John Wirthlin Hickey

Research Themes

Biomaterials, Biomedical & Health Data Sciences, Biomedical Imaging & Biophotonics, Computational Modeling of Biological Systems, Immune Engineering, Synthetic & Systems Biology, Tissue Engineering & Regenerative Medicine

Research Interests

Using and developing systems biology tools and technologies to describe and control spatial relationships between cells in tissues, particularly in cell therapies.

Bio

The Hickey Lab sits at the interface of engineering and immunology, using and developing systems immunology tools to investigate tissue structure in situ. We also use multiplexed imaging and computational techniques to characterize spatial cellular responses related to the effectiveness of anti-cancer cell or biomaterial therapies.  John has received a number of awards for his work, including the NSF Graduate Research Fellowship, ARCS Scholar, Siebel Scholar, NCI Postdoctoral Fellowship, and American Cancer Society Postdoctoral Fellowship.

Education

• Ph.D. Johns Hopkins University, School of Medicine, 2019

Positions

• Assistant Professor of Biomedical Engineering
• Assistant Professor in Biostatistics & Bioinformatics
• Member of the Duke Cancer Institute

Awards, Honors, and Distinctions

• American Cancer Society Postdoctoral Fellowship. American Cancer Society. 2020

Courses Taught

• EGR 393: Research Projects in Engineering
• BME 791: Graduate Independent Study
• BME 590: Special Topics in Biomedical Engineering
• BME 493: Projects in Biomedical Engineering (GE)

