1
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Krissanaprasit A, Mihalko E, Meinhold K, Simpson A, Sollinger J, Pandit S, Dupont DM, Kjems J, Brown AC, LaBean TH. A functional RNA-origami as direct thrombin inhibitor with fast-acting and specific single-molecule reversal agents in vivo model. Mol Ther 2024; 32:2286-2298. [PMID: 38720458 PMCID: PMC11286819 DOI: 10.1016/j.ymthe.2024.05.002] [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: 07/17/2023] [Revised: 03/29/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Injectable anticoagulants are widely used in medical procedures to prevent unwanted blood clotting. However, many lack safe, effective reversal agents. Here, we present new data on a previously described RNA origami-based, direct thrombin inhibitor (HEX01). We describe a new, fast-acting, specific, single-molecule reversal agent (antidote) and present in vivo data for the first time, including efficacy, reversibility, preliminary safety, and initial biodistribution studies. HEX01 contains multiple thrombin-binding aptamers appended on an RNA origami. It exhibits excellent anticoagulation activity in vitro and in vivo. The new single-molecule, DNA antidote (HEX02) reverses anticoagulation activity of HEX01 in human plasma within 30 s in vitro and functions effectively in a murine liver laceration model. Biodistribution studies of HEX01 in whole mice using ex vivo imaging show accumulation mainly in the liver over 24 h and with 10-fold lower concentrations in the kidneys. Additionally, we show that the HEX01/HEX02 system is non-cytotoxic to epithelial cell lines and non-hemolytic in vitro. Furthermore, we found no serum cytokine response to HEX01/HEX02 in a murine model. HEX01 and HEX02 represent a safe and effective coagulation control system with a fast-acting, specific reversal agent showing promise for potential drug development.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, NC 27695, USA.
| | - Emily Mihalko
- Joint Department of Biomedical Engineering, College of Engineering, North Carolina State University and University of North Carolina-Chapel Hill, Raleigh, NC 27695, USA
| | - Katherine Meinhold
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Aryssa Simpson
- Joint Department of Biomedical Engineering, College of Engineering, North Carolina State University and University of North Carolina-Chapel Hill, Raleigh, NC 27695, USA
| | - Jennifer Sollinger
- Joint Department of Biomedical Engineering, College of Engineering, North Carolina State University and University of North Carolina-Chapel Hill, Raleigh, NC 27695, USA
| | - Sanika Pandit
- Joint Department of Biomedical Engineering, College of Engineering, North Carolina State University and University of North Carolina-Chapel Hill, Raleigh, NC 27695, USA
| | - Daniel M Dupont
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000 Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000 Aarhus, Denmark
| | - Ashley C Brown
- Joint Department of Biomedical Engineering, College of Engineering, North Carolina State University and University of North Carolina-Chapel Hill, Raleigh, NC 27695, USA; Comparative Medicine Institute, North Carolina State University and University of North Carolina, Chapel Hill, NC 27695, USA
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, NC 27695, USA; Comparative Medicine Institute, North Carolina State University and University of North Carolina, Chapel Hill, NC 27695, USA.
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2
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Huang X, Wu F, Ye J, Wang L, Wang X, Li X, He G. Expanding the horizons of targeted protein degradation: A non-small molecule perspective. Acta Pharm Sin B 2024; 14:2402-2427. [PMID: 38828146 PMCID: PMC11143490 DOI: 10.1016/j.apsb.2024.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 06/05/2024] Open
Abstract
Targeted protein degradation (TPD) represented by proteolysis targeting chimeras (PROTACs) marks a significant stride in drug discovery. A plethora of innovative technologies inspired by PROTAC have not only revolutionized the landscape of TPD but have the potential to unlock functionalities beyond degradation. Non-small-molecule-based approaches play an irreplaceable role in this field. A wide variety of agents spanning a broad chemical spectrum, including peptides, nucleic acids, antibodies, and even vaccines, which not only prove instrumental in overcoming the constraints of conventional small molecule entities but also provided rapidly renewing paradigms. Herein we summarize the burgeoning non-small molecule technological platforms inspired by PROTACs, including three major trajectories, to provide insights for the design strategies based on novel paradigms.
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Affiliation(s)
- Xiaowei Huang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fengbo Wu
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jing Ye
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lian Wang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoyun Wang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiang Li
- Department of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Gu He
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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3
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He C, Hu C, He WZ, Sun YC, Jiang Y, Liu L, Hou J, Chen KX, Jiao YR, Huang M, Huang M, Yang M, Lu Q, Wei J, Zeng C, Lei GH, Li CJ. Macrophage-derived extracellular vesicles regulate skeletal stem/progenitor Cell lineage fate and bone deterioration in obesity. Bioact Mater 2024; 36:508-523. [PMID: 39072285 PMCID: PMC11282946 DOI: 10.1016/j.bioactmat.2024.06.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/07/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024] Open
Abstract
Obesity-induced chronic inflammation exacerbates multiple types of tissue/organ deterioration and stem cell dysfunction; however, the effects on skeletal tissue and the underlying mechanisms are still unclear. Here, we show that obesity triggers changes in the microRNA profile of macrophage-secreted extracellular vesicles, leading to a switch in skeletal stem/progenitor cell (SSPC) differentiation between osteoblasts and adipocytes and bone deterioration. Bone marrow macrophage (BMM)-secreted extracellular vesicles (BMM-EVs) from obese mice induced bone deterioration (decreased bone volume, bone microstructural deterioration, and increased adipocyte numbers) when administered to lean mice. Conversely, BMM-EVs from lean mice rejuvenated bone deterioration in obese recipients. We further screened the differentially expressed microRNAs in obese BMM-EVs and found that among the candidates, miR-140 (with the function of promoting adipogenesis) and miR-378a (with the function of enhancing osteogenesis) coordinately determine SSPC fate of osteogenic and adipogenic differentiation by targeting the Pparα-Abca1 axis. BMM miR-140 conditional knockout mice showed resistance to obesity-induced bone deterioration, while miR-140 overexpression in SSPCs led to low bone mass and marrow adiposity in lean mice. BMM miR-378a conditional depletion in mice led to obesity-like bone deterioration. More importantly, we used an SSPC-specific targeting aptamer to precisely deliver miR-378a-3p-overloaded BMM-EVs to SSPCs via an aptamer-engineered extracellular vesicle delivery system, and this approach rescued bone deterioration in obese mice. Thus, our study reveals the critical role of BMMs in mediating obesity-induced bone deterioration by transporting selective extracellular-vesicle microRNAs into SSPCs and controlling SSPC fate.
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Affiliation(s)
- Chen He
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Chen Hu
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Wen-Zhen He
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Yu-Chen Sun
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Yangzi Jiang
- School of Biomedical Sciences, Institute for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine (CNRM), The Chinese University of Hong Kong, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ling Liu
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Jing Hou
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Kai-Xuan Chen
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Yu-Rui Jiao
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Mei Huang
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Min Huang
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Mi Yang
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
| | - Qiong Lu
- Department of Pharmacy, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Jie Wei
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Joint Degeneration and Injury, Changsha, Hunan, 410008, China
- Key Laboratory of Aging-related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital, Central South University, Changsha, China
| | - Chao Zeng
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Joint Degeneration and Injury, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Key Laboratory of Aging-related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital, Central South University, Changsha, China
| | - Guang-Hua Lei
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
- Hunan Key Laboratory of Joint Degeneration and Injury, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Key Laboratory of Aging-related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital, Central South University, Changsha, China
| | - Chang-Jun Li
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Key Laboratory of Aging-related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital, Central South University, Changsha, China
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4
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Tang J, Liu J, Wang F, Yao Y, Hu R. Colorimetric and photothermal dual-mode aptasensor with redox cycling amplification for the detection of ochratoxin A in corn samples. Food Chem 2024; 439:137968. [PMID: 38043279 DOI: 10.1016/j.foodchem.2023.137968] [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: 07/27/2023] [Revised: 10/15/2023] [Accepted: 11/09/2023] [Indexed: 12/05/2023]
Abstract
Ochratoxin A (OTA) detection is critical for public health safety. This study proposes a G-quadruplex-Hemin/iodide (G4-Hemin/I-)-mediated non-enzyme redox cycling amplification (RCA) system for dual-modal (colorimetric and photothermal thermometer) OTA analysis. The proposed aptasensor platform for point-of-care testing employs a common thermometer for quantitative signal readouts. The OTA aptamer folds into a G4 structure, which significantly enhances the catalytic activity in the presence of I- after RCA reaction. Moreover, a notable temperature enhancement causes color changes, providing an ultrasensitive and label-free platform for OTA detection. Further, the designed sensor was applied to OTA content determination in corn samples and achieved satisfactory results compared to a commercial enzyme-linked immunoassay kit. The proposed dual-mode aptasensor is simple, highly sensitive (1 pg/mL for colorimetric method, 0.8 pg/mL for photothermal method), selective, and suitable for low-cost instrument-free bioanalysis in low-resource settings.
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Affiliation(s)
- Jian Tang
- National Engineering Research Center of Vacuum Metallurgy, Faculty of Metallurgy and Energy Engineering, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
| | - Jiali Liu
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Fupeng Wang
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Yaochun Yao
- National Engineering Research Center of Vacuum Metallurgy, Faculty of Metallurgy and Energy Engineering, Kunming University of Science and Technology, Kunming 650093, Yunnan, China.
| | - Rong Hu
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, Yunnan 650500, China.
