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Hutchings CJ, Sato AK. Phage display technology and its impact in the discovery of novel protein-based drugs. Expert Opin Drug Discov 2024; 19:887-915. [PMID: 39074492 DOI: 10.1080/17460441.2024.2367023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/07/2024] [Indexed: 07/31/2024]
Abstract
INTRODUCTION Phage display technology is a well-established versatile in vitro display technology that has been used for over 35 years to identify peptides and antibodies for use as reagents and therapeutics, as well as exploring the diversity of alternative scaffolds as another option to conventional therapeutic antibody discovery. Such successes have been responsible for spawning a range of biotechnology companies, as well as many complementary technologies devised to expedite the drug discovery process and resolve bottlenecks in the discovery workflow. AREAS COVERED In this perspective, the authors summarize the application of phage display for drug discovery and provide examples of protein-based drugs that have either been approved or are being developed in the clinic. The amenability of phage display to generate functional protein molecules to challenging targets and recent developments of strategies and techniques designed to harness the power of sampling diverse repertoires are highlighted. EXPERT OPINION Phage display is now routinely combined with cutting-edge technologies to deep-mine antibody-based repertoires, peptide, or alternative scaffold libraries generating a wealth of data that can be leveraged, e.g. via artificial intelligence, to enable the potential for clinical success in the discovery and development of protein-based therapeutics.
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2
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Kim SM, Heo HR, Kim CS, Shin HH. Genetically engineered bacteriophages as novel nanomaterials: applications beyond antimicrobial agents. Front Bioeng Biotechnol 2024; 12:1319830. [PMID: 38725991 PMCID: PMC11079243 DOI: 10.3389/fbioe.2024.1319830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Abstract
Bacteriophages, also known as phages, are viruses that replicate in bacteria and archaea. Phages were initially discovered as antimicrobial agents, and they have been used as therapeutic agents for bacterial infection in a process known as "phage therapy." Recently, phages have been investigated as functional nanomaterials in a variety of areas, as they can function not only as therapeutic agents but also as biosensors and tissue regenerative materials. Phages are nontoxic to humans, and they possess self-assembled nanostructures and functional properties. Additionally, phages can be easily genetically modified to display specific peptides or to screen for functional peptides via phage display. Here, we demonstrated the application of phage nanomaterials in the context of tissue engineering, sensing, and probing.
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Affiliation(s)
- Seong-Min Kim
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Hye Ryoung Heo
- Department of Chemical and Biochemical Engineering, Dongguk University, Seoul, Republic of Korea
| | - Chang Sup Kim
- Department of Chemical and Biochemical Engineering, Dongguk University, Seoul, Republic of Korea
| | - Hwa Hui Shin
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
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3
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Dogra P, Schiavone C, Wang Z, Ruiz-Ramírez J, Caserta S, Staquicini DI, Markosian C, Wang J, Sostman HD, Pasqualini R, Arap W, Cristini V. A modeling-based approach to optimize COVID-19 vaccine dosing schedules for improved protection. JCI Insight 2023; 8:e169860. [PMID: 37227783 PMCID: PMC10371350 DOI: 10.1172/jci.insight.169860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/23/2023] [Indexed: 05/27/2023] Open
Abstract
While the development of different vaccines slowed the dissemination of SARS-CoV-2, the occurrence of breakthrough infections has continued to fuel the COVID-19 pandemic. To secure at least partial protection in the majority of the population through 1 dose of a COVID-19 vaccine, delayed administration of boosters has been implemented in many countries. However, waning immunity and emergence of new variants of SARS-CoV-2 suggest that such measures may induce breakthrough infections due to intermittent lapses in protection. Optimizing vaccine dosing schedules to ensure prolonged continuity in protection could thus help control the pandemic. We developed a mechanistic model of immune response to vaccines as an in silico tool for dosing schedule optimization. The model was calibrated with clinical data sets of acquired immunity to COVID-19 mRNA vaccines in healthy and immunocompromised participants and showed robust validation by accurately predicting neutralizing antibody kinetics in response to multiple doses of COVID-19 mRNA vaccines. Importantly, by estimating population vulnerability to breakthrough infections, we predicted tailored vaccination dosing schedules to minimize breakthrough infections, especially for immunocompromised individuals. We identified that the optimal vaccination schedules vary from CDC-recommended dosing, suggesting that the model is a valuable tool to optimize vaccine efficacy outcomes during future outbreaks.
