John Hickey received his PhD in Biomedical Engineering from Johns Hopkins University in 2019, mentored under Dr. Jonathan Schneck and Hai-quan Mao. There he engineered biomaterials to solve challenges facing T cell immunotherapies and was a recipient of the NSF graduate research fellowship, INBT cancer research fellowship, ARCS foundation scholarship, Siebel scholar award, and Young Investigators' Day award. Dr. Hickey is a Postdoctoral Fellow in Dr. Garry Nolan's lab and comes with an interest in technology development that can provide systems-level data to immune responses.
Honors & Awards
ACS Postdoctoral Fellowship, American Cancer Society (2020)
Young Investigators' Day Hans J. Prochaska Award, Johns Hopkins School of Medicine (2019)
Siebel Scholar, Siebel Foundation (2018)
JCM Foundation ARCS Scholar, ARCS Foundation (2017)
Teaching Shark Tank Award, Center for Educational Resources (2016)
NSF Graduate Research Fellow, National Science Foundation (2015)
NIH Cancer Nanotechnology Predoctoral Fellow, JHU Institute for Nanobiotechnology (2014)
Boards, Advisory Committees, Professional Organizations
Member, Biomedical Engineering Society (2017 - Present)
Doctor of Philosophy, Johns Hopkins University (2019)
PhD, Johns Hopkins University, Biomedical Engineering (2019)
BS, Brigham Young University, Chemical Engineering (2013)
Garry Nolan, Postdoctoral Faculty Sponsor
Current Research and Scholarly Interests
I am interested in engineering and using tools which can capture the complex interactions of the immune system more holistically. Understanding the immune system at a systems level will be even more critical as we try to engineer it for therapy. This will enable unique innovations in therapies overcoming several challenges of current immunotherapies: (1) ineffective for a large subset of patients, (2) non-specific, causing immunocompromised or autoimmune states, (3) costly, (4) not well modeled or predicted by in vitro tests and animal models, and (5) treat symptoms rather than cure disease.
Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction.
European journal of immunology
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, we streamlined and simplified the multiplexed imaging method CO-Detection by indEXing (CODEX) by validating 58 unique oligonucleotide barcodes that can be conjugated to antibodies. We showed that barcoded antibodies retained their specificity for staining cognate targets in human tissue. Antibodies were visualized one at a time by adding a fluorescently labeled oligonucleotide complementary to oligonucleotide barcode, imaging, stripping, and repeating this cycle. With this we developed a panel of 46 antibodies that was used to stain five human lymphoid tissues: three tonsils, a spleen, and a lymph node. To analyze the data produced, an image processing and analysis pipeline was developed that enabled single-cell analysis on the data, including unsupervised clustering that revealed 31 cell types across all tissues. We compared cell-type compositions within and directly surrounding follicles from the different lymphoid organs and evaluated cell-cell density correlations. This sequential oligonucleotide exchange technique enables a facile imaging of tissues that leverages pre-existing imaging infrastructure to decrease the barriers to broad use of multiplexed imaging. This article is protected by copyright. All rights reserved.
View details for DOI 10.1002/eji.202048891
View details for PubMedID 33548142
Adaptive Nanoparticle Platforms for High Throughput Expansion and Detection of Antigen-Specific T cells
2020; 20 (9): 6289–98
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 translatability of magnetic nanoparticle-based artificial antigen presenting cells (aAPCs) to enrich and expand (E+E) murine or human antigen-specific T cells. We streamlined enrichment, expansion, and aAPC production processes by enriching CD8+ T cells directly from unpurified immune cells, increasing parallel processing capacity of aAPCs in a 96-well plate format, and designing an adaptive aAPC that enables multiplexed aAPC construction for E+E and detection. We applied these adaptive platforms to process and detect CD8+ T cells specific for rare cancer neoantigens, commensal bacterial cross-reactive epitopes, and human viral and melanoma antigens. These innovations dramatically increase the multiplexing ability and decrease the barrier to adopt for investigating antigen-specific T cell responses.
