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Filippova TA, Masamrekh RA, Khudoklinova YY, Shumyantseva VV, Kuzikov AV. The multifaceted role of proteases and modern analytical methods for investigation of their catalytic activity. Biochimie 2024; 222:169-194. [PMID: 38494106 DOI: 10.1016/j.biochi.2024.03.006] [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: 09/25/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
We discuss the diverse functions of proteases in the context of their biotechnological and medical significance, as well as analytical approaches used to determine the functional activity of these enzymes. An insight into modern approaches to studying the kinetics and specificity of proteases, based on spectral (absorption, fluorescence), mass spectrometric, immunological, calorimetric, and electrochemical methods of analysis is given. We also examine in detail electrochemical systems for determining the activity and specificity of proteases. Particular attention is given to exploring innovative electrochemical systems based on the detection of the electrochemical oxidation signal of amino acid residues, thereby eliminating the need for extra redox labels in the process of peptide synthesis. In the review, we highlight the main prospects for the further development of electrochemical systems for the study of biotechnologically and medically significant proteases, which will enable the miniaturization of the analytical process for determining the catalytic activity of these enzymes.
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Affiliation(s)
- Tatiana A Filippova
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Rami A Masamrekh
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Yulia Yu Khudoklinova
- Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Alexey V Kuzikov
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia.
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2
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Zhong Q, Tan EKW, Martin-Alonso C, Parisi T, Hao L, Kirkpatrick JD, Fadel T, Fleming HE, Jacks T, Bhatia SN. Inhalable point-of-care urinary diagnostic platform. SCIENCE ADVANCES 2024; 10:eadj9591. [PMID: 38181080 PMCID: PMC10776015 DOI: 10.1126/sciadv.adj9591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024]
Abstract
Although low-dose computed tomography screening improves lung cancer survival in at-risk groups, inequality remains in lung cancer diagnosis due to limited access to and high costs of medical imaging infrastructure. We designed a needleless and imaging-free platform, termed PATROL (point-of-care aerosolizable nanosensors with tumor-responsive oligonucleotide barcodes), to reduce resource disparities for early detection of lung cancer. PATROL formulates a set of DNA-barcoded, activity-based nanosensors (ABNs) into an inhalable format. Lung cancer-associated proteases selectively cleave the ABNs, releasing synthetic DNA reporters that are eventually excreted via the urine. The urinary signatures of barcoded nanosensors are quantified within 20 min at room temperature using a multiplexable paper-based lateral flow assay. PATROL detects early-stage tumors in an autochthonous lung adenocarcinoma mouse model with high sensitivity and specificity. Tailoring the library of ABNs may enable not only the modular PATROL platform to lower the resource threshold for lung cancer early detection tools but also the rapid detection of chronic pulmonary disorders and infections.
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Affiliation(s)
- Qian Zhong
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Marble Center of Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward K. W. Tan
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Marble Center of Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carmen Martin-Alonso
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Tiziana Parisi
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Liangliang Hao
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Marble Center of Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jesse D. Kirkpatrick
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tarek Fadel
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Marble Center of Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather E. Fleming
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tyler Jacks
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sangeeta N. Bhatia
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Marble Center of Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division Health Sciences and Technology, Cambridge, MA 02139, USA
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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3
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Zhou C, Li X, Tang SW, Liu C, Lam MHW, Lam YW. A Dual-Enzyme Amplification Loop for the Sensitive Biosensing of Endopeptidases. ACS OMEGA 2023; 8:25592-25600. [PMID: 37483190 PMCID: PMC10357553 DOI: 10.1021/acsomega.3c03533] [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: 05/24/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023]
Abstract
A rapid and sensitive approach for the detection of endopeptidases via a new analyte-triggered mutual emancipation of linker-immobilized enzymes (AMELIE) mechanism has been developed and demonstrated using a matrix metallopeptidase, a collagenase, as the model endopeptidase analyte. AMELIE involves an autocatalytic loop created by a pair of selected enzymes immobilized on solid substrates via linkers with specific sites that can be proteolyzed by one another. These bound enzymes are spatially separated so that they cannot act upon their corresponding substrates until the introduction of the target endopeptidase analyte that can also cleave one of the linkers. This triggers the self-sustained loop of enzymatic activities to emancipate all the immobilized enzymes. In this proof of concept, signal transduction was achieved by a colorimetric horseradish peroxidase-tetramethylbenzidine (HRP-TMB-H2O2) reaction with HRP that are also being immobilized by one of the linkers. The pair of immobilized enzymes were collagenase and alginate lyase, and they were immobilized by an alginate linker and a short peptide chain containing the amino acid sequence of Leu-Gly-Pro-Ala for collagenase. A detection limit of 2.5 pg collagenase mL-1 with a wide linear range up to 4 orders of magnitude was achieved. The AMELIE biosensor can detect extracellular collagenase in the supernatant of various bacteria cultures, with a sensitivity as low as 103 cfu mL-1 of E. coli. AMELIE can readily be adapted to provide the sensitive detection of other endopeptidases.
