Topic Summaries and Readings

Unit 1: Vaccine Engineering: Vaccines are one of the most successful biomedical advances of the modern age. Current engineering approaches are working towards developing new, synthetic vaccine formulations that are safer and more effective than classical preparations. These approaches are especially critical in the development of therapeutic vaccines to prevent and treat cancer or more complex pathogens such as HIV and for vaccines aimed at fighting autoimmune diseases.
1 Introduction No Readings
2 Immunogenic particle vaccines

Moon, J. J., H. Suh, et al. “Interbilayer-Crosslinked Multilamellar Vesicles as Synthetic Vaccines for Potent Humoral and Cellular Immune Responses.” Nature Materials 10, no. 3 (2011): 243–51.

Immune responses are generated most efficiently to live pathogens in the most effective vaccine preparations. In this manuscript, Moon et al. introduce a novel lipid nanoparticle-based platform with unique design properties that enable construction of vaccines that stably incorporate multiple immunogenic components from live pathogens.

Sexton, A., P. G. Whitney, et al. “A Protective Vaccine Delivery System for in Vivo T Cell Stimulation using Nanoengineered Polymer Hydrogel Capsules.” ACS Nano 3, no. 11 (2009): 3391–400.

Hydrogels are a specific class of biomaterials consisting of three-dimensional polymer networks filled with water (90–98%). Sexton et al. creatively utilized an approach using a highly tunable (i.e. simple control over crosslinking density to dictate release of payload) polymer hydrogel capsule (more recently being utilized by engineers for slow-release delivery of various growth factors and drugs for tissue regeneration and blood vessel formation in wounds) to efficiently deliver antigens to immune cells.

3 Tolerogenic particle vaccines

Getts, D. R., A. J. Martin, et al. “Microparticles Bearing Encephalitogenic Peptides Induce T-cell Tolerance and Ameliorate Experimental Autoimmune Encephalomyelitis.” Nature Biotechnology 30, no. 12 (2012): 1217–24.

In this manuscript, Getts et al. show that both degradable and non-degradable microparticles coupled to encephalitogenic myelin epitopes (i.e. regions of myelin proteins which produce an encephalitogenic mmune response) prevent and treat the clinical symptoms of experimental autoimmune encephalomyelitis (EAE), a mouse model of multiple sclerosis. Antigen-decorated microparticles are specifically able to induce long-term T cell tolerance.

Yeste, A., M. Nadeau. “Nanoparticle-Mediated Codelivery of Myelin Antigen and A Tolerogenic Small Molecule Suppresses Experimental Autoimmune Encephalomyelitis.” Proceedings of the National Academy of Sciences 109, no. 28 (2012): 11270–5.

Regulatory T cells (Tregs) prevent the immune system from attacking natural proteins in our bodies maintaining tolerance towards healthy cells and tissues. Deficits in Tregs are a characteristic of many autoimmune diseases. While there are known factors that can induce activation and production of Tregs, independent and soluble delivery of these factors is ineffective. Yeste et al. describe a gold nanoparticle-based system that allows codelivery of multiple factors that synergize to induce antigen-specific Tregs.

4 Novel vaccine platforms

Ali, O. A., N. Huebsch, et al. “Infection-Mimicking Materials to Program Dendritic Cells in Situ.” Nature Materials 8 (2009): 151–8.

Provenge is the first FDA-approved, cell-based cancer immunotherapy, taking a patient’s immune cells, reprogramming them in vitro to attack prostate tumors and then re-infusing them. This therapy is appealing, but has numerous disadvantages. Ali et al. have developed a novel approach to such therapy, taking cues from tissue engineering and developing polymer-based implants that achieve cell reprogramming in situ. These implants are now entering human clinical trials.

Tezel, A., S. Paliwal, et al. “Low-Frequency Ultrasound as a Transcutaneous Immunization Adjuvant.” Vaccine 23, no. 29 (2005): 3800–7.

Traditional vaccine administration has several potential drawbacks, including the requirement for needle-based delivery (complicated by the high prevalence of needle-phobia and potential for non-sterile administration) and the inclusion of potentially toxic immunostimulatory agents. In this study by Tezel et al., the authors develop a transcutaneous immunization method based on low-frequency ultrasound to provide a physical immunostimulatory signal, to painlessly disrupt the skin barrier without needles and to deliver antigens through passive diffusion.

5 Field trip to Vedantra Pharmaceuticals No Readings

Unit 2: Engineering Immunotherapies: Immunotherapies are a broad class of treatments that can be defined as any strategy that utilizes or targets the immune system to treat disease. Vaccines based on particles or novel delivery methods, as discussed in Unit 1, represent only a fraction of the spectrum of therapies being developed. In this unit, we will explore how engineering approaches have been more broadly applied to develop novel techniques as well as methods that synergize with existing approaches to advance the field on many fronts. Sessions will cover the use of tools from materials science and genetic engineering to enhance cellular immune functions.
6 Materials-based immunotherapies

Stephan, M. T., J. J. Moon, et al. “Therapeutic Cell Engineering with Surface-Conjugated Synthetic Nanoparticles.” Nature Medicine 16, no. 9 (2010): 1035–41.