View details for DOI 10.1021/acs.nanolett.0c01511
View details for Web of Science ID 000571442000008
View details for PubMedID 32594746
- Engineering an Artificial T-Cell Stimulating Matrix for Immunotherapy ADVANCED MATERIALS 2019; 31 (23)
Efficient magnetic enrichment of antigen-specific T cells by engineering particle properties
2018; 187: 105–16
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 particle design for positive isolation is necessary. Antigen-specific immune cells have low frequencies, which has made studying, identifying, and utilizing these cells for therapy a challenge. Here we demonstrate the importance of magnetic particle design based on the biology of T cells. We create magnetic particles which recognize rare antigen-specific T cells and quantitatively investigate important particle properties including size, concentration, ligand density, and ligand choice in enriching these rare cells. We observe competing optima among particle parameters, with 300 nm particles functionalized with a high density of antigen-specific ligand achieving the highest enrichment and recovery of target cells. In enriching and then activating an endogenous response, 300 nm aAPCs generate nearly 65% antigen-specific T cells with at least 450-fold expansion from endogenous precursors and a 5-fold increase in numbers of antigen-specific cells after only seven days. This systematic study of particle properties in magnetic enrichment provides a case study for the engineering design principles of particles for the isolation of rare cells through biological ligands.
View details for PubMedID 30312851
View details for PubMedCentralID PMC6284398
Biologically Inspired Design of Nanoparticle Artificial Antigen-Presenting Cells for Immunomodulation
2017; 17 (11): 7045–54
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 artificial antigen-presenting cells (aAPCs) for use in immunotherapy. While much has been learned about mimicking antigen presenting cell biology, as we decrease the size of aAPCs to the nanometer scale, we need to extend biomimetic design to include considerations of T cell biology-including T-cell receptor (TCR) organization. Here we describe the first quantitative analysis of particle size effect on aAPCs with both Signals 1 and 2 based on T cell biology. We show that aAPCs, larger than 300 nm, activate T cells more efficiently than smaller aAPCs, 50 nm. The 50 nm aAPCs require saturating doses or require artificial magnetic clustering to activate T cells. Increasing ligand density alone on the 50 nm aAPCs did not increase their ability to stimulate CD8+ T cells, confirming the size-dependent phenomenon. These data support the need for multireceptor ligation and activation of T-cell receptor (TCR) nanoclusters of similar sizes to 300 nm aAPCs. Quantitative analysis and modeling of a nanoparticle system provides insight into engineering constraints of aAPCs for T cell immunotherapy applications and offers a case study for other cell-modulating particles.
View details for PubMedID 28994285
Application of machine learning in understanding atherosclerosis: Emerging insights.
2021; 5 (1): 011505
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 the development of several disease processes including atherosclerosis. We have significantly advanced our understanding of bioprocesses in atherosclerosis, and in doing so, we are beginning to appreciate the complexities, intricacies, and heterogeneity atherosclerosi. We are also now better equipped to acquire, store, and process the vast amount of biological data needed to shed light on the biological circuitry involved. Such data can be analyzed within machine learning frameworks to better tease out such complex relationships. Indeed, there has been an increasing number of studies applying machine learning methods for patient risk stratification based on comorbidities, multi-modality image processing, and biomarker discovery pertaining to atherosclerotic plaque formation. Here, we focus on current applications of machine learning to provide insight into atherosclerotic plaque formation and better understand atherosclerotic plaque progression in patients with cardiovascular disease.
View details for DOI 10.1063/5.0028986
View details for PubMedID 33644628
Improving Biomedical Engineering Undergraduate Learning Through Use of Online Graduate Engineering Courses During the COVID-19 Pandemic.
Biomedical engineering education
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 were designed using published methodologies and held to a high level of rigor of a Masters-level curriculum. Adapting pre-existing online course material enabled us to more rapidly adapt to the COVID-19 shutdown of in-person education. We adapted content to meet the majority of lab-based learning objectives rather than generating self-recorded lecture material and allowing us to focus faculty time on addressing student needs. Here we discuss benefits, challenges, and methods for replicating these courses, and lessons to be applied in future offerings from this experience.
View details for DOI 10.1007/s43683-020-00041-w
View details for PubMedID 33554220
Biodegradable Cationic Polymer Blends for Fabrication of Enhanced Artificial Antigen Presenting Cells to Treat Melanoma.
