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Han Q, Li Z, Fu Y, Liu H, Guo H, Guan X, Niu M, Zhang C. Analyzing the research landscape: Mapping frontiers and hot spots in anti-cancer research using bibliometric analysis and research network pharmacology. Front Pharmacol 2023; 14:1256188. [PMID: 37745055 PMCID: PMC10512719 DOI: 10.3389/fphar.2023.1256188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction: Network pharmacology has emerged as a forefront and hotspot in anti-cancer. Traditional anti-cancer drugs are limited by the paradigm of "one cancer, one target, one drug," making it difficult to address the challenges of recurrence and drug resistance. However, the main advantage of network pharmacology lies in its approach from the perspective of molecular network relationships, employing a "one arrow, multiple targets" strategy, which provides a novel pathway for developing anti-cancer drugs. This study employed a bibliometric analysis method to examine network pharmacology's application and research progress in cancer treatment from January 2008 to May 2023. This research will contribute to revealing its forefront and hotspots, offering new insights and methodologies for future investigations. Methods: We conducted a literature search on network pharmacology research in anti-cancer (NPART) from January 2008 to May 2023, utilizing scientific databases such as Web of Science Core Collection (WoSCC) and PubMed to retrieve relevant research articles and reviews. Additionally, we employed visualization tools such as Citespace, SCImago Graphica, and VOSviewer to perform bibliometric analysis. Results: This study encompassed 3,018 articles, with 2,210 articles from WoSCC and 808 from PubMed. Firstly, an analysis of the annual national publication trends and citation counts indicated that China and the United States are the primary contributing countries in this field. Secondly, the recent keyword analysis revealed emerging research hotspots in "tumor microenvironment," "anti-cancer drugs," and "traditional Chinese medicine (TCM). " Furthermore, the literature clustering analysis demonstrated that "calycosin," "molecular mechanism," "molecular docking," and "anti-cancer agents" were widely recognized research hotspots and forefront areas in 2023, garnering significant attention and citations in this field. Ultimately, we analyzed the application of NPART and the challenges. Conclusion: This study represents the first comprehensive analysis paper based on bibliometric methods, aiming to investigate the forefront hotspots of network pharmacology in anti-cancer research. The findings of this study will facilitate researchers in swiftly comprehending the current research trends and forefront hotspots in the domain of network pharmacology in cancer research.
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Affiliation(s)
- Qi Han
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Zhongxun Li
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yang Fu
- Department of Cardiology, Shanxi Cardiovascular Hospital, Taiyuan, China
| | - Hongliang Liu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
- Department of Otolaryngology Head and Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, China
- Department of Cell Biology and Genetics, The Basic Medical School of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Huina Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiaoya Guan
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Min Niu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Chunming Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
- Department of Otolaryngology Head and Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, China
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Rosenblum S, Richardson A, Meyer S, Nevo T, Sinai M, Hassin-Baer S. DailyCog: A Real-World Functional Cognitive Mobile Application for Evaluating Mild Cognitive Impairment (MCI) in Parkinson's Disease. SENSORS (BASEL, SWITZERLAND) 2021; 21:1788. [PMID: 33806548 PMCID: PMC7961428 DOI: 10.3390/s21051788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 11/21/2022]
Abstract
Parkinson's disease (PD) is the second most common progressive neurodegenerative disorder affecting patient functioning and quality of life. Aside from the motor symptoms of PD, cognitive impairment may occur at early stages of PD and has a substantial impact on patient emotional and physical health. Detecting these early signs through actual daily functioning while the patient is still functionally independent is challenging. We developed DailyCog-a smartphone application for the detection of mild cognitive impairment. DailyCog includes an environment that simulates daily tasks, such as making a drink and shopping, as well as a self-report questionnaire related to daily events performed at home requiring executive functions and visual-spatial abilities, and psychomotor speed. We present the detailed design of DailyCog and discuss various considerations that influenced the design. We tested DailyCog on patients with mild cognitive impairment in PD. Our case study demonstrates how the markers we used coincide with the cognitive levels of the users. We present the outcome of our usability study that found that most users were able to use our app with ease, and provide details on how various features were used, along with some of the difficulties that were identified.