Publications

• Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, et al. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data. ArXiv. 2024 Aug 30;
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S4 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Table S1 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S9 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Data from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S1 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S4 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Data from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Table S2 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S6 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S5 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S3 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S3 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Table S3 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Table S3 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S8 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Table S1 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S6 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Table S2 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S7 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S2 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S9 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S2 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S7 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S5 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S1 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Figure S8 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. 2024.
• Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, et al. Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. Cancer discovery. 2024 Aug;14(8):1418–39.
• Aihara G, Clifton K, Chen M, Li Z, Atta L, Miller BF, et al. SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis. Bioinformatics (Oxford, England). 2024 Jul;40(7):btae412.
• Chen S, Zhu B, Huang S, Hickey JW, Lin KZ, Snyder M, et al. Integration of spatial and single-cell data across modalities with weakly linked features. Nature biotechnology. 2024 Jul;42(7):1096–106.
• Livingston NK, Hickey JW, Sim H, Salathe SF, Choy J, Kong J, et al. In Vivo Stimulation of Therapeutic Antigen-Specific T Cells in an Artificial Lymph Node Matrix. Advanced materials (Deerfield Beach, Fla). 2024 Jun;36(23):e2310043.
• Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, et al. Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nature cell biology. 2024 May;26(5):839.
• Hickey JW, Agmon E, Horowitz N, Tan T-K, Lamore M, Sunwoo JB, et al. Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy. Cell systems. 2024 Apr;15(4):322-338.e5.
• Börner K, Blood P, Silverstein J, Ruffalo M, Satija R, Teichmann S, et al. Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. bioRxiv. 2024.
• Caraccio C, Mukherjee N, Nolan GP, Hickey JW. Contributing to consortia human tissue mapping efforts with multiplexed imaging. In: Revealing Uncharted Biology with Single Cell Multiplex Proteomic Technologies: Applications. 2024. p. 21–46.
• Hickey JW, Agmon E, Horowitz N, Lamore M, Sunwoo J, Covert M, et al. Integrating Multiplexed Imaging and Multiscale Modeling Identifies Tumor Phenotype Transformation as a Critical Component of Therapeutic T Cell Efficacy. 2023.
• Hickey JW, Haist M, Horowitz N, Caraccio C, Tan Y, Rech AJ, et al. T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response. Cell reports. 2023 Dec;42(12):113494.
• Alvarez-Breckenridge C, Anderson KG, Correia AL, Demehri S, Dinh HQ, Dixon KO, et al. Lessons for the Next Generation of Scientists from the Second Annual Arthur and Sandra Irving Cancer Immunology Symposium. Cancer immunology research. 2023 Dec;11(12):1571–7.
• Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, et al. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nature cell biology. 2023 Aug;25(8):1089–100.
• Quardokus EM, Saunders DC, McDonough E, Hickey JW, Werlein C, Surrette C, et al. Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging. Nature methods. 2023 Aug;20(8):1174–8.
• Hickey JW, Becker WR, Nevins SA, Horning A, Perez AE, Zhu C, et al. Organization of the human intestine at single-cell resolution. Nature. 2023 Jul;619(7970):572–84.
• Jain Y, Godwin LL, Ju Y, Sood N, Quardokus EM, Bueckle A, et al. Segmentation of human functional tissue units in support of a Human Reference Atlas. Communications biology. 2023 Jul;6(1):717.
• Igarashi KJ, Kucinski I, Chan YY, Tan T-K, Khoo HM, Kealy D, et al. Physioxia improves the selectivity of hematopoietic stem cell expansion cultures. Blood advances. 2023 Jul;7(14):3366–77.
• Ben-Akiva E, Hickey JW, Meyer RA, Isser A, Shannon SR, Livingston NK, et al. Shape matters: Biodegradable anisotropic nanoparticle artificial antigen presenting cells for cancer immunotherapy. Acta biomaterialia. 2023 Apr;160:187–97.
• Matusiak M, Hickey JW, Luca B, Lu G, Kidziński L, Zhu S, et al. A spatial map of human macrophage niches reveals context-dependent macrophage functions in colon and breast cancer. 2023.
• Brbić M, Cao K, Hickey JW, Tan Y, Snyder MP, Nolan GP, et al. Annotation of spatially resolved single-cell data with STELLAR. Nature methods. 2022 Nov;19(11):1411–8.
• Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, et al. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nature methods. 2022 Mar;19(3):284–95.
• Baertsch M-A, Nolan GP, Hickey JW. Multicellular modules as clinical diagnostic and therapeutic targets. Trends in cancer. 2022 Mar;8(3):164–73.
• Livingston N, Hickey J, Sim H, Mao H-Q, Schneck J. IN VIVO EXPANSION OF ENDOGENOUS ANTIGENSPECIFIC CD8+T CELLS USING ARTIFICIAL T-CELL STIMULATING MICROPARTICLES. In: JOURNAL FOR IMMUNOTHERAPY OF CANCER. 2022. p. A271–A271.
