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Dr Kelvin Tuong

Senior Research Fellow

Child Health Research Centre
Faculty of Medicine
z.tuong@uq.edu.au
+61 7 3069 7506

Overview

Dr. Kelvin Tuong is a Senior Research Fellow/Group Leader at the Ian Frazer Centre for Children’s Immunotherapy Research (IFCCIR), Child Health Research Centre. He is interested in single-cell analysis of immune cells and harnessing adaptive immune receptors for understanding immune cell development and function in health and in cancer.

Dr. Tuong was born and raised in Singapore and moved to Brisbane, Australia, after completing national service in Singapore and obtaining a Diploma in Biomedical Laboratory Technology (Ngee Ann Polytechnic).

Dr. Tuong was originally trained as a molecular cell biologist and gradually transitioned into bioinformatics during his post-doctoral training. He has been very prolific for an early career researcher, having published >50 articles since 2013, with nearly a third of them as first/co-first or last author and has a stellar track record of pushing out highly collaborative work in prestigious journals including Nature, Cell, Science, Nature Medicine, Nature Biotechnology J Exp Med etc. He has the rare combination of having excellent laboratory and bioinformatics skill sets which provide him a strong command of both fundamental immunology and computational approaches.

Dr. Tuong completed his undergraduate Bachelor's degree in Biomedical science with Class I Honours, followed by his PhD in macrophage cell biology and endocrinology at UQ (Prof. Jenny Stow lab and Emiritus Prof. George Muscat lab, IMB, UQ). He then went on to a post-doc position with Emiritus Prof. Ian Frazer (co-inventor of the Gardasil cervical cancer vaccine, UQ Frazer Institute, Translational Research Institute) where he worked on HPV immunology, cervical cancer and skin cancer. In his time in the Frazer lab, he developed an interest in bioinformatics analyses as a means to tackle and understanding immunology problems in health and disease. He then moved to the UK and joined Prof. Menna Clatworthy's lab at the University of Cambridge and Dr. Sarah Teichmann's lab at the Wellcome Trust Sanger Institute. He has focused his interests on single-cell analyses of tissue immune cells, including T and B cells and their specific receptors (TCR/BCR). He has developed bespoke bioinformatics software, including one tailored for single-cell B Cell Receptor sequencing analysis, Dandelion, which he used in one of the largest combined single-cell transcriptomic, surface proteomic and TCR/BCR sequencing dataset in the world, published in Nature Medicine, and more recently in Nature Biotechnology where we introduced a TCR-based pseudotime trajectory analysis method.

Dr. Tuong is now leading the Computational Immunology group at the IFCCIR and his lab is focused on investigating how pediatric immunity is perturbed during cancer at the cellular level and how this information can be used for creating novel warning systems for children with cancer. For potential students/post-docs/trainees interested in joining the team, please contact Dr. Tuong at z.tuong@uq.edu.au.

Research Interests

  • Single-cell analysis of immune repertoires
    Specialized immune cells known as T-cells and B-cells use specific receptors to recognize tumor antigens and fight cancerous cells. My vision is to harness these cells and their receptors to enable early cancer detection and disease monitoring. These specific adaptive immune receptors are essential for all aspects of the T- and B-cell’s life cycle, serving as natural ‘time-keepers’ of the immune response against cancer progression. My research team will explore the properties that define how effective these immune cells are in childhood cancer by performing high resolution gene expression profiling at the single-cell level. To achieve this, we will develop critical software and algorithms for analyzing these immune cells and their receptors. We will develop highly advanced computer models that can be used to detect adaptive immune receptors that are targeted towards cancer. These models will learn and identify cancer-specific patterns and we will apply it onto predicting and monitoring response to therapy in children with blood cancer. This will allow for a highly precise mechanism that could be deployed early for initial cancer detection and monitoring of childhood cancer progression.

Qualifications

  • Doctor of Philosophy, The University of Queensland

Publications

  • Journal Article: Atypical B cells and impaired SARS-CoV-2 neutralization following heterologous vaccination in the elderly

    Ferreira, Isabella A.T.M., Lee, Colin Y.C., Foster, William S., Abdullahi, Adam, Dratva, Lisa M., Tuong, Zewen Kelvin, Stewart, Benjamin J., Ferdinand, John R., Guillaume, Stephane M., Potts, Martin O.P., Perera, Marianne, Krishna, Benjamin A., Peñalver, Ana, Cabantous, Mia, Kemp, Steven A., Ceron-Gutierrez, Lourdes, Ebrahimi, Soraya, Lyons, Paul, Smith, Kenneth G.C., Bradley, John, Collier, Dami A., McCoy, Laura E., van der Klaauw, Agatha, Thaventhiran, James E.D., Farooqi, I. Sadaf, Teichmann, Sarah A., MacAry, Paul A., Doffinger, Rainer, Wills, Mark R. ... Gupta, Ravindra K. (2023). Atypical B cells and impaired SARS-CoV-2 neutralization following heterologous vaccination in the elderly. Cell Reports, 42 (8) 112991, 112991. doi: 10.1016/j.celrep.2023.112991

  • Journal Article: A novel multifunctional radioprotective strategy using P7C3 as a countermeasure against ionizing radiation-induced bone loss

    Wei, Fei, Tuong, Zewen Kelvin, Omer, Mahmoud, Ngo, Christopher, Asiatico, Jackson, Kinzel, Michael, Pugazhendhi, Abinaya Sindu, Khaled, Annette R., Ghosh, Ranajay and Coathup, Melanie (2023). A novel multifunctional radioprotective strategy using P7C3 as a countermeasure against ionizing radiation-induced bone loss. Bone Research, 11 (1) 34, 34. doi: 10.1038/s41413-023-00273-w

  • Journal Article: Venous plexus-associated lymphoid hubs support meningeal humoral immunity