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Affiliation(s)
- Prashant Dogra
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
| | - Carmine Schiavone
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
| | - Zhihui Wang
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas, USA
| | - Javier Ruiz-Ramírez
- Centro de Ciencias de la Salud, Universidad Autónoma de Aguascalientes, Aguascalientes, Mexico
| | - Sergio Caserta
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Daniela I. Staquicini
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Christopher Markosian
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Jin Wang
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - H. Dirk Sostman
- Weill Cornell Medicine, New York, New York, USA
- Houston Methodist Research Institute, Houston, Texas, USA
- Houston Methodist Academic Institute, Houston, Texas, USA
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, USA
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Vittorio Cristini
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, Texas, USA
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Imaging Physics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Physiology, Biophysics, and Systems Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
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4
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Sarkar S, Mishra A, Periasamy S, Dyett B, Dogra P, Ball AS, Yeo LY, White JF, Wang Z, Cristini V, Jagannath C, Khan A, Soni SK, Drummond CJ, Conn CE. Prospective Subunit Nanovaccine against Mycobacterium tuberculosis Infection─Cubosome Lipid Nanocarriers of Cord Factor, Trehalose 6,6' Dimycolate. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37262346 DOI: 10.1021/acsami.3c04063] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
An improved vaccine is urgently needed to replace the now more than 100-year-old Bacillus Calmette-Guérin (BCG) vaccine against tuberculosis (TB) disease, which represents a significant burden on global public health. Mycolic acid, or cord factor trehalose 6,6' dimycolate (TDM), a lipid component abundant in the cell wall of the pathogen Mycobacterium tuberculosis (MTB), has been shown to have strong immunostimulatory activity but remains underexplored due to its high toxicity and poor solubility. Herein, we employed a novel strategy to encapsulate TDM within a cubosome lipid nanocarrier as a potential subunit nanovaccine candidate against TB. This strategy not only increased the solubility and reduced the toxicity of TDM but also elicited a protective immune response to control MTB growth in macrophages. Both pre-treatment and concurrent treatment of the TDM encapsulated in lipid monoolein (MO) cubosomes (MO-TDM) (1 mol %) induced a strong proinflammatory cytokine response in MTB-infected macrophages, due to epigenetic changes at the promoters of tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6) in comparison to the untreated control. Furthermore, treatment with MO-TDM (1 mol %) cubosomes significantly improved antigen processing and presentation capabilities of MTB-infected macrophages to CD4 T cells. The ability of MO-TDM (1 mol %) cubosomes to induce a robust innate and adaptive response in vitro was further supported by a mathematical modeling study predicting the vaccine efficacy in vivo. Overall, these results indicate a strong immunostimulatory effect of TDM when delivered through the lipid nanocarrier, suggesting its potential as a novel TB vaccine.
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Affiliation(s)
- Sampa Sarkar
- School of Science, STEM College, RMIT University, Melbourne 3001, Victoria, Australia
| | - Abhishek Mishra
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston, Texas 77030, United States
| | - Selvakannan Periasamy
- School of Science, STEM College, RMIT University, Melbourne 3001, Victoria, Australia
| | - Brendan Dyett
- School of Science, STEM College, RMIT University, Melbourne 3001, Victoria, Australia
| | - Prashant Dogra
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, Texas 77030, United States
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10021, United States
| | - Andrew S Ball
- School of Science, STEM College, RMIT University, Melbourne 3001, Victoria, Australia
| | - Leslie Y Yeo
- School of Engineering, STEM College, RMIT University, Melbourne 3001, Victoria, Australia
| | - Jacinta F White
- The Commonwealth Scientific and Industrial Research Organisation, Clayton 3169, Victoria, Australia
| | - Zhihui Wang
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, Texas 77030, United States
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10021, United States
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas 77030, United States
| | - Vittorio Cristini
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, Texas 77030, United States
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas 77030, United States
- Department of Imaging Physics, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, United States