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Affiliation(s)
- Sara Rosenblum
- The Laboratory of Complex Human Activity and Participation (CHAP), Department of Occupational Therapy, University of Haifa, Haifa 3498838, Israel
| | - Ariella Richardson
- Department of Industrial Engineering, Jerusalem College of Technology, Jerusalem 93721, Israel;
| | - Sonya Meyer
- Department of Occupational Therapy, Ariel University, Ariel 40700, Israel;
| | - Tal Nevo
- Movement Disorders Institute, Sheba Medical Center, Ramat-Gan 5262000, Israel; (T.N.); (S.H.-B.)
| | - Maayan Sinai
- Department of Industrial Engineering, Jerusalem College of Technology, Jerusalem 93721, Israel;
| | - Sharon Hassin-Baer
- Movement Disorders Institute, Sheba Medical Center, Ramat-Gan 5262000, Israel; (T.N.); (S.H.-B.)
- Department of Neurology, Sheba Medical Center, Ramat-Gan 5262000, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
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Abstract
In conditional microbial screening, a limited number of candidate strains are tested at different conditions searching for the optimal operation strategy in production (e.g., temperature and pH shifts, media composition as well as feeding and induction strategies). To achieve this, cultivation volumes of >10 mL and advanced control schemes are required to allow appropriate sampling and analyses. Operations become even more complex when the analytical methods are integrated into the robot facility. Among other multivariate data analysis methods, principal component analysis (PCA) techniques have especially gained popularity in high throughput screening. However, an important issue specific to high throughput bioprocess development is the lack of so-called golden batches that could be used as a basis for multivariate analysis. In this study, we establish and present a program to monitor dynamic parallel cultivations in a high throughput facility. PCA was used for process monitoring and automated fault detection of 24 parallel running experiments using recombinant E. coli cells expressing three different fluorescence proteins as the model organism. This approach allowed for capturing events like stirrer failures and blockage of the aeration system and provided a good signal to noise ratio. The developed application can be easily integrated in existing data- and device-infrastructures, allowing automated and remote monitoring of parallel bioreactor systems.
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Chmelař J, Kotál J, Kovaříková A, Kotsyfakis M. The Use of Tick Salivary Proteins as Novel Therapeutics. Front Physiol 2019; 10:812. [PMID: 31297067 PMCID: PMC6607933 DOI: 10.3389/fphys.2019.00812] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
The last three decades of research into tick salivary components have revealed several proteins with important pharmacological and immunological activities. Two primary interests have driven research into tick salivary secretions: the search for suitable pathogen transmission blocking or “anti-tick” vaccine candidates and the search for novel therapeutics derived from tick salivary components. Intensive basic research in the field of tick salivary gland transcriptomics and proteomics has identified several major protein families that play important roles in tick feeding and overcoming vertebrate anti-tick responses. Moreover, these families contain members with unrealized therapeutic potential. Here we review the major tick salivary protein families exploitable in medical applications such as immunomodulation, inhibition of hemostasis and inflammation. Moreover, we discuss the potential, opportunities, and challenges in searching for novel tick-derived drugs.
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Affiliation(s)
- Jindřich Chmelař
- Department of Medical Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Jan Kotál
- Department of Medical Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia.,Laboratory of Genomics and Proteomics of Disease Vectors, Biology Centre CAS, Institute of Parasitology, České Budějovice, Czechia
| | - Anna Kovaříková
- Department of Medical Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Michail Kotsyfakis
- Department of Medical Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia.,Laboratory of Genomics and Proteomics of Disease Vectors, Biology Centre CAS, Institute of Parasitology, České Budějovice, Czechia
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Aouiche C, Chen B, Shang X. Predicting stage-specific cancer related genes and their dynamic modules by integrating multiple datasets. BMC Bioinformatics 2019; 20:194. [PMID: 31074385 PMCID: PMC6509867 DOI: 10.1186/s12859-019-2740-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The mechanism of many complex diseases has not been detected accurately in terms of their stage evolution. Previous studies mainly focus on the identification of associations between genes and individual diseases, but less is known about their associations with specific disease stages. Exploring biological modules through different disease stages could provide valuable knowledge to genomic and clinical research. RESULTS In this study, we proposed a powerful and versatile framework to identify stage-specific cancer related genes and their dynamic modules by integrating multiple datasets. The discovered modules and their specific-signature genes were significantly enriched in many relevant known pathways. To further illustrate the dynamic evolution of these clinical-stages, a pathway network was built by taking individual pathways as vertices and the overlapping relationship between their annotated genes as edges. CONCLUSIONS The identified pathway network not only help us to understand the functional evolution of complex diseases, but also useful for clinical management to select the optimum treatment regimens and the appropriate drugs for patients.
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Affiliation(s)
- Chaima Aouiche
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China.,Key Laboratory of Big Data Storage and Management, Northwestern Polytechnical University Ministry of Industry and Information Technology, Xi'an, China
| | - Bolin Chen
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China. .,Key Laboratory of Big Data Storage and Management, Northwestern Polytechnical University Ministry of Industry and Information Technology, Xi'an, China.
