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Pot D, Worman Z, Baumann A, Pathak S, Beck R, Beck E, Thayer K, Davidsen TM, Kim E, Davis-Dusenbery B, Otridge J, Pihl T, Barnholtz-Sloan JS, Kerlavage AR. NCI Cancer Research Data Commons: Cloud-Based Analytic Resources. Cancer Res 2024; 84:1396-1403. [PMID: 38488504 PMCID: PMC11063685 DOI: 10.1158/0008-5472.can-23-2657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/26/2024] [Accepted: 03/05/2024] [Indexed: 03/19/2024]
Abstract
The NCI's Cloud Resources (CR) are the analytical components of the Cancer Research Data Commons (CRDC) ecosystem. This review describes how the three CRs (Broad Institute FireCloud, Institute for Systems Biology Cancer Gateway in the Cloud, and Seven Bridges Cancer Genomics Cloud) provide access and availability to large, cloud-hosted, multimodal cancer datasets, as well as offer tools and workspaces for performing data analysis where the data resides, without download or storage. In addition, users can upload their own data and tools into their workspaces, allowing researchers to create custom analysis workflows and integrate CRDC-hosted data with their own. See related articles by Brady et al., p. 1384, Wang et al., p. 1388, and Kim et al., p. 1404.
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Affiliation(s)
- David Pot
- General Dynamics Information Technology, Falls Church, Virginia
| | - Zelia Worman
- Velsera (Seven Bridges), Charlestown, Massachusetts
| | | | - Shirish Pathak
- Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Rowan Beck
- Velsera (Seven Bridges), Charlestown, Massachusetts
| | - Erin Beck
- Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland
| | | | - Tanja M. Davidsen
- Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland
| | - Erika Kim
- Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland
| | | | - John Otridge
- Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Todd Pihl
- Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | | | - Jill S. Barnholtz-Sloan
- Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland
- Trans Divisional Research Program, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Anthony R. Kerlavage
- Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland
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Crist RM, Clogston JD, Stern ST, Dobrovolskaia MA. Advancements in Nanoparticle Characterization. Methods Mol Biol 2024; 2789:3-17. [PMID: 38506986 DOI: 10.1007/978-1-0716-3786-9_1] [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] [Indexed: 03/22/2024]
Abstract
Nanotechnology for drug delivery has made significant advancements over the last two decades. Innovations have been made in cancer research and development, including chemotherapies, imaging agents, and vaccine strategies, as well as other therapeutic areas, e.g., the recent commercialization of mRNA lipid nanoparticles as vaccines against the SARS-CoV-2 virus. The field has also seen technological advancements to aid in addressing the complex questions posed by these novel therapies. In this latest edition of protocols and methods for nanoparticle characterization, we highlight both old and new methodologies for defining physicochemical properties, present both in vitro and in vivo methods to test for a variety of immunotoxicities, and describe assays used for pharmacological studies to assess drug release and tissue distribution.
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Affiliation(s)
- Rachael M Crist
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Jeffrey D Clogston
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Stephan T Stern
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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Ma X, Mao M, He J, Liang C, Xie HY. Nanoprobe-based molecular imaging for tumor stratification. Chem Soc Rev 2023; 52:6447-6496. [PMID: 37615588 DOI: 10.1039/d3cs00063j] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The responses of patients to tumor therapies vary due to tumor heterogeneity. Tumor stratification has been attracting increasing attention for accurately distinguishing between responders to treatment and non-responders. Nanoprobes with unique physical and chemical properties have great potential for patient stratification. This review begins by describing the features and design principles of nanoprobes that can visualize specific cell types and biomarkers and release inflammatory factors during or before tumor treatment. Then, we focus on the recent advancements in using nanoprobes to stratify various therapeutic modalities, including chemotherapy, radiotherapy (RT), photothermal therapy (PTT), photodynamic therapy (PDT), chemodynamic therapy (CDT), ferroptosis, and immunotherapy. The main challenges and perspectives of nanoprobes in cancer stratification are also discussed to facilitate probe development and clinical applications.
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Affiliation(s)
- Xianbin Ma
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Mingchuan Mao
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Jiaqi He
- School of Life Science, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Chao Liang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Hai-Yan Xie
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Chemical Biology Center, Peking University, Beijing, 100191, P. R. China.
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Tian B, Hua S, Liu J. Multi-functional chitosan-based nanoparticles for drug delivery: Recent advanced insight into cancer therapy. Carbohydr Polym 2023; 315:120972. [PMID: 37230614 DOI: 10.1016/j.carbpol.2023.120972] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/27/2023]
Abstract
Cancer therapy continues to be a major global concern, with conventional treatments suffering from low efficacy, untargeted drug delivery, and severe side effects. Recent research in nanomedicine suggests that nanoparticles' unique physicochemical properties can be leveraged to surmount the limitations of conventional cancer treatment. Chitosan-based nanoparticles have gained significant attention due to their high drug-carrying capacity, non-toxicity, biocompatibility, and long circulation time. Chitosan is utilized in cancer therapies as a carrier to accurately deliver active ingredients to tumor sites. This review focuses on clinical studies and current market offerings of anticancer drugs. The unique nature of tumor microenvironments presents new opportunities for the development of smart drug delivery systems, and this review explores the design and preparation of chitosan-based smart nanoparticles. Further, we discuss the therapeutic efficacies of these nanoparticles based on various in vitro and in vivo findings. Finally, we present a forward-looking perspective on the challenges and prospects of chitosan-based nanoparticles in cancer therapy, intending to provide fresh ideas for advancing cancer treatment strategies.
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Affiliation(s)
- Bingren Tian
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, China; Key Laboratory of Ningxia Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, China.
| | - Shiyao Hua
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Jiayue Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao.
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Afonin KA, Dokholyan NV. Editorial to "Molecular engineering of biomaterials programmed to operate in living systems". Adv Drug Deliv Rev 2023; 193:114669. [PMID: 36529189 PMCID: PMC10015611 DOI: 10.1016/j.addr.2022.114669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kirill A Afonin
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033-0850, USA.
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Ag/TiNPS nanocatalyst: biosynthesis, characterization and photocatalytic activity. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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