- Physiology, Biophysics, and Systems Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York 10021, United States
| | - Chinnaswamy Jagannath
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston, Texas 77030, United States
| | - Arshad Khan
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston, Texas 77030, United States
| | - Sarvesh K Soni
- School of Science, STEM College, RMIT University, Melbourne 3001, Victoria, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Melbourne 3001, Victoria, Australia
| | - Charlotte E Conn
- School of Science, STEM College, RMIT University, Melbourne 3001, Victoria, Australia
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Heslop R, Gao M, Brito Lira A, Sternlieb T, Loock M, Sanghi SR, Cestari I. Genome-Wide Libraries for Protozoan Pathogen Drug Target Screening Using Yeast Surface Display. ACS Infect Dis 2023; 9:1078-1091. [PMID: 37083339 PMCID: PMC10187560 DOI: 10.1021/acsinfecdis.2c00568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 04/22/2023]
Abstract
The lack of genetic tools to manipulate protozoan pathogens has limited the use of genome-wide approaches to identify drug or vaccine targets and understand these organisms' biology. We have developed an efficient method to construct genome-wide libraries for yeast surface display (YSD) and developed a YSD fitness screen (YSD-FS) to identify drug targets. We show the efficacy of our method by generating genome-wide libraries for Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia parasites. Each library has a diversity of ∼105 to 106 clones, representing ∼6- to 30-fold of the parasite's genome. Nanopore sequencing confirmed the libraries' genome coverage with multiple clones for each parasite gene. Western blot and imaging analysis confirmed surface expression of the G. lamblia library proteins in yeast. Using the YSD-FS assay, we identified bonafide interactors of metronidazole, a drug used to treat protozoan and bacterial infections. We also found enrichment in nucleotide-binding domain sequences associated with yeast increased fitness to metronidazole, indicating that this drug might target multiple enzymes containing nucleotide-binding domains. The libraries are valuable biological resources for discovering drug or vaccine targets, ligand receptors, protein-protein interactions, and pathogen-host interactions. The library assembly approach can be applied to other organisms or expression systems, and the YSD-FS assay might help identify new drug targets in protozoan pathogens.
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Affiliation(s)
- Rhiannon Heslop
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
- Faculté
de Pharmacie de Tours, 31, Avenue Monge, 37200 Tours, France
| | - Mengjin Gao
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
| | - Andressa Brito Lira
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
| | - Tamara Sternlieb
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
| | - Mira Loock
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
| | - Sahil Rao Sanghi
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
| | - Igor Cestari
- Institute
of Parasitology, McGill University, Ste Anne de Bellevue, Montreal, QC H9X 3V9, Canada
- Division
of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
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Palma M. Aspects of Phage-Based Vaccines for Protein and Epitope Immunization. Vaccines (Basel) 2023; 11:vaccines11020436. [PMID: 36851313 PMCID: PMC9967953 DOI: 10.3390/vaccines11020436] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Because vaccine development is a difficult process, this study reviews aspects of phages as vaccine delivery vehicles through a literature search. The results demonstrated that because phages have adjuvant properties and are safe for humans and animals, they are an excellent vaccine tool for protein and epitope immunization. The phage genome can easily be manipulated to display antigens or create DNA vaccines. Additionally, they are easy to produce on a large scale, which lowers their manufacturing costs. They are stable under various conditions, which can facilitate their transport and storage. However, no medicine regulatory agency has yet authorized phage-based vaccines despite the considerable preclinical data confirming their benefits. The skeptical perspective of phages should be overcome because humans encounter bacteriophages in their environment all the time without suffering adverse effects. The lack of clinical trials, endotoxin contamination, phage composition, and long-term negative effects are some obstacles preventing the development of phage vaccines. However, their prospects should be promising because phages are safe in clinical trials; they have been authorized as a food additive to avoid food contamination and approved for emergency use in phage therapy against difficult-to-treat antibiotic-resistant bacteria. Therefore, this encourages the use of phages in vaccines.