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5
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Mahmoudian F, Ahmari A, Shabani S, Sadeghi B, Fahimirad S, Fattahi F. Aptamers as an approach to targeted cancer therapy. Cancer Cell Int 2024; 24:108. [PMID: 38493153 PMCID: PMC10943855 DOI: 10.1186/s12935-024-03295-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Conventional cancer treatments can cause serious side effects because they are not specific to cancer cells and can damage healthy cells. Aptamers often are single-stranded oligonucleotides arranged in a unique architecture, allowing them to bind specifically to target sites. This feature makes them an ideal choice for targeted therapeutics. They are typically produced through the systematic evolution of ligands by exponential enrichment (SELEX) and undergo extensive pharmacological revision to modify their affinity, specificity, and therapeutic half-life. Aptamers can act as drugs themselves, directly inhibiting tumor cells. Alternatively, they can be used in targeted drug delivery systems to transport drugs directly to tumor cells, minimizing toxicity to healthy cells. In this review, we will discuss the latest and most advanced approaches to using aptamers for cancer treatment, particularly targeted therapy overcoming resistance to conventional therapies.
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Affiliation(s)
- Fatemeh Mahmoudian
- Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
| | - Azin Ahmari
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
- Department of Radiation Oncology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Shiva Shabani
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
- Department of Infectious Diseases, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Bahman Sadeghi
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
- Department of Community Medicine, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Shohreh Fahimirad
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran.
| | - Fahimeh Fattahi
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran.
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
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6
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Kang B, Park SV, Oh SS. Ionic liquid-caged nucleic acids enable active folding-based molecular recognition with hydrolysis resistance. Nucleic Acids Res 2024; 52:73-86. [PMID: 37994697 PMCID: PMC10783497 DOI: 10.1093/nar/gkad1093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023] Open
Abstract
Beyond storage and transmission of genetic information in cellular life, nucleic acids can perform diverse interesting functions, including specific target recognition and biochemical reaction acceleration; the versatile biopolymers, however, are acutely vulnerable to hydrolysis-driven degradation. Here, we demonstrate that the cage effect of choline dihydrogen phosphate permits active folding of nucleic acids like water, but prevents their phosphodiester hydrolysis unlike water. The choline-based ionic liquid not only serves as a universal inhibitor of nucleases, exceptionally extending half-lives of nucleic acids up to 6 500 000 times, but highly useful tasks of nucleic acids (e.g. mRNA detection of molecular beacons, ligand recognition of aptamers, and transesterification reaction of ribozymes) can be also conducted with well-conserved affinities and specificities. As liberated from the function loss and degradation risk, the presence of undesired and unknown nucleases does not undermine desired molecular functions of nucleic acids without hydrolysis artifacts even in nuclease cocktails and human saliva.
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Affiliation(s)
- Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
- Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon 21983, South Korea
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7
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Han Y, Wu Y, He B, Wu D, Hua J, Qian H, Zhang J. DNA nanoparticles targeting FOXO4 selectively eliminate cigarette smoke-induced senescent lung fibroblasts. NANOSCALE ADVANCES 2023; 5:5965-5973. [PMID: 37881696 PMCID: PMC10597553 DOI: 10.1039/d3na00547j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023]
Abstract
The pathogenesis and development of chronic obstructive pulmonary disease (COPD) are significantly related to cellular senescence. Strategies to eliminate senescent cells have been confirmed to benefit several senescence-related diseases. However, there are few reports of senolytic drugs in COPD management. In this study, we demonstrated elevated FOXO4 expression in cigarette smoke-induced senescent lung fibroblasts both in vitro and in vivo. Additionally, self-assembled DNA nanotubes loaded with single-stranded FOXO4 siRNA (siFOXO4-NT) were designed and synthesized to knockdown FOXO4 in senescent fibroblasts. We found that siFOXO4-NT can concentration- and time-dependently enter human lung fibroblasts (HFL-1 cells), thereby reducing FOXO4 levels in vitro. Most importantly, siFOXO4-NT selectively cleared senescent HFL-1 cells by reducing BCLXL expression and the BCL2/BAX ratio, which were increased in CSE-induced senescent HFL-1 cells. The findings from our work present a novel strategy for senolytic drug development for COPD therapy.
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Affiliation(s)
- Yaopin Han
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai 200032 China
| | - Yixing Wu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai 200032 China
| | - Binfeng He
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai 200032 China
- Department of General Practice, Xinqiao Hospital, Third Military Medical University Chongqing 400037 China
| | - Di Wu
- Institute of Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Xinqiao Hospital, Third Military Medical University Chongqing 400037 China
| | - Jianlan Hua
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai 200032 China
| | - Hang Qian
- Institute of Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Xinqiao Hospital, Third Military Medical University Chongqing 400037 China
| | - Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai 200032 China
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Chehelgerdi M, Chehelgerdi M, Allela OQB, Pecho RDC, Jayasankar N, Rao DP, Thamaraikani T, Vasanthan M, Viktor P, Lakshmaiya N, Saadh MJ, Amajd A, Abo-Zaid MA, Castillo-Acobo RY, Ismail AH, Amin AH, Akhavan-Sigari R. Progressing nanotechnology to improve targeted cancer treatment: overcoming hurdles in its clinical implementation. Mol Cancer 2023; 22:169. [PMID: 37814270 PMCID: PMC10561438 DOI: 10.1186/s12943-023-01865-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023] Open
Abstract
The use of nanotechnology has the potential to revolutionize the detection and treatment of cancer. Developments in protein engineering and materials science have led to the emergence of new nanoscale targeting techniques, which offer renewed hope for cancer patients. While several nanocarriers for medicinal purposes have been approved for human trials, only a few have been authorized for clinical use in targeting cancer cells. In this review, we analyze some of the authorized formulations and discuss the challenges of translating findings from the lab to the clinic. This study highlights the various nanocarriers and compounds that can be used for selective tumor targeting and the inherent difficulties in cancer therapy. Nanotechnology provides a promising platform for improving cancer detection and treatment in the future, but further research is needed to overcome the current limitations in clinical translation.
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Affiliation(s)
- Mohammad Chehelgerdi
- Novin Genome (NG) Institute, Research and Development Center for Biotechnology, Shahrekord, Chaharmahal and Bakhtiari, Iran.
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Chaharmahal and Bakhtiari, Iran.
| | - Matin Chehelgerdi
- Novin Genome (NG) Institute, Research and Development Center for Biotechnology, Shahrekord, Chaharmahal and Bakhtiari, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Chaharmahal and Bakhtiari, Iran
| | | | | | - Narayanan Jayasankar
- Department of Pharmacology, SRM Institute of Science and Technology, SRM College Of Pharmacy, Chengalpattu District, Kattankulathur, Tamil Nadu, 603203, India
| | - Devendra Pratap Rao
- Department of Chemistry, Coordination Chemistry Laboratory, Dayanand Anglo-Vedic (PG) College, Kanpur-208001, U.P, India
| | - Tamilanban Thamaraikani
- Department of Pharmacology, SRM Institute of Science and Technology, SRM College Of Pharmacy, Chengalpattu District, Kattankulathur, Tamil Nadu, 603203, India
| | - Manimaran Vasanthan
- Department of Pharmaceutics, SRM Institute of Science and Technology, SRM College Of Pharmacy, Chengalpattu District, Kattankulathur, Tamil Nadu, 603203, India
| | - Patrik Viktor
- Keleti Károly Faculty of Business and Management, Óbuda University, Tavaszmező U. 15-17, 1084, Budapest, Hungary
| | - Natrayan Lakshmaiya
- Department of Mechanical Engineering, Saveetha School of Engineering, SIMATS, Chennai, Tamil Nadu, India
| | - Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman, 11831, Jordan
| | - Ayesha Amajd
- Faculty of Organization and Management, Silesian University of Technology, 44-100, Gliwice, Poland
- Department of Mechanical Engineering, CEMMPRE, University of Coimbra, Polo II, 3030-788, Coimbra, Portugal
| | - Mabrouk A Abo-Zaid
- Department of Biology, College of Science, Jazan University, 82817, Jazan, Saudi Arabia
| | | | - Ahmed H Ismail
- Department of Biology, College of Science, Jazan University, 82817, Jazan, Saudi Arabia
| | - Ali H Amin
- Deanship of Scientific Research, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center, Tuebingen, Germany
- Department of Health Care Management and Clinical Research, Collegium Humanum Warsaw Management University Warsaw, Warsaw, Poland
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9
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Mehryab F, Taghizadeh F, Goshtasbi N, Merati F, Rabbani S, Haeri A. Exosomes as cutting-edge therapeutics in various biomedical applications: An update on engineering, delivery, and preclinical studies. Biochimie 2023; 213:139-167. [PMID: 37207937 DOI: 10.1016/j.biochi.2023.05.010] [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: 12/24/2022] [Revised: 04/29/2023] [Accepted: 05/16/2023] [Indexed: 05/21/2023]
Abstract
Exosomes are cell-derived nanovesicles, circulating in different body fluids, and acting as an intercellular mechanism. They can be purified from culture media of different cell types and carry an enriched content of various protein and nucleic acid molecules originating from their parental cells. It was indicated that the exosomal cargo can mediate immune responses via many signaling pathways. Over recent years, the therapeutic effects of various exosome types were broadly investigated in many preclinical studies. Herein, we present an update on recent preclinical studies on exosomes as therapeutic and/or delivery agents for various applications. The exosome origin, structural modifications, natural or loaded active ingredients, size, and research outcomes were summarized for various diseases. Overall, the present article provides an overview of the latest exosome research interests and developments to clear the way for the clinical study design and application.