    Zanluqui, Nagela Ghabdan, Fitzpatrick, Zachary, Rosenblum, Jared S, Tuong, Zewen Kelvin, Chandrashekhar, Vikram, Negro-Demontel, Maria Luciana, Allinson, Kieren S. J., Mastorakos, Panagiotis, Chittiboina, Prashant, Maric, Dragan, Donahue, Danielle, Ferdinand, John R, Portet, Anais, Penalver, Ana, Gillman, Eleanor, Zhuang, Zhengping, Clatworthy, Menna R and McGavern, Dorian B (2023). Venous plexus-associated lymphoid hubs support meningeal humoral immunity. The Journal of Immunology, 210 (1_Supplement), 76.23-76.23. doi: 10.4049/jimmunol.210.supp.76.23

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Grants

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Supervision

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Available Projects

  • Developing single-cell analysis methods harnessing adaptive immune receptors

    The direct linkage of adaptive immune receptor repertoire with cellular phenotypes from single-cell sequencing technology has proven to be a powerful tool in understanding lymphocyte development and function in healthy and disease contexts. Multi-omics analysis leverages data from different modalities e.g. transcriptomics, epigenetics, proteomics. Recent advances has successfully integrated the data modalities to study cellular biology at an unprecedented resolution. However, unlike the other data modalities, which are largely continuous data, single-cell adaptive immune receptor sequencing (scVDJ-seq) data are a mixture of categorical and continuous data which poses additional challenges for integration. It consists of annotations of variable (V), diversity (D) and joining (J) genes, which are selected and recombined during B/T-cell development. The technology to profile this at the single cell level with paired gene expression data is relatively new. I have led the development of Dandelion, a scVDJ-seq software framework which has been used to deeply profile single-cell lymphocyte biology and I aim to expand on the its capabilities for immunology research.

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Publications

Journal Article

  • Atypical B cells and impaired SARS-CoV-2 neutralization following heterologous vaccination in the elderly

    Ferreira, Isabella A.T.M., Lee, Colin Y.C., Foster, William S., Abdullahi, Adam, Dratva, Lisa M., Tuong, Zewen Kelvin, Stewart, Benjamin J., Ferdinand, John R., Guillaume, Stephane M., Potts, Martin O.P., Perera, Marianne, Krishna, Benjamin A., Peñalver, Ana, Cabantous, Mia, Kemp, Steven A., Ceron-Gutierrez, Lourdes, Ebrahimi, Soraya, Lyons, Paul, Smith, Kenneth G.C., Bradley, John, Collier, Dami A., McCoy, Laura E., van der Klaauw, Agatha, Thaventhiran, James E.D., Farooqi, I. Sadaf, Teichmann, Sarah A., MacAry, Paul A., Doffinger, Rainer, Wills, Mark R. ... Gupta, Ravindra K. (2023). Atypical B cells and impaired SARS-CoV-2 neutralization following heterologous vaccination in the elderly. Cell Reports, 42 (8) 112991, 112991. doi: 10.1016/j.celrep.2023.112991

  • A novel multifunctional radioprotective strategy using P7C3 as a countermeasure against ionizing radiation-induced bone loss

    Wei, Fei, Tuong, Zewen Kelvin, Omer, Mahmoud, Ngo, Christopher, Asiatico, Jackson, Kinzel, Michael, Pugazhendhi, Abinaya Sindu, Khaled, Annette R., Ghosh, Ranajay and Coathup, Melanie (2023). A novel multifunctional radioprotective strategy using P7C3 as a countermeasure against ionizing radiation-induced bone loss. Bone Research, 11 (1) 34, 34. doi: 10.1038/s41413-023-00273-w

  • Venous plexus-associated lymphoid hubs support meningeal humoral immunity

    Zanluqui, Nagela Ghabdan, Fitzpatrick, Zachary, Rosenblum, Jared S, Tuong, Zewen Kelvin, Chandrashekhar, Vikram, Negro-Demontel, Maria Luciana, Allinson, Kieren S. J., Mastorakos, Panagiotis, Chittiboina, Prashant, Maric, Dragan, Donahue, Danielle, Ferdinand, John R, Portet, Anais, Penalver, Ana, Gillman, Eleanor, Zhuang, Zhengping, Clatworthy, Menna R and McGavern, Dorian B (2023). Venous plexus-associated lymphoid hubs support meningeal humoral immunity. The Journal of Immunology, 210 (1_Supplement), 76.23-76.23. doi: 10.4049/jimmunol.210.supp.76.23

  • Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

    Suo, Chenqu, Polanski, Krzysztof, Dann, Emma, Lindeboom, Rik G. H., Vilarrasa-Blasi, Roser, Vento-Tormo, Roser, Haniffa, Muzlifah, Meyer, Kerstin B., Dratva, Lisa M., Tuong, Zewen Kelvin, Clatworthy, Menna R. and Teichmann, Sarah A. (2023). Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins. Nature Biotechnology. doi: 10.1038/s41587-023-01734-7

  • Low-dose IL-2 enhances the generation of IL-10-producing immunoregulatory B cells

    Inaba, Akimichi, Tuong, Zewen Kelvin, Zhao, Tian X., Stewart, Andrew P., Mathews, Rebeccah, Truman, Lucy, Sriranjan, Rouchelle, Kennet, Jane, Saeb-Parsy, Kourosh, Wicker, Linda, Waldron-Lynch, Frank, Cheriyan, Joseph, Todd, John A., Mallat, Ziad and Clatworthy, Menna R. (2023). Low-dose IL-2 enhances the generation of IL-10-producing immunoregulatory B cells. Nature Communications, 14 (1) 2071, 1-11. doi: 10.1038/s41467-023-37424-w

  • Heparan sulfate regulates IL-21 bioavailability and signal strength that control germinal center B cell selection and differentiation

