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Holt BA, Lim HS, Sivakumar A, Phuengkham H, Su M, Tuttle M, Xu Y, Liakakos H, Qiu P, Kwong GA. Embracing enzyme promiscuity with activity-based compressed biosensing. CELL REPORTS METHODS 2023; 3:100372. [PMID: 36814844 PMCID: PMC9939361 DOI: 10.1016/j.crmeth.2022.100372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 10/11/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022]
Abstract
The development of protease-activatable drugs and diagnostics requires identifying substrates specific to individual proteases. However, this process becomes increasingly difficult as the number of target proteases increases because most substrates are promiscuously cleaved by multiple proteases. We introduce a method-substrate libraries for compressed sensing of enzymes (SLICE)-for selecting libraries of promiscuous substrates that classify protease mixtures (1) without deconvolution of compressed signals and (2) without highly specific substrates. SLICE ranks substrate libraries using a compression score (C), which quantifies substrate orthogonality and protease coverage. This metric is predictive of classification accuracy across 140 in silico (Pearson r = 0.71) and 55 in vitro libraries (r = 0.55). Using SLICE, we select a two-substrate library to classify 28 samples containing 11 enzymes in plasma (area under the receiver operating characteristic curve [AUROC] = 0.93). We envision that SLICE will enable the selection of libraries that capture information from hundreds of enzymes using fewer substrates for applications like activity-based sensors for imaging and diagnostics.
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Affiliation(s)
- Brandon Alexander Holt
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Hong Seo Lim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Anirudh Sivakumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Hathaichanok Phuengkham
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Melanie Su
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - McKenzie Tuttle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Yilin Xu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Haley Liakakos
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Peng Qiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Gabriel A. Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
- Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, GA 30332, USA
- Institute for Electronics and Nanotechnology, Georgia Tech, Atlanta, GA 30332, USA
- Integrated Cancer Research Center, Georgia Tech, Atlanta, GA 30332, USA
- Georgia ImmunoEngineering Consortium, Georgia Tech and Emory University, Atlanta, GA 30332, USA
- Emory School of Medicine, Atlanta, GA 30332, USA
- Emory Winship Cancer Institute, Atlanta, GA 30322, USA
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Mac QD, Sivakumar A, Phuengkham H, Xu C, Bowen JR, Su FY, Stentz SZ, Sim H, Harris AM, Li TT, Qiu P, Kwong GA. Urinary detection of early responses to checkpoint blockade and of resistance to it via protease-cleaved antibody-conjugated sensors. Nat Biomed Eng 2022; 6:310-324. [PMID: 35241815 DOI: 10.1038/s41551-022-00852-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 01/28/2022] [Indexed: 12/15/2022]
Abstract
Immune checkpoint blockade (ICB) therapy does not benefit the majority of treated patients, and those who respond to the therapy can become resistant to it. Here we report the design and performance of systemically administered protease activity sensors conjugated to anti-programmed cell death protein 1 (αPD1) antibodies for the monitoring of antitumour responses to ICB therapy. The sensors consist of a library of mass-barcoded protease substrates that, when cleaved by tumour proteases and immune proteases, are released into urine, where they can be detected by mass spectrometry. By using syngeneic mouse models of colorectal cancer, we show that random forest classifiers trained on mass spectrometry signatures from a library of αPD1-conjugated mass-barcoded activity sensors for differentially expressed tumour proteases and immune proteases can be used to detect early antitumour responses and discriminate resistance to ICB therapy driven by loss-of-function mutations in either the B2m or Jak1 genes. Biomarkers of protease activity may facilitate the assessment of early responses to ICB therapy and the classification of refractory tumours based on resistance mechanisms.
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Affiliation(s)
- Quoc D Mac
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Anirudh Sivakumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Hathaichanok Phuengkham
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Congmin Xu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - James R Bowen
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Fang-Yi Su
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Samuel Z Stentz
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Hyoungjun Sim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Adrian M Harris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Tonia T Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Peng Qiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA.,Parker H. Petit Institute for Bioengineering and Bioscience, Atlanta, GA, USA.,The Georgia Immunoengineering Consortium, Emory University and Georgia Tech, Atlanta, GA, USA.,Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA. .,Parker H. Petit Institute for Bioengineering and Bioscience, Atlanta, GA, USA. .,The Georgia Immunoengineering Consortium, Emory University and Georgia Tech, Atlanta, GA, USA. .,Winship Cancer Institute, Emory University, Atlanta, GA, USA. .,Institute for Electronics and Nanotechnology, Georgia Tech, Atlanta, GA, USA. .,Integrated Cancer Research Center, Georgia Tech, Atlanta, GA, USA.