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Affiliation(s)
- Fatemeh Mehryab
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Taghizadeh
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nazanin Goshtasbi
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Faezeh Merati
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahram Rabbani
- Research Center for Advanced Technologies in Cardiovascular Medicine, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Azadeh Haeri
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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10
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Liao YC, Cheng TC, Tu SH, Chang J, Guo P, Chen LC, Ho YS. Tumor targeting and therapeutic assessments of RNA nanoparticles carrying α9-nAChR aptamer and anti-miR-21 in triple-negative breast cancers. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:351-366. [PMID: 37547295 PMCID: PMC10400867 DOI: 10.1016/j.omtn.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Triple-negative breast cancer (TNBC) is highly aggressive with a poor prognosis because of a lack of cell markers as drug targets. α9-Nicotinic acetylcholine receptor (nAChR) is expressed abundantly in TNBC; thus, it is a valuable biomarker for TNBC detection and treatment. In this study, we utilized thermodynamically stable three-way junction (3WJ) packaging RNA (pRNA) as the core to construct RNA nanoparticles with an α9-nAChR RNA aptamer as a targeting ligand and an anti-microRNA-21 (miR-21) as a therapeutic module. We compared the configuration of the two RNA nanoparticles and found that 3WJ-B-α9-nAChR-aptamer fluorescent RNA nanoparticles (3WJ-B-α9-apt-Alexa) exhibited better specificity for α9-nAChR in TNBC cells compared with 3WJ-C-α9-nAChR. Furthermore, 3WJ-B-α9-apt-Alexa bound more efficiently to TNBC patient-derived xenograft (PDX) tumors than 3WJ fluorescent RNA nanoparticles (3WJ-Alexa) with little or no accumulation in healthy organs after systemic injection in mice. Moreover, 3WJ-B-α9-nAChR-aptamer RNA nanoparticles carrying anti-miR-21 (3WJ-B-α9-apt-anti-miR-21) significantly suppressed TNBC-PDX tumor growth and induced cell apoptosis because of reduced miR-21 gene expression and upregulated the phosphatase and tensin homolog (PTEN) and programmed cell death 4 (PDCD4) proteins. In addition, no pathological changes were detected upon toxicity examination of treated mice. In conclusion, the 3WJ-B-α9-nAChR-aptamer RNA nanoparticles established in this study efficiently deliver therapeutic anti-miR-21, indicating their potential as a novel TNBC therapy.
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Affiliation(s)
- You-Cheng Liao
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
| | - Tzu-Chun Cheng
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 406040, Taiwan
| | - Shih-Hsin Tu
- Department of Surgery, Taipei Medical University Hospital, Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Jungshan Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
- International Master/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- College of Medicine, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Li-Ching Chen
- Department of Biological Science & Technology, College of Life Sciences, China Medical University, Taichung 406040, Taiwan
| | - Yuan-Soon Ho
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 406040, Taiwan
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11
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Hartung J, McCann N, Doe E, Hayth H, Benkato K, Johnson MB, Viard M, Afonin KA, Khisamutdinov EF. Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25300-25312. [PMID: 37204867 PMCID: PMC10331730 DOI: 10.1021/acsami.3c01604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We introduce a toehold-mediated strand displacement strategy for regulated shape-switching of nucleic acid nanoparticles (NANPs) enabling their sequential transformation from triangular to hexagonal architectures at isothermal conditions. The successful shape transitions were confirmed by electrophoretic mobility shift assays, atomic force microscopy, and dynamic light scattering. Furthermore, implementation of split fluorogenic aptamers allowed for monitoring the individual transitions in real time. Three distinct RNA aptamers─malachite green (MG), broccoli, and mango─were embedded within NANPs as reporter domains to confirm shape transitions. While MG "lights up" within the square, pentagonal, and hexagonal constructs, the broccoli is activated only upon formation of pentagon and hexagon NANPs, and mango reports only the presence of hexagons. Moreover, the designed RNA fluorogenic platform can be employed to construct a logic gate that performs an AND operation with three single-stranded RNA inputs by implementing a non-sequential polygon transformation approach. Importantly, the polygonal scaffolds displayed promising potential as drug delivery agents and biosensors. All polygons exhibited effective cellular internalization followed by specific gene silencing when decorated with fluorophores and RNAi inducers. This work offers a new perspective for the design of toehold-mediated shape-switching nanodevices to activate different light-up aptamers for the development of biosensors, logic gates, and therapeutic devices in the nucleic acid nanotechnology.
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Affiliation(s)
- Jordan Hartung
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Nathan McCann
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
- Basic Science Program, Leidos Biomedical Research Inc. National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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12
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Hu Z, Jiang Z, Yang Z, Liu L, Zhu Z, Jin Y, Yin Y. Development of a modularized aptamer targeting the nuclear T-cell suppressor PAC1. Analyst 2023; 148:2616-2625. [PMID: 37191022 DOI: 10.1039/d3an00011g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Aptamers associated with cancer targeting therapy are commonly focused on cell membrane proteins; however, the study of intracellular, particularly, nuclear proteins is limited. The nuclear phosphatase PAC1 has been reported to be a potential T cell-related immunotherapeutic target. Here, we identified an aptamer, designated as PA5, with high affinity and specificity for PAC1 through the systematic evolution of ligands by exponential enrichment (SELEX) procedure. We then developed a dual-module aptamer PAC1-AS consisting of a cell-internalizing module and a targeting module, which can recognize PAC1 in the nucleus under physiological conditions. This modularized aptamer raises the possibility of manipulating endosomes and provides insights into the exploration and development of an efficient cancer immunotherapy approach.
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Affiliation(s)
- Zixi Hu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Zhongyu Jiang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Zeliang Yang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Liang Liu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Zhenyu Zhu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Yan Jin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
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13
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Chang Y, Wang Y, Li W, Wei Z, Tang S, Chen R. Mechanisms, Techniques and Devices of Airborne Virus Detection: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085471. [PMID: 37107752 PMCID: PMC10138381 DOI: 10.3390/ijerph20085471] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/13/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Airborne viruses, such as COVID-19, cause pandemics all over the world. Virus-containing particles produced by infected individuals are suspended in the air for extended periods, actually resulting in viral aerosols and the spread of infectious diseases. Aerosol collection and detection devices are essential for limiting the spread of airborne virus diseases. This review provides an overview of the primary mechanisms and enhancement techniques for collecting and detecting airborne viruses. Indoor virus detection strategies for scenarios with varying ventilations are also summarized based on the excellent performance of existing advanced comprehensive devices. This review provides guidance for the development of future aerosol detection devices and aids in the control of airborne transmission diseases, such as COVID-19, influenza and other airborne transmission viruses.
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Affiliation(s)
- Yuqing Chang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Yuqian Wang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Wen Li
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (W.L.); (Z.W.)
| | - Zewen Wei
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (W.L.); (Z.W.)
| | - Shichuan Tang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Rui Chen
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
- Correspondence:
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14
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Zhang M, Guo X, Wang J. Advanced biosensors for mycotoxin detection incorporating miniaturized meters. Biosens Bioelectron 2023; 224:115077. [PMID: 36669289 DOI: 10.1016/j.bios.2023.115077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Advanced biosensors, considered as emerging technologies, are capable of accurate, quantitative and real-time analysis for point-of-care testing (POCT) applications. Moreover, the integrating of miniaturized meters into these advanced biosensors makes them ideally appropriate for portable, sensitive and selective detection of biomolecules. Miniaturized meters including PGMs (personal glucose meters), thermometer, pressuremeter, pH meter, etc. are the most accurate devices and wide availability in the market, exhibiting a promising potential towards detection of small molecule mycotoxins. In this article, we introduce and analyze the recent advancements for sensing of mycotoxins measured by handheld meters since the first report in 2012. Furthermore, limitations and challenges for versatile meters application against mycotoxins in food matrix are highlighted. By overcoming the bottleneck problems, we believe the miniaturized meters-based biosensor platform will provide great possibilities for mycotoxins analysis and launch them to the market.
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Affiliation(s)
- Mengke Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Xiaodong Guo
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
| | - Jiaqi Wang
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agriculture Sciences, Beijing, 100193, China.
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15
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Convenient Solid-Phase Attachment of Small-Molecule Ligands to Oligonucleotides via a Biodegradable Acid-Labile P-N-Bond. Molecules 2023; 28:molecules28041904. [PMID: 36838892 PMCID: PMC9961013 DOI: 10.3390/molecules28041904] [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: 01/26/2023] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
One of the key problems in the design of therapeutic and diagnostic oligonucleotides is the attachment of small-molecule ligands for targeted deliveries in such a manner that provides the controlled release of the oligonucleotide at a certain moment. Here, we propose a novel, convenient approach for attaching ligands to the 5'-end of the oligonucleotide via biodegradable, acid-labile phosphoramide linkage. The method includes the activation of the 5'-terminal phosphate of the fully protected, support-bound oligonucleotide, followed by interaction with a ligand bearing the primary amino group. This technique is simple to perform, allows for forcing the reaction to completion by adding excess soluble reactant, eliminates the problem of the limited solubility of reagents, and affords the possibility of using different solvents, including water/organic media. We demonstrated the advantages of this approach by synthesizing and characterizing a wide variety of oligonucleotide 5'-conjugates with different ligands, such as cholesterol, aliphatic oleylamine, and p-anisic acid. The developed method suits different types of oligonucleotides (deoxyribo-, 2'-O-methylribo-, ribo-, and others).