    Chen, Zhian, Cui, Yanfang, Yao, Yin, Liu, Bo, Yunis, Joseph, Gao, Xin, Wang, Naiqi, Cañete, Pablo F., Tuong, Zewen Kelvin, Sun, Hongjian, Wang, Hao, Yang, Siling, Wang, Runli, Leong, Yew Ann, Simon Davis, David, Qin, Jiahuan, Liang, Kaili, Deng, Jun, Wang, Conan K., Huang, Yen-Hua, Roco, Jonathan A., Nettelfield, Sam, Zhu, Huaming, Xu, Huajun, Yu, Zhijia, Craik, David, Liu, Zheng, Qi, Hai, Parish, Christopher and Yu, Di (2023). Heparan sulfate regulates IL-21 bioavailability and signal strength that control germinal center B cell selection and differentiation. Science immunology, 8 (80) eadd1728, 1-17. doi: 10.1126/sciimmunol.add1728

  • Dimensionality reduction under scrutiny

    Yang, Yang, Tuong, Zewen K. and Yu, Di (2023). Dimensionality reduction under scrutiny. Nature Computational Science, 3 (1), 8-9. doi: 10.1038/s43588-022-00383-1

  • Autoimmune uveitis in Behçet's disease and Vogt‐Koyanagi‐Harada disease differ in tissue immune infiltration and T cell clonality

    Kang, Hao, Sun, Hongjian, Yang, Yang, Tuong, Zewen K, Shu, Minglei, Wei, Yunbo, Zhang, Yu, Yu, Di and Tao, Yong (2023). Autoimmune uveitis in Behçet's disease and Vogt‐Koyanagi‐Harada disease differ in tissue immune infiltration and T cell clonality. Clinical & Translational Immunology, 12 (9). doi: 10.1002/cti2.1461

  • A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates

    He, Peng, Lim, Kyungtae, Sun, Dawei, Pett, Jan Patrick, Jeng, Quitz, Polanski, Krzysztof, Dong, Ziqi, Bolt, Liam, Richardson, Laura, Mamanova, Lira, Dabrowska, Monika, Wilbrey-Clark, Anna, Madissoon, Elo, Tuong, Zewen Kelvin, Dann, Emma, Suo, Chenqu, Goh, Isaac, Yoshida, Masahiro, Nikolić, Marko Z., Janes, Sam M., He, Xiaoling, Barker, Roger A., Teichmann, Sarah A., Marioni, John C., Meyer, Kerstin B. and Rawlins, Emma L. (2022). A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates. Cell, 185 (25), 4841-4860.e25. doi: 10.1016/j.cell.2022.11.005

  • Distinct pathogenic roles for resident and monocyte-derived macrophages in lupus nephritis

    Richoz, Nathan, Tuong, Zewen K., Loudon, Kevin W., Patiño-Martínez, Eduardo, Ferdinand, John R., Portet, Anaïs, Bashant, Kathleen R., Thevenon, Emeline, Rucci, Francesca, Hoyler, Thomas, Junt, Tobias, Kaplan, Mariana J., Siegel, Richard M. and Clatworthy, Menna R. (2022). Distinct pathogenic roles for resident and monocyte-derived macrophages in lupus nephritis. JCI Insight, 7 (21) e159751, 1-19. doi: 10.1172/jci.insight.159751

  • Obesity is associated with attenuated tissue immunity in COVID-19

    Guo, Shuang A., Bowyer, Georgina S., Ferdinand, John R., Maes, Mailis, Tuong, Zewen K., Gillman, Eleanor, Liao, Mingfeng, Lindeboom, Rik G H, Yoshida, Masahiro, Worlock, Kaylee, Gopee, Hudaa, Stephenson, Emily, Gao, Catherine A, Lyons, Paul A, Smith, Kenneth G C, Haniffa, Muzlifah, Meyer, Kerstin B, Nikolić, Marko Z, Zhang, Zheng, Wunderink, Richard G, Misharin, Alexander V, Dougan, Gordon, Navapurkar, Vilas, Teichmann, Sarah A, Conway Morris, Andrew and Clatworthy, Menna R (2022). Obesity is associated with attenuated tissue immunity in COVID-19. American Journal of Respiratory and Critical Care Medicine, 207 (5), 566-576. doi: 10.1164/rccm.202204-0751OC

  • Fracture hematoma micro-architecture influences transcriptional profile and plays a crucial role in determining bone healing outcomes

    Woloszyk, Anna, Tuong, Zewen K., Perez, Louis, Aguilar, Leonardo, Bankole, Abraham I., Evans, Christopher H. and Glatt, Vaida (2022). Fracture hematoma micro-architecture influences transcriptional profile and plays a crucial role in determining bone healing outcomes. Biomaterials Advances, 139 213027, 1-15. doi: 10.1016/j.bioadv.2022.213027

  • A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages

    Tran, M., Yoon, S., Teoh, M., Andersen, S., Lam, PY., Purdue, B. W., Raghubar, A., Hanson, S.J., Devitt, K., Jones, K., Walters, S., Monkman, J., Kulasinghe, A., Tuong, Z.K., Soyer, H.P., Frazer, I. H. and Nguyen, Q. (2022). A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages. Frontiers in Immunology, 13 911873, 911873. doi: 10.3389/fimmu.2022.911873

  • Group 3 innate lymphocytes make a distinct contribution to type 17 immunity in bladder defence

    Riding, Alexandra M., Loudon, Kevin W., Guo, Andrew, Ferdinand, John R., Lok, Laurence S.C., Richoz, Nathan, Stewart, Andrew, Castro-Dopico, Tomas, Tuong, Zewen Kelvin, Fiancette, Remi, Bowyer, Georgina S., Fleming, Aaron, Gillman, Eleanor S., Suchanek, Ondrej, Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Withers, David, Dougan, Gordan, Clare, Simon and Clatworthy, Menna R. (2022). Group 3 innate lymphocytes make a distinct contribution to type 17 immunity in bladder defence. iScience, 25 (7) 104660, 1-30. doi: 10.1016/j.isci.2022.104660