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China.,Key Laboratory of Big Data Storage and Management, Northwestern Polytechnical University Ministry of Industry and Information Technology, Xi'an, China
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Jørgensen JT. Twenty Years with Personalized Medicine: Past, Present, and Future of Individualized Pharmacotherapy. Oncologist 2019; 24:e432-e440. [PMID: 30940745 PMCID: PMC6656435 DOI: 10.1634/theoncologist.2019-0054] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
On April 16, 1999, a short article appeared in The Wall Street Journal entitled "New Era of Personalized Medicine: Targeting Drugs for Each Unique Genetic Profile," and here, the public was introduced to the term "personalized medicine" for the first time. A few months after publication of the article, it was reprinted in The Oncologist. The article describes the formation of the Single Nucleotide Polymorphisms Consortium, which was established as a collaboration between a number of major pharmaceutical companies and several academic research institutions, with support from the Wellcome Trust Foundation. Reading the article today, one will find that several of the important arguments for an individualized therapy are described in a similar way as we have known it from the past 20 years of discussion. The article mentioned the poor efficacy of the current pharmacotherapy, disease heterogeneity, and genetic variability, a showdown with the "one-size-fits-all" approach, and the use of predictive safety and efficacy biomarkers. Today, personal medicine is in competition with other terms such as "precision medicine" and "stratified medicine" and is no longer the preferred term for describing the individualized health care approach. Even though personalized medicine arose from the idea of improving and individualizing pharmacotherapy, the concept has influenced most other areas of our health care system. No matter if we use the term precision medicine or personalized medicine, the ideas that originated 20 years ago have greatly impacted the way we develop and implement new initiatives in relation to diagnosis, prevention, and treatment today. IMPLICATIONS FOR PRACTICE: Since the publication of the ideas behind personalized medicine in The Wall Street Journal and The Oncologist 20 year ago, they have permeated medical research and innovation. This review will provide an overview of the background, definitions, and terminology and will describe some of the achievements in relation to the treatment of malignant diseases.
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Feng W, Ao H, Yue S, Peng C. Systems pharmacology reveals the unique mechanism features of Shenzhu Capsule for treatment of ulcerative colitis in comparison with synthetic drugs. Sci Rep 2018; 8:16160. [PMID: 30385774 PMCID: PMC6212405 DOI: 10.1038/s41598-018-34509-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/16/2018] [Indexed: 12/17/2022] Open
Abstract
In clinic, both synthetic drugs and Shenzhu Capsule (SZC), one kind of traditional Chinese medicines (TCMs), are used to treat ulcerative colitis (UC). In our study, a systems pharmacology approach was employed to elucidate the chemical and mechanism differences between SZC and synthetic drugs in treating UC. First, the compound databases were constructed for SZC and synthetic drugs. Then, the targets of SZC were predicted with on-line tools and validated using molecular docking method. Finally, chemical space, targets, and pathways of SZC and synthetic drugs were compared. Results showed that atractylenolide I, atractylone, kaempferol, etc., were bioactive compounds of SZC. Comparison of SZC and synthetic drugs showed that (1) in chemical space, the area of SZC encompasses the area of synthetic drugs; (2) SZC can act on more targets and pathways than synthetic drugs; (3) SZC can not only regulate immune and inflammatory reactions but also act on ulcerative colitis complications (bloody diarrhea) and prevent UC to develop into colorectal cancer whereas synthetic drugs mainly regulate immune and inflammatory reactions. Our study could help us to understand the compound and mechanism differences between TCM and synthetic drugs.
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Affiliation(s)
- Wuwen Feng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hui Ao
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shijun Yue
- College of Pharmacy and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Cheng Peng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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Strategic R&D transactions in personalized drug development. Drug Discov Today 2018; 23:1334-1339. [PMID: 29574213 DOI: 10.1016/j.drudis.2018.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/21/2018] [Accepted: 03/19/2018] [Indexed: 12/17/2022]
Abstract
Although external collaboration capability influences the development of personalized medicine, key transactions in the pharmaceutical industry have not been addressed. To explore specific trends in interorganizational transactions and key players, we longitudinally surveyed strategic transactions, comparing them with other advanced medical developments, such as antibody therapy, as controls. We found that the financing deals of start-ups have surged over the past decade, accelerating intellectual property (IP) creation. Our correlation and regression analyses identified determinants of financing deals among alliance deals, acquisition deals, patents, research and development (R&D) licenses, market licenses, and scientific papers. They showed that patents positively correlated with transactions, and that the number of R&D licenses significantly predicted financing deals. This indicates, for the first time, that start-ups and investors lead progress in personalized medicine.