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Affiliation(s)
- Marco Palma
- Institute for Globally Distributed Open Research and Education (IGDORE), 03181 Torrevieja, Spain;
- Creative Biolabs Inc., Shirley, NY 11967, USA
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7
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Dogra P, Schiavone C, Wang Z, Ruiz-Ramírez J, Caserta S, Staquicini DI, Markosian C, Wang J, Sostman HD, Pasqualini R, Arap W, Cristini V. A modeling-based approach to optimize COVID-19 vaccine dosing schedules for improved protection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2022.09.14.22279959. [PMID: 36415468 PMCID: PMC9681049 DOI: 10.1101/2022.09.14.22279959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
While the development of different vaccines has slowed the dissemination of SARS-CoV-2, the occurrence of breakthrough infections continues to fuel the pandemic. As a strategy to secure at least partial protection, with a single dose of a given COVID-19 vaccine to maximum possible fraction of the population, delayed administration of subsequent doses (or boosters) has been implemented in many countries. However, waning immunity and emergence of new variants of SARS-CoV-2 suggest that such measures may jeopardize the attainment of herd immunity due to intermittent lapses in protection. Optimizing vaccine dosing schedules could thus make the difference between periodic occurrence of breakthrough infections or effective control of the pandemic. To this end, we have developed a mechanistic mathematical model of adaptive immune response to vaccines and demonstrated its applicability to COVID-19 mRNA vaccines as a proof-of-concept for future outbreaks. The model was thoroughly calibrated against multiple clinical datasets involving immune response to SARS-CoV-2 infection and mRNA vaccines in healthy and immunocompromised subjects (cancer patients undergoing therapy); the model showed robust clinical validation by accurately predicting neutralizing antibody kinetics, a correlate of vaccine-induced protection, in response to multiple doses of mRNA vaccines. Importantly, we estimated population vulnerability to breakthrough infections and predicted tailored vaccination dosing schedules to maximize protection and thus minimize breakthrough infections, based on the immune status of a sub-population. We have identified a critical waiting window for cancer patients (or, immunocompromised subjects) to allow recovery of the immune system (particularly CD4+ T-cells) for effective differentiation of B-cells to produce neutralizing antibodies and thus achieve optimal vaccine efficacy against variants of concern, especially between the first and second doses. Also, we have obtained optimized dosing schedules for subsequent doses in healthy and immunocompromised subjects, which vary from the CDC-recommended schedules, to minimize breakthrough infections. The developed modeling tool is based on generalized adaptive immune response to antigens and can thus be leveraged to guide vaccine dosing schedules during future outbreaks.
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Affiliation(s)
- Prashant Dogra
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Carmine Schiavone
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
| | - Zhihui Wang
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Javier Ruiz-Ramírez
- Centro de Ciencias de la Salud, Universidad Autónoma de Aguascalientes, Aguascalientes, Mexico
| | - Sergio Caserta
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Daniela I. Staquicini
- Rutgers Cancer Institute of New Jersey, Newark, NJ, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Christopher Markosian
- Rutgers Cancer Institute of New Jersey, Newark, NJ, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Jin Wang
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston, TX, USA
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - H. Dirk Sostman
- Weill Cornell Medicine, New York, NY, USA
- Houston Methodist Research Institute, Houston, TX, USA
- Houston Methodist Academic Institute, Houston, TX, USA
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, NJ, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, NJ, USA
- Department of Medicine, Division of Hematology/Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Vittorio Cristini
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX, USA
- Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
- Department of Imaging Physics, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
- Physiology, Biophysics, and Systems Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
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8
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Capsule-Based Dry Powder Inhaler Evaluation Using CFD-DEM Simulations and Next Generation Impactor Data. Eur J Pharm Sci 2022; 175:106226. [DOI: 10.1016/j.ejps.2022.106226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/03/2022] [Accepted: 05/23/2022] [Indexed: 11/24/2022]
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Soraci L, Lattanzio F, Soraci G, Gambuzza ME, Pulvirenti C, Cozza A, Corsonello A, Luciani F, Rezza G. COVID-19 Vaccines: Current and Future Perspectives. Vaccines (Basel) 2022; 10:608. [PMID: 35455357 PMCID: PMC9025326 DOI: 10.3390/vaccines10040608] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 12/16/2022] Open
Abstract
Currently available vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are highly effective but not able to keep the coronavirus disease 2019 (COVID-19) pandemic completely under control. Alternative R&D strategies are required to induce a long-lasting immunological response and to reduce adverse events as well as to favor rapid development and large-scale production. Several technological platforms have been used to develop COVID-19 vaccines, including inactivated viruses, recombinant proteins, DNA- and RNA-based vaccines, virus-vectored vaccines, and virus-like particles. In general, mRNA vaccines, protein-based vaccines, and vectored vaccines have shown a high level of protection against COVID-19. However, the mutation-prone nature of the spike (S) protein affects long-lasting vaccine protection and its effectiveness, and vaccinated people can become infected with new variants, also showing high virus levels. In addition, adverse effects may occur, some of them related to the interaction of the S protein with the angiotensin-converting enzyme 2 (ACE-2). Thus, there are some concerns that need to be addressed and challenges regarding logistic problems, such as strict storage at low temperatures for some vaccines. In this review, we discuss the limits of vaccines developed against COVID-19 and possible innovative approaches.