  • Mapping the developing human immune system across organs

    Suo, Chenqu, Dann, Emma, Goh, Issac, Jardine, Laura, Kleshchevnikov, Vitalii, Park, Jong-Eun, Botting, Rachel A., Stephenson, Emily, Engelbert, Justin, Tuong, Zewen Kelvin, Polanski, Krzysztof, Yayon, Nadav, Xu, Chuan, Suchanek, Ondrej, Elmentaite, Rasa, Domínguez Conde, Cecilia, He, Peng, Pritchard, Sophie, Miah, Mohi, Moldovan, Corina, Steemers, Alexander S., Mazin, Pavel, Prete, Martin, Horsfall, Dave, Marioni, John C., Clatworthy, Menna R., Haniffa, Muzlifah and Teichmann, Sarah A. (2022). Mapping the developing human immune system across organs. Science, 376 (6597), eabo0510. doi: 10.1126/science.abo0510

  • Cross-tissue immune cell analysis reveals tissue-specific features in humans

    Domínguez Conde, C., Xu, C., Jarvis, L. B., Rainbow, D. B., Wells, S. B., Gomes, T., Howlett, S. K., Suchanek, O., Polanski, K., King, H. W., Mamanova, L., Huang, N., Szabo, P. A., Richardson, L., Bolt, L., Fasouli, E. S., Mahbubani, K. T., Prete, M., Tuck, L., Richoz, N., Tuong, Z. K., Campos, L., Mousa, H. S., Needham, E. J., Pritchard, S., Li, T., Elmentaite, R., Park, J., Rahmani, E. ... Teichmann, S. A. (2022). Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science, 376 (6594) eabl5197, eabl5197. doi: 10.1126/science.abl5197

  • GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans

    Yao, Yikun, Du Jiang, Ping, Chao, Brittany N., Cagdas, Deniz, Kubo, Satoshi, Balasubramaniyam, Arasu, Zhang, Yu, Shadur, Bella, NaserEddin, Adeeb, Folio, Les R., Schwarz, Benjamin, Bohrnsen, Eric, Zheng, Lixin, Lynberg, Matthew, Gottlieb, Simone, Leney-Greene, Michael A., Park, Ann Y., Tezcan, Ilhan, Akdogan, Ali, Gocmen, Rahsan, Onder, Sevgen, Rosenberg, Avi, Soilleux, Elizabeth J., Johnson, Errin, Jackson, Peter K., Demeter, Janos, Chauvin, Samuel D., Paul, Florian, Selbach, Matthias ... Lenardo, Michael J. (2022). GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans. Journal of Experimental Medicine, 219 (6) e20201405, 1-29. doi: 10.1084/jem.20201405

  • In vivo labeling reveals continuous trafficking of TCF-1+ T cells between tumor and lymphoid tissue

    Li, Zhi, Tuong, Zewen K., Dean, Isaac, Willis, Claire, Gaspal, Fabrina, Fiancette, Rémi, Idris, Suaad, Kennedy, Bethany, Ferdinand, John R., Peñalver, Ana, Cabantous, Mia, Murtuza Baker, Syed, Fry, Jeremy W., Carlesso, Gianluca, Hammond, Scott A., Dovedi, Simon J., Hepworth, Matthew R., Clatworthy, Menna R. and Withers, David R. (2022). In vivo labeling reveals continuous trafficking of TCF-1+ T cells between tumor and lymphoid tissue. Journal of Experimental Medicine, 219 (6) e20210749, 1-27. doi: 10.1084/jem.20210749

  • The impact of hypoxia on B cells in COVID-19

    Kotagiri, Prasanti, Mescia, Federica, Hanson, Aimee L., Turner, Lorinda, Bergamaschi, Laura, Peñalver, Ana, Richoz, Nathan, Moore, Stephen D., Ortmann, Brian M., Dunmore, Benjamin J., Morgan, Michael D., Tuong, Zewen Kelvin, Göttgens, Berthold, Toshner, Mark, Hess, Christoph, Maxwell, Patrick. H., Clatworthy, Menna. R., Nathan, James A., Bradley, John R., Lyons, Paul A., Burrows, Natalie and Smith, Kenneth G.C. (2022). The impact of hypoxia on B cells in COVID-19. eBioMedicine, 77 103878, 103878. doi: 10.1016/j.ebiom.2022.103878

  • B cell receptor repertoire kinetics after SARS-CoV-2 infection and vaccination

    Kotagiri, Prasanti, Mescia, Federica, Rae, William M., Bergamaschi, Laura, Tuong, Zewen K., Turner, Lorinda, Hunter, Kelvin, Gerber, Pehuén P., Hosmillo, Myra, Hess, Christoph, Clatworthy, Menna R., Goodfellow, Ian G., Matheson, Nicholas J., McKinney, Eoin F., Wills, Mark R., Gupta, Ravindra K., Bradley, John R., Bashford-Rogers, Rachael J.M., Lyons, Paul A. and Smith, Kenneth G.C. (2022). B cell receptor repertoire kinetics after SARS-CoV-2 infection and vaccination. Cell Reports, 38 (7) 110393, 110393. doi: 10.1016/j.celrep.2022.110393

  • Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity

    Uzzan, Mathieu, Martin, Jerome C., Mesin, Luka, Livanos, Alexandra E., Castro-Dopico, Tomas, Huang, Ruiqi, Petralia, Francesca, Magri, Giuliana, Kumar, Shashi, Zhao, Qing, Rosenstein, Adam K., Tokuyama, Minami, Sharma, Keshav, Ungaro, Ryan, Kosoy, Roman, Jha, Divya, Fischer, Jeremy, Singh, Harpriya, Keir, Mary E., Ramamoorthi, Nandhini, Gorman, William E. O’, Cohen, Benjamin L., Rahman, Adeeb, Cossarini, Francesca, Seki, Akihiro, Leyre, Louise, Vaquero, Sonia Tejedor, Gurunathan, Sakteesh, Grasset, Emilie K. ... Mehandru, Saurabh (2022). Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity. Nature Medicine, 28 (4), 766-779. doi: 10.1038/s41591-022-01680-y

