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Basu S, Hendler-Neumark A, Bisker G. Rationally Designed Functionalization of Single-Walled Carbon Nanotubes for Real-Time Monitoring of Cholinesterase Activity and Inhibition in Plasma. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309481. [PMID: 38358018 DOI: 10.1002/smll.202309481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/25/2024] [Indexed: 02/16/2024]
Abstract
Enzymes play a pivotal role in regulating numerous bodily functions. Thus, there is a growing need for developing sensors enabling real-time monitoring of enzymatic activity and inhibition. The activity and inhibition of cholinesterase (CHE) enzymes in blood plasma are fluorometrically monitored using near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) as probes, strategically functionalized with myristoylcholine (MC)- the substrate of CHE. A significant decrease in the fluorescence intensity of MC-suspended SWCNTs upon interaction with CHE is observed, attributed to the hydrolysis of the MC corona phase of the SWCNTs by CHE. Complementary measurements for quantifying choline, the product of MC hydrolysis, reveal a correlation between the fluorescence intensity decrease and the amount of released choline, rendering the SWCNTs optical sensors with real-time feedback in the NIR biologically transparent spectral range. Moreover, when synthetic and naturally abundant inhibitors inhibit the CHE enzymes present in blood plasma, no significant modulations of the MC-SWCNT fluorescence are observed, allowing effective detection of CHE inhibition. The rationally designed SWCNT sensors platform for monitoring of enzymatic activity and inhibition in clinically relevant samples is envisioned to not only advance the field of clinical diagnostics but also deepen further understanding of enzyme-related processes in complex biological fluids.
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Affiliation(s)
- Srestha Basu
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Adi Hendler-Neumark
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gili Bisker
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, 6997801, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 6997801, Israel
- Center for Light-Matter Interaction, Tel Aviv University, Tel Aviv, 6997801, Israel
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2
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Stollmann A, Garcia-Guirado J, Hong JS, Rüedi P, Im H, Lee H, Ortega Arroyo J, Quidant R. Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform. Nat Commun 2024; 15:4109. [PMID: 38750038 PMCID: PMC11096335 DOI: 10.1038/s41467-024-48132-4] [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: 09/22/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Label-free detection of multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. First, we characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles are required.
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Affiliation(s)
- Alexia Stollmann
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Jose Garcia-Guirado
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Jae-Sang Hong
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Pascal Rüedi
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Jaime Ortega Arroyo
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland.
| | - Romain Quidant
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland.
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3
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Geng S, Guo P, Wang J, Zhang Y, Shi Y, Li X, Cao M, Song Y, Zhang H, Zhang Z, Zhang K, Song H, Shi J, Liu J. Ultrasensitive Optical Detection and Elimination of Residual Microtumors with a Postoperative Implantable Hydrogel Sensor for Preventing Cancer Recurrence. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307923. [PMID: 38174840 DOI: 10.1002/adma.202307923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/16/2023] [Indexed: 01/05/2024]
Abstract
In vivo optical imaging of trace biomarkers in residual microtumors holds significant promise for cancer prognosis but poses a formidable challenge. Here, a novel hydrogel sensor is designed for ultrasensitive and specific imaging of the elusive biomarker. This hydrogel sensor seamlessly integrates a molecular beacon nanoprobe with fibroblasts, offering both high tissue retention capability and an impressive signal-to-noise ratio for imaging. Signal amplification is accomplished through exonuclease I-mediated biomarker recycling. The resulting hydrogel sensor sensitively detects the biomarker carcinoembryonic antigen with a detection limit of 1.8 pg mL-1 in test tubes. Moreover, it successfully identifies residual cancer nodules with a median diameter of less than 2 mm in mice bearing partially removed primary triple-negative breast carcinomas (4T1). Notably, this hydrogel sensor is proven effective for the sensitive diagnosis of invasive tumors in post-surgical mice with infiltrating 4T1 cells, leveraging the role of fibroblasts in locally enriching tumor cells. Furthermore, the residual microtumor is rapidly photothermal ablation by polydopamine-based nanoprobe under the guidance of visualization, achieving ≈100% suppression of tumor recurrence and lung metastasis. This work offers a promising alternative strategy for visually detecting residual microtumors, potentially enhancing the prognosis of cancer patients following surgical interventions.