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10
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Abstract
Companion diagnostics (CDx) is a positive attempt in the direction of improving the drug development process, especially in the field of oncology, with the advent of newer targeted therapies. It helps the oncologist in deciding the choice of treatment for the individual patient. The role of CDx assays has attracted the attention of regulators, and especially the US Food and Drug Administration developed regulatory strategies for CDx and the drug-diagnostic codevelopment project. For an increasing number of cancer patients, the treatment selection will depend on the result generated by a CDx assay, and consequently this type of assay has become critical for the care and safety of the patients. In addition to the assay-based approach, molecular imaging with its ability to image at the genetic and receptor level has made foray into the field of drug development and personalized medicine. We shall review these aspects of CDx, with special focus on molecular imaging and the upcoming concept of Theranostics.
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Plant Natural Products Calycosin and Gallic Acid Synergistically Attenuate Neutrophil Infiltration and Subsequent Injury in Isoproterenol-Induced Myocardial Infarction: A Possible Role for Leukotriene B4 12-Hydroxydehydrogenase? OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:434052. [PMID: 26265982 PMCID: PMC4523677 DOI: 10.1155/2015/434052] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 06/16/2015] [Accepted: 06/24/2015] [Indexed: 01/29/2023]
Abstract
Leukotriene B4 12-hydroxydehydrogenase (LTB4DH) catalyzes the oxidation of proinflammatory LTB4 into less bioactive 12-oxo-LTB4. We recently discovered that LTB4DH was induced by two different natural products in combination. We previously isolated gallic acid from Radix Paeoniae through a bioactivity-guided fractionation procedure. The purpose of this study is to test the hypothesis that LTB4DH inducers may suppress neutrophil-mediated inflammation in myocardial infarction. We first isolated the active compound(s) from another plant, Radix Astragali, by the similar strategy. By evaluating LTB4DH induction, we identified calycosin and formononetin from Radix Astragali by HPLC-ESI-MS technique. We confirmed that gallic acid and commercial calycosin or formononetin could synergistically induce LTB4DH expression in HepG2 cells and human neutrophils. Moreover, calycosin and gallic acid attenuated the effects of LTB4 on the survival and chemotaxis of neutrophil cell culture. We further demonstrated that calycosin and gallic acid synergistically suppressed neutrophil infiltration and protected cardiac integrity in the isoproterenol-induced mice model of myocardial infarction. Calycosin and gallic acid dramatically suppressed isoproterenol-induced increase in myeloperoxidase (MPO) activity and malondialdehyde (MDA) level. Collectively, our results suggest that LTB4DH inducers (i.e., calycosin and gallic acid) may be a novel combined therapy for the treatment of neutrophil-mediated myocardial injury.
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Everett JR. Pharmacometabonomics in humans: a new tool for personalized medicine. Pharmacogenomics 2015; 16:737-54. [PMID: 25929853 DOI: 10.2217/pgs.15.20] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Pharmacogenomics is now over 50 years old and has had some impact in clinical practice, through its use to select patient subgroups who will enjoy efficacy without side effects when treated with certain drugs. However, pharmacogenomics, has had less impact than initially predicted. One reason for this is that many diseases, and the way in which the patients respond to drug treatments, have both genetic and environmental elements. Pure genomics is almost blind to the environmental elements. A new methodology has emerged, termed pharmacometabonomics that is concerned with the prediction of drug effects through the analysis of predose, biofluid metabolite profiles, which reflect both genetic and environmental influences on human physiology. In this review we will cover what pharmacometabonomics is, how it works, what applications exist and what the future might hold in this exciting new area.
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ICan: an integrated co-alteration network to identify ovarian cancer-related genes. PLoS One 2015; 10:e0116095. [PMID: 25803614 PMCID: PMC4372216 DOI: 10.1371/journal.pone.0116095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 12/04/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Over the last decade, an increasing number of integrative studies on cancer-related genes have been published. Integrative analyses aim to overcome the limitation of a single data type, and provide a more complete view of carcinogenesis. The vast majority of these studies used sample-matched data of gene expression and copy number to investigate the impact of copy number alteration on gene expression, and to predict and prioritize candidate oncogenes and tumor suppressor genes. However, correlations between genes were neglected in these studies. Our work aimed to evaluate the co-alteration of copy number, methylation and expression, allowing us to identify cancer-related genes and essential functional modules in cancer. RESULTS We built the Integrated Co-alteration network (ICan) based on multi-omics data, and analyzed the network to uncover cancer-related genes. After comparison with random networks, we identified 155 ovarian cancer-related genes, including well-known (TP53, BRCA1, RB1 and PTEN) and also novel cancer-related genes, such as PDPN and EphA2. We compared the results with a conventional method: CNAmet, and obtained a significantly better area under the curve value (ICan: 0.8179, CNAmet: 0.5183). CONCLUSION In this paper, we describe a framework to find cancer-related genes based on an Integrated Co-alteration network. Our results proved that ICan could precisely identify candidate cancer genes and provide increased mechanistic understanding of carcinogenesis. This work suggested a new research direction for biological network analyses involving multi-omics data.
