Publications

Publications are listed in reverse chronological order.

[1] A. Kothurkar, G. S. Patient, N. C. L. Noel, C. J. Chu, and R. B. MacDonald, “Iterative bleaching extends multiplexity (IBEX) imaging facilitates simultaneous identification of all cell types in the vertebrate retina,” bioRxiv, 2024, doi: 10.1101/2024.02.28.582563. [Corresponding authors: Colin J. Chu, Ryan B. MacDonald]

[2] A. J. Radtke, I. Anidi, L. Arakkal, A. Arroyo-Mejias, R. T. Beuschel, K. Börner, C. J. Chu, B. Clark, M. R. Clatworthy, J. Colautti, J. Croteau, S. Denha, R. Dever, W. O. Dutra, S. Fritzsche, S. Fullam, M. Y. Gerner, A. Gola, K. J. Gollob, J. M. Hernandez, J. L. Hor, H. Ichise, Z. Jing, D. Jonigk, E. Kandov, W. Kastenmüller, J. F. E. Koenig, A. Kothurkar, A. Y. Kreins, I. Lamborn, Y. Lin, K. L. P. Morais, A. Lunich, J. C. S. Luz, R. B. MacDonald, C. Makranz, V. I. Maltez, R. V. Moriaty, J. M. Ocampo-Godinez, V. M. Olyntho, K. Padhan, K. Remmert, N. Richoz, E. C. Schrom, W. Shang, L. Shi, R. M. Shih, E. Speranza, S. Stierli, S. A. Teichmann, T. Z. Veres, M. Vierhout, B. T. Wachter, A. K. WadeVallance, M. Williams, N. Zangger, R. N. Germain, and Z. Yaniv, “The IBEX knowledge-base: Achieving more together with open science,” aRxiv, 2024, doi: 10.48550/arXiv.2407.19059. [Corresponding authors: Andrea J. Radtke, Ronald N. Germain, Ziv Yaniv]

[3] A. J. Radtke, E. Postovalova, A. Varlamova, A. Bagaev, M. Sorokina, O. Kudryashova, M. Meerson, M. Polyakova, I. Galkin, V. Svekolkin, S. Isaev, D. Wiebe, A. Sharun, A. Sarachakov, G. Perelman, Y. Lozinsky, Z. Yaniv, B. C. Lowekamp, E. Speranza, L. Yao, S. Pittaluga, A. L. Shaffer III, D. Jonigk, J. D. Phelan, T. Davies-Hill, D. W. Huang, P. Ovcharov, K. Nomie, E. Nuzhdina, N. Kotlov, R. Ataullakhanov, N. Fowler, M. Kelly, J. Muppidi, J. L. Davis, J. M. Hernandez, W. H. Wilson, E. S. Jaffe, L. M. Staudt, M. Roschewski, and R. N. Germain, “Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients,” Cancer Cell, no. 3, 42, pp. 444–463, 2024, doi: 10.1016/j.ccell.2024.02.001. [Corresponding authors: Andrea J. Radtke]

[4] C. Y. C. Lee, B. C. Kennedy, N. Richoz, I. Dean, Z. K. Tuong, F. Gaspal, Z. Li, C. Willis, T. Hasegawa, S. K. Whiteside, D. A. Posner, G. Carlesso, S. A. Hammond, S. J. Dovedi, R. Roychoudhuri, D. R. Withers, and M. R. Clatworthy, “Tumour-retained activated CCR7⁺ dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activity,” Nat Commun, vol. 15, no. 1, 2024, doi: 10.1038/s41467-024-44787-1. [Corresponding authors: David R. Withers, Menna R. Clatworthy]

[5] H. Ichise, E. Speranza, F. La Russa, T. Z. Veres, C. J. Chu, A. Gola, and R. N. Germain, “Rebalancing viral and immune damage versus tissue repair prevents death from lethal influenza infection,” bioRxiv, 2024, doi: 10.1101/2024.07.04.601620. [Corresponding authors: Hiroshi Ichise, Ronald N. Germain]

[6] A. Shapiro, N. W. S. Caballes, R. N. Vera, B. S. Klein, P. J. Brennan, Y.-F. Wu, and D. L. Wiesner, “Sensitization with Fungal Protease Allergen Establishes Long-Lived, Allergenic Th Cell Memory in the Lung,” The Journal of Immunology, vol. 212, no. 9, pp. 1420–1427, Mar. 2024, doi: 10.4049/jimmunol.2300694. [Corresponding authors: Darin L. Wiesner]