Systemic injection of tumor-targeting T cells (known as adoptive transfer) is an attractive immunotherapy approach, particularly for aggressive solid tumors that are resistant to traditional therapies. However, these therapies encounter many barriers at tumor sites that suppress cellular functions; drugs that can support these cells are often toxic when given systemically. Stephan et al. utilized a simple, robust strategy for functionalizing the surface of tumor-targeting T cells to enhance their performance and persistence in vivo in a cell-specific manner.

Singh, A., H. Qin, et al. “An Injectable Synthetic Immune-Priming Center Mediates Efficient T-cell Class Switching and T-helper 1 Hesponse Against B Cell Lymphoma.” Journal of Controlled Release 155, no. 2 (2011): 184–92.

Singh et al. develop a multi-faceted materials construct approach incorporating both a matrix and drug particles to program the functions of recruited immature immune cells during immunotherapy. Protection against a subsequent tumor challenge in mice is also demonstrated.

7 Genetic engineering approaches

Carpenito, C., M. C. Milone, et al. “Control of Large, Established Tumor Xenografts with Genetically Retargeted Human T cells Containing CD28 and CD137 Domains.” Proceedings of the National Academy of Sciences 106, no. 9 (2009): 3360–5.

In this landmark study, Carpenito et al. designed a novel type of receptor composed of components from adaptive immune cells (B and T cells). They developed and utilized a highly sensitive and specific chimeric receptor based on an antibody-like domain targeting tumor cell proteins and intracellular domains from receptors used to support the functions of T cells. These re-engineered anti-cancer T cells proved robust and self-sustained, with enhanced tumor-killing abilities. This strategy is now entering clinical trials in an academic/industry collaboration between UPenn and Novartis.

Moulin, V., M. E. Morgan, et al. “Targeting Dendritic Cells with Antigen via Dendritic Cell-Associated Promoters.” Cancer Gene Therapy 19 (2012): 303–11.

The induction of tumor-specific immune responses is largely dependent on the ability of dendritic cells (DCs, antigen-presenting immune cells) to present tumor-associated antigens to T lymphocytes. To enhance the specificity of displayed antigen, Moulin et al. utilized dendritic cell-associated promoters to restrict expression of specific genes incorporated within the vaccine to dendritic cells.

8 Cell-based vaccines for immunomodulation

Dranoff, G., E. Jaffee, et al. “Vaccination with Irradiated Tumor Cells Engineered to Secrete Murine Granulocyte-Macrophage Colony-Stimulating Factor Stimulates Potent, Specific, and Long-Lasting Anti-Tumor Immunity.” Proceedings of the National Academy of Sciences 90, no. 8 (1993): 3539–43.

Irradiated autologous (e.g., self-derived) tumor cells provide a safer alternative to live tumor cells as cell-based immunomodulators. In this early example, Dranoff et al. improve upon the mild immune responses elicited by irradiated tumor cells alone by expressing the cytokine GM-CSF. This approach generates effective, systemic anti-tumor immunity from engineered, irradiated tumor cells that is equivalent to previous responses attained using live tumor cells.

Kim, Y. S., Y. J. Kim, et al. “CD40-Targeted Recombinant Adenovirus Significantly Enhances the Efficacy of Antitumor Vaccines Based on Dendritic Cells and B Cells.” Human Gene Therapy 21, no. 12 (2010): 1697–706.

Dendritic cells have been widely investigated as anti-tumor vaccines. Until now, short-comings using this approach have resulted from the suboptimal conditions for producing immunostimulatory dendritic cells. Dendritic cells and B cells lack surface expression of the viral receptor for the common viral vector adenovirus, limiting its use as a gene transfer system. In this study, Kim et al. address this limitation by developing a fusion CD40L-adenovirus to target CD40 on dendritic cells and B cells. This approach significantly enhances adenoviral infection of these cells, and results in increased expression of the viral-encoded antigen.

9 HIV specific immunotherapies

Perez, E. E., J. Wang, et al. “Establishment of HIV-1 Resistance in CD4+ T Cells by Genome Editing Using Zinc-Finger Nucleases.” Nature Biotechnology 26, no. 7 (2008): 808–16.

HIV transmission and the infectivity of target immune cells rely on the expression of viral receptors. Studies in the field have discovered a subset of the population is resistant to HIV infection due to a specific genetic mutation in the co-receptor, chemokine receptor CCR5. In this study, Perez et al. capitalize on this knowledge by using engineered enzymes to introduce a genetic disruption in CCR5 that functions similar to the naturally-occurring delta32 mutation, rendering the engineered T cells resistant to HIV infection.