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Affiliation(s)
- Chuanwen Zhou
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Xiaomin Li
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Sze Wing Tang
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Chunxi Liu
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Michael H. W. Lam
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Yun Wah Lam
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
- School
of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, U.K.
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4
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DeColli AA, Koolik IM, Seminara AB, Hatzios SK. A propeptide-based biosensor for the selective detection of Vibrio cholerae using an environment-sensitive fluorophore. Cell Chem Biol 2022; 29:1505-1516.e7. [DOI: 10.1016/j.chembiol.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 07/29/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022]
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Anahtar M, Chan LW, Ko H, Rao A, Soleimany AP, Khatri P, Bhatia SN. Host protease activity classifies pneumonia etiology. Proc Natl Acad Sci U S A 2022; 119:e2121778119. [PMID: 35696579 PMCID: PMC9231472 DOI: 10.1073/pnas.2121778119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/18/2022] [Indexed: 01/26/2023] Open
Abstract
Community-acquired pneumonia (CAP) has been brought to the forefront of global health priorities due to the COVID-19 pandemic. However, classification of viral versus bacterial pneumonia etiology remains a significant clinical challenge. To this end, we have engineered a panel of activity-based nanosensors that detect the dysregulated activity of pulmonary host proteases implicated in the response to pneumonia-causing pathogens and produce a urinary readout of disease. The nanosensor targets were selected based on a human protease transcriptomic signature for pneumonia etiology generated from 33 unique publicly available study cohorts. Five mouse models of bacterial or viral CAP were developed to assess the ability of the nanosensors to produce etiology-specific urinary signatures. Machine learning algorithms were used to train diagnostic classifiers that could distinguish infected mice from healthy controls and differentiate those with bacterial versus viral pneumonia with high accuracy. This proof-of-concept diagnostic approach demonstrates a way to distinguish pneumonia etiology based solely on the host proteolytic response to infection.
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Affiliation(s)
- Melodi Anahtar
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Leslie W. Chan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332
| | - Henry Ko
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Aditya Rao
- Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305
| | - Ava P. Soleimany
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Graduate Program in Biophysics, Harvard University, Boston, MA 02115
- Microsoft Research New England, Cambridge, MA 02142
| | - Purvesh Khatri
- Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305
| | - Sangeeta N. Bhatia
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Hansjörg Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115
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Lawson J, Nakhleh M, Smolinska A. Reproducibility and reporting, the routes to progress in breath research - highlights from the Breath Biopsy Conference 2021. J Breath Res 2022; 16. [PMID: 35405666 DOI: 10.1088/1752-7163/ac661d] [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: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/11/2022]
Abstract
With the continued presence of COVID-19 worldwide, it has been a challenge for the breath research community to progress with clinical studies and travel restrictions have also limited the opportunities to meet up, share ideas and celebrate the latest advances. The Breath Biopsy Conference 2021 provided a much-needed opportunityoffered the chance to catch up with the latest breath research and to share the researchprogress that researchers in the community have been able to progress make in these difficult times. Limited opportunities for clinical research have provided opportunitiesled many in the field to look more closely at different methods for breath collection and have contributed to the growing calls for consistent standards in how results are reported, shared and even how breath studies themselves are carried out. As such, standardization was a key theme for this year's event and featured prominently in the keynotes, discussions and throughout many of the presentation sessions. With over 900 registrants, almost 400 live attendees and 16 speakers, the Breath Biopsy Conference continues to bring together breath research leaders from around the world. This article provides an overview of the highlights from this event.