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Shimazawa R, Ikeda M. International differences in companion diagnostic approvals: how are we able to manage the differences? Expert Rev Mol Diagn 2014; 15:157-9. [PMID: 25308218 DOI: 10.1586/14737159.2015.969243] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
One would expect regulations for drugs and diagnostics not to differ significantly between countries, given that regulatory authorities evaluate the same scientific data generated in an increasingly globally harmonized context. However, studies of our own and others have provided compelling evidence of differences in regulations for drugs and in vitro companion diagnostics in personalized medicine. Differing regulatory processes create hurdles for both pharmaceutical and companion diagnostics companies with different platforms that employ different technologies. The rising cost of healthcare caused by improvements in technology is another issue that faces all advanced countries. To address these issues and to facilitate access to personalized medicine, regulatory authorities, academia and the pharmaceutical industry should increase dialogue on the differences on an international platform.
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Jørgensen JT. Drug-diagnostics co-development in oncology. Front Oncol 2014; 4:208. [PMID: 25136515 PMCID: PMC4120852 DOI: 10.3389/fonc.2014.00208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 07/22/2014] [Indexed: 01/21/2023] Open
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Jones RC, Greek R. A review of the Institute of Medicine's analysis of using chimpanzees in biomedical research. SCIENCE AND ENGINEERING ETHICS 2014; 20:481-504. [PMID: 23616243 PMCID: PMC4033812 DOI: 10.1007/s11948-013-9442-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 03/17/2013] [Indexed: 05/05/2023]
Abstract
We argue that the recommendations made by the Institute of Medicine's 2011 report, Chimpanzees in Biomedical and Behavioral Research: Assessing the Necessity, are methodologically and ethically confused. We argue that a proper understanding of evolution and complexity theory in terms of the science and ethics of using chimpanzees in biomedical research would have had led the committee to recommend not merely limiting but eliminating the use of chimpanzees in biomedical research. Specifically, we argue that a proper understanding of the difference between the gross level of examination of species and examinations on finer levels can shed light on important methodological and ethical inconsistencies leading to ignorance of potentially unethical practices and policies regarding the use of animals in scientific research.
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Affiliation(s)
- Robert C. Jones
- Department of Philosophy, California State University, Chico, Chico, CA 95929-0730 USA
| | - Ray Greek
- Americans For Medical Advancement, 2251 Refugio Rd, Goleta, CA 93117 USA
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Dimitrakopoulou K, Dimitrakopoulos GN, Sgarbas KN, Bezerianos A. Tamoxifen integromics and personalized medicine: dynamic modular transformations underpinning response to tamoxifen in breast cancer treatment. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 18:15-33. [PMID: 24299457 DOI: 10.1089/omi.2013.0055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recent advances in pharmacogenomics technologies allow bold steps to be taken towards personalized medicine, more accurate health planning, and personalized drug development. In this framework, systems pharmacology network-based approaches offer an appealing way for integrating multi-omics data and set the basis for defining systems-level drug response biomarkers. On the road to individualized tamoxifen treatment in estrogen receptor-positive breast cancer patients, we examine the dynamics of the attendant pharmacological response mechanisms. By means of an "integromics" network approach, we assessed the tamoxifen effect through the way the high-order organization of interactome (i.e., the modules) is perturbed. To accomplish that, first we integrated the time series transcriptome data with the human protein interaction data, and second, an efficient module-detecting algorithm was applied onto the composite graphs. Our findings show that tamoxifen induces severe modular transformations on specific areas of the interactome. Our modular biomarkers in response to tamoxifen attest to the immunomodulatory role of tamoxifen, and further reveal that it deregulates cell cycle and apoptosis pathways, while coordinating the proteasome and basal transcription factors. To the best of our knowledge, this is the first report that informs the fields of personalized medicine and clinical pharmacology about the actual dynamic interactome response to tamoxifen administration.