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Affiliation(s)
- Shizhen Geng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Pengke Guo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Jing Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yunya Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yaru Shi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Xinling Li
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Mengnian Cao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yutong Song
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Hongling Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China
| | - Haiwei Song
- Department of Biochemistry, National University of Singapore, SingaporeCity, 138673, Singapore
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China
| | - Junjie Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China
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4
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Macchia E, Torricelli F, Caputo M, Sarcina L, Scandurra C, Bollella P, Catacchio M, Piscitelli M, Di Franco C, Scamarcio G, Torsi L. Point-Of-Care Ultra-Portable Single-Molecule Bioassays for One-Health. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309705. [PMID: 38108547 DOI: 10.1002/adma.202309705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/20/2023] [Indexed: 12/19/2023]
Abstract
Screening asymptomatic organisms (humans, animals, plants) with a high-diagnostic accuracy using point-of-care-testing (POCT) technologies, though still visionary holds great potential. Convenient surveillance requires easy-to-use, cost-effective, ultra-portable but highly reliable, in-vitro-diagnostic devices that are ready for use wherever they are needed. Currently, there are not yet such devices available on the market, but there are a couple more promising technologies developed at readiness-level 5: the Clustered-Regularly-Interspaced-Short-Palindromic-Repeats (CRISPR) lateral-flow-strip tests and the Single-Molecule-with-a-large-Transistor (SiMoT) bioelectronic palmar devices. They both hold key features delineated by the World-Health-Organization for POCT systems and an occurrence of false-positive and false-negative errors <1-5% resulting in diagnostic-selectivity and sensitivity >95-99%, while limit-of-detections are of few markers. CRISPR-strip is a molecular assay that, can detect down to few copies of DNA/RNA markers in blood while SiMoT immunometric and molecular test can detect down to a single oligonucleotide, protein marker, or pathogens in 0.1mL of blood, saliva, and olive-sap. These technologies can prospectively enable the systematic and reliable surveillance of asymptomatic ones prior to worsening/proliferation of illnesses allowing for timely diagnosis and swift prognosis. This could establish a proactive healthcare ecosystem that results in effective treatments for all living organisms generating diffuse and well-being at efficient costs.
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Affiliation(s)
- Eleonora Macchia
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Fabrizio Torricelli
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Mariapia Caputo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Lucia Sarcina
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Cecilia Scandurra
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Paolo Bollella
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Michele Catacchio
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Matteo Piscitelli
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
- CNR IFN, Bari, 70126, Italy
| | | | - Gaetano Scamarcio
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
- CNR IFN, Bari, 70126, Italy
| | - Luisa Torsi
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
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5
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Seddighi S, Qi YA, Brown AL, Wilkins OG, Bereda C, Belair C, Zhang YJ, Prudencio M, Keuss MJ, Khandeshi A, Pickles S, Kargbo-Hill SE, Hawrot J, Ramos DM, Yuan H, Roberts J, Sacramento EK, Shah SI, Nalls MA, Colón-Mercado JM, Reyes JF, Ryan VH, Nelson MP, Cook CN, Li Z, Screven L, Kwan JY, Mehta PR, Zanovello M, Hallegger M, Shantaraman A, Ping L, Koike Y, Oskarsson B, Staff NP, Duong DM, Ahmed A, Secrier M, Ule J, Jacobson S, Reich DS, Rohrer JD, Malaspina A, Dickson DW, Glass JD, Ori A, Seyfried NT, Maragkakis M, Petrucelli L, Fratta P, Ward ME. Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD. Sci Transl Med 2024; 16:eadg7162. [PMID: 38277467 DOI: 10.1126/scitranslmed.adg7162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Functional loss of TDP-43, an RNA binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to the inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote the degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43-depleted human iPSC-derived neurons in vitro, and de novo peptides were found in cerebrospinal fluid (CSF) samples from patients with ALS or FTD. Using coordinated transcriptomic and proteomic studies of TDP-43-depleted human iPSC-derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43-depleted human iPSC-derived neurons were predictive of cryptic exons expressed in postmortem brain tissue from patients with TDP-43 proteinopathy. These cryptic exons produced transcript variants that generated de novo proteins. We found that the inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Last, we showed that 18 de novo peptides across 13 genes were present in CSF samples from patients with ALS/FTD spectrum disorders. The demonstration of cryptic exon translation suggests new mechanisms for ALS/FTD pathophysiology downstream of TDP-43 dysfunction and may provide a potential strategy to assay TDP-43 function in patient CSF.
