1
|
Park C, Chung S, Kim H, Kim N, Son HY, Kim R, Lee S, Park G, Rho HW, Park M, Han J, Song Y, Lee J, Jun SH, Huh YM, Jeong HH, Lim EK, Kim E, Haam S. All-in-One Fusogenic Nanoreactor for the Rapid Detection of Exosomal MicroRNAs for Breast Cancer Diagnosis. ACS NANO 2024. [PMID: 39248519 DOI: 10.1021/acsnano.4c08339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Molecular-profiling-based cancer diagnosis has significant implications for predicting disease prognosis and selecting targeted therapeutic interventions. The analysis of cancer-derived extracellular vesicles (EVs) provides a noninvasive and sequential method to assess the molecular landscape of cancer. Here, we developed an all-in-one fusogenic nanoreactor (FNR) encapsulating DNA-fueled molecular machines (DMMs) for the rapid and direct detection of EV-associated microRNAs (EV miRNAs) in a single step. This platform was strategically designed to interact selectively with EVs and induce membrane fusion under a specific trigger. After fusion, the DMMs recognized the target miRNA and initiated nonenzymatic signal amplification within a well-defined reaction volume, thus producing an amplified fluorescent signal within 30 min. We used the FNRs to analyze the unique expression levels of three EV miRNAs in various biofluids, including cell culture, urine, and plasma, and obtained an accuracy of 86.7% in the classification of three major breast cancer (BC) cell lines and a diagnostic accuracy of 86.4% in the distinction between patients with cancer and healthy donors. Notably, a linear discriminant analysis revealed that increasing the number of miRNAs from one to three improved the accuracy of BC patient discrimination from 78.8 to 95.4%. Therefore, this all-in-one diagnostic platform performs nondestructive EV processing and signal amplification in one step, providing a straightforward, accurate, and effective individual EV miRNA analysis strategy for personalized BC treatment.
Collapse
Affiliation(s)
- Chaewon Park
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Soohyun Chung
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hansol Kim
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Nayoung Kim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
- Institute for Medical Engineering and Science, MIT, Cambridge, Massachusetts 02139, United States
| | - Hye Young Son
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, Republic of Korea
- YUHS-KRIBB Medical Convergence Research Institute, Seoul 03722, Republic of Korea
| | - Ryunhyung Kim
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Sojeong Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Geunseon Park
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyun Wook Rho
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, Republic of Korea
| | - Mirae Park
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, Republic of Korea
| | - Jueun Han
- Department of Bioengineering and Nano-Bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon 22012, Republic of Korea
| | - Yejin Song
- Department of Bioengineering and Nano-Bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon 22012, Republic of Korea
| | - Jihee Lee
- Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Sung-Hoon Jun
- Electron Microscopy & Spectroscopy Team, Korea Basic Science Institute, Chungbuk 28119, Republic of Korea
| | - Yong-Min Huh
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, Republic of Korea
- YUHS-KRIBB Medical Convergence Research Institute, Seoul 03722, Republic of Korea
| | | | - Eun-Kyung Lim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology(KRIBB), Daejeon 34141, Republic of Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Eunjung Kim
- Department of Bioengineering and Nano-Bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon 22012, Republic of Korea
- Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Seungjoo Haam
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| |
Collapse
|
2
|
Lim K, Kodera N, Wang H, Mohamed MS, Hazawa M, Kobayashi A, Yoshida T, Hanayama R, Yano S, Ando T, Wong RW. High-Speed AFM Reveals Molecular Dynamics of Human Influenza A Hemagglutinin and Its Interaction with Exosomes. NANO LETTERS 2020; 20:6320-6328. [PMID: 32787163 DOI: 10.1021/acs.nanolett.0c01755] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Influenza A hemagglutinin (HA) is one of the crucial virulence factors that mediate host tropism and viral infectivity. Presently, the mechanism of the fusogenic transition of HA remains elusive. Here, we used high-speed atomic force microscopy (HS-AFM) to decipher the molecular dynamics of HA and its interaction with exosomes. Our data reveal that the native conformation of HA in the neutral buffer is ellipsoidal, and HA undergoes a conformational change in an acidic buffer. Real-time visualization of the fusogenic transition by HS-AFM suggests that the mechanism is possibly fit to the "uncaging" model, and HA intermediate appears as Y-shaped. A firm interaction between the HA and exosome in an acidic buffer indicates the insertion of a fusion peptide into the exosomal layer and subsequently destabilizes the layer, resulting in the deformation or rupture of exosomes, releasing exosomal contents. In contrast, the HA-exosome interaction is weak in a neutral buffer because the interaction is mediated by weak bonds between the HA receptor-binding site and receptors on the exosome.
Collapse
Affiliation(s)
- Keesiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hanbo Wang
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Mahmoud Shaaban Mohamed
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaharu Hazawa
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Akiko Kobayashi
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Takeshi Yoshida
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department of Immunology, Kanazawa University Graduate School of Medical Sciences, 13-1 Takara, Kanazawa, Ishikawa 920-8640, Japan
| | - Rikinari Hanayama
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department of Immunology, Kanazawa University Graduate School of Medical Sciences, 13-1 Takara, Kanazawa, Ishikawa 920-8640, Japan
| | - Seiji Yano
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Division of Medical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Toshio Ando
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Richard W Wong
- WPI-Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| |
Collapse
|
3
|
Jeyaram RA, Radha CA, Gromiha MM, Veluraja K. Design of fluorinated sialic acid analog inhibitor to H5 hemagglutinin of H5N1 influenza virus through molecular dynamics simulation study. J Biomol Struct Dyn 2019; 38:3504-3513. [PMID: 31594458 DOI: 10.1080/07391102.2019.1677500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Influenza epidemics and pandemics are caused by influenza A virus. The cell surface protein of hemagglutinin and neuraminidase is responsible for viral infection and release of progeny virus on the host cell membrane. Now 18 hemagglutinin and 11 neuraminidase subtypes are identified. The avian influenza virus of H5N1 is an emergent threat to public health issues. To control the influenza viral infection it is necessary to develop antiviral inhibitors and vaccination. In the present investigation we carried out 50 ns Molecular Dynamics simulation on H5 hemagglutinin of Influenza A virus H5N1 complexed with fluorinated sialic acid by substituting fluorine atoms at any two hydroxyls of sialic acid by considering combinatorial combination. The binding affinity between the protein-ligand complex system is investigated by calculating pair interaction energy and MM-PBSA binding free energy. All the complex structures are stabilized by hydrogen bonding interactions between the H5 protein and the ligand fluorinated sialic acid. It is concluded from all the analyses that the fluorinated complexes enhance the inhibiting potency against H5 hemagglutinin and the order of inhibiting potency is SIA-F9 ≫ SIA-F2 ≈ SIA-F7 ≈ SIA-F2F4 ≈ SIA-F2F9 ≈ SIA-F7F9 > SIA-F7F8 ≈ SIA-F2F8 ≈ SIA-F8F9 > SIA-F4 ≈ SIA-F4F7 ≈ SIA-F4F8 ≈ SIA-F8 ≈ SIA-F2F7 ≈ SIA > SIA-F4F9. This study suggests that one can design the inhibitor by using the mono fluorinated models SIA-F9, SIA-F2 and SIA-F7 and difluorinated models SIA-F2F4, SIA-F2F9 and SIA-F7F9 to inhibit H5 of H5N1 to avoid Influenza A viral infection.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- R A Jeyaram
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - K Veluraja
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| |
Collapse
|