[7] M. Vierhout, A. Ayoub, P. Ali, V. Kumaran, S. Naiel, T. Isshiki, J. F. Koenig, M. R. J. Kolb, and K. Ask, “A novel ex vivo approach for investigating profibrotic macrophage polarization using murine precision-cut lung slices,” bioRxiv, 2024, doi: 10.1101/2024.07.05.602278. [Corresponding authors: Kjetil Ask]

[8] E. M. Quardokus, D. C. Saunders, E. McDonough, J. W. Hickey, C. Werlein, C. Surrette, P. Rajbhandari, A. M. Casals, H. Tian, L. Lowery, E. K. Neumann, F. Björklund, T. V. Neelakantan, J. Croteau, A. E. Wiblin, J. Fisher, A. J. Livengood, K. G. Dowell, J. C. Silverstein, J. M. Spraggins, G. S. Pryhuber, G. Deutsch, F. Ginty, G. P. Nolan, S. Melov, D. Jonigk, M. A. Caldwell, I. S. Vlachos, W. Muller, N. Gehlenborg, B. R. Stockwell, E. Lundberg, M. P. Snyder, R. N. Germain, J. M. Camarillo, N. L. Kelleher, K. Börner, and A. J. Radtke, “Organ mapping antibody panels: A community resource for standardized multiplexed tissue imaging,” Nat Methods, vol. 20, no. 8, pp. 1174–1178, 2023, doi: 10.1038/s41592-023-01846-7. [Corresponding authors: Andrea J. Radtke]

[9] A.-M. Globig, S. Zhao, J. Roginsky, V. I. Maltez, J. Guiza, N. Avina-Ochoa, M. Heeg, F. Araujo Hoffmann, O. Chaudhary, J. Wang, G. Senturk, D. Chen, C. O’Connor, S. Pfaff, R. N. Germain, K. A. Schalper, B. Emu, and S. M. Kaech, “The β1-adrenergic receptor links sympathetic nerves to Tcell exhaustion,” Nature, vol. 622, no. 7982, pp. 383–392, Oct. 2023, doi: 10.1038/s41586-023-06568-6. [Corresponding authors: Susan M. Kaech]

[10] J. Gu, A. Iyer, B. Wesley, A. Taglialatela, G. Leuzzi, S. Hangai, A. Decker, R. Gu, N. Klickstein, Y. Shuai, K. Jankovic, L. Parker-Burns, Y. Jin, J. Y. Zhang, J. Hong, S. Niu, J. Chou, D. A. Landau, E. Azizi, E. M. Chan, A. Ciccia, and J. T. Gaublomme, “CRISPRmap: Sequencing-free optical pooled screens mapping multi-omic phenotypes in cells and tissue,” bioRxiv, 2023, doi: 10.1101/2023.12.26.572587. [Corresponding authors: Jellert T. Gaublomme]

[11] L. Arakkal, “IBEX: A user-friendly and open-source solution for high-plex immunostaining,” Nat Rev Immunol, 2023, doi: 10.1038/s41577-023-00963-w. [Corresponding authors: Leanne Arakkal]

[12] N. Yayon, V. R. Kedlian, L. Boehme, C. Suo, B. Wachter, R. T. Beuschel, O. Amsalem, K. Polanski, S. Koplev, E. Tuck, E. Dann, J. V. Hulle, S. Perera, T. Putteman, A. V. Predeus, M. Dabrowska, L. Richardson, C. Tudor, A. Y. Kreins, J. Engelbert, E. Stephenson, V. Kleshchevnikov, F. D. Rita, D. Crossland, M. Bosticardo, F. Pala, E. Prigmore, N.-J. Chipampe, M. Prete, L. Fei, K. To, R. A. Barker, X. He, F. V. Nieuwerburgh, O. Bayraktar, M. Patel, G. E. Davies, M. A. Haniffa, V. Uhlmann, L. D. Notarangelo, R. N. Germain, A. J. Radtke, J. C. Marioni, T. Taghon, and S. A. Teichmann, “A spatial human thymus cell atlas mapped to a continuous tissue axis,” bioRxiv, 2023, doi: 10.1101/2023.10.25.562925. [Corresponding authors: Ronald N. Germain, Andrea J. Radtke, John C. Marioni, Tom Taghon, Sarah A. Teichmann]