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Affiliation(s)
- Jonathan Lawson
- Owlstone Medical Ltd, 183 Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire, CB4 0GJ, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Morad Nakhleh
- Owlstone Ltd, 183 Cambridge Science Park, Milton Road, Cambridge, CB4 0GD, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Agnieszka Smolinska
- Toxicology Department, Maastricht University, Universiteitssingel, Maastricht, Maastricht, 6229 ER, NETHERLANDS
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7
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Gruba N, Rachubik P, Piwkowska A, Lesner A. Analysis of urinary kallikrein-related peptidase 13 for monitoring bladder cancer. Biomarkers 2021; 26:770-779. [PMID: 34704886 DOI: 10.1080/1354750x.2021.1999502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Bladder cancer (BC) is one of the 10 most common types of cancer worldwide, with approximately 550,000 new cases each year. Early detection and appropriate diagnosis are important factors in successful treatment of the disease. MATERIAL AND METHODS We used specific fluorogenic substrate for the quantitative determination of urine kallikrein 13 (KLK13) activity in healthy (n = 15) and BC (n = 54) patients. The proteolytic activity in individual urine samples was determined by fluorescence measurements. Then, immunoenzymatic analyses (ELISA, Western blot) were performed to confirm the presence of KLK13 in the tested samples. RESULTS Urine samples from patients with G2 and G3 grade BC contained proteolytically active KLK13, as confirmed by kinetic analysis and immunochemical detection. KLK13 was not detected in the urine of patients with G1 grade BC. DISCUSSION Previous clinical study reveals the KLK13 significance for BC prognosis as increased KLK13 expression was highlighted in bladder tumours compared to normal adjacent tissues. Our findings correlate to the report. KLK13 activity was confirmed in BC patients with G2 and G3 stage of disease development. CONCLUSIONS Using specific chromogenic/fluorogenic peptides could be useful for the non-invasive disease monitoring of BC progress.
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Affiliation(s)
- Natalia Gruba
- Department of Environmental Technology, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Patrycja Rachubik
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Gdańsk, Poland
| | - Agnieszka Piwkowska
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Gdańsk, Poland.,Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Adam Lesner
- Department of Environmental Technology, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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8
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Affiliation(s)
- Matthew Bogyo
- Departments of Pathology and Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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9
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Chan LW. Advances in activity-based diagnostics for infectious disease and microbiome health. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 19:100296. [PMID: 34179594 PMCID: PMC8224833 DOI: 10.1016/j.cobme.2021.100296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In the human body, pathogens and the endogenous microbiome produce enzymes that aid in replication and survival. The activity from these enzymes as well as energy-dependent transport processes can be used as functional biomarkers for pathogen identification, antimicrobial treatment monitoring, and surveillance of microbiome health. To produce visual and/or quantifiable readouts from this activity, concepts from chemical biology and nanomedicine have been utilized to develop signal-producing probes for patient samples or for direct administration in vivo. In the context of infection, activity-based diagnostics offer several potential advantages over current diagnostics including the ability to differentiate between active infection and sterile inflammation, which is made possible by targeting microbial enzymes with orthogonal activity to that of the host. In this review, we discuss new developments in the making of activity-based infection diagnostics and the beginnings of microbiome activity-based diagnostics.
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Affiliation(s)
- Leslie W. Chan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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10
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Kirkpatrick JD, Warren AD, Soleimany AP, Westcott PMK, Voog JC, Martin-Alonso C, Fleming HE, Tammela T, Jacks T, Bhatia SN. Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling. Sci Transl Med 2021; 12:12/537/eaaw0262. [PMID: 32238573 DOI: 10.1126/scitranslmed.aaw0262] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 08/06/2019] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Lung cancer is the leading cause of cancer-related death, and patients most commonly present with incurable advanced-stage disease. U.S. national guidelines recommend screening for high-risk patients with low-dose computed tomography, but this approach has limitations including high false-positive rates. Activity-based nanosensors can detect dysregulated proteases in vivo and release a reporter to provide a urinary readout of disease activity. Here, we demonstrate the translational potential of activity-based nanosensors for lung cancer by coupling nanosensor multiplexing with intrapulmonary delivery and machine learning to detect localized disease in two immunocompetent genetically engineered mouse models. The design of our multiplexed panel of sensors was informed by comparative transcriptomic analysis of human and mouse lung adenocarcinoma datasets and in vitro cleavage assays with recombinant candidate proteases. Intrapulmonary administration of the nanosensors to a Kras- and Trp53-mutant lung adenocarcinoma mouse model confirmed the role of metalloproteases in lung cancer and enabled accurate detection of localized disease, with 100% specificity and 81% sensitivity. Furthermore, this approach generalized to an alternative autochthonous model of lung adenocarcinoma, where it detected cancer with 100% specificity and 95% sensitivity and was not confounded by lipopolysaccharide-driven lung inflammation. These results encourage the clinical development of activity-based nanosensors for the detection of lung cancer.