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Affiliation(s)
- Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Oscar G Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Colleen Bereda
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Matthew J Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Aditya Khandeshi
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Sarah E Kargbo-Hill
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - James Hawrot
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Hebao Yuan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Roberts
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Erika Kelmer Sacramento
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Syed I Shah
- Data Tecnica International, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Jennifer M Colón-Mercado
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Joel F Reyes
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Veronica H Ryan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Casey N Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Ziyi Li
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Laurel Screven
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Justin Y Kwan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Puja R Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Martina Hallegger
- Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | | | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Björn Oskarsson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Nathan P Staff
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Aisha Ahmed
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, UCL, London, UK
| | - Jernej Ule
- Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | - Steven Jacobson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel S Reich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan D Rohrer
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Andrea Malaspina
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Jonathan D Glass
- Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, USA
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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6
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Stollmann A, Garcia-Guirado J, Hong JS, Im H, Lee H, Arroyo JO, Quidant R. Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform. RESEARCH SQUARE 2023:rs.3.rs-3309306. [PMID: 37886549 PMCID: PMC10602063 DOI: 10.21203/rs.3.rs-3309306/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Label-free detecting multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. Herein, we first thoroughly characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles is required.
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Affiliation(s)
- Alexia Stollmann
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Jose Garcia-Guirado
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Jae-Sang Hong
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jaime Ortega Arroyo
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Romain Quidant
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
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7
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Fang H, Zhou Y, Ma Y, Chen Q, Tong W, Zhan S, Guo Q, Xiong Y, Tang BZ, Huang X. M13 Bacteriophage-Assisted Recognition and Signal Spatiotemporal Separation Enabling Ultrasensitive Light Scattering Immunoassay. ACS NANO 2023; 17:18596-18607. [PMID: 37698300 DOI: 10.1021/acsnano.3c07194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
The demand for the ultrasensitive and rapid quantitative analysis of trace target analytes has become increasingly urgent. However, the sensitivity of traditional immunoassay-based detection methods is limited due to the contradiction between molecular recognition and signal amplification caused by the size effect of nanoprobes. To address this dilemma, we describe versatile M13 phage-assisted immunorecognition and signal transduction spatiotemporal separation that enable ultrasensitive light-scattering immunoassay systems for the quantitative detection of low-abundance target analytes. The newly developed immunoassay strategy combines the M13 phage-assisted light scattering signal fluctuations of gold nanoparticles (AuNPs) with gold in situ growth (GISG) technology. Given the synergy of M13 phage-mediated leverage effect and GISG-amplified light scattering signal modulation, the practical detection capability of this strategy can achieve the ultrasensitive and rapid quantification of ochratoxin A and alpha-fetoprotein in real samples at the subfemtomolar level within 50 min, displaying about 4 orders of magnitude enhancement in sensitivity compared with traditional phage-based ELISA. To further improve the sensitivity of our immunoassay, the biotin-streptavidin amplification scheme is implemented to detect severe acute respiratory syndrome coronavirus 2 spike protein down to the attomolar range. Overall, this study offers a direction for ultrasensitive quantitative detection of target analytes by the synergistic combination of M13 phage-mediated leverage effect and GISG-amplified light scattering signal modulation.
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Affiliation(s)
- Hao Fang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Yaofeng Zhou
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Yanbing Ma
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Qi Chen
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Weipeng Tong
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Shengnan Zhan
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
| | - Qian Guo
- Jiangxi Province Centre for Disease Control and Prevention, Nanchang 330029, P. R. China
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
- Jiangxi Medicine Academy of Nutrition and Health Management, Nanchang 330006, P. R. China
| | - Ben Zhong Tang
- Shenzhen Institute of Aggregate Science and Technology, School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
| | - Xiaolin Huang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China
- Jiangxi Medicine Academy of Nutrition and Health Management, Nanchang 330006, P. R. China
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8
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Stollmann A, Garcia-Guirado J, Hong JS, Im H, Lee H, Arroyo JO, Quidant R. Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform. ARXIV 2023:arXiv:2308.06117v1. [PMID: 37608933 PMCID: PMC10441434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Label-free detecting multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. Herein, we first thoroughly characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles is required.