ACS applied materials & interfaces
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 precisely engineered to exhibit defined characteristics including biodegradability, physical size, and tuned surface presentation of immunomodulatory signals. In particular, modulating the interface between the biomaterial surface and the target biological cell is key to enabling biological functions. Synthetic artificial antigen presenting cells (aAPCs) are promising as a cancer immunotherapy but are limited in clinical translation by the requirement of ex vivo cell manipulation and adoptive transfer of antigen-specific CD8+ T cells. To move toward acellular aAPC technology for in vivo use, we combine poly(lactic-co-glycolic acid) (PLGA) and cationic poly(beta-amino-ester) (PBAE) to form a biodegradable blend based on the hypothesis that therapeutic aAPCs fabricated from a cationic blend may have improved functions. PLGA/PBAE aAPCs demonstrate enhanced surface interactions with antigen-specific CD8+ T cells that increase T cell activation and expansion ex vivo, associated with significantly increased conjugation efficiency of T cell stimulatory signals to the aAPCs. Critically, these PLGA/PBAE aAPCs also expand antigen-specific cytotoxic CD8+ T cells in vivo without the need of adoptive transfer. Treatment with PLGA/PBAE aAPCs in combination with checkpoint therapy decreases tumor growth and extends survival in a B16-F10 melanoma mouse model. These results demonstrate the potential of PLGA/PBAE aAPCs as a biocompatible, directly injectable acellular therapy for cancer immunotherapy.
View details for DOI 10.1021/acsami.0c19955
View details for PubMedID 33573372
Commensal bacteria stimulate antitumor responses via T cell cross-reactivity.
2020; 5 (8)
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 in the commensal bacterium Bifidobacterium breve (B. breve), cross-react with a model neoantigen, SIYRYYGL (SIY). Mice lacking B. breve had decreased SVY-reactive T cells compared with B. breve-colonized mice, and the T cell response was transferable by SVY immunization or by cohousing mice without Bifidobacterium with ones colonized with Bifidobacterium. Tumors expressing the model SIY neoantigen also grew faster in mice lacking B. breve compared with Bifidobacterium-colonized animals. B. breve colonization also shaped the SVY-reactive TCR repertoire. Finally, SVY-specific T cells recognized SIY-expressing melanomas in vivo and led to decreased tumor growth and extended survival. Our work demonstrates that commensal bacteria can stimulate antitumor immune responses via cross-reactivity and how bacterial antigens affect the T cell landscape.
View details for DOI 10.1172/jci.insight.135597
View details for PubMedID 32324171
- Collagen fiber structure guides 3D motility of cytotoxic T lymphocytes MATRIX BIOLOGY 2020; 85-86: 147–59
Collagen fiber structure guides 3D motility of cytotoxic T lymphocytes.
Matrix biology : journal of the International Society for Matrix Biology
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 remodeling. Three dimensional studies of human lymphocytes in such environments are lacking. We hypothesized that aligned collagenous environment modulates CD8+ T cells motility. We encapsulated activated CD8+ T cells in collagen hydrogels of distinct fiber alignment, a characteristic of tumor microenvironments. We found that human CD8+ T cells move faster and more persistently in aligned collagen fibers compared with nonaligned collagen fibers. Moreover, CD8+ T cells move along the axis of collagen alignment. We showed that myosin light chain kinase (MLCK) inhibition could nullify the effect of aligned collagen on CD8+ T cell motility patterns by decreasing T cell turning in unaligned collagen fiber gels. Finally, as an example of a tertiary lymphoid site, we found that xenograft prostate tumors exhibit highly aligned collagen fibers. We observed CD8+ T cells alongside aligned collagen fibers, and found that they are mostly concentrated in the periphery of tumors. Overall, using an in vitro controlled hydrogel system, we show that collagen fiber organization modulates CD8+ T cells movement via MLCK activation thus providing basis for future studies into relevant therapeutics.
View details for PubMedID 30776427
Enrich and Expand Rare Antigen-specific T Cells with Magnetic Nanoparticles
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
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-specific responses affect disease state such as autoimmunity, D) demystify heterogeneous responses for antigen-specific T cells, or E) utilize antigen-specific cells for therapy. The tool is based on a magnetic particle that we conjugate antigen-specific and T cell co-stimulatory signals, and that we term as artificial antigen presenting cells (aAPCs). Consequently, since the technology is simple to produce, it can easily be adopted by other laboratories; thus, our purpose here is to describe in detail the fabrication and subsequent use of the aAPCs. We explain how to attach antigen-specific and co-stimulatory signals to the aAPCs, how to utilize them to enrich for antigen-specific T cells, and how to expand antigen-specific T cells. Furthermore, we will highlight engineering design considerations based on experimental and biological information of our experience with characterizing antigen-specific T cells.