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Affiliation(s)
- Luca Soraci
- Unit of Geriatric Medicine, Italian National Research Center on Aging (IRCCS INRCA), 87100 Cosenza, Italy; (L.S.); (A.C.)
| | - Fabrizia Lattanzio
- Scientific Direction, Italian National Research Center on Aging (IRCCS INRCA), 60121 Ancona, Italy;
| | - Giulia Soraci
- Department of Obstetrics and Gynecology, University of Ferrara, 44121 Ferrara, Italy;
| | - Maria Elsa Gambuzza
- Territorial Office of Messina, Italian Ministry of Health, 98122 Messina, Italy
| | | | - Annalisa Cozza
- Laboratory of Pharmacoepidemiology and Biostatistics, Italian National Research Center on Aging (IRCCS INRCA), 87100 Cosenza, Italy;
| | - Andrea Corsonello
- Unit of Geriatric Medicine, Italian National Research Center on Aging (IRCCS INRCA), 87100 Cosenza, Italy; (L.S.); (A.C.)
- Laboratory of Pharmacoepidemiology and Biostatistics, Italian National Research Center on Aging (IRCCS INRCA), 87100 Cosenza, Italy;
| | - Filippo Luciani
- Infectious Diseases Unit of Annunziata Hospital, 87100 Cosenza, Italy;
| | - Giovanni Rezza
- Health Prevention Directorate, Italian Ministry of Health, 00144 Rome, Italy;
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10
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Xu HM, Xu WM, Zhang L. Current Status of Phage Therapy against Infectious Diseases and Potential Application beyond Infectious Diseases. Int J Clin Pract 2022; 2022:4913146. [PMID: 36263241 PMCID: PMC9550513 DOI: 10.1155/2022/4913146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/19/2022] [Indexed: 12/02/2022] Open
Abstract
Intestinal microbiota plays a key role in regulating the pathogenesis of human disease and maintaining health. Many diseases, mainly induced by bacteria, are on the rise due to the emergence of antibiotic-resistant strains. Intestinal microorganisms include organisms such as bacteria, viruses, and fungi. They play an important role in maintaining human health. Among these microorganisms, phages are the main members of intestinal viromes. In particular, the viral fraction, composed essentially of phages, affects homeostasis by exerting selective pressure on bacterial communities living in the intestinal tract. In recent years, with the widespread use and even abuse of antibacterial drugs, more and more drug-resistant bacteria have been found, and they show a trend of high drug resistance and multidrug resistance. Therefore, it has also become increasingly difficult to treat serious bacterial infections. Phages, a natural antibacterial agent with strong specificity and rapid proliferation, have come back to the field of vision of clinicians and scholars. In this study, the current state of research on intestinal phages was discussed, with an exploration of the impact of phage therapy against infectious diseases, as well as potential application beyond infectious diseases.
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Affiliation(s)
- Hao-Ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Wen-Min Xu
- Department of Endoscopy, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510091, China
| | - Long Zhang
- Department of Endoscopy, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510091, China
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11
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Markosian C, Staquicini DI, Dogra P, Dodero-rojas E, Tang FHF, Smith TL, Contessoto VG, Libutti SK, Wang Z, Cristini V, Whitford PC, Burley SK, Onuchic JN, Pasqualini R, Arap W. Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools.. [PMID: 34676381 PMCID: PMC8529634 DOI: 10.1101/2021.08.30.458222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Targeted bacteriophage (phage) particles are potentially attractive yet inexpensive platforms for immunization. Herein, we describe targeted phage capsid display of an immunogenically relevant epitope of the SARS-CoV-2 Spike protein that is empirically conserved, likely due to the high mutational cost among all variants identified to date. This observation may herald an approach to developing vaccine candidates for broad-spectrum, towards universal, protection against multiple emergent variants of coronavirus that cause COVID-19.
