Scholars@Duke
John Wirthlin Hickey

John Wirthlin Hickey

Assistant Professor of Biomedical Engineering
Biomedical Engineering

Selected Publications

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage.

Journal Article Nat Methods · April 2025 The Human BioMolecular Atlas Program (HuBMAP) aims to construct a 3D Human Reference Atlas (HRA) of the healthy adult body. Experts from 20+ consortia collaborate to develop a Common Coordinate Framework (CCF), knowledge graphs and tools that describe the ... Full text Link to item Cite

High-throughput multiplexed serology via the mass-spectrometric analysis of isotopically barcoded beads.

Journal Article Nature biomedical engineering · February 2025 In serology, each sample is typically tested individually, one antigen at a time. This is costly and time consuming. Serology techniques should ideally allow recurrent measurements in parallel in small sample volumes and be inexpensive and fast. Here we sh ... Full text Cite

mRNA lipid nanoparticle-incorporated nanofiber-hydrogel composite generates a local immunostimulatory niche for cancer immunotherapy.

Journal Article bioRxiv · January 29, 2025 Hydrogel materials have emerged as versatile platforms for various biomedical applications. Notably, the engineered nanofiber-hydrogel composite (NHC) has proven effective in mimicking the soft tissue extracellular matrix, facilitating substantial recruitm ... Full text Link to item Cite

Ex vivo expansion and hydrogel-mediated in vivo delivery of tissue-resident memory T cells for immunotherapy.

Journal Article Science advances · December 2024 Tissue-resident memory T (TRM) cells preferentially reside in peripheral tissues, serving as key players in tumor immunity and immunotherapy. The lack of effective approaches for expanding TRM cells and delivering these cells in vivo ... Full text Cite

Harmonizing the Generation and Pre-publication Stewardship of FAIR bioimage data.

Journal Article ArXiv · August 30, 2024 Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For t ... Link to item Cite

Data from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <div>Abstract<p>Tumor-associated macrophages are transcriptionally heterogeneous, but the spatial distribution and cell interactions that shape macrophage tissue roles remain poorly characterized. Here, we spatially resolve five distinc ... Full text Cite

Table S1 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Supplementary Table 1. List of IHC antibodies</p> ... Full text Cite

Figure S8 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure shows Kaplan-Meier plots of CRC patient samples stratified by IL4I1+ macrophage counts.</p> ... Full text Cite

Figure S5 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Thus Figure illustrates how macrophage subsets detected using scRNAseq, 4-color IF, and CODEX correspond to each other and shows representative examples of protein marker expression across macrophage niches.</p> ... Full text Cite

Figure S4 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure shows protein marker expression across different cell types detected in CODEX experiment, macrophage distance to the closest tumor cell, macrophage distribution across different tissue niches, and tissue niche distribution acro ... Full text Cite

Figure S8 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure shows Kaplan-Meier plots of CRC patient samples stratified by IL4I1+ macrophage counts.</p> ... Full text Cite

Figure S2 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure illustrates spatial segregation of IL4I1+ vs FOLR2+ macrophages in BC and CRC tumor metastasis to the LN, and across eight different tumor types.</p> ... Full text Cite

Figure S1 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure shows the distribution of scRNAseq macrophage clusters across different datasets, tissue locations, and tumor types.</p> ... Full text Cite

Figure S6 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure shows the spatial interaction of FOLR2+ macrophages with Plasma Cells in normal colon lamina propria, normal breast, normal lymph node, and breast cancer adjacent normal tissue. It also illustrates ligand-receptor interactions ... Full text Cite

Table S3 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Supplementary Table 3. CODEX imiging cycles record</p> ... Full text Cite

Table S1 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Supplementary Table 1. List of IHC antibodies</p> ... Full text Cite

Figure S9 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure is a visual summary of this work’s findings and shows the spatial distribution of distinct macrophage subsets in the tumor microenvironment and the clinical significance of IL4I1+ and SPP1+ macrophages in breast and colon tumor ... Full text Cite