View details for PubMedID 30507913
Separating T Cell Targeting Components onto Magnetically Clustered Nanoparticles Boosts Activation
2018; 18 (3): 1916–24
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 cell functionality for applications such as adoptive cell therapy (ACT), but the large diversity in these molecules complicates these studies. Here, we develop and validate a reductionist T cell activation platform that enables streamlined customization of stimulatory conditions. This platform is useful for the optimization of ACT protocols as well as the more general study of immune T cell activation. Rather than decorating particles with both signal 1 antigen and signal 2 costimulus, we use distinct, monospecific, paramagnetic nanoparticles, which are then clustered on the cell surface by a magnetic field. This allows for rapid synthesis and characterization of a small number of single-signal nanoparticles which can be systematically combined to explore and optimize T cell activation. By increasing cognate T cell enrichment and incorporating additional costimulatory molecules using this platform, we find significantly higher frequencies and numbers of cognate T cells stimulated from an endogenous population. The magnetic field-induced association of separate particles thus provides a tool for optimizing T cell activation for adoptive immunotherapy and other immunological studies.
View details for DOI 10.1021/acs.nanolett.7b05284
View details for Web of Science ID 000427910600050
View details for PubMedID 29488768
Engineering Platforms for T Cell Modulation
BIOLOGY OF T CELLS, PT A
2018; 341: 277–362
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 toxicities, limited efficacy, biological variability, and high costs. As T cell therapeutics continue to develop, the application of engineering concepts to control their delivery and presentation will be critical for their success. Here, we outline the engineer's toolbox and contextualize it with the biology of T cells. We focus on the design principles of T cell modulation platforms regarding size, shape, material, and ligand choice. Furthermore, we review how application of these design principles has already impacted T cell immunotherapies and our understanding of T cell biology. Recent, salient examples from protein engineering, synthetic particles, cellular and genetic engineering, and scaffolds and surfaces are provided to reinforce the importance of design considerations. Our aim is to provide a guide for immunologists, engineers, clinicians, and the pharmaceutical sector for the design of T cell-targeting platforms.
View details for PubMedID 30262034
Biomimetic Artificial Antigen Presenting Cells Synergize with Anti-PD1 in the Treatment of Melanoma
CELL PRESS. 2017: 269–70
View details for Web of Science ID 000401083600580
Biomimetic biodegradable artificial antigen presenting with PD-1 blockade to treat melanoma cells synergize
2017; 118: 16–26
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 and size, and controlled release of immune-modulators. As these new platforms enter the playing field, it is imperative to understand their interaction with existing immunotherapies since single-targeted approaches have limited efficacy. Here, we investigate the synergy between a PLGA-based artificial antigen presenting cell (aAPC) and a checkpoint blockade molecule, anti-PD1 monoclonal antibody (mAb). The combination of antigen-specific aAPC-based activation and anti-PD-1 mAb checkpoint blockade induced the greatest IFN-γ secretion by CD8+ T cells in vitro. Combination treatment also acted synergistically in an in vivo murine melanoma model to result in delayed tumor growth and extended survival, while either treatment alone had no effect. This was shown mechanistically to be due to decreased PD-1 expression and increased antigen-specific proliferation of CD8+ T cells within the tumor microenvironment and spleen. Thus, biomaterial-based therapy can synergize with other immunotherapies and motivates the translation of biomimetic combinatorial treatments.
View details for DOI 10.1016/j.biomaterials.2016.11.038
View details for Web of Science ID 000393254700002
View details for PubMedID 27940380
View details for PubMedCentralID PMC5207804
Control of polymeric nanoparticle size to improve therapeutic delivery
JOURNAL OF CONTROLLED RELEASE
2015; 219: 536–47
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 engineer new NPs, impart unique functionalities, identify novel utilities, and improve the clinical translation of NP formulations. One key design parameter is NP size. New methods have been developed to produce NPs with increased control of NP size between 10 and 200nm, a size range most relevant to physical and biochemical targeting through both intravascular and site-specific deliveries. Three notable techniques best suited for generating polymeric NPs with narrow size distributions are highlighted in this review: self-assembly, microfluidics-based preparation, and flash nanoprecipitation. Furthermore, the effect of NP size on the biological fate and transport properties at the molecular scale (protein-NP interactions) and the tissue and systemic scale (convective and diffusive transport of NPs) are analyzed here. These analyses underscore the importance of NP size control in considering clinical translation and assessment of therapeutic outcomes of NP delivery vehicles.