• Lu G, Baertsch MA, Hickey JW, Goltsev Y, Rech AJ, Mani L, et al. A real-time GPU-accelerated parallelized image processor for large-scale multiplexed fluorescence microscopy data. Frontiers in immunology. 2022 Jan;13:981825.
• Hickey J, Nolan G, Covert M, Agmon E, Horowitz N, Sunwoo J. 180 T cell phenotype drives restructuring of tumor microenvironment to balance T cell longevity and tumor control: insights from multiplexed imaging and multi-scale agent based modeling. In: Regular and Young Investigator Award Abstracts. BMJ Publishing Group Ltd; 2021. p. A192–A192.
• Horowitz N, Hickey J, Sunwoo J. 181 Intraepithelial group 1 innate lymphoid cells generated in vitro exhibit enhanced cytotoxicity and infiltration into solid tumoroids. Regular and Young Investigator Award Abstracts. 2021 Nov;A193–A193.
• Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, et al. Anatomical structures, cell types and biomarkers of the Human Reference Atlas. Nature cell biology. 2021 Nov;23(11):1117–28.
• Black S, Phillips D, Hickey JW, Kennedy-Darling J, Venkataraaman VG, Samusik N, et al. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nature protocols. 2021 Aug;16(8):3802–35.
• Kennedy-Darling J, Bhate SS, Hickey JW, Black S, Barlow GL, Vazquez G, et al. Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. European journal of immunology. 2021 May;51(5):1262–77.
• Munger E, Hickey JW, Dey AK, Jafri MS, Kinser JM, Mehta NN. Application of machine learning in understanding atherosclerosis: Emerging insights. APL bioengineering. 2021 Mar;5(1):011505.
• Rhodes KR, Isser A, Hickey JW, Ben-Akiva E, Meyer RA, Kosmides AK, et al. Biodegradable Cationic Polymer Blends for Fabrication of Enhanced Artificial Antigen Presenting Cells to Treat Melanoma. ACS applied materials & interfaces. 2021 Feb;13(7):7913–23.
• Jiang S, Mukherjee N, Bennett RS, Chen H, Logue J, Dighero-Kemp B, et al. Rhesus Macaque CODEX Multiplexed Immunohistochemistry Panel for Studying Immune Responses During Ebola Infection. Frontiers in immunology. 2021 Jan;12:729845.
• Brbić M, Cao K, Hickey J, Tan Y, Snyder M, Nolan G, et al. Annotation of Spatially Resolved Single-cell Data with STELLAR. bioRxiv. 2021.
• Hickey JW, Tan Y, Nolan GP, Goltsev Y. Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data. Frontiers in immunology. 2021 Jan;12:727626.
• Nesmith JE, Hickey JW, Haase E. Improving Biomedical Engineering Undergraduate Learning Through Use of Online Graduate Engineering Courses During the COVID-19 Pandemic. Biomedical engineering education. 2021 Jan;1(2):317–24.
• Hickey JW, Isser A, Salathe SF, Gee KM, Hsiao M-H, Shaikh W, et al. Adaptive Nanoparticle Platforms for High Throughput Expansion and Detection of Antigen-Specific T cells. Nano letters. 2020 Sep;20(9):6289–98.
• Bessell CA, Isser A, Havel JJ, Lee S, Bell DR, Hickey JW, et al. Commensal bacteria stimulate antitumor responses via T cell cross-reactivity. JCI insight. 2020 Apr;5(8):135597.
• Pruitt HC, Lewis D, Ciccaglione M, Connor S, Smith Q, Hickey JW, et al. Collagen fiber structure guides 3D motility of cytotoxic T lymphocytes. Matrix biology : journal of the International Society for Matrix Biology. 2020 Jan;85–86:147–59.
• Hickey JW, Dong Y, Chung JW, Salathe SF, Pruitt HC, Li X, et al. Engineering an Artificial T-Cell Stimulating Matrix for Immunotherapy. Advanced materials (Deerfield Beach, Fla). 2019 Jun;31(23):e1807359.
• Hickey JW, Isser AY, Vicente FP, Warner SB, Mao H-Q, Schneck JP. Efficient magnetic enrichment of antigen-specific T cells by engineering particle properties. Biomaterials. 2018 Dec;187:105–16.
• Hickey JW, Schneck JP. Enrich and Expand Rare Antigen-specific T Cells with Magnetic Nanoparticles. Journal of visualized experiments : JoVE. 2018 Nov;(141).
• Kosmides AK, Necochea K, Hickey JW, Schneck JP. Separating T Cell Targeting Components onto Magnetically Clustered Nanoparticles Boosts Activation. Nano letters. 2018 Mar;18(3):1916–24.
• Hickey JW, Kosmides AK, Schneck JP. Engineering Platforms for T Cell Modulation. In 2018. p. 277–362.
• Hickey JW, Vicente FP, Howard GP, Mao H-Q, Schneck JP. Biologically Inspired Design of Nanoparticle Artificial Antigen-Presenting Cells for Immunomodulation. Nano letters. 2017 Nov;17(11):7045–54.
• Kosmides AK, Meyer RA, Hickey JW, Aje K, Cheung KN, Green JJ, et al. Biomimetic biodegradable artificial antigen presenting cells synergize with PD-1 blockade to treat melanoma. Biomaterials. 2017 Feb;118:16–26.
• Meyer RA, Kosmides AK, Hickey JW, Aje K, Cheung KHN, Schneck JP, et al. Biomimetic Artificial Antigen Presenting Cells Synergize with Anti-PD1 in the Treatment of Melanoma. In: MOLECULAR THERAPY. 2017. p. 269–70.
• Hickey JW, Santos JL, Williford J-M, Mao H-Q. Control of polymeric nanoparticle size to improve therapeutic delivery. Journal of controlled release : official journal of the Controlled Release Society. 2015 Dec;219:536–47.
• Tam NK, Pitt WG, Perez KX, Handly E, Glenn AA, Hickey JW, et al. The role of multi-purpose solutions in prevention and removal of lipid depositions on contact lenses. Contact lens & anterior eye : the journal of the British Contact Lens Association. 2014 Dec;37(6):405–14.
• Tam NK, Pitt WG, Perez KX, Hickey JW, Glenn AA, Chinn J, et al. Prevention and removal of lipid deposits by lens care solutions and rubbing. Optometry and vision science : official publication of the American Academy of Optometry. 2014 Dec;91(12):1430–9.
• Liu J, Geng Y, Pound E, Gyawali S, Ashton JR, Hickey J, et al. Metallization of branched DNA origami for nanoelectronic circuit fabrication. ACS nano. 2011 Mar;5(3):2240–7.

In The News

• John Hickey: When It Comes to Studying Cells, Location is Everything (Aug 21, 2023 | Duke Engineering News)
• It’s a beautiful day in the intestinal neighborhood (Jul 19, 2023 | )