  • Secreted toxins from Staphylococcus aureus strains isolated from keratinocyte skin cancers mediate pro-tumorigenic inflammatory responses in the skin

    Krueger, Annika, Zaugg, Julian, Chisholm, Sarah, Linedale, Richard, Lachner, Nancy, Teoh, Siok Min, Tuong, Zewen K., Lukowski, Samuel W., Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Hill, Michelle M. and Frazer, Ian H. (2022). Secreted toxins from Staphylococcus aureus strains isolated from keratinocyte skin cancers mediate pro-tumorigenic inflammatory responses in the skin. Frontiers in Microbiology, 12 789042, 789042. doi: 10.3389/fmicb.2021.789042

  • Epigenetics and tissue immunity—translating environmental cues into functional adaptations*

    Tuong, Zewen Kelvin, Stewart, Benjamin J., Guo, Shuang Andrew and Clatworthy, Menna R. (2022). Epigenetics and tissue immunity—translating environmental cues into functional adaptations*. Immunological Reviews, 305 (1), 111-136. doi: 10.1111/imr.13036

  • Resolving the immune landscape of human prostate at a single-cell level in health and cancer

    Tuong, Zewen Kelvin, Loudon, Kevin W., Berry, Brendan, Richoz, Nathan, Jones, Julia, Tan, Xiao, Nguyen, Quan, George, Anne, Hori, Satoshi, Field, Sarah, Lynch, Andy G., Kania, Katarzyna, Coupland, Paul, Babbage, Anne, Grenfell, Richard, Barrett, Tristan, Warren, Anne Y., Gnanapragasam, Vincent, Massie, Charlie and Clatworthy, Menna R. (2021). Resolving the immune landscape of human prostate at a single-cell level in health and cancer. Cell Reports, 37 (12) 110132, 110132. doi: 10.1016/j.celrep.2021.110132

  • Aldehyde-driven transcriptional stress triggers an anorexic DNA damage response

    Mulderrig, Lee, Garaycoechea, Juan I., Tuong, Zewen K., Millington, Christopher L., Dingler, Felix A., Ferdinand, John R., Gaul, Liam, Tadross, John A., Arends, Mark J., O’Rahilly, Stephen, Crossan, Gerry P., Clatworthy, Menna R. and Patel, Ketan J. (2021). Aldehyde-driven transcriptional stress triggers an anorexic DNA damage response. Nature, 600 (7887), 158-163. doi: 10.1038/s41586-021-04133-7

  • A model of impaired Langerhans cell maturation associated with HPV induced epithelial hyperplasia

    Tuong, Zewen K., Lukowski, Samuel W., Nguyen, Quan H., Chandra, Janin, Zhou, Chenhao, Gillinder, Kevin, Bashaw, Abate A., Ferdinand, John R., Stewart, Benjamin J., Teoh, Siok Min, Hanson, Sarah J., Devitt, Katharina, Clatworthy, Menna R., Powell, Joseph E. and Frazer, Ian H. (2021). A model of impaired Langerhans cell maturation associated with HPV induced epithelial hyperplasia. iScience, 24 (11) 103326, 103326. doi: 10.1016/j.isci.2021.103326

  • B-cells are abnormal in psychosocial stress and regulate meningeal myeloid cell activation

    Lynall, Mary-Ellen, Kigar, Stacey L., Lehmann, Michael L., DePuyt, Allison E., Tuong, Zewen Kelvin, Listwak, Samuel J., Elkahloun, Abdel G., Bullmore, Edward T., Herkenham, Miles and Clatworthy, Menna R. (2021). B-cells are abnormal in psychosocial stress and regulate meningeal myeloid cell activation. Brain, Behavior, and Immunity, 97, 226-238. doi: 10.1016/j.bbi.2021.08.002

  • IFN-γ critically enables the intratumoural infiltration of CXCR3+ CD8+ T cells to drive squamous cell carcinoma regression

    Zeng, Zhen, Veitch, Margaret, Kelly, Gabrielle A., Tuong, Zewen K., Cruz, Jazmina G., Frazer, Ian H. and Wells, James W. (2021). IFN-γ critically enables the intratumoural infiltration of CXCR3+ CD8+ T cells to drive squamous cell carcinoma regression. Cancers, 13 (9) 2131, 2131. doi: 10.3390/cancers13092131

  • Antigen nonspecific induction of distinct regulatory T cell states in oncogene-driven hyperproliferative skin

    Zhou, Chenhao, Tuong, Zewen Kelvin, Lukowski, Samuel Wieslaw, Chandra, Janin and Frazer, Ian H. (2021). Antigen nonspecific induction of distinct regulatory T cell states in oncogene-driven hyperproliferative skin. ImmunoHorizons, 5 (2), 102-116. doi: 10.4049/immunohorizons.2100006

  • Manganese-doped silica-based nanoparticles promote the efficacy of antigen-specific immunotherapy

    Chandra, Janin, Teoh, Siok Min, Kuo, Paula, Tolley, Lynn, Bashaw, Abate Assefa, Tuong, Zewen Kelvin, Liu, Yang, Chen, Zibin, Wells, James W., Yu, Chengzhong, Frazer, Ian H. and Yu, Meihua (2021). Manganese-doped silica-based nanoparticles promote the efficacy of antigen-specific immunotherapy. The Journal of Immunology, 206 (5), ji2000355-998. doi: 10.4049/jimmunol.2000355