[13] Q. Xu, P. Milanez-Almeida, A. J. Martins, A. J. Radtke, K. B. Hoehn, C. Oguz, J. Chen, C. Liu, J. Tang, G. Grubbs, S. Stein, S. Ramelli, J. Kabat, H. Behzadpour, M. Karkanitsa, J. Spathies, H. Kalish, L. Kardava, M. Kirby, F. Cheung, S. Preite, P. C. Duncker, M. M. Kitakule, N. Romero, D. Preciado, L. Gitman, G. Koroleva, G. Smith, A. Shaffer, I. T. McBain, P. J. McGuire, S. Pittaluga, R. N. Germain, R. Apps, D. M. Schwartz, K. Sadtler, S. Moir, D. S. Chertow, S. H. Kleinstein, S. Khurana, J. S. Tsang, P. Mudd, P. L. Schwartzberg, and K. Manthiram, “Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children,” Nat Immunol., vol. 24, no. 1, pp. 186–199, 2023, doi: 10.1038/s41590-022-01367-z. [Corresponding authors: Pamela L. Schwartzberg, Kalpana Manthiram]

[14] T. Kudo, A. M. Meireles, R. Moncada, Y. Chen, P. Wu, J. Gould, X. Hu, O. Kornfeld, R. Jesudason, C. Foo, B. Höckendorf, H. C. Bravo, J. P. Town, R. Wei, A. Rios, V. Chandrasekar, M. Heinlein, S. Cai, C. S. Lu, C. Celen, N. Kljavin, J. Jiang, J. S. Hleap, N. Kayagaki, F. de Sousa e Melo, L. McGinnis, B. Li, A. Singh, L. Garraway, O. Rozenblatt-Rosen, A. Regev, and E. Lubeck, “Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView,” bioRxiv, 2023, doi: 10.1101/2023.12.26.573143. [Corresponding authors: Aviv Regev, Eric Lubeck]

[15] J. W. Hickey, E. K. Neumann, A. J. Radtke, J. M. Camarillo, R. T. Beuschel, A. Albanese, E. McDonough, J. Hatler, A. E. Wiblin, J. Fisher, J. Croteau, E. C. Small, A. Sood, R. M. Caprioli, R. M. Angelo, G. P. Nolan, K. Chung, S. M. Hewitt, R. N. Germain, J. M. Spraggins, E. Lundberg, M. P. Snyder, N. L. Kelleher, and S. K. Saka, “Spatial mapping of protein composition and tissue organization: A primer for multiplexed antibody-based imaging,” Nature Methods, vol. 19, no. 2, pp. 284–295, 2022, doi: 10.1038/s41592-021-01316-y. [Corresponding authors: Andrea J. Radtke, Sinem K. Saka]

[16] N. Richoz, Z. K. Tuong, K. W. Loudon, E. Patiño-Martínez, J. R. Ferdinand, A. Portet, K. R. Bashant, E. Thevenon, F. Rucci, T. Hoyler, T. Junt, M. J. Kaplan, R. M. Siegel, and M. R. Clatworthy, “Distinct pathogenic roles for resident and monocyte-derived macrophages in lupus nephritis,” JCI Insight, vol. 7, no. 21, p. e159751, 2022, doi: 10.1172/jci.insight.159751. [Corresponding authors: Richard M. Siegel, Menna R. Clatworthy]

[17] A. J. Radtke, C. J. Chu, Z. Yaniv, L. Yao, J. Marr, R. T. Beuschel, H. Ichise, A. Gola, J. Kabat, B. Lowekamp, E. Speranza, J. Croteau, N. Thakur, D. Jonigk, J. Davis, J. M. Hernandez, and R. N. Germain, “IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues,” Nat Protoc, vol. 17, no. 2, pp. 378–401, 2022, doi: 10.1038/s41596-021-00644-9. [Corresponding authors: Andrea J. Radtke, Ronald N. Germain]

[18] A. J. Radtke, E. Postovalova, A. Varlamova, A. Bagaev, M. Sorokina, O. Kudryashova, M. Meerson, M. Polyakova, I. Galkin, V. Svekolkin, S. Isaev, G. Perelman, Y. Lozinsky, Z. Yaniv, B. C. Lowekamp, E. Speranza, L. Yao, S. Pittaluga, A. L. Shaffer, D. Jonigk, J. D. Phelan, T. Davies-Hill, D. W. Huang, P. Ovcharov, K. Nomie, E. Nuzhdina, N. Kotlov, R. Ataullakhanov, N. Fowler, M. Kelly, J. Muppidi, J. Davis, J. M. Hernandez, W. H. Wilson, E. S. Jaffe, L. M. Staudt, M. Roschewski, and R. N. Germain, “A multi-scale, multiomic atlas of human normal and follicular lymphoma lymph nodes,” bioRxiv, 2022, doi: 10.1101/2022.06.03.494716. [Corresponding authors: Andrea J. Radtke]