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16
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Chen M, Zhou P, Kong Y, Li J, Li Y, Zhang Y, Ran J, Zhou J, Chen Y, Xie S. Inducible Degradation of Oncogenic Nucleolin Using an Aptamer-Based PROTAC. J Med Chem 2023; 66:1339-1348. [PMID: 36608275 DOI: 10.1021/acs.jmedchem.2c01557] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
While proteolysis-targeting chimeras (PROTACs) are showing promise for targeting previously undruggable molecules, their application has been limited by difficulties in identifying suitable ligands and undesired on-target toxicity. Aptamers can virtually recognize any protein through their unique and switchable conformations. Here, by exploiting aptamers as targeting warheads, we developed a novel strategy for inducible degradation of undruggable proteins. As a proof of concept, we chose oncogenic nucleolin (NCL) as the target and generated a series of NCL degraders, and demonstrated that dNCL#T1 induced NCL degradation in a ubiquitin-proteasome-dependent manner, thereby inhibiting NCL-mediated breast cancer cell proliferation. To reduce on-target toxicity, we further developed a light-controllable PROTAC, opto-dNCL#T1, by introducing a photolabile complementary oligonucleotide to hybridize with dNCL#T1. UVA irradiation liberated dNCL#T1 from caged opto-dNCL#T1, leading to dNCL#T1 activation and NCL degradation. These results indicate that aptamer-based PROTACs are a viable alternative approach to degrade proteins of interest in a highly tunable manner.
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Affiliation(s)
- Miao Chen
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Ping Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yun Kong
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jingrui Li
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Yan Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yao Zhang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jie Ran
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China.,College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Yan Chen
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Songbo Xie
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, China.,Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
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17
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Perez Tobia J, Huang PJJ, Ding Y, Saran Narayan R, Narayan A, Liu J. Machine Learning Directed Aptamer Search from Conserved Primary Sequences and Secondary Structures. ACS Synth Biol 2023; 12:186-195. [PMID: 36594697 DOI: 10.1021/acssynbio.2c00462] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Computer-aided prediction of aptamer sequences has been focused on primary sequence alignment and motif comparison. We observed that many aptamers have a conserved hairpin, yet the sequence of the hairpin can be highly variable. Taking such secondary structure information into consideration, a new algorithm combining conserved primary sequences and secondary structures is developed, which combines three scores based on sequence abundance, stability, and structure, respectively. This algorithm was used in the prediction of aptamers from the caffeine and theophylline selections. In the late rounds of the selections, when the libraries were converged, the predicted sequences matched well with the most abundant sequences. When the libraries were far from convergence and the sequences were deemed challenging for traditional analysis methods, this algorithm still predicted aptamer sequences that were experimentally verified by isothermal titration calorimetry. This algorithm paves a new way to look for patterns in aptamer selection libraries and mimics the sequence evolution process. It will help shorten the aptamer selection time and promote the biosensor and chemical biology applications of aptamers.
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Affiliation(s)
- Javier Perez Tobia
- Department of Computer Science, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran Narayan
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Apurva Narayan
- Department of Computer Science, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada.,Department of Computer Science, Western University, London, Ontario N6A 3K7, Canada.,Systems Design Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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18
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Soni R, Krishna AM, More SH, Sharma A. Reversible Modulation of Aptamer-Ligand Binding in RNA Light-Up Aptamers Containing G-Quadruplex Using Chemical Stimuli. Chembiochem 2023; 24:e202200574. [PMID: 36352557 DOI: 10.1002/cbic.202200574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/07/2022] [Indexed: 11/11/2022]
Abstract
Regulating a system in equilibrium transiently to out-of-equilibrium by using certain stimuli is the strategy used by natural biomolecules to function. Herein, we showed that the interaction of synthetic RNA aptamers, having a G-quadruplex core structure, with their corresponding ligands could be regulated from their equilibrium state to non-equilibrium state in a reversible manner using simple chemical stimuli (Ag+ and cysteine). The approach would be useful for designing aptamer regulators that work in a dynamic nucleic acid network, where a strict control on aptamer-ligand interaction is needed. In addition, to the best of our knowledge, this is the first report which shows that RNA G-quadruplexes can be disrupted by the addition of silver ions. This would be useful not only in designing RNA-based sensors or regulators but would also be useful for understanding the role of metal ions in RNA folding and catalysis.
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Affiliation(s)
- Rashi Soni
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - A Murali Krishna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Shahaji H More
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Ashwani Sharma
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India.,Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
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19
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Feng Y, Yang Y, Xiao Y, Fu T, He L, Qi L, Yang Q, Peng R, Tan W. Multi-parameter Inputted Logic-Gating on Aptamer-Encoded Extracellular Vesicles for Colorectal Cancer Diagnosis. Anal Chem 2023; 95:1132-1139. [PMID: 36533834 DOI: 10.1021/acs.analchem.2c03883] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Extracellular vesicles (EVs) have emerged as a potential biomarker in liquid biopsy. However, cancer heterogeneity poses significant challenge to precise molecular diagnosis based on single-parameter input. Hence, strategies for analyzing multiple inputs with molecular computing were developed with the aim of improving diagnostic accuracy in liquid biopsy. In the present study, based on the surface of aptamer-encoded EVs, three toe-hold extended DNA aptamers served as specific inputs to perform AND-logic-gating to distinguish between healthy and cancerous EVs. In addition, this strategy has been successfully employed to analyze circulating EVs in clinical samples from colorectal cancer patients and healthy donors. The developed method has a promising future in the analysis of multiplex EV membrane proteins and the identification of early cancer.
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Affiliation(s)
- Yawei Feng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yunshan Yang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yating Xiao
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Lei He
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Lubin Qi
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Qiuxia Yang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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20
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Radwan Y, Rebolledo LP, Panigaj M, Afonin KA. Dynamic Nanostructures for Conditional Activation and Deactivation of Biological Pathways. Methods Mol Biol 2023; 2709:309-318. [PMID: 37572291 PMCID: PMC10482318 DOI: 10.1007/978-1-0716-3417-2_22] [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] [Indexed: 08/14/2023]
Abstract
Nucleic acid nanotechnology utilizes natural and synthetic structural motifs to build versatile nucleic acid nanoparticles (NANPs). These rationally designed assemblies can be further equipped with functional nucleic acids and other molecules such as peptides, fluorescent dyes, etc. In addition to nucleic acids that directly interact with the regulated target gene transcripts, NANPs can display decoys, wherein the oligonucleotide stretches with transcription factor binding sequences, preventing transcription initiation. The nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is a group of five crucial transcription factors regulating the pathogenesis of inflammatory diseases and cancer; as such, they are relevant targets for therapy. One therapeutic approach involves interdependent self-recognizing hybridized DNA/RNA fibers designed to bind NF-κB and prevent its interaction with the promotor region of NF-κB-dependent genes involved in inflammatory responses. Decoying NF-κB results in the inability to initiate transcription of regulated genes, showing a promising approach to gene regulation and gene therapy. The protocol described herein provides detailed steps for the synthesis of NF-κB decoy fibers, as well as their characterization using polyacrylamide gel electrophoresis (to confirm desired physicochemical properties and purity) and functional bioassays (to confirm desired biological activity).
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Affiliation(s)
- Yasmine Radwan
- Department of Chemistry, University of North Carolina, Charlotte, NC, USA
| | - Laura P Rebolledo
- Department of Chemistry, University of North Carolina, Charlotte, NC, USA
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, USA
| | - Martin Panigaj
- Department of Chemistry, University of North Carolina, Charlotte, NC, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina, Charlotte, NC, USA.
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21
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Rolband LA, Ke W, Afonin KA. Aptamer Conjugated RNA/DNA Hybrid Nanostructures Designed for Efficient Regulation of Blood Coagulation. Methods Mol Biol 2023; 2709:277-286. [PMID: 37572288 PMCID: PMC10498824 DOI: 10.1007/978-1-0716-3417-2_19] [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] [Indexed: 08/14/2023]
Abstract
Disruptions to the hemostatic pathway can cause a variety of serious or even life-threatening complications. Situations in which the coagulation of blood has become disturbed necessitate immediate care. Thrombin-binding aptamers are single-stranded nucleic acids that bind to thrombin with high specificity and affinity. While they can effectively inhibit thrombin, they suffer from rapid degradation and clearance in vivo. These issues are resolved, however, by attaching the therapeutic aptamer to a nucleic acid nanostructure. The increased size of the nanostructure-aptamer complex elongates the post-infusion half-life of the aptamer. These complexes are also immunoquiescent. A significant benefit of using nucleic acids as anticoagulants is their rapid deactivation by the introduction of a nanostructure made fully from the reverse complement of the therapeutically active nanostructure. These advantages make nanoparticle conjugated antithrombin aptamers a promising candidate for a rapidly reversible anticoagulant therapy.
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Affiliation(s)
- Lewis A Rolband
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Weina Ke
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- University of North Carolina at Charlotte, Charlotte, NC, USA.
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22
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Panigaj M, Skelly E, Beasock D, Marriott I, Johnson MB, Salotti J, Afonin KA. Therapeutic immunomodulation by rationally designed nucleic acids and nucleic acid nanoparticles. Front Immunol 2023; 14:1053550. [PMID: 36798121 PMCID: PMC9927404 DOI: 10.3389/fimmu.2023.1053550] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 01/18/2023] [Indexed: 02/01/2023] Open
Abstract
The immune system has evolved to defend organisms against exogenous threats such as viruses, bacteria, fungi, and parasites by distinguishing between "self" and "non-self". In addition, it guards us against other diseases, such as cancer, by detecting and responding to transformed and senescent cells. However, for survival and propagation, the altered cells and invading pathogens often employ a wide range of mechanisms to avoid, inhibit, or manipulate the immunorecognition. As such, the development of new modes of therapeutic intervention to augment protective and prevent harmful immune responses is desirable. Nucleic acids are biopolymers essential for all forms of life and, therefore, delineating the complex defensive mechanisms developed against non-self nucleic acids can offer an exciting avenue for future biomedicine. Nucleic acid technologies have already established numerous approaches in therapy and biotechnology; recently, rationally designed nucleic acids nanoparticles (NANPs) with regulated physiochemical properties and biological activities has expanded our repertoire of therapeutic options. When compared to conventional therapeutic nucleic acids (TNAs), NANP technologies can be rendered more beneficial for synchronized delivery of multiple TNAs with defined stabilities, immunological profiles, and therapeutic functions. This review highlights several recent advances and possible future directions of TNA and NANP technologies that are under development for controlled immunomodulation.