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12
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Staquicini DI, Tang FHF, Markosian C, Yao VJ, Staquicini FI, Dodero-Rojas E, Contessoto VG, Davis D, O'Brien P, Habib N, Smith TL, Bruiners N, Sidman RL, Gennaro ML, Lattime EC, Libutti SK, Whitford PC, Burley SK, Onuchic JN, Arap W, Pasqualini R. Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain. Proc Natl Acad Sci U S A 2021; 118:e2105739118. [PMID: 34234013 PMCID: PMC8325333 DOI: 10.1073/pnas.2105739118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Development of effective vaccines against coronavirus disease 2019 (COVID-19) is a global imperative. Rapid immunization of the entire human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and different vaccine approaches are being pursued. Engineered filamentous bacteriophage (phage) particles have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for large-scale production, and proven safety profile in humans. Herein we report the development and initial evaluation of two targeted phage-based vaccination approaches against SARS-CoV-2: dual ligand peptide-targeted phage and adeno-associated virus/phage (AAVP) particles. For peptide-targeted phage, we performed structure-guided antigen design to select six solvent-exposed epitopes of the SARS-CoV-2 spike (S) protein. One of these epitopes displayed on the major capsid protein pVIII of phage induced a specific and sustained humoral response when injected in mice. These phage were further engineered to simultaneously display the peptide CAKSMGDIVC on the minor capsid protein pIII to enable their transport from the lung epithelium into the systemic circulation. Aerosolization of these "dual-display" phage into the lungs of mice generated a systemic and specific antibody response. In the second approach, targeted AAVP particles were engineered to deliver the entire S protein gene under the control of a constitutive CMV promoter. This induced tissue-specific transgene expression, stimulating a systemic S protein-specific antibody response in mice. With these proof-of-concept preclinical experiments, we show that both targeted phage- and AAVP-based particles serve as robust yet versatile platforms that can promptly yield COVID-19 vaccine prototypes for translational development.
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Affiliation(s)
- Daniela I Staquicini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Fenny H F Tang
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Christopher Markosian
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Virginia J Yao
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Fernanda I Staquicini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | | | - Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, SP 15054, Brazil
| | - Deodate Davis
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Paul O'Brien
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Nazia Habib
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Tracey L Smith
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Natalie Bruiners
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Richard L Sidman
- Department of Neurology, Harvard Medical School, Boston, MA 02115
| | - Maria L Gennaro
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Edmund C Lattime
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Steven K Libutti
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Paul C Whitford
- Department of Physics and Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115
| | - Stephen K Burley
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- RCSB Protein Data Bank, San Diego Supercomputer Center and Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92067
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005;
- Department of Biosciences, Rice University, Houston, TX 77005
- Department of Chemistry, Rice University, Houston, TX 77005
- Department of Physics and Astronomy, Rice University, Houston, TX 77005
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101;
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101;
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
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Dogra P, Koay EJ, Wang Z, Vahidy FS, Ferrari M, Pasqualini R, Arap W, Boom ML, Dirk Sostman H, Cristini V. Is the worst of the COVID-19 global pandemic yet to come? Application of financial mathematics as candidate predictive tools. Transl Psychiatry 2021; 11:299. [PMID: 34016952 PMCID: PMC8134815 DOI: 10.1038/s41398-021-01429-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/21/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
The Elliott Wave principle is a time-honored, oft-used method for predicting variations in the financial markets. It is based on the notion that human emotions drive financial decisions. In the fight against the COVID-19 global pandemic, human emotions are similarly decisive, for instance in that they determine one's willingness to be vaccinated, and/or to follow preventive measures including the personal wearing of masks, the application of social distancing protocols, and frequent handwashing. On this basis, we postulated that the Elliott Wave Principle may similarly be used to predict the future evolution of the COVID-19 pandemic. We demonstrated that this method reproduces the data pattern for various countries and the world (daily new cases). Potential scenarios were then extrapolated, from the best-case corresponding to a rapid, full vaccination of the population, to the utterly disastrous case of slow vaccination, and poor adherence to preventive protocols.
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Affiliation(s)
- Prashant Dogra
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA
| | - Eugene J Koay
- Department of Gastrointestinal Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhihui Wang
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA
| | - Farhaan S Vahidy
- Center for Outcomes Research, Houston Methodist Research Institute, Houston, TX, USA
- Houston Methodist Neurological Institute, Houston Methodist, Houston, TX, USA
| | - Mauro Ferrari
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
- Dompé X-Therapeutics, San Mateo, CA, USA
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, NJ, USA
- Department of Radiation Oncology, Division of Cancer Biology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, NJ, USA
- Department of Medicine, Division of Hematology/Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Marc L Boom
- Department of Medicine, Houston Methodist, Houston, TX, USA
| | - H Dirk Sostman
- Weill Cornell Medicine, New York, NY, USA
- Houston Methodist Research Institute, Houston, TX, USA
- Houston Methodist Academic Institute, Houston, TX, USA
| | - Vittorio Cristini
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA.
