*co-first author; †corresponding author; group members in bold.
Key publications
Cui A†, Huang T, Li S, Ma A, Pérez JL, Sander C, Keskin DB, Wu CJ, Fraenkel E, Hacohen N†. Dictionary of immune responses to cytokines at single-cell resolution. Nature. 2024 Jan; 625(7994):377-384. PMID: 38057668; PMCID: PMC10781646. PDF
- Broad Institute of MIT and Harvard News: New “dictionary” of immune responses reveals far more complexity in the immune system than previously thought.
- Harvard School of Dental Medicine News: Immune Dictionary reveals deepest-yet view into workings of the immune system.
- International Cytokine & Interferon Society News: Gigantic cytokines paper is out recently in Nature! A comprehensive study of how every immune cell type responds to each of 86 cytokines in vivo at single-cell resolution.
- Antibuddies Blog: A Periodic Table for Cytokines.
- MicrobeTV Immune Podcast: Ang Cui unveils the cytokine symphony.
Cui A*†, Li B*, Wallace MS, Gonye ALK, Oetheimer C, Patel H, Tonnerre P, Holmes JA, Lieb D, Yao BS, Ma A, Roberts K, Damasio M, Chen JH, Piou D, Carlton-Smith C, Brown J, Mylvaganam R, Hon Fung JM, Sade-Feldman M, Aneja J, Gustafson J, Epstein ET, Salloum S, Brisac C, Thabet A, Kim AY, Lauer GM, Hacohen N†, Chung RT†, Alatrakchi N†. Single-cell atlas of the liver myeloid compartment before and after cure of chronic viral hepatitis. Journal of Hepatology. 2024 02; 80(2):251-267. PMID: 36972796. PDF
- Featured in Editorial: Crouchet E and Baumert TF, Unraveling the role of the liver myeloid compartment during hepatitis C virus cure. Journal of Hepatology. 2024 02; 80(2):184-187. PMID: 37088307.
Cui A†, Chawla DG, Kleinstein SH†. Sex-biased aging effects on Ig somatic hypermutation targeting. Journal of Immunology. 2021 01 01; 206(1):101-108. PMID: 33288546; PMCID: PMC8582005. PDF
Cui A, Di Niro R, Vander Heiden JA, Briggs AW, Adams K, Gilbert T, O’Connor KC, Vigneault F, Shlomchik MJ, Kleinstein SH. A model of somatic hypermutation targeting in mice based on high-throughput Ig sequencing data. Journal of Immunology. 2016 11 01; 197(9):3566-3574. PMID: 27707999; PMCID: PMC5161250. PDF
Cui A*, Quon G*, Rosenberg AM, Yeung RS, Morris Q, BBOP Study Consortium. Gene expression deconvolution for uncovering molecular signatures in response to therapy in juvenile idiopathic arthritis. Plos One. 2016; 11(5):e0156055. PMID: 27244050; PMCID: PMC4887077. PDF
All publications
Cui A†, Huang T, Li S, Ma A, Pérez JL, Sander C, Keskin DB, Wu CJ, Fraenkel E, Hacohen N†. Dictionary of immune responses to cytokines at single-cell resolution. Nature. 2024 Jan; 625(7994):377-384. PMID: 38057668; PMCID: PMC10781646. PDF
Cui A*†, Li B*, Wallace MS, Gonye ALK, Oetheimer C, Patel H, Tonnerre P, Holmes JA, Lieb D, Yao BS, Ma A, Roberts K, Damasio M, Chen JH, Piou D, Carlton-Smith C, Brown J, Mylvaganam R, Hon Fung JM, Sade-Feldman M, Aneja J, Gustafson J, Epstein ET, Salloum S, Brisac C, Thabet A, Kim AY, Lauer GM, Hacohen N†, Chung RT†, Alatrakchi N†. Single-cell atlas of the liver myeloid compartment before and after cure of chronic viral hepatitis. Journal of Hepatology. 2024 02; 80(2):251-267. PMID: 36972796. PDF
Chudnovskiy A, Castro TBR, Nakandakari-Higa S, Cui A, Lin CH, Sade-Feldman M, Phillips BK, Pae J, Mesin L, Bortolatto J, Schweitzer LD, Pasqual G, Lu LF, Hacohen N, Victora GD. Proximity-dependent labeling identifies dendritic cells that drive the tumor-specific CD4+ T cell response. Science Immunology. 2024 10 04; 9 (100):eadq8843. PMID: 39365874. PDF
Aung A, Cui A, Maiorino L, Amini AP, Gregory JR, Bukenya M, Zhang Y, Lee H, Cottrell CA, Morgan DM, Silva M, Suh H, Kirkpatrick JD, Amlashi P, Remba T, Froehle LM, Xiao S, Abraham W, Adams J, Love JC, Huyett P, Kwon DS, Hacohen N, Schief WR, Bhatia SN, Irvine DJ. Low protease activity in B cell follicles promotes retention of intact antigens after immunization. Science. 2023 01 27; 379(6630):eabn8934. PMID: 36701450; PMCID: PMC10041875. PDF
Cui A†, Chawla DG, Kleinstein SH†. Sex-biased aging effects on Ig somatic hypermutation targeting. Journal of Immunology. 2021 01 01; 206(1):101-108. PMID: 33288546; PMCID: PMC8582005. PDF
Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, Kang HY, Cui A, Ray JP, Eisenhaure TM, Collins RL, Dey K, Pfister H, Price AL, Epstein CB, Kundaje A, Xavier RJ, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM. Genome-wide enhancer maps link risk variants to disease genes. Nature. 2021 05; 593(7858):238-243. PMID: 33828297; PMCID: PMC9153265. PDF