Figure S4 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure shows protein marker expression across different cell types detected in CODEX experiment, macrophage distance to the closest tumor cell, macrophage distribution across different tissue niches, and tissue niche distribution acro ... Full text Cite

Figure S6 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure shows the spatial interaction of FOLR2+ macrophages with Plasma Cells in normal colon lamina propria, normal breast, normal lymph node, and breast cancer adjacent normal tissue. It also illustrates ligand-receptor interactions ... Full text Cite

Data from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <div>Abstract<p>Tumor-associated macrophages are transcriptionally heterogeneous, but the spatial distribution and cell interactions that shape macrophage tissue roles remain poorly characterized. Here, we spatially resolve five distinc ... Full text Cite

Table S3 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Supplementary Table 3. CODEX imiging cycles record</p> ... Full text Cite

Figure S1 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure shows the distribution of scRNAseq macrophage clusters across different datasets, tissue locations, and tumor types.</p> ... Full text Cite

Figure S3 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Thus Figure shows CD274 gene scRNAseq expression across different cell types and datasets.</p> ... Full text Cite

Figure S5 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Thus Figure illustrates how macrophage subsets detected using scRNAseq, 4-color IF, and CODEX correspond to each other and shows representative examples of protein marker expression across macrophage niches.</p> ... Full text Cite

Table S2 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Supplementary Table 2. List of CODEX antibodies</p> ... Full text Cite

Figure S7 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Thus Figure shows spatial enrichment of NLRP3+ macrophages with neutrophils in Crohn’s Disease, and immunostimulatory and immunosuppressive protein marker expression in NLRP3+ vs SPP1+ macrophages.</p> ... Full text Cite

Figure S9 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure is a visual summary of this work’s findings and shows the spatial distribution of distinct macrophage subsets in the tumor microenvironment and the clinical significance of IL4I1+ and SPP1+ macrophages in breast and colon tumor ... Full text Cite

Table S2 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Supplementary Table 2. List of CODEX antibodies</p> ... Full text Cite

Figure S3 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Thus Figure shows CD274 gene scRNAseq expression across different cell types and datasets.</p> ... Full text Cite

Figure S2 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>This Figure illustrates spatial segregation of IL4I1+ vs FOLR2+ macrophages in BC and CRC tumor metastasis to the LN, and across eight different tumor types.</p> ... Full text Cite

Figure S7 from Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Other · August 2, 2024 <p>Thus Figure shows spatial enrichment of NLRP3+ macrophages with neutrophils in Crohn’s Disease, and immunostimulatory and immunosuppressive protein marker expression in NLRP3+ vs SPP1+ macrophages.</p> ... Full text Cite

Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer.

Journal Article Cancer discovery · August 2024 Tumor-associated macrophages are transcriptionally heterogeneous, but the spatial distribution and cell interactions that shape macrophage tissue roles remain poorly characterized. Here, we spatially resolve five distinct human macrophage populations in no ... Full text Cite

Integration of spatial and single-cell data across modalities with weakly linked features.

Journal Article Nature biotechnology · July 2024 Although single-cell and spatial sequencing methods enable simultaneous measurement of more than one biological modality, no technology can capture all modalities within the same cell. For current data integration methods, the feasibility of cross-modal in ... Full text Cite

SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis.

Journal Article Bioinformatics (Oxford, England) · July 2024 MotivationSpatial omics data demand computational analysis but many analysis tools have computational resource requirements that increase with the number of cells analyzed. This presents scalability challenges as researchers use spatial omics tech ... Full text Cite

In Vivo Stimulation of Therapeutic Antigen-Specific T Cells in an Artificial Lymph Node Matrix.

Journal Article Advanced materials (Deerfield Beach, Fla.) · June 2024 T cells are critical mediators of antigen-specific immune responses and are common targets for immunotherapy. Biomaterial scaffolds have previously been used to stimulate antigen-presenting cells to elicit antigen-specific immune responses; however, struct ... Full text Cite

Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy.

