crisis Standards of Care Guidelines

Author

Bharadwaj, Maheetha, primary, Jezmir, Julia L., additional, Kishore, Sandeep P., additional, Winkler, Marisa, additional, Diephus, Bradford, additional, Haider, Hibah, additional, Crowley, Conor P., additional, Pinilla-Vera, Mayra, additional, Varon, Jack, additional, Baron, Rebecca M., additional, Feldman, William B., additional, and Kim, Edy Y., additional

Published
2021
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44. Persistent activation of an innate immune response translates respiratory viral infection into chronic lung disease

Author

Kim, Edy Y., Battaile, John T., Patel, Anand C., You, Yingjian, Agapov, Eugene, Grayson, Mitchell H., Benoit, Loralyn A., Byers, Derek E., Alevy, Yael, Tucker, Jennifer, Swanson, Suzanne, Tidwell, Rose, Tyner, Jeffrey W., Morton, Jeffrey D., Castro, Mario, Polineni, Deepika, Patterson, G. Alexander, Schwendener, Reto A., Allard, John D., Peltz, Gary, and Holtzman, Michael J.

Subjects
Prevention, Care and treatment, Usage, Models, Research, Risk factors, Health aspects, Lung diseases -- Risk factors -- Care and treatment -- Prevention -- Research, Immune response -- Health aspects -- Research -- Models -- Usage, House mouse -- Usage -- Models -- Research -- Health aspects, T cells -- Health aspects -- Research -- Usage -- Models, Mice -- Usage -- Models -- Research -- Health aspects
Abstract

It has been widely speculated that infections are linked to the development of chronic inflammatory diseases. Although the connection between infection and chronic disease is uncertain, it probably depends on [...], To understand the pathogenesis of chronic inflammatory disease, we analyzed an experimental mouse model of chronic lung disease with pathology that resembles asthma and chronic obstructive pulmonary disease (COPD) in humans. In this model, chronic lung disease develops after an infection with a common type of respiratory virus is cleared to only trace levels of noninfectious virus. Chronic inflammatory disease is generally thought to depend on an altered adaptive immune response. However, here we find that this type of disease arises independently of an adaptive immune response and is driven instead by interleukin-13 produced by macrophages that have been stimulated by CD1d-dependent T cell receptor-invariant natural killer T (NKT) cells. This innate immune axis is also activated in the lungs of humans with chronic airway disease due to asthma or COPD. These findings provide new insight into the pathogenesis of chronic inflammatory disease with the discovery that the transition from respiratory viral infection into chronic lung disease requires persistent activation of a previously undescribed NKT cell-macrophage innate immune axis.