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Affiliation(s)
- Alexia Stollmann
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Jose Garcia-Guirado
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Jae-Sang Hong
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jaime Ortega Arroyo
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Romain Quidant
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
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9
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Natalia A, Zhang L, Sundah NR, Zhang Y, Shao H. Analytical device miniaturization for the detection of circulating biomarkers. NATURE REVIEWS BIOENGINEERING 2023; 1:1-18. [PMID: 37359772 PMCID: PMC10064972 DOI: 10.1038/s44222-023-00050-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 06/28/2023]
Abstract
Diverse (sub)cellular materials are secreted by cells into the systemic circulation at different stages of disease progression. These circulating biomarkers include whole cells, such as circulating tumour cells, subcellular extracellular vesicles and cell-free factors such as DNA, RNA and proteins. The biophysical and biomolecular state of circulating biomarkers carry a rich repertoire of molecular information that can be captured in the form of liquid biopsies for disease detection and monitoring. In this Review, we discuss miniaturized platforms that allow the minimally invasive and rapid detection and analysis of circulating biomarkers, accounting for their differences in size, concentration and molecular composition. We examine differently scaled materials and devices that can enrich, measure and analyse specific circulating biomarkers, outlining their distinct detection challenges. Finally, we highlight emerging opportunities in biomarker and device integration and provide key future milestones for their clinical translation.
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Affiliation(s)
- Auginia Natalia
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Li Zhang
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Noah R. Sundah
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
| | - Yan Zhang
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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10
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Seddighi S, Qi YA, Brown AL, Wilkins OG, Bereda C, Belair C, Zhang Y, Prudencio M, Keuss MJ, Khandeshi A, Pickles S, Hill SE, Hawrot J, Ramos DM, Yuan H, Roberts J, Kelmer Sacramento E, Shah SI, Nalls MA, Colon-Mercado J, Reyes JF, Ryan VH, Nelson MP, Cook C, Li Z, Screven L, Kwan JY, Shantaraman A, Ping L, Koike Y, Oskarsson B, Staff N, Duong DM, Ahmed A, Secrier M, Ule J, Jacobson S, Rohrer J, Malaspina A, Glass JD, Ori A, Seyfried NT, Maragkakis M, Petrucelli L, Fratta P, Ward ME. Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525149. [PMID: 36747793 PMCID: PMC9900763 DOI: 10.1101/2023.01.23.525149] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Functional loss of TDP-43, an RNA-binding protein genetically and pathologically linked to ALS and FTD, leads to inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. However, the possibility of de novo protein synthesis from cryptic exon transcripts has not been explored. Here, we show that mRNA transcripts harboring cryptic exons generate de novo proteins both in TDP-43 deficient cellular models and in disease. Using coordinated transcriptomic and proteomic studies of TDP-43 depleted iPSC-derived neurons, we identified numerous peptides that mapped to cryptic exons. Cryptic exons identified in iPSC models were highly predictive of cryptic exons expressed in brains of patients with TDP-43 proteinopathy, including cryptic transcripts that generated de novo proteins. We discovered that inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Finally, we showed that these de novo peptides were present in CSF from patients with ALS. The demonstration of cryptic exon translation suggests new mechanisms for ALS pathophysiology downstream of TDP-43 dysfunction and may provide a strategy for novel biomarker development.