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Holt BA, Tuttle M, Xu Y, Su M, Røise JJ, Wang X, Murthy N, Kwong GA. Dimensionless parameter predicts bacterial prodrug success. Mol Syst Biol 2022; 18:e10495. [PMID: 35005851 PMCID: PMC8744131 DOI: 10.15252/msb.202110495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding mechanisms of antibiotic failure is foundational to combating the growing threat of multidrug-resistant bacteria. Prodrugs-which are converted into a pharmacologically active compound after administration-represent a growing class of therapeutics for treating bacterial infections but are understudied in the context of antibiotic failure. We hypothesize that strategies that rely on pathogen-specific pathways for prodrug conversion are susceptible to competing rates of prodrug activation and bacterial replication, which could lead to treatment escape and failure. Here, we construct a mathematical model of prodrug kinetics to predict rate-dependent conditions under which bacteria escape prodrug treatment. From this model, we derive a dimensionless parameter we call the Bacterial Advantage Heuristic (BAH) that predicts the transition between prodrug escape and successful treatment across a range of time scales (1-104 h), bacterial carrying capacities (5 × 104 -105 CFU/µl), and Michaelis constants (KM = 0.747-7.47 mM). To verify these predictions in vitro, we use two models of bacteria-prodrug competition: (i) an antimicrobial peptide hairpin that is enzymatically activated by bacterial surface proteases and (ii) a thiomaltose-conjugated trimethoprim that is internalized by bacterial maltodextrin transporters and hydrolyzed by free thiols. We observe that prodrug failure occurs at BAH values above the same critical threshold predicted by the model. Furthermore, we demonstrate two examples of how failing prodrugs can be rescued by decreasing the BAH below the critical threshold via (i) substrate design and (ii) nutrient control. We envision such dimensionless parameters serving as supportive pharmacokinetic quantities that guide the design and administration of prodrug therapeutics.
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Affiliation(s)
- Brandon Alexander Holt
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Tech College of Engineering and Emory School of MedicineAtlantaGAUSA
| | - McKenzie Tuttle
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Tech College of Engineering and Emory School of MedicineAtlantaGAUSA
| | - Yilin Xu
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Tech College of Engineering and Emory School of MedicineAtlantaGAUSA
| | - Melanie Su
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Tech College of Engineering and Emory School of MedicineAtlantaGAUSA
| | - Joachim J Røise
- Department of BioengineeringInnovative Genomics InstituteUniversity of CaliforniaBerkeleyCAUSA
| | - Xioajian Wang
- Institute of Advanced SynthesisSchool of Chemistry and Molecular EngineeringNanjing Tech UniversityNanjingChina
| | - Niren Murthy
- Department of BioengineeringInnovative Genomics InstituteUniversity of CaliforniaBerkeleyCAUSA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Tech College of Engineering and Emory School of MedicineAtlantaGAUSA
- Parker H. Petit Institute of Bioengineering and BioscienceAtlantaGAUSA
- Institute for Electronics and NanotechnologyGeorgia TechAtlantaGAUSA
- Integrated Cancer Research CenterGeorgia TechAtlantaGAUSA
- Georgia ImmunoEngineering ConsortiumGeorgia Tech and Emory UniversityAtlantaGAUSA
- Emory School of MedicineAtlantaGAUSA
- Emory Winship Cancer InstituteAtlantaGAUSA
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Su FY, Mac QD, Sivakumar A, Kwong GA. Interfacing Biomaterials with Synthetic T Cell Immunity. Adv Healthc Mater 2021; 10:e2100157. [PMID: 33887123 PMCID: PMC8349871 DOI: 10.1002/adhm.202100157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/28/2021] [Indexed: 12/14/2022]
Abstract
The clinical success of cancer immunotherapy is providing exciting opportunities for the development of new methods to detect and treat cancer more effectively. A new generation of biomaterials is being developed to interface with molecular and cellular features of immunity and ultimately shape or control anti-tumor responses. Recent advances that are supporting the advancement of engineered T cells are focused here. This class of cancer therapy has the potential to cure disease in subsets of patients, yet there remain challenges such as the need to improve response rates and safety while lowering costs to expand their use. To provide a focused overview, recent strategies in three areas of biomaterials research are highlighted: low-cost cell manufacturing to broaden patient access, noninvasive diagnostics for predictive monitoring of immune responses, and strategies for in vivo control that enhance anti-tumor immunity. These research efforts shed light on some of the challenges associated with T cell immunotherapy and how engineered biomaterials that interface with synthetic immunity are gaining traction to solve these challenges.
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Affiliation(s)
- Fang-Yi Su
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, Atlanta, GA, 30332, USA
| | - Quoc D Mac
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, Atlanta, GA, 30332, USA
| | - Anirudh Sivakumar
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, Atlanta, GA, 30332, USA
| | - Gabriel A Kwong
- The Wallace H. Coulter Department of Biomedical Engineering, Institute for Electronics and Nanotechnology, Parker H. Petit Institute of Bioengineering and Bioscience, Integrated Cancer Research Center, Georgia Immunoengineering Consortium, Winship Cancer Institute, Emory University, Georgia Institute of Technology & Emory University, Atlanta, GA, 30332, USA
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