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14
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Staquicini DI, Tang FHF, Markosian C, Yao VJ, Staquicini FI, Dodero-Rojas E, Contessoto VG, Davis D, O’Brien P, Habib N, Smith TL, Bruiners N, Sidman RL, Gennaro ML, Lattime EC, Libutti SK, Whitford PC, Burley SK, Onuchic JN, Arap W, Pasqualini R. Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.15.435496. [PMID: 33758865 PMCID: PMC7987025 DOI: 10.1101/2021.03.15.435496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Development of effective vaccines against Coronavirus Disease 2019 (COVID-19) is a global imperative. Rapid immunization of the world human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and many different vaccine approaches are being pursued to meet this task. Engineered filamentous bacteriophage (phage) have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for large-scale production, and proven safety profile in humans. Herein we report the design, development, and initial evaluation of targeted phage-based vaccination approaches against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) by using dual ligand peptide-targeted phage and adeno-associated virus/phage (AAVP) particles. Towards a unique phage- and AAVP-based dual-display candidate approach, we first performed structure-guided antigen design to select six solvent-exposed epitopes of the SARS-CoV-2 spike (S) protein for display on the recombinant major capsid coat protein pVIII. Targeted phage particles carrying one of these epitopes induced a strong and specific humoral response. In an initial experimental approach, when these targeted phage particles were further genetically engineered to simultaneously display a ligand peptide (CAKSMGDIVC) on the minor capsid protein pIII, which enables receptor-mediated transport of phage particles from the lung epithelium into the systemic circulation (termed "dual-display"), they enhanced a systemic and specific spike (S) protein-specific antibody response upon aerosolization into the lungs of mice. In a second line of investigation, we engineered targeted AAVP particles to deliver the entire S protein gene under the control of a constitutive cytomegalovirus (CMV) promoter, which induced tissue-specific transgene expression stimulating a systemic S protein-specific antibody response. As proof-of-concept preclinical experiments, we show that targeted phage- and AAVP-based particles serve as robust yet versatile enabling platforms for ligand-directed immunization and promptly yield COVID-19 vaccine prototypes for further translational development. SIGNIFICANCE The ongoing COVID-19 global pandemic has accounted for over 2.5 million deaths and an unprecedented impact on the health of mankind worldwide. Over the past several months, while a few COVID-19 vaccines have received Emergency Use Authorization and are currently being administered to the entire human population, the demand for prompt global immunization has created enormous logistical challenges--including but not limited to supply, access, and distribution--that justify and reinforce the research for additional strategic alternatives. Phage are viruses that only infect bacteria and have been safely administered to humans as antibiotics for decades. As experimental proof-of-concept, we demonstrated that aerosol pulmonary vaccination with lung-targeted phage particles that display short epitopes of the S protein on the capsid as well as preclinical vaccination with targeted AAVP particles carrying the S protein gene elicit a systemic and specific immune response against SARS-CoV-2 in immunocompetent mice. Given that targeted phage- and AAVP-based viral particles are sturdy yet simple to genetically engineer, cost-effective for rapid large-scale production in clinical grade, and relatively stable at room temperature, such unique attributes might perhaps become additional tools towards COVID-19 vaccine design and development for immediate and future unmet needs.
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Affiliation(s)
- Daniela I. Staquicini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Fenny H. F. Tang
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Christopher Markosian
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Virginia J. Yao
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Fernanda I. Staquicini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | | | - Vinícius G. Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, SP 15054, Brazil. Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Deodate Davis
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Paul O’Brien
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Nazia Habib
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Tracey L. Smith
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Natalie Bruiners
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
| | | | - Maria L. Gennaro
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Edmund C. Lattime
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Steven K. Libutti
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Paul C. Whitford
- Department of Physics and Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115
| | - Stephen K. Burley
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- RCSB Protein Data Bank, San Diego Supercomputer Center and Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92067
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
- Department of Biosciences, Rice University, Houston, TX 77005
- Department of Chemistry, Rice University, Houston, TX 77005
- Department of Physics and Astronomy, Rice University, Houston, TX 77005
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
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