Clark, M. R., H. A. Aliyan, et al. “Enzymatic Triggered Release of an HIV-1 Entry Inhibitor from Prostate Specific Antigen Degradable Microparticles.” International Journal of Pharmaceutics 413, no. 1–2 (2011): 10–8.

HIV transmission through heterosexual contact often occurs nonconsensually, prompting the development of microbicides and other prophylactic approaches that can be used by women. In this paper by Clark et al., the authors describe a controlled drug delivery system that utilizes the physiology of the transmission site and event, namely vaginal exposure to infectious semen, by incorporating HIV-1 inhibitors into particles that are selectively degraded when exposed to semen.

Unit 3: Systems-Level Approaches to the Immune System: Engineering has also introduced uniquely quantitative and distinct perspectives concerning the functions of the immune system. Computational and analytical approaches often used in systems control and fields such as chemical engineering are now being brought to bear on the function of the immune system to define its behavior at the systems level.
10 Immune signatures and models

Querec, T. D., R. S. Akondy, et al. “Systems Biology Approach Predicts Immunogenicity of the Yellow Fever Vaccine in Humans.” Nature Immunology 10, no. 1 (2008): 116–25.

Computational modeling holds the potential to guide development of new vaccines and predict patient responses to existing ones by profiling aspects of the immune response. In this study, Querec et al. focus on yellow fever vaccine, one of the most effective vaccines ever developed. They provide predictive signatures that correlate with different aspects of a patient’s immune response to the vaccine and identify potential mechanistic explanations for the vaccine’s efficacy, paving the way for improved prognostics and reverse engineering to inform future vaccine designs.

Lau, K. S., V. Cortez-Retamozo, et al. “Multi-Scale In Vivo Systems Analysis Reveals the Influence of Immune Cells on TNF-α-Induced Apoptosis in the Intestinal Epithelium.” PLOS Biology 10, no. 9 (2012): 1–14.

In this elegant study, Lau et al. demonstrate the deconvolution of a complex signaling network of cell death and turnover in the intestinal epithelium using a systems biology approach to dissect the different contributions of various cell subsets and mediators within the microenvironment of the gut. Combined modeling and experimentation revealed the complex dynamics between immune cells, their secreted products, and interactions with epithelial cells mediating apoptotic cell death in homeostasis and disease.

11 Methods and devices

Bendall, S. C., E. F. Simonds, et al. “Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum.” Science 332, no. 6030 (2011): 687–96.

In this impressive study, Bendall et al. apply a novel platform for multiparametric measurement of cell states based on integrating the techniques of flow cytometry and mass spectrometry. The authors 1) reveal the surprisingly heterogeneous response of single-cell signaling within similar cell populations, 2) identify new insights into how various signaling pathways are regulated among different cell types and 3) provide a novel perspective on how different immune cell populations are distinct and related to each other.

Han, Q., N. Bagheri, et al. “Polyfunctional Responses by Human T Cells Result from Sequential Release of Cytokines.” Proceedings of the National Academy of Sciences 109, no. 5 (2012): 1607–12.

Han et al. utilize a novel method in this study to characterize a commonly analyzed response: cytokine secretion. They identify novel temporal regulation and heterogeneity of single-cells within phenotypically similar populations and reveal the temporal nature of single-cell cytokine secretions in response to canonical stimuli. This study provides insight into how population behaviors are significantly more diverse than previously appreciated.

12 Novel mechanisms

Garcia-Cordero, J. L., C. Nembrini, et al. “A High-Throughput Nanoimmunoassay Chip Applied to Large-Scale Vaccine Adjuvant Screening.” Integrative Biology 5, no. 4 (2013): 650–8.

Many innate immune components are being investigated as potential vaccine adjuvants (i.e. substances that can be added to vaccines to boost the body’s immune response to the vaccine). However, all natural pathogens present a combination of signals to the immune system that result in a concerted response. Garcia-Cordero et al. develop a novel, high-throughput functional screening assay to identify synergistic combinations of potential vaccine adjuvants in vitro, and they further show that hese results translate into synergistic effects in vivo. This platform and analysis provide a new method for unbiased screening and identification of novel therapeutic approaches for vaccine development.

Yosef, N., A. K. Shalek, et al. “Dynamic Regulatory Network Controlling TH17 Cell Differentiation.” Nature 496 (2013): 461–8.

T cells are known to have diverse functional fates; among T cells, Th17 cells are particularly interesting in their rarity in circulation compared to tissue sites and their specific involvement in multiple autoimmune diseases. In this study by Yosef et al., the authors systematically reconstruct the networks driving differentiation and function of the Th17 cell subset in mice using a combination of computational modeling, transcriptional profiling and engineering-based perturbations. The resulting model of differentiation identifies critical mediators that may also serve as drug targets and reconstructs short and long-term temporal mechanisms directing Th17 differentiation.

13 Final student presentations, course retrospective No Readings