View details for PubMedID 26450667
View details for PubMedCentralID PMC4656075
Prevention and Removal of Lipid Deposits by Lens Care Solutions and Rubbing
OPTOMETRY AND VISION SCIENCE
2014; 91 (12): 1430–39
Despite 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 on the removal. Therefore, we used an in vitro soaking and rubbing model to compare the effectiveness of borate buffered saline (BBS) and two commercial MPSs, PureMoist and Biotrue, in preventing sorption of representative polar and nonpolar lipids.Radiolabeled cholesterol (CH) and dipalmitoylphosphatidylcholine (DPPC) were sorbed on two SiHy lenses (senofilcon A and balafilcon A) from an artificial tear fluid. Deposition and removal were evaluated by quantitative solvent extraction and scintillation counting.The efficiencies of the MPSs in reducing lipid deposition are somewhat dependent on lens material. Both DPPC and CH sorption on senofilcon A are greater when lenses are preconditioned in BBS compared with preconditioning in either MPS (p < 0.05). However, neither MPS affects lipid sorption on balafilcon A lenses (p > 0.05). As for removal of presorbed lipids, neither PureMoist, Biotrue, nor BBS removed CH in the absence of rubbing. When a simulated rubbing protocol was used, minimal but detectible CH was removed (p < 0.05) from senofilcon A and balafilcon A lenses (likely only from the lens surface). These commercial solutions were not substantially better than BBS in removing DPPC, with or without rubbing (p > 0.05).These data suggest that MPSs do not appreciably alter lipid sorption. Rubbing lenses removes a small amount of sorbed lipids. Yet, we recommend that MPSs be used as they may disinfect SiHy lenses and may clean their surfaces of large particles.
View details for PubMedID 25325760
The role of multi-purpose solutions in prevention and removal of lipid depositions on contact lenses
CONTACT LENS & ANTERIOR EYE
2014; 37 (6): 405–14
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 buffered saline and two commercial multi-purpose lens-care solutions (MPSs) on reducing the lipid (DPPC and CH) sorption and increasing the lipid removal were examined. The results showed that silicone hydrogel (SiHy) lenses accumulated the most lipids, sorbing over an order of magnitude more than polymacon, a conventional hydrogel lens. Pre-soaking the SiHy lenses for 16h in MPSs reduced the DPPC sorption by up to 13% and the CH sorption by up to 11%, compared to controls that were not pre-soaked. However neither these reductions nor those on polymacon were statistically significant (p>0.05). In sorption experiments without presoaking, subsequent exposure to the MPSs removed some DPPC from the lenses (0-3.1% for SiHy lenses and 14-55% for polymacon), but CH removal was 0.0-0.8% for SiHy lenses and 0.6-28% for polymacon lenses. Some of these removals were statistically significant (p<0.05).
View details for PubMedID 25081521
Metallization of Branched DNA Origami for Nanoelectronic Circuit Fabrication
2011; 5 (3): 2240-2247
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, makes possible the increased complexity and flexibility needed for both the design and assembly of useful circuit templates. In addition, selective metallization of the DNA template is essential for circuit fabrication. Metallization of DNA origami presents several challenges over and above those associated with the metallization of other DNA templates such as λ-DNA. These challenges include (1) the stability of the origami in the processes used for metallization, (2) the enhanced selectivity required to metallize small origami structures, (3) the increased difficulty of adhering small structures to the surface so that they will not be removed when subject to multiple metallization steps, and (4) the influence of excess staple strands present with the origami. This paper describes our efforts to understand and address these challenges. Specifically, the influence of experimental conditions on template stability and on the selectivity of metal deposition was investigated for small DNA origami templates. These templates were seeded with Ag and then plated with Au via an electroless deposition process. Both staple strand concentration and the concentration of ions in solution were found to have a significant impact. Selective continuous metal deposition was achieved, with an average metallized height as small as 32 nm. The shape of branched origami was also retained after metallization. These results represent important progress toward the realization of DNA-templated nanocircuits.
View details for DOI 10.1021/nn1035075
View details for Web of Science ID 000288570600083
View details for PubMedID 21323323