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Affiliation(s)
- Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Oscar G Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
| | - Colleen Bereda
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Yongjie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Matthew J Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Aditya Khandeshi
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Sarah E Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - James Hawrot
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Hebao Yuan
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Jessica Roberts
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | | | - Syed I Shah
- Data Tecnica International, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Jenn Colon-Mercado
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Joel F Reyes
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Veronica H Ryan
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Casey Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Ziyi Li
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Laurel Screven
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Justin Y Kwan
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | | | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Björn Oskarsson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Nathan Staff
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Aisha Ahmed
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, UCL, London, UK
| | - Jerneg Ule
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Steven Jacobson
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Jonathan Rohrer
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Andrea Malaspina
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Jonathan D Glass
- Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, USA
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
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11
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He H, Wu C, Saqib M, Hao R. Single-molecule fluorescence methods for protein biomarker analysis. Anal Bioanal Chem 2023:10.1007/s00216-022-04502-9. [PMID: 36609860 DOI: 10.1007/s00216-022-04502-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Abstract
Proteins have been considered key building blocks of life. In particular, the protein content of an organism and a cell offers significant information for the in-depth understanding of the disease and biological processes. Single-molecule protein detection/sequencing tools will revolutionize clinical (proteomics) research, offering ultrasensitivity for low-abundance biomarker (protein) detection, which is important for the realization of early-stage disease diagnosis and single-cell proteomics. This improved detection/measurement capability delivers new sets of techniques to explore new frontiers and address important challenges in various interdisciplinary areas including nanostructured materials, molecular medicine, molecular biology, and chemistry. Importantly, fluorescence-based methods have emerged as indispensable tools for single protein detection/sequencing studies, providing a higher signal-to-noise ratio (SNR). Improvements in fluorescent dyes/probes and detector capabilities coupled with advanced (image) analysis strategies have fueled current developments for single protein biomarker detections. For example, in comparison to conventional ELISA (i.e., based on ensembled measurements), single-molecule fluorescence detection is more sensitive, faster, and more accurate with reduced background, high-throughput, and so on. In comparison to MS sequencing, fluorescence-based single-molecule protein sequencing can achieve the sequencing of peptides themselves with higher sensitivity. This review summarizes various typical single-molecule detection technologies including their methodology (modes of operation), detection limits, advantages and drawbacks, and current challenges with recent examples. We describe the fluorescence-based single-molecule protein sequencing/detection based on five kinds of technologies such as fluorosequencing, N-terminal amino acid binder, nanopore light sensing, and DNA nanotechnology. Finally, we present our perspective for developing high-performance fluorescence-based sequencing/detection techniques.
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Affiliation(s)
- Haihan He
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chuhong Wu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Muhammad Saqib
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.,Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | - Rui Hao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China. .,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
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12
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Liu Y, Li B, Liu B, Zhang K. Single-Particle Optical Imaging for Ultrasensitive Bioanalysis. BIOSENSORS 2022; 12:1105. [PMID: 36551072 PMCID: PMC9775667 DOI: 10.3390/bios12121105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The quantitative detection of critical biomolecules and in particular low-abundance biomarkers in biofluids is crucial for early-stage diagnosis and management but remains a challenge largely owing to the insufficient sensitivity of existing ensemble-sensing methods. The single-particle imaging technique has emerged as an important tool to analyze ultralow-abundance biomolecules by engineering and exploiting the distinct physical and chemical property of individual luminescent particles. In this review, we focus and survey the latest advances in single-particle optical imaging (OSPI) for ultrasensitive bioanalysis pertaining to basic biological studies and clinical applications. We first introduce state-of-the-art OSPI techniques, including fluorescence, surface-enhanced Raman scattering, electrochemiluminescence, and dark-field scattering, with emphasis on the contributions of various metal and nonmetal nano-labels to the improvement of the signal-to-noise ratio. During the discussion of individual techniques, we also highlight their applications in spatial-temporal measurement of key biomarkers such as proteins, nucleic acids and extracellular vesicles with single-entity sensitivity. To that end, we discuss the current challenges and prospective trends of single-particle optical-imaging-based bioanalysis.