  • Single-cell multi-omics analysis of the immune response in COVID-19

    Stephenson, Emily, Reynolds, Gary, Botting, Rachel A., Calero-Nieto, Fernando J., Morgan, Michael D., Tuong, Zewen Kelvin, Bach, Karsten, Sungnak, Waradon, Worlock, Kaylee B., Yoshida, Masahiro, Kumasaka, Natsuhiko, Kania, Katarzyna, Engelbert, Justin, Olabi, Bayanne, Spegarova, Jarmila Stremenova, Wilson, Nicola K., Mende, Nicole, Jardine, Laura, Gardner, Louis C. S., Goh, Issac, Horsfall, Dave, McGrath, Jim, Webb, Simone, Mather, Michael W., Lindeboom, Rik G. H., Dann, Emma, Huang, Ni, Polanski, Krzysztof, Prigmore, Elena ... Haniffa, Muzlifah (2021). Single-cell multi-omics analysis of the immune response in COVID-19. Nature Medicine, 27 (5), 904-916. doi: 10.1038/s41591-021-01329-2

  • Increased lipid metabolism impairs NK cell function and mediates adaptation to the lymphoma environment

    Kobayashi, Takumi, Lam, Pui Yeng, Jiang, Hui, Bednarska, Karolina, Gloury, Renee Elyse, Murigneux, Valentine, Tay, Joshua, Jacquelot, Nicolas, Li, Rui, Tuong, Zewen Kelvin, Leggatt, Graham, Gandhi, Maher K., Hill, Michelle M, Belz, Gabrielle T., Ngo, Shyuan, Kallies, Axel and Mattarollo, Stephen R. (2020). Increased lipid metabolism impairs NK cell function and mediates adaptation to the lymphoma environment. Blood, 136 (26), 3004-3017. doi: 10.1182/blood.2020005602

  • Gut-educated IgA plasma cells defend the meningeal venous sinuses

    Fitzpatrick, Zachary, Frazer, Gordon, Ferro, Ashley, Clare, Simon, Bouladoux, Nicolas, Ferdinand, John, Tuong, Zewen Kelvin, Negro-Demontel, Maria Luciana, Kumar, Nitin, Suchanek, Ondrej, Tajsic, Tamara, Harcourt, Katherine, Scott, Kirsten, Bashford-Rogers, Rachel, Helmy, Adel, Reich, Daniel S, Belkaid, Yasmine, Lawley, Trevor D, McGavern, Dorian B and Clatworthy, Menna R (2020). Gut-educated IgA plasma cells defend the meningeal venous sinuses. Nature, 587 (7834), 472-476. doi: 10.1038/s41586-020-2886-4

  • B lymphocyte-derived CCL7 augments neutrophil and monocyte recruitment, exacerbating acute kidney injury

    Inaba, Akimichi, Tuong, Zewen K., Riding, Alexandra M., Mathews, Rebeccah J., Martin, Jack L., Saeb-Parsy, Kourosh and Clatworthy, Menna R. (2020). B lymphocyte-derived CCL7 augments neutrophil and monocyte recruitment, exacerbating acute kidney injury. Journal of Immunology, 205 (5), 1376-1384. doi: 10.4049/jimmunol.2000454

  • Organ immune responses — don’t forget the structural cells

    Tuong, Zewen Kelvin and Clatworthy, Menna R. (2020). Organ immune responses — don’t forget the structural cells. Nature Reviews Nephrology, 16 (10), 570-571. doi: 10.1038/s41581-020-00334-x

  • GM-CSF Calibrates Macrophage Defense and Wound Healing Programs during Intestinal Infection and Inflammation

    Castro-Dopico, Tomas, Fleming, Aaron, Dennison, Thomas W., Ferdinand, John R., Harcourt, Katherine, Stewart, Benjamin J., Cader, Zaeem, Tuong, Zewen K., Jing, Chenzhi, Lok, Laurence S. C., Mathews, Rebeccah J., Portet, Anaïs, Kaser, Arthur, Clare, Simon and Clatworthy, Menna R. (2020). GM-CSF Calibrates Macrophage Defense and Wound Healing Programs during Intestinal Infection and Inflammation. Cell Reports, 32 (1) 107857, 107857. doi: 10.1016/j.celrep.2020.107857

  • Macrophage metabolic reprogramming presents a therapeutic target in lupus nephritis

    Jing, Chenzhi, Castro-Dopico, Tomas, Richoz, Nathan, Tuong, Zewen K., Ferdinand, John R., Lok, Laurence S C, Loudon, Kevin W., Banham, Gemma D., Mathews, Rebeccah J., Cader, Zaeem, Fitzpatrick, Susan, Bashant, Kathleen R., Kaplan, Mariana J., Kaser, Arthur, Johnson, Randall S., Murphy, Michael P., Siegel, Richard M. and Clatworthy, Menna R. (2020). Macrophage metabolic reprogramming presents a therapeutic target in lupus nephritis. Proceedings of the National Academy of Sciences of the United States of America, 117 (26), 15160-15171. doi: 10.1073/pnas.2000943117

  • Cytokine/chemokine profiles in squamous cell carcinoma correlate with precancerous and cancerous disease stage

    Tuong, Zewen, Lewandowski, Andrew, Bridge, Jennifer, Gonzalez-Cruz, Jazmina, Yamada, Miko, Lambie, Duncan, Lewandowski, Richard, Steptoe, Raymond, Leggatt, Graham, Simpson, Fiona, Frazer, Ian, Soyer, Peter and Wells, James W. (2019). Cytokine/chemokine profiles in squamous cell carcinoma correlate with precancerous and cancerous disease stage. Scientific Reports, 9 (1) 17754, 17754. doi: 10.1038/s41598-019-54435-0

  • HPV16 E7-driven epithelial hyperplasia promotes impaired antigen presentation and regulatory T cell development

    Bashaw, Abate Assefa, Teoh, Siok M., Tuong, Zewen K., Leggatt, Graham R., Frazer, Ian H. and Chandra, Janin (2019). HPV16 E7-driven epithelial hyperplasia promotes impaired antigen presentation and regulatory T cell development. Journal of Investigative Dermatology, 139 (12), 2467-2476.e3. doi: 10.1016/j.jid.2019.03.1162