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Affiliation(s)
- Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrew D Warren
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard Graduate Program in Biophysics, Harvard University, Boston, MA 02115, USA
| | - Peter M K Westcott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin C Voog
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tuomas Tammela
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. .,Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA 02139, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02139, USA.,Wyss Institute at Harvard, Boston, MA 02115, USA
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11
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Piovarci I, Melikishvili S, Tatarko M, Hianik T, Thompson M. Detection of Sub-Nanomolar Concentration of Trypsin by Thickness-Shear Mode Acoustic Biosensor and Spectrophotometry. BIOSENSORS 2021; 11:117. [PMID: 33920444 PMCID: PMC8070231 DOI: 10.3390/bios11040117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 05/03/2023]
Abstract
The determination of protease activity is very important for disease diagnosis, drug development, and quality and safety assurance for dairy products. Therefore, the development of low-cost and sensitive methods for assessing protease activity is crucial. We report two approaches for monitoring protease activity: in a volume and at surface, via colorimetric and acoustic wave-based biosensors operated in the thickness-shear mode (TSM), respectively. The TSM sensor was based on a β-casein substrate immobilized on a piezoelectric quartz crystal transducer. After an enzymatic reaction with trypsin, it cleaved the surface-bound β-casein, which increased the resonant frequency of the crystal. The limit of detection (LOD) was 0.48 ± 0.08 nM. A label-free colorimetric assay for trypsin detection has also been performed using β-casein and 6-mercaptohexanol (MCH) functionalized gold nanoparticles (AuNPs/MCH-β-casein). Due to the trypsin cleavage of β-casein, the gold nanoparticles lost shelter, and MCH increased the attractive force between the modified AuNPs. Consequently, AuNPs aggregated, and the red shift of the absorption spectra was observed. Spectrophotometric assay enabled an LOD of 0.42 ± 0.03 nM. The Michaelis-Menten constant, KM, for reverse enzyme reaction has also been estimated by both methods. This value for the colorimetric assay (0.56 ± 0.10 nM) is lower in comparison with those for the TSM sensor (0.92 ± 0.44 nM). This is likely due to the better access of the trypsin to the β-casein substrate at the surface of AuNPs in comparison with those at the TSM transducer.
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Affiliation(s)
- Ivan Piovarci
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina F1, 84248 Bratislava, Slovakia; (I.P.); (S.M.); (M.T.)
| | - Sopio Melikishvili
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina F1, 84248 Bratislava, Slovakia; (I.P.); (S.M.); (M.T.)
| | - Marek Tatarko
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina F1, 84248 Bratislava, Slovakia; (I.P.); (S.M.); (M.T.)
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina F1, 84248 Bratislava, Slovakia; (I.P.); (S.M.); (M.T.)
| | - Michael Thompson
- Lash Miller Laboratories, Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
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12
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Doroudian M, O' Neill A, Mac Loughlin R, Prina-Mello A, Volkov Y, Donnelly SC. Nanotechnology in pulmonary medicine. Curr Opin Pharmacol 2020; 56:85-92. [PMID: 33341460 PMCID: PMC7746087 DOI: 10.1016/j.coph.2020.11.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/23/2022]
Abstract
Nanotechnology in medicine—nanomedicine—is extensively employed to diagnose, treat, and prevent pulmonary diseases. Over the last few years, this brave new world has made remarkable progress, offering opportunities to address historical clinical challenges in pulmonary diseases including multidrug resistance, adverse side effects of conventional therapeutic agents, novel imaging, and earlier disease detection. Nanomedicine is also being applied to tackle the new emerging infectious diseases, including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), influenza A virus subtype H1N1 (A/H1N1), and more recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this review we provide both a historical overview of the application of nanomedicine to respiratory diseases and more recent cutting-edge approaches such as nanoparticle-mediated combination therapies, novel double-targeted nondrug delivery system for targeting, stimuli-responsive nanoparticles, and theranostic imaging in the diagnosis and treatment of pulmonary diseases.
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Affiliation(s)
- Mohammad Doroudian
- Department of Medicine, Tallaght University Hospital & Trinity College Dublin, Ireland; Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Andrew O' Neill
- Department of Medicine, Tallaght University Hospital & Trinity College Dublin, Ireland
| | - Ronan Mac Loughlin
- Aerogen, IDA Business Park, Dangan, Galway, Ireland; School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland; School of Pharmacy and Pharmaceutical Sciences, Trinity College, Dublin, Ireland
| | - Adriele Prina-Mello
- Laboratory for Biological Characterization of Advanced Materials (LBCAM), Department of Medicine, Trinity College Dublin, Ireland; Nanomedicine Group, Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Ireland; CRANN Institute and AMBER Centre, Trinity College Dublin, Ireland
| | - Yuri Volkov
- Laboratory for Biological Characterization of Advanced Materials (LBCAM), Department of Medicine, Trinity College Dublin, Ireland; Nanomedicine Group, Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Ireland; CRANN Institute and AMBER Centre, Trinity College Dublin, Ireland; Department of Histology, Cytology and Embryology, First Moscow State Sechenov Medical University, Moscow, Russian Federation
| | - Seamas C Donnelly
- Department of Medicine, Tallaght University Hospital & Trinity College Dublin, Ireland.