Journal Article Cell systems · April 2024 Cancer progression is a complex process involving interactions that unfold across molecular, cellular, and tissue scales. These multiscale interactions have been difficult to measure and to simulate. Here, we integrated CODEX multiplexed tissue imaging wit ... Full text Cite

Contributing to consortia human tissue mapping efforts with multiplexed imaging

Chapter · January 1, 2024 Consortia projects are harnessing the power of single-cell, spatially resolved imaging technologies for large-scale tissue mapping projects. We have participated in normal and disease tissue mapping consortia by contributing to the development of tools, st ... Full text Cite

Lessons for the Next Generation of Scientists from the Second Annual Arthur and Sandra Irving Cancer Immunology Symposium.

Journal Article Cancer immunology research · December 2023 The Arthur and Sandra Irving Cancer Immunology Symposium has been created as a platform for established cancer immunologists to mentor trainees and young investigators as they launch their research career in the field. By sharing their different paths to s ... Full text Cite

T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.

Journal Article Cell reports · December 2023 Antigen-specific T cells traffic to, are influenced by, and create unique cellular microenvironments. Here we characterize these microenvironments over time with multiplexed imaging in a melanoma model of adoptive T cell therapy and human patients with mel ... Full text Cite

Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP).

Journal Article Nature cell biology · August 2023 The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale spatial atlas of the healthy human body at single-cell resolution by applying advanced technologies and disseminating resources to the community. As the HuBMAP moves past its first ... Full text Cite

Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.

Journal Article Nature methods · August 2023 Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed ... Full text Cite

Organization of the human intestine at single-cell resolution.

Journal Article Nature · July 2023 The intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall health1. The intesting has a length of over nine me ... Full text Cite

Physioxia improves the selectivity of hematopoietic stem cell expansion cultures.

Journal Article Blood advances · July 2023 Hematopoietic stem cells (HSCs) are a rare type of hematopoietic cell that can entirely reconstitute the blood and immune system after transplantation. Allogeneic HSC transplantation (HSCT) is used clinically as a curative therapy for a range of hematolymp ... Full text Cite

Segmentation of human functional tissue units in support of a Human Reference Atlas.

Journal Article Communications biology · July 2023 The Human BioMolecular Atlas Program (HuBMAP) aims to compile a Human Reference Atlas (HRA) for the healthy adult body at the cellular level. Functional tissue units (FTUs), relevant for HRA construction, are of pathobiological significance. Manual segment ... Full text Cite

Shape matters: Biodegradable anisotropic nanoparticle artificial antigen presenting cells for cancer immunotherapy.

Journal Article Acta biomaterialia · April 2023 Artificial antigen presenting cells are biomimetic particles that recapitulate the signals presented by natural antigen presenting cells in order to stimulate T cells in an antigen-specific manner using an acellular platform. We have engineered an enhanced ... Full text Cite

Annotation of spatially resolved single-cell data with STELLAR.

Journal Article Nature methods · November 2022 Accurate cell-type annotation from spatially resolved single cells is crucial to understand functional spatial biology that is the basis of tissue organization. However, current computational methods for annotating spatially resolved single-cell data are t ... Full text Cite

Multicellular modules as clinical diagnostic and therapeutic targets.

Journal Article Trends in cancer · March 2022 The complex determinants of health and disease can be determined when approached as a system of interactions of biological agents at different scales. Similar to the physicochemical properties that govern nucleic acids and proteins, there should be a finit ... Full text Cite

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging.

Journal Article Nature methods · March 2022 Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which ... Full text Cite

A real-time GPU-accelerated parallelized image processor for large-scale multiplexed fluorescence microscopy data.

Journal Article Frontiers in immunology · January 2022 Highly multiplexed, single-cell imaging has revolutionized our understanding of spatial cellular interactions associated with health and disease. With ever-increasing numbers of antigens, region sizes, and sample sizes, multiplexed fluorescence imaging exp ... Full text Cite

Anatomical structures, cell types and biomarkers of the Human Reference Atlas.