[19] E. Madissoon, A. J. Oliver, V. Kleshchevnikov, A. Wilbrey-Clark, K. Polanski, A. R. Orsi, L. Mamanova, L. Bolt, N. Richoz, R. Elmentaite, J. P. Pett, N. Huang, P. He, M. Dabrowska, S. Pritchard, L. Tuck, E. Prigmore, A. Knights, A. Oszlanczi, A. Hunter, S. F. Vieira, M. Patel, N. Georgakopoulos, K. Mahbubani, K. Saeb-Parsy, M. Clatworthy, O. A. Bayraktar, O. Stegle, N. Kumasaka, S. A. Teichmann, and K. B. Meyer, “A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche,” bioRxiv, 2021, doi: 10.1101/2021.11.26.470108. [Corresponding authors: Sarah A. Teichmann, Kerstin B. Meyer]

[20] Z. K. Tuong, K. W. Loudon, B. Berry, N. Richoz, J. Jones, X. Tan, Q. Nguyen, A. George, S. Hori, S. Field, A. G. Lynch, K. Kania, P. Coupland, A. Babbage, R. Grenfell, T. Barrett, A. Y. Warren, V. Gnanapragasam, C. Massie, and M. R. Clatworthy, “Resolving the immune landscape of human prostate at a single-cell level in health and cancer,” Cell Rep., vol. 37, no. 12, p. 110132, 2021, doi: 10.1016/j.celrep.2021.110132. [Corresponding authors: Charlie Massie, Menna R. Clatworthy]

[21] C. R. Stoltzfus, J. Filipek, B. H. Gern, B. E. Olin, J. M. Leal, Y. Wu, M. R. Lyons-Cohen, J. Y. Huang, C. L. Paz-Stoltzfus, C. R. Plumlee, T. Pöschinger, K. B. Urdahl, M. Perro, and M. Y. Gerner, “CytoMAP: A spatial analysis toolbox reveals features of myeloid cell organization in lymphoid tissues,” Cell Rep., vol. 31, no. 3, p. 107523, 2020, doi: 10.1016/j.celrep.2020.107523. [Corresponding authors: Michael Y. Gerner]

[22] A. Gola, M. G. Dorrington, E. Speranza, C. Sala, R. M. Shih, A. J. Radtke, H. S. Wong, A. P. Baptista, J. M. Hernandez, G. Castellani, I. D. C. Fraser, and R. N. Germain, “Commensal-driven immune zonation of the liver promotes host defence,” Nature, vol. 589, no. 7840, pp. 131–136, 2020, doi: 10.1038/s41586-020-2977-2. [Corresponding authors: Anita Gola, Ronald N. Germain]

[23] A. J. Radtke, E. Kandov, B. Lowekamp, E. Speranza, C. J. Chu, A. Gola, N. Thakur, R. Shih, L. Yao, Z. R. Yaniv, R. T. Beuschel, J. Kabat, J. Croteau, J. Davis, J. M. Hernandez, and R. N. Germain, “IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues,” Proceedings of the National Academy of Sciences, vol. 117, no. 52, pp. 33455–33465, 2020, doi: 10.1073/pnas.2018488117. [Corresponding authors: Andrea J. Radtke, Ronald N. Germain]

[24] E. Speranza, J. N. Purushotham, J. R. Port, B. Schwarz, M. Flagg, B. N. Williamson, F. Feldmann, M. Singh, L. Pérez-Pérez, G. L. Sturdevant, L. M. Roberts, A. Carmody, J. E. Schulz, N. van Doremalen, A. Okumura, J. Lovaglio, P. W. Hanley, C. Shaia, R. N. Germain, S. M. Best, V. J. Munster, C. M. Bosio, and E. de Wit, “Age-related differences in immune dynamics during SARS-CoV-2 infection in rhesus macaques,” Life Sci Alliance, vol. 5, no. 4, p. e202101314, 2020, doi: 10.26508/lsa.202101314. [Corresponding authors: Emmie de Wit]