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Differential Markers of Bacterial and Viral Infections in Children for Point-of-Care Testing. Trends Mol Med 2020; 26:1118-1132. [PMID: 33008730 PMCID: PMC7522093 DOI: 10.1016/j.molmed.2020.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/22/2020] [Accepted: 09/02/2020] [Indexed: 02/08/2023]
Abstract
Children suffering from infectious diseases, both bacterial and viral, are often treated with empirical antibiotics. Keeping in mind both the menace of microorganisms and antibiotic toxicity, it is imperative to develop point-of-care testing (POCT) to discriminate bacterial from viral infections, and to define indications for antibiotic treatment. This article reviews potential protein biomarkers and host-derived gene expression signatures for differentiating between bacterial and viral infections in children, and focuses on emerging multiplex POCT devices for the simultaneous detection of sets of protein biomarkers or streamlined gene expression signatures that may provide rapid and cost-effective pathogen-discriminating tools. Bacteria and viruses activate or inhibit different signaling pathways in the cells they infect, and further give rise to different host transcriptional signatures as well as to unique protein biomarkers. Many of the newly evaluated protein biomarkers, especially in combination, have better discriminative value for distinguishing between bacterial and viral infections than the biomarkers that are currently used for examining infections in children. The transcriptomes of children undergo remarkable changes when they are infected by different types of bacteria and viruses. Approaches based on host-derived DNA/RNA signatures can accurately discriminate bacterial from viral infections. Emerging multiplex POCT techniques allow simultaneous testing of protein- or gene-based biomarkers in an outpatient setting.
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Chan LW, Anahtar MN, Ong TH, Hern KE, Kunz RR, Bhatia SN. Engineering synthetic breath biomarkers for respiratory disease. NATURE NANOTECHNOLOGY 2020; 15:792-800. [PMID: 32690884 PMCID: PMC8173716 DOI: 10.1038/s41565-020-0723-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/02/2020] [Indexed: 05/10/2023]
Abstract
Human breath contains many volatile metabolites. However, few breath tests are currently used in the clinic to monitor disease due to bottlenecks in biomarker identification. Here we engineered breath biomarkers for respiratory disease by local delivery of protease-sensing nanoparticles to the lungs. The nanosensors shed volatile reporters upon cleavage by neutrophil elastase, an inflammation-associated protease with elevated activity in lung diseases such as bacterial infection and alpha-1 antitrypsin deficiency. After intrapulmonary delivery into mouse models with acute lung inflammation, the volatile reporters are released and expelled in breath at levels detectable by mass spectrometry. These breath signals can identify diseased mice with high sensitivity as early as 10 min after nanosensor administration. Using these nanosensors, we performed serial breath tests to monitor dynamic changes in neutrophil elastase activity during lung infection and to assess the efficacy of a protease inhibitor therapy targeting neutrophil elastase for the treatment of alpha-1 antitrypsin deficiency.
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Affiliation(s)
- Leslie W Chan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Melodi N Anahtar
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ta-Hsuan Ong
- Biological and Chemical Technologies Group, Massachusetts Institute of Technology Lincoln Laboratory, Lexington, MA, USA
| | - Kelsey E Hern
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roderick R Kunz
- Biological and Chemical Technologies Group, Massachusetts Institute of Technology Lincoln Laboratory, Lexington, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute, Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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Soleimany AP, Bhatia SN. Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring. Trends Mol Med 2020; 26:450-468. [PMID: 32359477 DOI: 10.1016/j.molmed.2020.01.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 12/26/2022]
Abstract
Diagnostics to accurately detect disease and monitor therapeutic response are essential for effective clinical management. Bioengineering, chemical biology, molecular biology, and computer science tools are converging to guide the design of diagnostics that leverage enzymatic activity to measure or produce biomarkers of disease. We review recent advances in the development of these 'activity-based diagnostics' (ABDx) and their application in infectious and noncommunicable diseases. We highlight efforts towards both molecular probes that respond to disease-specific catalytic activity to produce a diagnostic readout, as well as diagnostics that use enzymes as an engineered component of their sense-and-respond cascade. These technologies exemplify how integrating techniques from multiple disciplines with preclinical validation has enabled ABDx that may realize the goals of precision medicine.
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Affiliation(s)
- Ava P Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard Graduate Program in Biophysics, Harvard University, Boston, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Wyss Institute at Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
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