Journal Article Nature cell biology · November 2021 The Human Reference Atlas (HRA) aims to map all of the cells of the human body to advance biomedical research and clinical practice. This Perspective presents collaborative work by members of 16 international consortia on two essential and interlinked part ... Full text Cite

CODEX multiplexed tissue imaging with DNA-conjugated antibodies.

Journal Article Nature protocols · August 2021 Advances in multiplexed imaging technologies have drastically improved our ability to characterize healthy and diseased tissues at the single-cell level. Co-detection by indexing (CODEX) relies on DNA-conjugated antibodies and the cyclic addition and remov ... Full text Cite

Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction.

Journal Article European journal of immunology · May 2021 Multiparameter tissue imaging enables analysis of cell-cell interactions in situ, the cellular basis for tissue structure, and novel cell types that are spatially restricted, giving clues to biological mechanisms behind tissue homeostasis and disease. Here ... Full text Cite

Application of machine learning in understanding atherosclerosis: Emerging insights.

Journal Article APL bioengineering · March 2021 Biological processes are incredibly complex-integrating molecular signaling networks involved in multicellular communication and function, thus maintaining homeostasis. Dysfunction of these processes can result in the disruption of homeostasis, leading to ... Full text Cite

Biodegradable Cationic Polymer Blends for Fabrication of Enhanced Artificial Antigen Presenting Cells to Treat Melanoma.

Journal Article ACS applied materials & interfaces · February 2021 Biomimetic biomaterials are being actively explored in the context of cancer immunotherapy because of their ability to directly engage the immune system to generate antitumor responses. Unlike cellular therapies, biomaterial-based immunotherapies can be pr ... Full text Cite

Improving Biomedical Engineering Undergraduate Learning Through Use of Online Graduate Engineering Courses During the COVID-19 Pandemic.

Journal Article Biomedical engineering education · January 2021 In order to provide undergraduate students with a full, rich online learning experience we adapted pre-existing online content including graduate courses from Johns Hopkins University Engineering for Professionals (JHU EP) program. These online courses wer ... Full text Cite

Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data.

Journal Article Frontiers in immunology · January 2021 Multiplexed imaging is a recently developed and powerful single-cell biology research tool. However, it presents new sources of technical noise that are distinct from other types of single-cell data, necessitating new practices for single-cell multiplexed ... Full text Cite

Rhesus Macaque CODEX Multiplexed Immunohistochemistry Panel for Studying Immune Responses During Ebola Infection.

Journal Article Frontiers in immunology · January 2021 Non-human primate (NHP) animal models are an integral part of the drug research and development process. For some biothreat pathogens, animal model challenge studies may offer the only possibility to evaluate medical countermeasure efficacy. A thorough und ... Full text Cite

Adaptive Nanoparticle Platforms for High Throughput Expansion and Detection of Antigen-Specific T cells.

Journal Article Nano letters · September 2020 T cells are critical players in disease; yet, their antigen-specificity has been difficult to identify, as current techniques are limited in terms of sensitivity, throughput, or ease of use. To address these challenges, we increased the throughput and tran ... Full text Cite

Commensal bacteria stimulate antitumor responses via T cell cross-reactivity.

Journal Article JCI insight · April 2020 Recent studies show gut microbiota modulate antitumor immune responses; one proposed mechanism is cross-reactivity between antigens expressed in commensal bacteria and neoepitopes. We found that T cells targeting an epitope called SVYRYYGL (SVY), expressed ... Full text Cite

Collagen fiber structure guides 3D motility of cytotoxic T lymphocytes.

Journal Article Matrix biology : journal of the International Society for Matrix Biology · January 2020 Lymphocyte motility is governed by a complex array of mechanisms, and highly dependent on external microenvironmental cues. Tertiary lymphoid sites in particular have unique physical structure such as collagen fiber alignment, due to matrix deposition and ... Full text Cite

Engineering an Artificial T-Cell Stimulating Matrix for Immunotherapy.