Braun DA, Street K, Burke KP, Cookmeyer DL, Denize T, Pedersen CB, Gohil SH, Schindler N, Pomerance L, Hirsch L, Bakouny Z, Hou Y, Forman J, Huang T, Li S, Cui A, Keskin DB, Steinharter J, Bouchard G, Sun M, Pimenta EM, Xu W, Mahoney KM, McGregor BA, Hirsch MS, Chang SL, Livak KJ, McDermott DF, Shukla SA, Olsen LR, Signoretti S, Sharpe AH, Irizarry RA, Choueiri TK, Wu CJ. Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. Cancer Cell. 2021 05 10; 39(5):632-648.e8. PMID: 33711273; PMCID: PMC8138872. PDF
Tonnerre P, Wolski D, Subudhi S, Aljabban J, Hoogeveen RC, Damasio M, Drescher HK, Bartsch LM, Tully DC, Sen DR, Bean DJ, Brown J, Torres-Cornejo A, Robidoux M, Kvistad D, Alatrakchi N, Cui A, Lieb D, Cheney JA, Gustafson J, Lewis-Ximenez LL, Massenet-Regad L, Eisenhaure T, Aneja J, Haining WN, Chung RT, Hacohen N, Allen TM, Kim AY, Lauer GM. Differentiation of exhausted CD8+ T cells after termination of chronic antigen stimulation stops short of achieving functional T cell memory. Nature Immunology. 2021 08; 22(8):1030-1041. PMID: 34312544; PMCID: PMC8323980. PDF
Wang C, Cui A, Bukenya M, Aung A, Pradhan D, Whittaker CA, Agarwal Y, Thomas A, Liang S, Amlashi P, Suh H, Spranger S, Hacohen N, Irvine DJ. Reprogramming NK cells and macrophages via combined antibody and cytokine therapy primes tumors for elimination by checkpoint blockade. Cell Reports. 2021 11 23; 37(8):110021. PMID: 34818534; PMCID: PMC8653865. PDF
Raychowdhury R, Gentili M, Cui A, Schweitzer LD, Li B, Hacohen N. Macrophages from Rosa26-Integrated Cas9-Expressing C57BL/6J Mice Have a Putative TRIF-Mediated Defect in the TLR-3/4 Signaling. Immunohorizons. 2021 10 19; 5(10):818-829. PMID: 34667099. PDF
Chia BS, Li B, Cui A, Eisenhaure T, Raychowdhury R, Lieb D, Hacohen N. Loss of the Nuclear Protein RTF2 Enhances Influenza Virus Replication. Journal of Virology. 2020 10 27; 94(22). PMID: 32878895; PMCID: PMC7592231. PDF
Li B, Clohisey SM, Chia BS, Wang B, Cui A, Eisenhaure T, Schweitzer LD, Hoover P, Parkinson NJ, Nachshon A, Smith N, Regan T, Farr D, Gutmann MU, Bukhari SI, Law A, Sangesland M, Gat-Viks I, Digard P, Vasudevan S, Lingwood D, Dockrell DH, Doench JG, Baillie JK, Hacohen N. Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection. Nature Communications. 2020 01 09; 11(1):164. PMID: 31919360; PMCID: PMC6952391. PDF
Pasqual G, Chudnovskiy A, Tas JMJ, Agudelo M, Schweitzer LD, Cui A, Hacohen N, Victora GD. Monitoring T cell-dendritic cell interactions in vivo by intercellular enzymatic labelling. Nature. 2018 01 25; 553(7689):496-500. PMID: 29342141. PDF
Hinks A, Bowes J, Cobb J, Ainsworth HC, Marion MC, Comeau ME, Sudman M, Han B, Juvenile Arthritis Consortium for Immunochip (including Cui A), Becker ML, Bohnsack JF, de Bakker PI, Haas JP, Hazen M, Lovell DJ, Nigrovic PA, Nordal E, Punnaro M, Rosenberg AM, Rygg M, Smith SL, Wise CA, Videm V, Wedderburn LR, Yarwood A, Yeung RS, Prahalad S, Langefeld CD, Raychaudhuri S, Thompson SD, Thomson W. Fine-mapping the MHC locus in juvenile idiopathic arthritis (JIA) reveals genetic heterogeneity corresponding to distinct adult inflammatory arthritic diseases. Annals of the Rheumatic Diseases. 2017 04; 76(4):765-772. PMID: 27998952; PMCID: PMC5530326. PDF
Cui A, Di Niro R, Vander Heiden JA, Briggs AW, Adams K, Gilbert T, O’Connor KC, Vigneault F, Shlomchik MJ, Kleinstein SH. A model of somatic hypermutation targeting in mice based on high-throughput Ig sequencing data. Journal of Immunology. 2016 11 01; 197(9):3566-3574. PMID: 27707999; PMCID: PMC5161250. PDF
Bohannon C, Powers R, Satyabhama L, Cui A, Tipton C, Michaeli M, Skountzou I, Mittler RS, Kleinstein SH, Mehr R, Lee FE, Sanz I, Jacob J. Long-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection. Nature Communications. 2016 06 07; 7:11826. PMID: 27270306; PMCID: PMC4899631. PDF
Cui A*, Quon G*, Rosenberg AM, Yeung RS, Morris Q, BBOP Study Consortium. Gene expression deconvolution for uncovering molecular signatures in response to therapy in juvenile idiopathic arthritis. Plos One. 2016; 11(5):e0156055. PMID: 27244050; PMCID: PMC4887077. PDF
Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q. Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. Genome Medicine. 2013 Mar 28; 5(3):29. PMID: 23537167; PMCID: PMC3706990. PDF