Published
2008

45. ImmGen at 15

Author

Aguilar, Stephanie Vargas, Aguilar, Oscar, Allan, Rhys, Amir, El Ad David, Angeli, Veronique, Artyomov, Maxim, Asinovski, Natasha, Astarita, Jilian, Austen, K. Frank, Bajpai, Geetika, Barrett, Nora, Baysoy, Alev, Benoist, Christophe, Bellemare-Pelletier, Angelique, Berg, Brad, Best, Adam, Bezman, Natalie, Blair, David, Blander, Julie, Bogunovic, Milena, Brennan, Patrick, Brenner, Michael, Brown, Brian, Buechler, Matthew, Buenrostro, Jason, Casanova, Maria Acebes, Choi, Kyunghee, Chow, Andrew, Chudnovskiy, Aleksey, Cipoletta, Daniela, Cohen, Nadia, Collins, James, Colonna, Marco, Cook, Alison, Costello, James, Cremasco, Viviana, Crowl, Ty, Crozat, Karine, Cruse, Richard, D’angelo, June, Dalod, Marc, Davis, Scott, Demiralp, Cagatay, Deng, Tianda, Desai, Jigar, Desland, Fiona, Dhainaut, Maxime, Ding, Jiarui, Doedens, Andrew, Dominguez, Claudia, Doran, Graeme, Dress, Regine, Dustin, Michael, Dwyer, Daniel, Dzhagalov, Ivan, Elpek, Kutlu, Ergun, Ayla, Ericson, Jeff, Esomonu, Eunice, Fairfax, Keke, Fletcher, Anne, Frascoli, Michela, Fuchs, Anja, Gainullina, Anastasiia, Gal-Oz, Shani, Gallagher, Michael, Gautier, Emmanuel, Gazit, Roi, Gibbings, Sophie, Giraud, Matthieu, Ginhoux, Florent, Goldrath, Ananda, Gotthardt, Dagmar, Gray, Daniel, Greter, Melanie, Grieshaber-Bouyer, Ricardo, Guilliams, Martin, Haidermota, Sara, Hardy, Randy, Hashimoto, Daigo, Helft, Julie, Hendricks, Deborah, Heng, Tracy, Hill, Jonathan, Hyatt, Gordon, Idoyaga, Juliana, Jakubzick, Claudia, Jarjoura, Jessica, Jepson, Daniel, Jia, Baosen, Jianu, Radu, Johanson, Tim, Jordan, Stefan, Jojic, Vladimir, Kamimura, Yosuke, Kana, Veronica, Kang, Joonsoo, Kapoor, Varun, Kenigsberg, Ephriam, Kent, Andrew, Kim, Charles, Kim, Edy, Kim, Francis, Kim, Joel, Kim, Kiwook, Kiner, Evgeny, Knell, Jamie, Koller, Daphne, Kozinn, Larry, Krchma, Karen, Kreslavsky, Taras, Kronenberg, Mitchell, Kwan, Wing-Hong, Laidlaw, David, Lam, Viola, Lanier, Lewis, Laplace, Catherine, Lareau, Caleb, Lavin, Yonit, Lavine, Kory, Leader, Andrew, Leboeuf, Marylene, Lee, Jacob, Lee, Jisu, Li, Bo, Li, Hu, Li, Yuesheng, Lionakis, Michail, Luche, Herve, Lynch, Lydia, Magen, Assaf, Maier, Barbara, Malhotra, Deepali, Malhotra, Nidhi, Malissen, Marie, Maslova, Alexandra, Mathis, Diane, Mcfarland, Adelle, Merad, Miriam, Meunier, Etienne, Miller, Jennifer, Milner, Justin, Mingueneau, Michael, Min-Oo, Gundula, Monach, Paul, Moodley, Devapregasan, Mortha, Arthur, Morvan, Maelig, Mostafavi, Sara, Muller, Soren, Muus, Christoph, Nabekura, Tsukasa, Rao, Tata Nageswara, Narang, Vipin, Narayan, Kavitha, Ner-Gaon, Hadas, Nguyen, Quyhn, Nigrovic, Peter, Novakovsky, German, Nutt, Stephan, Omilusik, Kayla, Ortiz-Lopez, Adriana, Paidassi, Helena, Paik, Henry, Painter, Michio, Paynich, Mallory, Peng, Vincent, Potempa, Marc, Pradhan, Rachana, Price, Jeremy, Qi, Yilin, Qi, Yiqing, Quon, Sara, Ramirez, Ricardo, Ramanan, Deepshika, Randolph, Gwendalyn, Regev, Aviv, Rhoads, Andrew, Robinette, Michelle, Rose, Samuel, Rossi, Derrick, Rothamel, Katie, Sachidanandam, Ravi, Sathe, Priyanka, Scott, Charlotte, Seddu, Kumba, See, Peter, Sergushichev, Alexey, Shaw, Laura, Shay, Tal, Shemesh, Avishai, Shinton, Susan, Shyer, Justin, Sieweke, Michael, Smillie, Chris, Spel, Lotte, Spidale, Nick, Stifano, Giuseppina, Subramanian, Ayshwarya, Sun, Joseph, Sylvia, Katelyn, Tellier, Julie, This, Sébastien, Tomasello, Elena, Todorov, Helena, Turley, Shannon, Vijaykumar, Brinda, Wagers, Amy, Wakamatsu, Ei, Wang, Chendi, Wang, Peter, Wroblewska, Aleksandra, Wu, Jun, Yang, Edward, Yang, Liang, Yim, Aldrin, Yng, Lim Sheau, Yoshida, Hideyuki, Yu, Bingfei, Zhou, Yan, Zhu, Yanan, Ziemkiewicz, Caroline, Microenvironment, Cell Differentiation, Immunology and Cancer (MICMAC), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), The Walter and Eliza Hall Institute of Medical Research (WEHI), Icahn School of Medicine at Mount Sinai [New York] (MSSM), National University of Singapore (NUS), Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), Harvard Medical School [Boston] (HMS), Genentech, Inc. [San Francisco], Brigham & Women’s Hospital [Boston] (BWH), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Brown University, Lymphocytes B effecteurs et à mémoire – Effector and memory B cells, Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Dresden = Dresden University of Technology (TU Dresden), Crozat, Karine, and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
0301 basic medicine, Regulation of gene expression, [SDV.IMM] Life Sciences [q-bio]/Immunology, Test data generation, Computer science, [SDV]Life Sciences [q-bio], Immunology, Gene regulatory network, Genomics, Genome project, Data science, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, microRNA, Immunology and Allergy, DECIPHER, [SDV.IMM]Life Sciences [q-bio]/Immunology, Scientific publishing, ComputingMilieux_MISCELLANEOUS, 030215 immunology
Abstract