  • Single-cell RNA sequencing reveals cell type-specific HPV expression in hyperplastic skin lesions

    Devitt, Katharina, Hanson, Sarah J., Tuong, Zewen K., McMeniman, Erin, Soyer, H. Peter, Frazer, Ian H. and Lukowski, Samuel W. (2019). Single-cell RNA sequencing reveals cell type-specific HPV expression in hyperplastic skin lesions. Virology, 537, 14-19. doi: 10.1016/j.virol.2019.08.007

  • Microprojection arrays applied to skin generate mechanical stress, induce an inflammatory transcriptome and cell death, and improve vaccine-induced immune responses

    Ng, Hwee-Ing, Tuong, Zewen K., Fernando, Germain J. P., Depelsenaire, Alexandra C. I., Meliga, Stefano C., Frazer, Ian H. and Kendall, Mark A. F. (2019). Microprojection arrays applied to skin generate mechanical stress, induce an inflammatory transcriptome and cell death, and improve vaccine-induced immune responses. npj Vaccines, 4 (1) 41, 41. doi: 10.1038/s41541-019-0134-4

  • Papillomavirus immune evasion strategies target the infected cell and the local immune system

    Zhou, Chenhao, Tuong, Zewen Kelvin and Frazer, Ian Hector (2019). Papillomavirus immune evasion strategies target the infected cell and the local immune system. Frontiers in Oncology, 9 682, 682. doi: 10.3389/fonc.2019.00682

  • Mechanism of iron oxide-induced macrophage activation: the impact of composition and the underlying signaling pathway

    Gu, Zhengying, Liu, Tianqing, Tang, Jie, Yang, Yannan, Song, Hao, Tuong, Zewen K., Fu, Jianye and Yu, Chengzhong (2019). Mechanism of iron oxide-induced macrophage activation: the impact of composition and the underlying signaling pathway. Journal of the American Chemical Society, 141 (15) jacs.8b10904, 6122-6126. doi: 10.1021/jacs.8b10904

  • Recruitment of antigen presenting cells to skin draining lymph node from HPV16E7-expressing skin requires E7-Rb interaction

    Kuo, Paula, Teoh, Siok Min, Tuong, Zewen K., Leggatt, Graham R., Mattarollo, Stephen R. and Frazer, Ian H. (2018). Recruitment of antigen presenting cells to skin draining lymph node from HPV16E7-expressing skin requires E7-Rb interaction. Frontiers in Immunology, 9 2896, 2896. doi: 10.3389/fimmu.2018.02896

  • Examining the contribution of smoking and HPV towards the etiology of oral cavity squamous cell carcinoma using high-throughput sequencing: a prospective observational study

    Zammit, Andrew P., Sinha, Rohit, Cooper, Caroline L., Perry, Christopher F. L., Frazer, Ian H. and Tuong, Zewen K. (2018). Examining the contribution of smoking and HPV towards the etiology of oral cavity squamous cell carcinoma using high-throughput sequencing: a prospective observational study. PLoS One, 13 (10) e0205406, e0205406. doi: 10.1371/journal.pone.0205406

  • Detection of HPV E7 transcription at single-cell resolution in epidermis

    Lukowski, S. W., Tuong, Z. K., Noske, K., Senabouth, A., Nguyen, Q. H., Andersen, S. B., Soyer, H. P., Frazer, I. H. and Powell, J. E. (2018). Detection of HPV E7 transcription at single-cell resolution in epidermis. The Journal of Investigative Dermatology, 138 (12), 2558-2567. doi: 10.1016/j.jid.2018.06.169

  • HPV16E7 Induced Hyperplasia Promotes CXCL9/10 Expression and Induces CXCR3+ T cell Migration to Skin

    Kuo, Paula, Tuong, Zewen K, Teoh, Siok Min, Frazer, Ian H, Mattarollo, Stephen and Leggatt, Graham R (2018). HPV16E7 Induced Hyperplasia Promotes CXCL9/10 Expression and Induces CXCR3+ T cell Migration to Skin. The Journal of investigative dermatology, 138 (6), 1348-1359. doi: 10.1016/j.jid.2017.12.021

  • Characterization of 7A7, an anti-mouse EGFR monoclonal antibody proposed to be the mouse equivalent of cetuximab

    He, Xuzhi, Cruz, Jazmina L., Joseph, Shannon, Pett, Nicola, Chew, Hui Yi, Tuong, Zewen K., Okano, Satomi, Kelly, Gabrielle, Veitch, Margaret, Simpson, Fiona and Wells, James W. (2018). Characterization of 7A7, an anti-mouse EGFR monoclonal antibody proposed to be the mouse equivalent of cetuximab. Oncotarget, 9 (15), 12250-12260. doi: 10.18632/oncotarget.24242

  • B cell lymphoma progression promotes the accumulation of circulating Ly6Clo monocytes with immunosuppressive activity

    McKee, Sara J., Tuong, Zewen K., Kobayashi, Takumi, Doff, Brianna L., Soon, Megan S. F ., Nissen, Michael, Lam, Pui Yeng, Keane, Colm, Vari, Frank, Moi, Davide, Mazzieri, Roberta, Leggatt, Graham, Gandhi, Maher K. and Mattarollo, Stephen R. (2018). B cell lymphoma progression promotes the accumulation of circulating Ly6Clo monocytes with immunosuppressive activity. OncoImmunology, 7 (2) e1393599, e1393599. doi: 10.1080/2162402X.2017.1393599

  • Modulation of antigen presenting cell functions during chronic HPV infection

    Bashaw, Abate Assefa, Leggatt, Graham R., Chandra, Janin, Tuong, Zewen K. and Frazer, Ian H. (2017). Modulation of antigen presenting cell functions during chronic HPV infection. Papillomavirus Research, 4, 58-65. doi: 10.1016/j.pvr.2017.08.002