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Affiliation(s)
- Martin Panigaj
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States.,Institute of Biology & Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, Slovakia
| | - Elizabeth Skelly
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Jacqueline Salotti
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States
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23
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Trammell SR. Light-Assisted Drying for the Thermal Stabilization of Nucleic Acid Nanoparticles and Other Biologics. Methods Mol Biol 2023; 2709:117-130. [PMID: 37572276 DOI: 10.1007/978-1-0716-3417-2_7] [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: 08/14/2023]
Abstract
Cold-chain storage can be challenging and expensive for the transportation and storage of biologics, especially in low-resource settings. Nucleic acid nanoparticles (NANPs) are an example of new biological products that require refrigerated storage. Light-assisted drying (LAD) is a new processing technique to prepare biologics for anhydrous storage in a trehalose amorphous solid matrix at ambient temperatures. Small volume samples (10 μL) containing NANPs are irradiated with a 1064 nm laser to speed the evaporation of water and create an amorphous trehalose preservation matrix. In previous studies, samples were stored for 1 month at 4 °C or 20 °C without degradation. A FLIR SC655 mid-IR camera is used to record the temperature of samples during processing. The trehalose matrix was characterized using polarized light imaging to determine if crystallization occurred during processing or storage. Damage to LAD-processed NANPs was assessed after processing and storage using gel electrophoresis.
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Affiliation(s)
- Susan R Trammell
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC, USA.
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24
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Yin X, He Z, Ge W, Zhao Z. Application of aptamer functionalized nanomaterials in targeting therapeutics of typical tumors. Front Bioeng Biotechnol 2023; 11:1092901. [PMID: 36873354 PMCID: PMC9978196 DOI: 10.3389/fbioe.2023.1092901] [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: 11/08/2022] [Accepted: 02/01/2023] [Indexed: 02/22/2023] Open
Abstract
Cancer is a major cause of human death all over the world. Traditional cancer treatments include surgery, radiotherapy, chemotherapy, immunotherapy, and hormone therapy. Although these conventional treatment methods improve the overall survival rate, there are some problems, such as easy recurrence, poor treatment, and great side effects. Targeted therapy of tumors is a hot research topic at present. Nanomaterials are essential carriers of targeted drug delivery, and nucleic acid aptamers have become one of the most important targets for targeted tumor therapy because of their high stability, high affinity, and high selectivity. At present, aptamer-functionalized nanomaterials (AFNs), which combine the unique selective recognition characteristics of aptamers with the high-loading performance of nanomaterials, have been widely studied in the field of targeted tumor therapy. Based on the reported application of AFNs in the biomedical field, we introduce the characteristics of aptamer and nanomaterials, and the advantages of AFNs first. Then introduce the conventional treatment methods for glioma, oral cancer, lung cancer, breast cancer, liver cancer, colon cancer, pancreatic cancer, ovarian cancer, and prostate cancer, and the application of AFNs in targeted therapy of these tumors. Finally, we discuss the progress and challenges of AFNs in this field.
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Affiliation(s)
- Xiujuan Yin
- Department of Radiology, Shaoxing People's Hospital, Shaoxing, China.,Key Laboratory of Functional Molecular Imaging of Tumor and Interventional Diagnosis and Treatment of Shaoxing City, Shaoxing, China
| | - Zhenqiang He
- Clinical Medical College of Hebei University, Baoding, China.,Department of Radiology, Hebei University Affiliated Hospital, Baoding, China
| | - Weiying Ge
- Department of Radiology, Hebei University Affiliated Hospital, Baoding, China
| | - Zhenhua Zhao
- Department of Radiology, Shaoxing People's Hospital, Shaoxing, China.,Key Laboratory of Functional Molecular Imaging of Tumor and Interventional Diagnosis and Treatment of Shaoxing City, Shaoxing, China.,Medical College of Zhejiang University, Hangzhou, China
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25
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Klotz K, Radwan Y, Chakrabarti K. Dissecting Functional Biological Interactions Using Modular RNA Nanoparticles. Molecules 2022; 28:molecules28010228. [PMID: 36615420 PMCID: PMC9821959 DOI: 10.3390/molecules28010228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022] Open
Abstract
Nucleic acid nanoparticles (NANPs) are an exciting and innovative technology in the context of both basic and biomedical research. Made of DNA, RNA, or their chemical analogs, NANPs are programmed for carrying out specific functions within human cells. NANPs are at the forefront of preventing, detecting, and treating disease. Their nucleic acid composition lends them biocompatibility that provides their cargo with enhanced opportunity for coordinated delivery. Of course, the NANP system of targeting specific cells and tissues is not without its disadvantages. Accumulation of NANPs outside of the target tissue and the potential for off-target effects of NANP-mediated cargo delivery present challenges to research and medical professionals and these challenges must be effectively addressed to provide safe treatment to patients. Importantly, development of NANPs with regulated biological activities and immunorecognition becomes a promising route for developing versatile nucleic acid therapeutics. In a basic research context, NANPs can assist investigators in fine-tuning the structure-function relationship of final formulations and in this review, we explore the practical applications of NANPs in laboratory and clinical settings and discuss how we can use established nucleic acid research techniques to design effective NANPs.
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Affiliation(s)
- Kaitlin Klotz
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Yasmine Radwan
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
- Correspondence:
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26
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Chandler M, Jain S, Halman J, Hong E, Dobrovolskaia MA, Zakharov AV, Afonin KA. Artificial Immune Cell, AI-cell, a New Tool to Predict Interferon Production by Peripheral Blood Monocytes in Response to Nucleic Acid Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204941. [PMID: 36216772 PMCID: PMC9671856 DOI: 10.1002/smll.202204941] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acid nanoparticles, or NANPs, rationally designed to communicate with the human immune system, can offer innovative therapeutic strategies to overcome the limitations of traditional nucleic acid therapies. Each set of NANPs is unique in their architectural parameters and physicochemical properties, which together with the type of delivery vehicles determine the kind and the magnitude of their immune response. Currently, there are no predictive tools that would reliably guide the design of NANPs to the desired immunological outcome, a step crucial for the success of personalized therapies. Through a systematic approach investigating physicochemical and immunological profiles of a comprehensive panel of various NANPs, the research team developes and experimentally validates a computational model based on the transformer architecture able to predict the immune activities of NANPs. It is anticipated that the freely accessible computational tool that is called an "artificial immune cell," or AI-cell, will aid in addressing the current critical public health challenges related to safety criteria of nucleic acid therapies in a timely manner and promote the development of novel biomedical tools.
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Affiliation(s)
- Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Sankalp Jain
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Justin Halman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Enping Hong
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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27
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Anh Lam P, Furr DP, Tran A, McKeough RQ, Beasock D, Chandler M, Afonin KA, Trammell SR. The Application of Light-Assisted Drying to the Thermal Stabilization of Nucleic Acid Nanoparticles. Biopreserv Biobank 2022; 20:451-460. [PMID: 36067075 PMCID: PMC9603253 DOI: 10.1089/bio.2022.0035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Cold-chain storage can be challenging and expensive for the transportation and storage of biologics, especially in low-resource settings. Nucleic acid nanoparticles (NANPs) are an example of new biological products that require refrigerated storage. Light-assisted drying (LAD) is a new processing technique to prepare biologics for anhydrous storage in a trehalose amorphous solid matrix at ambient temperatures. In this study, LAD was used to thermally stabilize four types of NANPs with differing structures and melting temperatures. Methods: Small volume samples (10 μL) containing NANPs were irradiated with a 1064 nm laser to speed the evaporation of water and create an amorphous trehalose preservation matrix. Samples were then stored for 1 month at 4°C or 20°C. A FLIR C655 mid-IR camera was used to record the temperature of samples during processing. The trehalose matrix was characterized using polarized light imaging (PLI) to determine if crystallization occurred during processing or storage. Damage to LAD-processed NANPs was assessed after processing and storage using gel electrophoresis. Results: Based on the end moisture content (EMC) as a function time and the thermal histories of samples, a LAD processing time of 30 min is sufficient to achieve low EMCs for the 10 μL samples used in this study. PLI demonstrates that the trehalose matrix was resistant to crystallization during processing and after storage at 4°C and at room temperature. The native-polyacrylamide gel electrophoresis results for DNA cubes, RNA cubes, and RNA rings indicate that the main structures of these NANPs were not damaged significantly after LAD processing and being stored at 4°C or at room temperature for 1 month. Conclusions: These preliminary studies indicate that LAD processing can stabilize NANPs for dry-state storage at room temperature, providing an alternative to refrigerated storage for these nanomedicine products.
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Affiliation(s)
- Phuong Anh Lam
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Daniel P. Furr
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Allison Tran
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Riley Q. McKeough
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Damian Beasock
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Susan R. Trammell
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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28
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Lu Q, Hu Y, Yin Li C, Kuang Y. Aptamer‐Array‐Guided Protein Assembly Enhances Synthetic mRNA Switch Performance. Angew Chem Int Ed Engl 2022; 61:e202207319. [PMID: 35703374 PMCID: PMC9544043 DOI: 10.1002/anie.202207319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Indexed: 11/17/2022]
Abstract
Synthetic messenger RNA (mRNA) switches are powerful synthetic biological tools that can sense cellular molecules to manipulate cell fate. However, their performances are limited by high output signal noise due to leaky output protein expression. Here, we designed a readout control module that disables protein leakage from generating signal. Aptamer array on the switch guides the inactive output protein to self‐assemble into functional assemblies that generate output signal. Leaky protein expression fails to saturate the array, thus produces marginal signal. In this study, we demonstrated that switches with this module exhibit substantially lower signal noise and, consequently, higher input sensitivity and wider output range. Such switches are applicable for different types of input molecules and output proteins. The work here demonstrates a new type of spatially guided protein self‐assembly, affording novel synthetic mRNA switches that promise accurate cell manipulation for biomedical applications.