International audience; 700 comment | SERIES ImmGen at 15 Nature Immunology's 20 th anniversary is a good opportunity to reminisce about the ImmGen collective endeavor-its goals, successes and horror stories-and the group's exploration of various modes of scientific publishing. The Immunological Genome Project T he Immunological Genome Project (ImmGen) is a collaborative group of immunology and computational biology laboratories that perform a thorough dissection of gene expression and its regulation in the immune system of the mouse. This activity first centered on mRNA expression and then expanded to microRNA (miRNA), chromatin structure, nuclear organization and protein-RNA relationships. Shared protocols, data generation and QC pipelines have yielded data that can be directly compared from >250 stem, lymphoid and myeloid cell types, at baseline or under challenge. The group develops and applies computational tools to decipher regulatory connections and transcriptional control. From its inception, data generated by ImmGen were meant to be a public resource, and they can be accessed through dedicated web and smartphone platforms that use interactive graphic displays that make the results intuitive to users.

Published
2020
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47. CCL5-CCR5 interaction provides antiapoptotic signals for macrophage survival during viral infection

Author

Tyner, Jeffrey W., Uchida, Osamu, Kajiwara, Naohiro, Kim, Edy Y., Patel, Anand C., O'Sullivan, Mary P., Walter, Michael J., Schwendener, Reto A., Cook, Donald N., Danoff, Theodore M., and Holtzman, Michael J.

Abstract

Author(s): Jeffrey W Tyner [1]; Osamu Uchida [1]; Naohiro Kajiwara [1]; Edy Y Kim [1]; Anand C Patel [2]; Mary P O'Sullivan [1]; Michael J Walter [1]; Reto A Schwendener [...]

Published
2005
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48. Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases

Author

Korsunsky, Ilya, primary, Wei, Kevin, additional, Pohin, Mathilde, additional, Kim, Edy Y., additional, Barone, Francesca, additional, Kang, Joyce B., additional, Friedrich, Matthias, additional, Turner, Jason, additional, Nayar, Saba, additional, Fisher, Benjamin A., additional, Raza, Karim, additional, Marshall, Jennifer L., additional, Croft, Adam P., additional, Sholl, Lynette M., additional, Vivero, Marina, additional, Rosas, Ivan O., additional, Bowman, Simon J., additional, Coles, Mark, additional, Frei, Andreas P., additional, Lassen, Kara, additional, Filer, Andrew, additional, Powrie, Fiona, additional, Buckley, Christopher D., additional, Brenner, Michael B., additional, and Raychaudhuri, Soumya, additional

Published
2021
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