  • Murine HPV16 E7-expressing transgenic skin effectively emulates the cellular and molecular features of human high-grade squamous intraepithelial lesions

    Tuong, Z. K., Noske, K., Kuo, P., Bashaw, A. A., Teoh, S. M. and Frazer, I. H. (2017). Murine HPV16 E7-expressing transgenic skin effectively emulates the cellular and molecular features of human high-grade squamous intraepithelial lesions. Papillomavirus Research, 5, 6-20. doi: 10.1016/j.pvr.2017.10.001

  • Transgenic adipose-specific expression of the nuclear receptor RORα drives a striking shift in fat distribution and impairs glycemic control

    Tuong, Zewen Kelvin, Fitzsimmons, Rebecca, Wang, Shu-Ching Mary, Oh, Tae Gyu, Lau, Patrick, Steyn, Frederik, Thomas, Gethin and Muscat, George E. O. (2016). Transgenic adipose-specific expression of the nuclear receptor RORα drives a striking shift in fat distribution and impairs glycemic control. EBioMedicine, 11, 101-117. doi: 10.1016/j.ebiom.2016.08.027

  • A mouse model of hyperproliferative human epithelium validated by keratin profiling ahows an aberrant cytoskeletal response to injury

    Zhussupbekova, Samal, Sinha, Rohit, Kuo, Paula, Lambert, Paul F., Frazer, Ian H. and Tuong, Zewen K. (2016). A mouse model of hyperproliferative human epithelium validated by keratin profiling ahows an aberrant cytoskeletal response to injury. Ebiomedicine, 9, 314-323. doi: 10.1016/j.ebiom.2016.06.011

  • The nuclear receptor, Nor-1, induces the physiological responses associated with excercise

    Goode, Joel M., Pearen, Michael A., Tuong, Zewen K., Wang, Shu-Ching M., Oh, Tae Gyu, Shao, Emily X. and Muscat, George E. (2016). The nuclear receptor, Nor-1, induces the physiological responses associated with excercise. Molecular Endocrinology, 30 (6), 660-676. doi: 10.1210/me.2015-1300

  • RORα and 25-hydroxycholesterol crosstalk regulates lipid droplet homeostasis in macrophages

    Tuong, Zewen Kelvin, Lau, Patrick, Du, Ximing, Condon, Nicholas D., Goode, Joel M., Oh, Tae Gyu, Yeo, Jeremy C., Muscat, George E. O. and Stow, Jennifer L. (2016). RORα and 25-hydroxycholesterol crosstalk regulates lipid droplet homeostasis in macrophages. PLoS ONE, 11 (1) e0147179, e0147179. doi: 10.1371/journal.pone.0147179

  • Ror-alpha deficiency and decreased adiposity are associated with induction of thermogenic gene expression in subcutaneous white and brown adipose tissue

    Lau, Patrick, Tuong, Zewen K., Wang, Shu-Ching, Fitzsimmons, Rebecca L., Goode, Joel M., Thomas, Gethin P., Cowin, Gary J., Pearen, Michael A., Mardon, Karine, Stow, Jennifer L. and Muscat, George E. O. (2015). Ror-alpha deficiency and decreased adiposity are associated with induction of thermogenic gene expression in subcutaneous white and brown adipose tissue. American Journal of Physiology: Endocrinology and Metabolism, 308 (2), E159-E171. doi: 10.1152/ajpendo.00056.2014

  • Muscle specific Nor-1 expression regulates multiple pathways that effect adiposity, metabolism and endurance

    Pearen, Michael A., Goode, Joel M., Fitzsimmons, Rebecca L., Eriksson, Natalie A., Thomas, Gethin P., Cowin, Gary J., Wang, S.-C. Mary, Tuong, Zewen K. and Muscat, George E. O. (2013). Muscle specific Nor-1 expression regulates multiple pathways that effect adiposity, metabolism and endurance. Molecular Endocrinology, 27 (11), 1897-1917. doi: 10.1210/me.2013-1205

  • Disruption of Rorα1 and cholesterol 25-hydroxylase expression attenuates phagocytosis in male Rorαsg/sg mice

    Tuong, Zewen K., Lau, Patrick, Yeo, Jeremy C., Pearen, Michael A., Wall, Adam A., Stanley, Amanda C., Stow, Jennifer L. and Muscat, George E. O. (2013). Disruption of Rorα1 and cholesterol 25-hydroxylase expression attenuates phagocytosis in male Rorαsg/sg mice. Endocrinology, 154 (1), 140-149. doi: 10.1210/en.2012-1889

Conference Publication

Other Outputs

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

  • Investigate T cell specificity and function in immune responses by systems immunology

    Doctor Philosophy — Associate Advisor

    Other advisors:

Possible Research Projects

Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.

  • Developing single-cell analysis methods harnessing adaptive immune receptors

    The direct linkage of adaptive immune receptor repertoire with cellular phenotypes from single-cell sequencing technology has proven to be a powerful tool in understanding lymphocyte development and function in healthy and disease contexts. Multi-omics analysis leverages data from different modalities e.g. transcriptomics, epigenetics, proteomics. Recent advances has successfully integrated the data modalities to study cellular biology at an unprecedented resolution. However, unlike the other data modalities, which are largely continuous data, single-cell adaptive immune receptor sequencing (scVDJ-seq) data are a mixture of categorical and continuous data which poses additional challenges for integration. It consists of annotations of variable (V), diversity (D) and joining (J) genes, which are selected and recombined during B/T-cell development. The technology to profile this at the single cell level with paired gene expression data is relatively new. I have led the development of Dandelion, a scVDJ-seq software framework which has been used to deeply profile single-cell lymphocyte biology and I aim to expand on the its capabilities for immunology research.

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ResearcherID: E-4419-2017

ORCID: 0000-0002-6735-6808

Scopus ID: 55539754100

Google Scholar ID: FxM6LDEAAAAJ

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