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Affiliation(s)
- Qiuyu Lu
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
| | - Yaxin Hu
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
| | - Cheuk Yin Li
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
| | - Yi Kuang
- Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay, Kowloon, Hong Kong Hong Kong
- HKUST Shenzhen Research Institute Shenzhen Guangdong China
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29
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Ke W, Chandler M, Cedrone E, Saito RF, Rangel MC, de Souza Junqueira M, Wang J, Shi D, Truong N, Richardson M, Rolband LA, Dréau D, Bedocs P, Chammas R, Dokholyan NV, Dobrovolskaia MA, Afonin KA. Locking and Unlocking Thrombin Function Using Immunoquiescent Nucleic Acid Nanoparticles with Regulated Retention In Vivo. NANO LETTERS 2022; 22:5961-5972. [PMID: 35786891 PMCID: PMC9511123 DOI: 10.1021/acs.nanolett.2c02019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The unbalanced coagulation of blood is a life-threatening event that requires accurate and timely treatment. We introduce a user-friendly biomolecular platform based on modular RNA-DNA anticoagulant fibers programmed for reversible extracellular communication with thrombin and subsequent control of anticoagulation via a "kill-switch" mechanism that restores hemostasis. To demonstrate the potential of this reconfigurable technology, we designed and tested a set of anticoagulant fibers that carry different thrombin-binding aptamers. All fibers are immunoquiescent, as confirmed in freshly collected human peripheral blood mononuclear cells. To assess interindividual variability, the anticoagulation is confirmed in the blood of human donors from the U.S. and Brazil. The anticoagulant fibers reveal superior anticoagulant activity and prolonged renal clearance in vivo in comparison to free aptamers. Finally, we confirm the efficacy of the "kill-switch" mechanism in vivo in murine and porcine models.
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Affiliation(s)
- Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Edward Cedrone
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Renata F Saito
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Maria Cristina Rangel
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Mara de Souza Junqueira
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Da Shi
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Nguyen Truong
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Melina Richardson
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Lewis A Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Didier Dréau
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Peter Bedocs
- Department of Anesthesiology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland 20817, United States
| | - Roger Chammas
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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30
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Li X, Bhullar AS, Binzel DW, Guo P. The dynamic, motile and deformative properties of RNA nanoparticles facilitate the third milestone of drug development. Adv Drug Deliv Rev 2022; 186:114316. [PMID: 35526663 DOI: 10.1016/j.addr.2022.114316] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/25/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022]
Abstract
Besides mRNA, rRNA, and tRNA, cells contain many other noncoding RNA that display critical roles in the regulation of cellular functions. Human genome sequencing revealed that the majority of non-protein-coding DNA actually codes for non-coding RNAs. The dynamic nature of RNA results in its motile and deformative behavior. These conformational transitions such as the change of base-pairing, breathing within complemented strands, and pseudoknot formation at the 2D level as well as the induced-fit and conformational capture at the 3D level are important for their biological functions including regulation, translation, and catalysis. The dynamic, motile and catalytic activity has led to a belief that RNA is the origin of life. We have recently reported that the deformative property of RNA nanoparticles enhances their penetration through the leaky blood vessel of cancers which leads to highly efficient tumor accumulation. This special deformative property also enables RNA nanoparticles to pass the glomerulus, overcoming the filtration size limit, resulting in fast renal excretion and rapid body clearance, thus low or no toxicity. The biodistribution of RNA nanoparticles can be further improved by the incorporation of ligands for cancer targeting. In addition to the favorable biodistribution profiles, RNA nanoparticles possess other properties including self-assembly, negative charge, programmability, and multivalency; making it a great material for pharmaceutical applications. The intrinsic negative charge of RNA nanoparticles decreases the toxicity of drugs by preventing nonspecific binding to the negative charged cell membrane and enhancing the solubility of hydrophobic drugs. The polyvalent property of RNA nanoparticles allows the multi-functionalization which can apply to overcome drug resistance. This review focuses on the summary of these unique properties of RNA nanoparticles, which describes the mechanism of RNA dynamic, motile and deformative properties, and elucidates and prepares to welcome the RNA therapeutics as the third milestone in pharmaceutical drug development.
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Affiliation(s)
- Xin Li
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Abhjeet S Bhullar
- Interdisciplinary Biophysics Graduate Program, College of Art and Science, The Ohio State University, Columbus, OH 43210, United States
| | - Daniel W Binzel
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
| | - Peixuan Guo
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, United States; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States; College of Medicine, The Ohio State University, Columbus, OH 43210, United States.
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31
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Lu Q, Hu Y, Li CY, Kuang Y. Aptamer‐Array‐Guided Protein Assembly Enhances Synthetic mRNA Switch Performance. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Qiuyu Lu
- Hong Kong University of Science and Technology School of Engineering Chemical and Biological Engineering HONG KONG
| | - Yaxin Hu
- Hong Kong University of Science and Technology School of Engineering Chemical and Biological Engineering HONG KONG
| | - Cheuk Yin Li
- Hong Kong University of Science and Technology School of Engineering Chemical and Biological Engineering HONG KONG
| | - Yi Kuang
- Hong Kong University of Science and Technology Chemical and Biological Engineering Room 5578, Academic Bldg,Clear Water Bay 000000 Kowloon HONG KONG
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32
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Chen S, Zhang L, Yuan Q, Tan J. Current Advances in Aptamer-based Biomolecular Recognition and Biological Process Regulation. Chem Res Chin Univ 2022; 38:847-855. [PMID: 35573821 PMCID: PMC9077342 DOI: 10.1007/s40242-022-2087-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 12/01/2022]
Abstract
The interaction between biomolecules with their target ligands plays a great role in regulating biological functions. Aptamers are short oligonucleotide sequences that can specifically recognize target biomolecules via structural complementarity and thus regulate related biological functions. In the past ten years, aptamers have made great progress in target biomolecule recognition, becoming a powerful tool to regulate biological functions. At present, there are many reviews on aptamers applied in biomolecular recognition, but few reviews pay attention to aptamer-based regulation of biological functions. Here, we summarize the approaches to enhancing aptamer affinity and the advancements of aptamers in regulating enzymatic activity, cellular immunity and cellular behaviors. Furthermore, this review discusses the challenges and future perspectives of aptamers in target recognition and biological functions regulation, aiming to provide some promising ideas for future regulation of biomolecular functions in a complex biological environment.
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Affiliation(s)
- Sisi Chen
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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33
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An ultrasensitive electrochemical aptasensor based on Pd@PCN-222 as a signal probe coupled with exonuclease III-assisted cycling amplification for the detection of ochratoxin A. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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34
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Tran AN, Chandler M, Halman J, Beasock D, Fessler A, McKeough RQ, Lam PA, Furr DP, Wang J, Cedrone E, Dobrovolskaia MA, Dokholyan NV, Trammell SR, Afonin KA. Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104814. [PMID: 35128787 PMCID: PMC8976831 DOI: 10.1002/smll.202104814] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/17/2021] [Indexed: 05/13/2023]
Abstract
Recent advances in nanotechnology now allow for the methodical implementation of therapeutic nucleic acids (TNAs) into modular nucleic acid nanoparticles (NANPs) with tunable physicochemical properties which can match the desired biological effects, provide uniformity, and regulate the delivery of multiple TNAs for combinatorial therapy. Despite the potential of novel NANPs, the maintenance of their structural integrity during storage and shipping remains a vital issue that impedes their broader applications. Cold chain storage is required to maintain the potency of NANPs in the liquid phase, which greatly increases transportation costs. To promote long-term storage and retention of biological activities at higher temperatures (e.g., +50 °C), a panel of representative NANPs is first exposed to three different drying mechanisms-vacuum concentration (SpeedVac), lyophilization (Lyo), and light-assisted drying (LAD)-and then rehydrated and analyzed. While SpeedVac primarily operates using heat, Lyo avoids temperature increases by taking advantage of pressure reduction and LAD involves a near-infrared laser for uniform drying in the presence of trehalose. This work compares and defines refinements crucial in formulating an optimal strategy for producing stable, fully functional NANPs and presents a forward advancement in their development for clinical applications.
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Affiliation(s)
- Allison N Tran
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Justin Halman
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Adam Fessler
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Riley Q McKeough
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Phuong Anh Lam
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Daniel P Furr
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Edward Cedrone
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, 21702, USA
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, 21702, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Susan R Trammell
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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Huang Y, Nguyen MK, Nguyen VH, Loo J, Lehtonen AJ, Kuzyk A. Characterizing Aptamers with Reconfigurable Chiral Plasmonic Assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2954-2960. [PMID: 35212547 PMCID: PMC8908738 DOI: 10.1021/acs.langmuir.1c03434] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Aptamers have emerged as versatile affinity ligands and as promising alternatives to protein antibodies. However, the inconsistency in the reported affinities and specificities of aptamers has greatly hindered the development of aptamer-based applications. Herein, we present a strategy to characterize aptamers by using DNA origami-based chiral plasmonic assemblies as reporters and establishing a competitive hybridization reaction-based thermodynamic model. We demonstrate the characterization of several DNA aptamers, including aptamers for small molecules and macromolecules, as well as aptamers with high and low affinities. The presented characterization scheme can be readily adapted to a wide selection of aptamers. We anticipate that our approach will advance the development of aptamer-based applications by enabling reliable and reproducible characterization of aptamers.