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Affiliation(s)
- Katrin Beyer
- Department of Pathology, Health Sciences Research Institute of the 'Germans Trias i Pujol' Foundation (IGTP), Badalona, Barcelona, Spain.
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Greek R, Hansen LA. Questions regarding the predictive value of one evolved complex adaptive system for a second: Exemplified by the SOD1 mouse. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:231-53. [DOI: 10.1016/j.pbiomolbio.2013.06.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 11/25/2022]
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Pailleux F, Vachon P, Lemoine J, Beaudry F. Targeted liquid chromatography quadrupole ion trap mass spectrometry analysis of tachykinin related peptides reveals significant expression differences in a rat model of neuropathic pain. Neuropeptides 2013; 47:261-71. [PMID: 23490005 DOI: 10.1016/j.npep.2013.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/07/2013] [Accepted: 02/14/2013] [Indexed: 12/26/2022]
Abstract
Animal models are widely used to perform basic scientific research in pain. The rodent chronic constriction injury (CCI) model is widely used to study neuropathic pain. Animals were tested prior and after CCI surgery using behavioral tests (von Frey filaments and Hargreaves test) to evaluate pain. The brain and the lumbar enlargement of the spinal cord were collected from neuropathic and normal animals. Tachykinin related peptides were analyzed by high performance liquid chromatography quadrupole ion trap mass spectrometry. Our results reveal that the β-tachykinin₅₈₋₇₁, SP and SP₃₋₁₁ up-regulation are closely related to pain behavior. The spinal β-tachykinin₅₈₋₇₁, SP and SP₃₋₁₁ concentrations were significantly up-regulated in neuropathic animals compared with normal animals (p<0.001; p<0.001 and p<0.05, respectively). In contrast, the spinal SP5₅₋₁₁ concentration in neuropathic animals revealed a significant down-regulation compared with normal animals (p<0.05). The brain β-tachykinin₅₈₋₇₁ and SP concentrations were significantly up-regulated (p<0.05 and p<0.001, respectively). Interestingly, no significant concentration differences were observed in the spinal cord and brain for NKA, β-tachykinin₅₈₋₇₁, SP₁₋₇ and SP₆₋₁₁ (p>0.05). The β-tachykinin₅₈₋₇₁, SP and C-terminal SP metabolites could potentially serve as biomarkers in early drug discovery.
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Affiliation(s)
- Floriane Pailleux
- Groupe de Recherche en Pharmacologie Animal du Québec-GREPAQ, Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
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Jørgensen JT. Companion diagnostics in oncology - current status and future aspects. Oncology 2013; 85:59-68. [PMID: 23860090 DOI: 10.1159/000353454] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 05/21/2013] [Indexed: 11/19/2022]
Abstract
A large number of targeted anticancer drugs are currently under development and most of them will have a companion diagnostic linked to their use. If a diagnostic assay is developed in conjunction with a targeted anticancer drug, such an assay will later end up determining the conditions for the use of the drug after its approval. The assay then becomes a kind of 'gatekeeper' in relation to which patients should be treated with the drug in question. This 'gatekeeper' role implies that companion diagnostic assays must live up to the same regulatory standards and requirements known from drug development. The assays must have proven to be analytically robust and reliable and to have demonstrated clinical utility before they are routinely used in the clinic. In the drug-diagnostic codevelopment model, several 'traditional' study designs have been used to demonstrate clinical utility. However, if we are to benefit from the increasing knowledge provided by molecular oncology, new ways should be developed to demonstrate the clinical utility of drug-diagnostic combinations. The development of such an approach will require a rethinking at different levels and is likely to include a number of ethical, regulatory and practical challenges.