Journal Article Advanced materials (Deerfield Beach, Fla.) · June 2019 T cell therapies require the removal and culture of T cells ex vivo to expand several thousand-fold. However, these cells often lose the phenotype and cytotoxic functionality for mediating effective therapeutic responses. The extracellular matrix (ECM) has ... Full text Cite

Efficient magnetic enrichment of antigen-specific T cells by engineering particle properties.

Journal Article Biomaterials · December 2018 Magnetic particles can enrich desired cell populations to aid in understanding cell-type functions and mechanisms, diagnosis, and therapy. As cells are heterogeneous in ligand type, location, expression, and density, careful consideration of magnetic parti ... Full text Cite

Enrich and Expand Rare Antigen-specific T Cells with Magnetic Nanoparticles.

Journal Article Journal of visualized experiments : JoVE · November 2018 We have developed a tool to both enrich and expand antigen-specific T cells. This can be helpful in cases such as to A) detect the existence of antigen-specific T cells, B) probe the dynamics of antigen-specific responses, C) understand how antigen-specifi ... Full text Cite

Separating T Cell Targeting Components onto Magnetically Clustered Nanoparticles Boosts Activation.

Journal Article Nano letters · March 2018 T cell activation requires the coordination of a variety of signaling molecules including T cell receptor-specific signals and costimulatory signals. Altering the composition and distribution of costimulatory molecules during stimulation greatly affects T ... Full text Cite

Engineering Platforms for T Cell Modulation.

Chapter · January 2018 T cells are crucial contributors to mounting an effective immune response and increasingly the focus of therapeutic interventions in cancer, infectious disease, and autoimmunity. Translation of current T cell immunotherapies has been hindered by off-target ... Full text Cite

Biologically Inspired Design of Nanoparticle Artificial Antigen-Presenting Cells for Immunomodulation.

Journal Article Nano letters · November 2017 Particles engineered to engage and interact with cell surface ligands and to modulate cells can be harnessed to explore basic biological questions as well as to devise cellular therapies. Biology has inspired the design of these particles, such as artifici ... Full text Cite

Biomimetic biodegradable artificial antigen presenting cells synergize with PD-1 blockade to treat melanoma.

Journal Article Biomaterials · February 2017 Biomimetic materials that target the immune system and generate an anti-tumor responses hold promise in augmenting cancer immunotherapy. These synthetic materials can be engineered and optimized for their biodegradability, physical parameters such as shape ... Full text Cite

Control of polymeric nanoparticle size to improve therapeutic delivery.

Journal Article Journal of controlled release : official journal of the Controlled Release Society · December 2015 As nanoparticle (NP)-mediated drug delivery research continues to expand, understanding parameters that govern NP interactions with the biological environment becomes paramount. The principles identified from the study of these parameters can be used to en ... Full text Cite

Prevention and removal of lipid deposits by lens care solutions and rubbing.

Journal Article Optometry and vision science : official publication of the American Academy of Optometry · December 2014 PurposeDespite the prevalence of silicone hydrogel (SiHy) contact lenses, there are relatively few studies that evaluate the efficacy of multipurpose lens care solutions (MPSs) in reducing lipid deposition on these lenses and the effect of rubbing ... Full text Cite

The role of multi-purpose solutions in prevention and removal of lipid depositions on contact lenses.

Journal Article Contact lens & anterior eye : the journal of the British Contact Lens Association · December 2014 The sorption and desorption of radiolabeled dipalmitoylphosphatidylcholine (DPPC) and cholesterol (CH) were measured on 5 types of commercial contact lenses. The lenses were soaked in vitro in an artificial tear fluid for 16h. The effects of borate buffere ... Full text Cite

Metallization of branched DNA origami for nanoelectronic circuit fabrication.

Journal Article ACS nano · March 2011 This work examines the metallization of folded DNA, known as DNA origami, as an enabling step toward the use of such DNA as templates for nanoelectronic circuits. DNA origami, a simple and robust method for creating a wide variety of shapes and patterns, m ... Full text Cite