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Affiliation(s)
- Yike Huang
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dist. 10, 700000 Ho Chi Minh City, Vietnam
- Vietnam
National University Ho Chi Minh City,
Linh Trung Ward, Thu Duc District, 700000 Ho Chi Minh City, Vietnam
| | - Vu Hoang Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Arttu J. Lehtonen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Department
of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
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Chen S, Xu Z, Li S, Liang H, Zhang C, Wang Z, Li J, Li J, Yang H. Systematic Interrogation of Cellular Signaling in Live Cells Using a Membrane‐Anchored DNA Multitasking Processor. Angew Chem Int Ed Engl 2022; 61:e202113795. [DOI: 10.1002/anie.202113795] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 12/11/2022]
Affiliation(s)
- Shan Chen
- Fujian Key Laboratory of Functional Marine Sensing Materials Fuzhou Institute of Oceanography Minjiang University Fuzhou 350108 P.R. China
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350108 P.R. China
| | - Zhifei Xu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350108 P.R. China
| | - Shiwei Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350108 P.R. China
| | - Hong Liang
- Fujian Key Laboratory of Functional Marine Sensing Materials Fuzhou Institute of Oceanography Minjiang University Fuzhou 350108 P.R. China
| | - Chen Zhang
- Fujian Key Laboratory of Functional Marine Sensing Materials Fuzhou Institute of Oceanography Minjiang University Fuzhou 350108 P.R. China
| | - Zonghua Wang
- Fujian Key Laboratory of Functional Marine Sensing Materials Fuzhou Institute of Oceanography Minjiang University Fuzhou 350108 P.R. China
| | - Jingying Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350108 P.R. China
- College of Biological Science and Engineering Fuzhou University Fuzhou 350108 P.R. China
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350108 P.R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350108 P.R. China
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Wan Q, Zeng Z, Qi J, Chen Z, Liu X, Zu Y. Aptamer-armed nanostructures improve the chemotherapy outcome of triple-negative breast cancer. Mol Ther 2022; 30:2242-2256. [PMID: 35143958 DOI: 10.1016/j.ymthe.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/10/2021] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
Triple-negative breast cancer is an aggressive subtype of breast cancer that is primarily treated using systemic chemotherapy due to the lack of a specific cell surface marker for drug delivery. Cancer cell-specific aptamer-mediated drug delivery is a promising targeted chemotherapy for marker-unknown cancers. Using a poorly differentiated carcinoma cell-specific DNA aptamer (PDGC21T), we formed a self-assembling circinate DNA nanoparticle (Apt21TNP) that binds triple-negative breast cancer cells. Using our previously designed pH-sensitive dendrimer-conjugated doxorubicin (DDOX) as the payload, we found that each nanoparticle loaded 30 doxorubicin molecules to form an Apt21TNP-DDOX nanomedicine that is stable in human plasma. Upon cell binding, Apt21TNP-DDOX is internalized by triple-negative breast cancer cells through the macropinocytosis pathway. Once inside cells, the low pH microenvironment in lysosomes induces doxorubicin drug payload release from Apt21TNP-DDOX. Our in vitro studies demonstrate that Apt21TNP-DDOX can preferentially bind triple-negative breast cancer cells to induce cell death. Further, we show that Apt21TNP-DDOX can accumulate in subcutaneous MDA-MB-231 tumors in mice following systemic administration to reduce tumor burden, minimize side effects, and improve animal survival. Together, our results demonstrate that Apt21TNP-mediated doxorubicin delivery is a potent, targeted chemotherapy for triple-negative breast cancer that may alleviate side effects in patients.
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Affiliation(s)
- Quanyuan Wan
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Zihua Zeng
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Jianjun Qi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Zhenghu Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Xiaohui Liu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.
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38
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Afonin KA, Dobrovolskaia MA, Ke W, Grodzinski P, Bathe M. Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation. Adv Drug Deliv Rev 2022; 181:114081. [PMID: 34915069 PMCID: PMC8886801 DOI: 10.1016/j.addr.2021.114081] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 01/01/2023]
Abstract
With numerous recent advances, the field of therapeutic nucleic acid nanotechnology is now poised for clinical translation supported by several examples of FDA-approved nucleic acid nanoformulations including two recent mRNA-based COVID-19 vaccines. Within this rapidly growing field, a new subclass of nucleic acid therapeutics called nucleic acid nanoparticles (NANPs) has emerged in recent years, which offers several unique properties distinguishing it from traditional therapeutic nucleic acids. Key unique aspects of NANPs include their well-defined 3D structure, their tunable multivalent architectures, and their ability to incorporate conditional activations of therapeutic targeting and release functions that enable diagnosis and therapy of cancer, regulation of blood coagulation disorders, as well as the development of novel vaccines, immunotherapies, and gene therapies. However, non-consolidated research developments of this highly interdisciplinary field create crucial barriers that must be overcome in order to impact a broader range of clinical indications. Forming a consortium framework for nucleic acid nanotechnology would prioritize and consolidate translational efforts, offer several unifying solutions to expedite their transition from bench-to-bedside, and potentially decrease the socio-economic burden on patients for a range of conditions. Herein, we review the unique properties of NANPs in the context of therapeutic applications and discuss their associated translational challenges.
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Affiliation(s)
- Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Weina Ke
- Biomedical Informatics and Data Science Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Piotr Grodzinski
- Nanodelivery Systems and Devices Branch, Cancer Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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39
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Xia F, He A, Zhao H, Sun Y, Duan Q, Abbas SJ, Liu J, Xiao Z, Tan W. Molecular Engineering of Aptamer Self-Assemblies Increases in Vivo Stability and Targeted Recognition. ACS NANO 2022; 16:169-179. [PMID: 34935348 DOI: 10.1021/acsnano.1c05265] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Functionally modified aptamer conjugates are promising tools for targeted imaging or treatment of various diseases. However, broad applications of aptamer molecules are limited by their in vivo instability. To overcome this challenge, current strategies mostly rely on covalent chemical modification of aptamers, a complicated process that requires case-by-case sequence design, multiple-step synthesis, and purification. Herein, we report a covalent modification-free strategy to enhance the in vivo stability of aptamers. This strategy simply utilizes one-step molecular engineering of aptamers with gold nanoclusters (GNCs) to form GNCs@aptamer self-assemblies. Using Sgc8 as a representative aptamer, the resulting GNCs@Sgc8 assemblies enhance cancer-cell-specific binding and sequential internalization by a receptor-mediated endocytosis pathway. Importantly, the GNCs@aptamer self-assemblies resist nuclease degradation for as long as 48 h, compared to the degradation of aptamer alone at 3 h. In parallel, the tumor-targeted recognition and retention of GNCs@aptamer self-assemblies are dramatically enhanced, indicated by a 9-fold signal increase inside the tumor compared to the aptamer alone. This strategy is to avoid complicated chemical modification of aptamers and can be extended to all aptamers. Our work provides a simple, effective, and universal strategy for enhancing the in vivo stability of any aptamer or its conjugates, thus expanding their imaging and therapeutic applications.
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Affiliation(s)
- Fangfang Xia
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Axin He
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haitao Zhao
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Sun
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiao Duan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sk Jahir Abbas
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianjun Liu
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zeyu Xiao
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
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40
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Chen S, Xu Z, Li S, Liang H, Zhang C, Wang Z, Li J, Li J, Yang H. Systematic Interrogation of Cellular Signaling in Live Cells using a Membrane‐anchored DNA Multitasking Processor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shan Chen
- Minjiang University Fujian Key Laboratory of Functional Marine Sensing Materials, Fuzhou Institute of Oceanography CHINA
| | - Zhifei Xu
- Fuzhou University College of Chemistry CHINA
| | - Shiwei Li
- Fuzhou University College of Chemistry CHINA
| | - Hong Liang
- Minjiang University Fujian Key Laboratory of Functional Marine Sensing Materials, Fuzhou Institute of Oceanography CHINA
| | - Chen Zhang
- Minjiang University Fujian Key Laboratory of Functional Sensing Materials, Fuzhou Institute of Oceanography CHINA
| | - Zonghua Wang
- Minjiang University Fujian Key Laboratory of Functional Sensing Materials, Fuzhou Institute of Oceanography CHINA
| | - Jingying Li
- Fuzhou University College of Biological Science and Engineering Qi Shan Campus of Fuzhou University,2 Xue Yuan Road 350108 Fuzhou CHINA
| | - Juan Li
- Fuzhou University College of Chemistry CHINA
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41
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Liu M, Wang L, Lo Y, Shiu SCC, Kinghorn AB, Tanner JA. Aptamer-Enabled Nanomaterials for Therapeutics, Drug Targeting and Imaging. Cells 2022; 11:159. [PMID: 35011722 PMCID: PMC8750369 DOI: 10.3390/cells11010159] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/06/2023] Open
Abstract
A wide variety of nanomaterials have emerged in recent years with advantageous properties for a plethora of therapeutic and diagnostic applications. Such applications include drug delivery, imaging, anti-cancer therapy and radiotherapy. There is a critical need for further components which can facilitate therapeutic targeting, augment their physicochemical properties, or broaden their theranostic applications. Aptamers are single-stranded nucleic acids which have been selected or evolved to bind specifically to molecules, surfaces, or cells. Aptamers can also act as direct biologic therapeutics, or in imaging and diagnostics. There is a rich field of discovery at the interdisciplinary interface between nanomaterials and aptamer science that has significant potential across biomedicine. Herein, we review recent progress in aptamer-enabled materials and discuss pending challenges for their future biomedical application.