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Andria B, Auriemma L, Attanasio C, Cozzolino S, Cristinziano A, Zeuli L, Mancini A. The impact of innovation for biotech drugs: an Italian analysis of products licensed in Europe between 2004 and 2011. Eur J Hosp Pharm 2013. [DOI: 10.1136/ejhpharm-2013-000293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Aplicación de la farmacogenómica y otras nuevas tecnologías al desarrollo de medicamentos. Med Clin (Barc) 2013; 140:558-63. [DOI: 10.1016/j.medcli.2013.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/14/2013] [Indexed: 11/23/2022]
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Greek R, Menache A. Systematic reviews of animal models: methodology versus epistemology. Int J Med Sci 2013; 10:206-21. [PMID: 23372426 PMCID: PMC3558708 DOI: 10.7150/ijms.5529] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 12/30/2012] [Indexed: 01/24/2023] Open
Abstract
Systematic reviews are currently favored methods of evaluating research in order to reach conclusions regarding medical practice. The need for such reviews is necessitated by the fact that no research is perfect and experts are prone to bias. By combining many studies that fulfill specific criteria, one hopes that the strengths can be multiplied and thus reliable conclusions attained. Potential flaws in this process include the assumptions that underlie the research under examination. If the assumptions, or axioms, upon which the research studies are based, are untenable either scientifically or logically, then the results must be highly suspect regardless of the otherwise high quality of the studies or the systematic reviews. We outline recent criticisms of animal-based research, namely that animal models are failing to predict human responses. It is this failure that is purportedly being corrected via systematic reviews. We then examine the assumption that animal models can predict human outcomes to perturbations such as disease or drugs, even under the best of circumstances. We examine the use of animal models in light of empirical evidence comparing human outcomes to those from animal models, complexity theory, and evolutionary biology. We conclude that even if legitimate criticisms of animal models were addressed, through standardization of protocols and systematic reviews, the animal model would still fail as a predictive modality for human response to drugs and disease. Therefore, systematic reviews and meta-analyses of animal-based research are poor tools for attempting to reach conclusions regarding human interventions.
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Affiliation(s)
- Ray Greek
- Americans For Medical Advancement, 2251 Refugio Rd, Goleta, CA 93117, USA.
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Thomas J, Stratton E, Keppens M. Companion diagnostics: emerging strategies and issues in pharmaceutical development. Expert Rev Mol Diagn 2012; 12:561-3. [PMID: 22845476 DOI: 10.1586/erm.12.49] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This article summarizes the broad messages from pharmaceutical and diagnostic companies on the collaborations required to support companion diagnostics. Since the groundbreaking herceptin HER2 diagnostic model in 1998, it has taken until 2011 for the US FDA to issue a draft guidance document, which was then immediately followed with approvals for two new drugs and their companion diagnostics. This conference summarized the current state of thinking in new projects and innovative technologies in pharmaceutical and diagnostic codevelopment. Attitudes are slowly changing and collaborations are rapidly ensuing, although the alignment between pharmaceutical and diagnostic understanding of value, timelines, outcomes and impact is difficult and remains a contentious area. The value of this conference has been to address these issues.
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Affiliation(s)
- Janette Thomas
- Integrated Medicines Ltd, Director of Programmes, Topfield House, Ermine Street, Caxton, Cambridge, CB23 3PQ, UK.
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Abstract
Personalized medicine is a novel medical model with all decisions and practices being tailored to individual patients in whatever ways possible. In the era of genomics, personalized medicine combines the genetic information for additional benefit in preventive and therapeutic strategies. Personalized medicine may allow the physician to provide a better therapy for patients in terms of efficiency, safety and treatment length to reduce the associated costs. There was a remarkable growth in scientific publication on personalized medicine within the past few years in the cardiovascular field. However, so far, only very few cardiologists in the USA are incorporating personalized medicine into clinical treatment. We review the concepts, strengths, limitations and challenges of personalized medicine with a particular focus on cardiovascular diseases (CVDs). There are many challenges from both scientific and policy perspectives to personalized medicine, which can overcome them by comprehensive concept and understanding, clinical application, and evidence based practices. Individualized medicine serves a pivotal role in the evolution of national and global healthcare reform, especially, in the CVDs fields. Ultimately, personalized medicine will affect the entire landscape of health care system in the near future.
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Affiliation(s)
- Moo-Sik Lee
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA. ; Department of Preventive Medicine, College of Medicine, Konyang University, Daejeon, Korea
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28
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Abstract
Biomarkers are of tremendous importance for the prediction, diagnosis, and observation of the therapeutic success of common complex multifactorial metabolic diseases, such as type II diabetes and obesity. However, the predictive power of the traditional biomarkers used (eg, plasma metabolites and cytokines, body parameters) is apparently not sufficient for reliable monitoring of stage-dependent pathogenesis starting with the healthy state via its initiation and development to the established disease and further progression to late clinical outcomes. Moreover, the elucidation of putative considerable differences in the underlying pathogenetic pathways (eg, related to cellular/tissue origin, epigenetic and environmental effects) within the patient population and, consequently, the differentiation between individual options for disease prevention and therapy - hallmarks of personalized medicine - plays only a minor role in the traditional biomarker concept of metabolic diseases. In contrast, multidimensional and interdependent patterns of genetic, epigenetic, and phenotypic markers presumably will add a novel quality to predictive values, provided they can be followed routinely along the complete individual disease pathway with sufficient precision. These requirements may be fulfilled by small membrane vesicles, which are so-called exosomes and microvesicles (EMVs) that are released via two distinct molecular mechanisms from a wide variety of tissue and blood cells into the circulation in response to normal and stress/pathogenic conditions and are equipped with a multitude of transmembrane, soluble and glycosylphosphatidylinositol-anchored proteins, mRNAs, and microRNAs. Based on the currently available data, EMVs seem to reflect the diverse functional and dysfunctional states of the releasing cells and tissues along the complete individual pathogenetic pathways underlying metabolic diseases. A critical step in further validation of EMVs as biomarkers will rely on the identification of unequivocal correlations between critical disease states and specific EMV signatures, which in future may be determined in rapid and convenient fashion using nanoparticle-driven biosensors.