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Affiliation(s)
- Yujie Liu
- Shanghai Institute of Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Binxiao Li
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Kun Zhang
- Shanghai Institute of Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
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13
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Briggs K, Bouhamidi MY, He L, Tabard-Cossa V. Efficient Simulation of Arbitrary Multicomponent First-Order Binding Kinetics for Improved Assay Design and Molecular Assembly. ACS MEASUREMENT SCIENCE AU 2022; 2:139-146. [PMID: 35479104 PMCID: PMC9026241 DOI: 10.1021/acsmeasuresciau.1c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Traditional enzyme-linked immunosorbent assay (ELISA), long the workhorse for specific target protein detection using microplate wells, is nearing its fundamental limit of sensitivity. New opportunities in health care call for in vitro diagnostic tests with ultrahigh sensitivity. Magnetic bead-based sandwich immunoassay formats have been developed that can reach unprecedented sensitivities, orders of magnitude better than are allowed for by the rate constants for a single ligand-receptor interaction. However, these ultrahigh sensitivity assays are vulnerable to a host of confounding factors, including nonspecific binding from background molecules and loss of low-abundance target to tube walls and during wash steps. Moreover, the optimization of workflow is often time-consuming and expensive. In this work, we present a simulation tool that allows users to graphically define arbitrary binding assays, including fully reversible first-order binding kinetics, timed addition of extra components, and timed wash steps. The tool is freely available as a user-friendly webapp. The framework is lightweight and fast, allowing for inexpensive simulation and visualization of arbitrarily complex assay schemes, including but not limited to digital immunoassays, DNA hybridization, and enzyme kinetics, for validation and optimization of assay designs without requiring any programming knowledge from the user. We demonstrate some of these capabilities and provide practical guidance on assay simulation design.
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14
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Ha T, Kaiser C, Myong S, Wu B, Xiao J. Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo. Mol Cell 2022; 82:304-314. [PMID: 35063098 DOI: 10.1016/j.molcel.2021.12.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022]
Abstract
Owing to their unique abilities to manipulate, label, and image individual molecules in vitro and in cellulo, single-molecule techniques provide previously unattainable access to elementary biological processes. In imaging, single-molecule fluorescence resonance energy transfer (smFRET) and protein-induced fluorescence enhancement in vitro can report on conformational changes and molecular interactions, single-molecule pull-down (SiMPull) can capture and analyze the composition and function of native protein complexes, and single-molecule tracking (SMT) in live cells reveals cellular structures and dynamics. In labeling, the abilities to specifically label genomic loci, mRNA, and nascent polypeptides in cells have uncovered chromosome organization and dynamics, transcription and translation dynamics, and gene expression regulation. In manipulation, optical tweezers, integration of single-molecule fluorescence with force measurements, and single-molecule force probes in live cells have transformed our mechanistic understanding of diverse biological processes, ranging from protein folding, nucleic acids-protein interactions to cell surface receptor function.
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Affiliation(s)
- Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
| | - Christian Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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15
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Fan Z, Li B, Wang YJ, Huang X, Li B, Wang S, Liu Y, Liu YJ, Liu B. Spatially resolved single-molecule profiling of microRNAs in migrating cells driven by microconfinement. Chem Sci 2022; 13:11197-11204. [PMID: 36320480 PMCID: PMC9517726 DOI: 10.1039/d2sc04132d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Cancer cells utilize a range of migration modes to navigate through a confined tissue microenvironment in vivo, while regulatory roles of key microRNAs (miRNAs) remain unclear. Precisely engineered microconfinement and the high spatial-resolution imaging strategy offer a promising avenue for deciphering the molecular mechanisms that drive cell migration. Here, enzyme-free signal-amplification nanoprobes as an effective tool are developed for three-dimensional (3D) high-resolution profiling of key miRNA molecules in single migrating cells, where distinct migration modes are precisely driven by microconfinement-engineered microchips. The constructed nanoprobes exhibit intuitive and ultrasensitive miRNA characterization in vitro by virtue of a single-molecule imaging microscope, and the differential expression and intracellular locations in different cell lines are successfully monitored. Furthermore, 3D spatial distribution of miR-141 at high resolution in flexible phenotypes of migrating cells is reconstructed in the engineered biomimetic microenvironment. The results indicate that miR-141 may be involved in the metastatic transition from a slow to a fast migration state. This work offers a new opportunity for investigating regulatory mechanisms of intracellular key biomolecules during cell migration in biomimetic microenvironments, which may advance in-depth understanding of cancer metastasis in vivo. Spatially resolved profiling of miRNAs was realized in migrating cells using enzyme-free signal-amplification nanoprobes, in which distinct migration modes of single living cells are driven by precisely engineered microchips.![]()
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Affiliation(s)
- Zihui Fan
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Bin Li
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Ya-Jun Wang
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Xuedong Huang
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Binxiao Li
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Shurong Wang
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Yixin Liu
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Yan-Jun Liu
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Baohong Liu
- Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Chemistry, State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
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