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Affiliation(s)
- Mengping Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Lin Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Young Lo
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Andrew B. Kinghorn
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Julian A. Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR 999077, China
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42
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Lin M, Zou S, Li T, Karges J, Chen Y, Zhao Y, Ji L, Chao H. Chiral rhodium(III)-azobenzene complexes as photoswitchable DNA molecular locks. Chem Commun (Camb) 2022; 58:4324-4327. [DOI: 10.1039/d2cc00932c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chiral rhodium(III)-azobenzene complexes which are able to intercalate into DNA were developed. Upon light exposure, the azobenzene moiety of the metal complex can photoisomerize from the trans- into the cis-form...
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43
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Jiang Y, Chen SJ. RLDOCK method for predicting RNA-small molecule binding modes. Methods 2022; 197:97-105. [PMID: 33549725 PMCID: PMC8333169 DOI: 10.1016/j.ymeth.2021.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
RNA molecules play critical roles in cellular functions at the level of gene expression and regulation. The intricate 3D structures and the functional roles of RNAs make RNA molecules ideal targets for therapeutic drugs. The rational design of RNA-targeted drug requires accurate modeling of RNA-ligand interactions. Recently a new computational tool, RLDOCK, was developed to predict ligand binding sites and binding poses. Using an iterative multiscale sampling and search algorithm and a energy-based evaluation of ligand poses, the method enables efficient and accurate predictions for RNA-ligand interactions. Here we present a detailed illustration of the computational procedure for the practical implementation of the RLDOCK method. Using Flavin mononucleotide (FMN) docking to F. nucleatum FMN riboswitch as an example, we illustrate the computational protocol for RLDOCK-based prediction of RNA- ligand interactions. The RLDOCK software is freely accessible at http://https://github.com/Vfold-RNA/RLDOCK.
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Affiliation(s)
- Yangwei Jiang
- Department of Physics, MU Institute for Data Science and Informatics, Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Shi-Jie Chen
- Department of Physics, MU Institute for Data Science and Informatics, Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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44
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Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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45
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Chandler M, Johnson B, Khisamutdinov E, Dobrovolskaia MA, Sztuba-Solinska J, Salem AK, Breyne K, Chammas R, Walter NG, Contreras LM, Guo P, Afonin KA. The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field. ACS NANO 2021; 15:16957-16973. [PMID: 34677049 PMCID: PMC9023608 DOI: 10.1021/acsnano.0c10240] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) hosts an annual meeting series focused on presenting the latest research achievements involving RNA-based therapeutics and strategies, aiming to expand their current biomedical applications while overcoming the remaining challenges of the burgeoning field of RNA nanotechnology. The most recent online meeting hosted a series of engaging talks and discussions from an international cohort of leading nanotechnologists that focused on RNA modifications and modulation, dynamic RNA structures, overcoming delivery limitations using a variety of innovative platforms and approaches, and addressing the newly explored potential for immunomodulation with programmable nucleic acid nanoparticles. In this Nano Focus, we summarize the main discussion points, conclusions, and future directions identified during this two-day webinar as well as more recent advances to highlight and to accelerate this exciting field.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47304, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Joanna Sztuba-Solinska
- Department of Biological Sciences, Auburn University, 120 W. Samford Avenue, Rouse Life Sciences Building, Auburn, Alabama 36849, United States
| | - Aliasger K Salem
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, Iowa 52242, United States
| | - Koen Breyne
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachussets 02114, United States
| | - Roger Chammas
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Centro de Investigação Translacional em Oncologia, Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de São Paulo - ICESP, Faculdade de Medicina da Universidade de São Paulo - FMUSP, Avenida Dr. Arnaldo 251, Cerqueira César, São Paulo 01246-000, São Paulo, Brazil
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering and Department of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78714, United States
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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Doroudian M, Azhdari MH, Goodarzi N, O'Sullivan D, Donnelly SC. Smart Nanotherapeutics and Lung Cancer. Pharmaceutics 2021; 13:1972. [PMID: 34834387 PMCID: PMC8619749 DOI: 10.3390/pharmaceutics13111972] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is a significant health problem worldwide. Unfortunately, current therapeutic strategies lack a sufficient level of specificity and can harm adjacent healthy cells. Consequently, to address the clinical need, novel approaches to improve treatment efficiency with minimal side effects are required. Nanotechnology can substantially contribute to the generation of differentiated products and improve patient outcomes. Evidence from previous research suggests that nanotechnology-based drug delivery systems could provide a promising platform for the targeted delivery of traditional chemotherapeutic drugs and novel small molecule therapeutic agents to treat lung cancer cells more effectively. This has also been found to improve the therapeutic index and reduce the required drug dose. Nanodrug delivery systems also provide precise control over drug release, resulting in reduced toxic side effects, controlled biodistribution, and accelerated effects or responses. This review highlights the most advanced and novel nanotechnology-based strategies, including targeted nanodrug delivery systems, stimuli-responsive nanoparticles, and bio-nanocarriers, which have recently been employed in preclinical and clinical investigations to overcome the current challenges in lung cancer treatments.
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Affiliation(s)
- Mohammad Doroudian
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran 15719-14911, Iran
| | - Mohammad H Azhdari
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran 15719-14911, Iran
| | - Nima Goodarzi
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran 15719-14911, Iran
| | - David O'Sullivan
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
| | - Seamas C Donnelly
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
- Department of Clinical Medicine, Trinity Centre for Health Sciences, Tallaght University Hospital, Tallaght, Dublin 24, Ireland
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47
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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48
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Redox manipulation of enzyme activity through physiologically active molecule. iScience 2021; 24:102977. [PMID: 34485859 PMCID: PMC8405983 DOI: 10.1016/j.isci.2021.102977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/01/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
The effective utility of physiologically active molecules is crucial in numerous biological processes. However, the regulation of enzyme functions through active substances remains challenging at present. Here, glutathione (GSH), produced in cells, was used to modulate the catalytic activity of thrombin without external stimulus. It was found that high concentrations of GSH was more conducive to initiate the cleavage of compound AzoDiTAB in the range of concentration used to mimic the difference between cancer and normal cells, which has practical implications for targeting cancel cells since GSH is overexpressed in cancer cells. Importantly, GSH treatment caused the deformation of G4 structure by cleaving AzoDiTAB and thus triggered the transition of thrombin from being free to be inhibited in complex biological systems. This work would open up a new route for the specific manipulation of enzyme-catalyzed systems in cancer cells. The transition of telomere DNA structures based on redox switch Achieving redox manipulation of thrombin activity through active substance This switch can be specifically used for enzyme regulation in cancer cells
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Ke W, Afonin KA. Exosomes as natural delivery carriers for programmable therapeutic nucleic acid nanoparticles (NANPs). Adv Drug Deliv Rev 2021; 176:113835. [PMID: 34144087 PMCID: PMC8440450 DOI: 10.1016/j.addr.2021.113835] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023]
Abstract
With recent advances in nanotechnology and therapeutic nucleic acids (TNAs), various nucleic acid nanoparticles (NANPs) have demonstrated great promise in diagnostics and therapeutics. However, the full realization of NANPs' potential necessitates the development of a safe, efficient, biocompatible, stable, tissue-specific, and non-immunogenic delivery system. Exosomes, the smallest extracellular vesicles and an endogenous source of nanocarriers, offer these advantages while avoiding complications associated with manufactured agents. The lipid membranes of exosomes surround a hydrophilic core, allowing for the simultaneous incorporation of hydrophobic and hydrophilic drugs, nucleic acids, and proteins. Additional capabilities for post-isolation exosome surface modifications with imaging agents, targeting ligands, and covalent linkages also pave the way for their diverse biomedical applications. This review focuses on exosomes: their biogenesis, intracellular trafficking, transportation capacities, and applications with emphasis on the delivery of TNAs and programmable NANPs. We also highlight some of the current challenges and discuss opportunities related to the development of therapeutic exosome-based formulations and their clinical translation.
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Affiliation(s)
- Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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50
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Chandler M, Minevich B, Roark B, Viard M, Johnson MB, Rizvi MH, Deaton TA, Kozlov S, Panigaj M, Tracy JB, Yingling YG, Gang O, Afonin KA. Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities. ACS APPLIED MATERIALS & INTERFACES 2021; 13:39030-39041. [PMID: 34402305 PMCID: PMC8654604 DOI: 10.1021/acsami.1c09230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Precise control over the assembly of biocompatible three-dimensional (3D) nanostructures would allow for programmed interactions within the cellular environment. Nucleic acids can be used as programmable crosslinkers to direct the assembly of quantum dots (QDs) and tuned to demonstrate different interparticle binding strategies. Morphologies of self-assembled QDs are evaluated via gel electrophoresis, transmission electron microscopy, small-angle X-ray scattering, and dissipative particle dynamics simulations, with all results being in good agreement. The controlled assembly of 3D QD organizations is demonstrated in cells via the colocalized emission of multiple assembled QDs, and their immunorecognition is assessed via enzyme-linked immunosorbent assays. RNA interference inducers are also embedded into the interparticle binding strategy to be released in human cells only upon QD assembly, which is demonstrated by specific gene silencing. The programmability and intracellular activity of QD assemblies offer a strategy for nucleic acids to imbue the structure and therapeutic function into the formation of complex networks of nanostructures, while the photoluminescent properties of the material allow for optical tracking in cells in vitro.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Brandon Roark
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702, United States
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mehedi H Rizvi
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas A Deaton
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Seraphim Kozlov
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Martin Panigaj
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice 04154, Slovak Republic
| | - Joseph B Tracy
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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