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Affiliation(s)
- Günter Müller
- Department of Biology I, Genetics, Ludwig-Maximilians University Munich, Biocenter, Munich, Germany
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Moore MW, Babu D, Cotter PD. Challenges in the codevelopment of companion diagnostics. Per Med 2012; 9:485-496. [DOI: 10.2217/pme.12.60] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Therapeutics harnessing the power of personalized medicine have the potential to revolutionize healthcare. Companion diagnostics are critical to this goal and are increasingly relied upon to ensure the effective, safe development and use of a personalized therapeutic. Companion diagnostics are the focus of several recent regulatory guidance documents; the drug–diagnostic codevelopment process has become increasingly relevant and necessary. Despite this, the promise of companion diagnostics has not been fully realized and there are multiple difficulties that still need resolution. The path to codevelop a successful companion diagnostic with its complementary drug is complex, fragmented and fraught with several challenges. In this article, we discuss the logistic, strategic business, regulatory and financial challenges involved in drug-companion diagnostic codevelopment.
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Affiliation(s)
- Mathew W Moore
- ResearchDx, 13766 Alton Parkway, Suite 147, Irvine, CA 92618, USA
| | - Deepti Babu
- University of Alberta, Department of Medical Genetics, Edmonton, Alberta, Canada
| | - Philip D Cotter
- ResearchDx, 13766 Alton Parkway, Suite 147, Irvine, CA 92618, USA
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Pailleux F, Beaudry F. Internal standard strategies for relative and absolute quantitation of peptides in biological matrices by liquid chromatography tandem mass spectrometry. Biomed Chromatogr 2012; 26:881-91. [DOI: 10.1002/bmc.2757] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 04/23/2012] [Indexed: 01/08/2023]
Affiliation(s)
| | - Francis Beaudry
- Groupe de Recherche en Pharmacologie Animal du Québec (GREPAQ), Département de biomédecine vétérinaire, Faculté de médecine vétérinaire; Université de Montréal, Saint-Hyacinthe; Québec; Canada
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Sosnik A, Seremeta KP, Imperiale JC, Chiappetta DA. Novel formulation and drug delivery strategies for the treatment of pediatric poverty-related diseases. Expert Opin Drug Deliv 2012; 9:303-23. [PMID: 22257003 DOI: 10.1517/17425247.2012.655268] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Due to a lack of approved drugs and formulations, children represent the most vulnerable patients. Magistral, unlicensed formulations obtained by the manipulation of solid forms should undergo clinical evaluation to ensure bioequivalence. The development of new pediatric medicines is complex and faces technological, economic and ethical challenges. This phenomenon has contributed to the emergence of an adult-children gap. To improve the situation, the World Health Organization launched the global campaign 'Make medicines child size' and a number of international initiatives have been established. The situation is more critical in the case of poverty-related diseases (PRDs) that mainly affect poor countries. AREAS COVERED This review critically discusses different strategies to develop pediatric formulations and drug delivery systems (DDS) in PRDs and their potential implementation in the current market. Readers will gain an updated perspective on the development of pediatric medicines for the treatment of PRDs and the proximate challenges and opportunities faced to ensure an effective pharmacotherapy. EXPERT OPINION There is an urgent need for the development of innovative, scalable and cost-viable formulations to ensure pediatric patients have access to appropriate medications for PRDs. The guidelines of the International Conference on Harmonisation constitute a very good orientation tool, as they emphasize physiological and developmental aspects that need to be considered in pediatric research. It is important to consider cultural, economic and ethical aspects that make developing nations facing PRDs different from the developed world. Thus, the best strategy would probably be to conceive and engage similar initiatives in the developing world, to address unattended therapeutic niches.
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Affiliation(s)
- Alejandro Sosnik
- University of Buenos Aires, Faculty of Pharmacy and Biochemistry, Department of Pharmaceutical Technology, The Group of Biomaterials and Nanotechnology for Improved Medicines, 956 Junín St., Buenos Aires CP1113, Argentina.
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