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Pandit S, Duchow M, Chao W, Capasso A, Samanta D. DNA-Barcoded Plasmonic Nanostructures for Activity-Based Protease Sensing. Angew Chem Int Ed Engl 2024; 63:e202310964. [PMID: 37985161 DOI: 10.1002/anie.202310964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
We report the development of a new class of protease activity sensors called DNA-barcoded plasmonic nanostructures. These probes are comprised of gold nanoparticles functionalized with peptide-DNA conjugates (GPDs), where the peptide is a substrate of the protease of interest. The DNA acts as a barcode identifying the peptide and facilitates signal amplification. Protease-mediated peptide cleavage frees the DNA from the nanoparticle surface, which is subsequently measured via a CRISPR/Cas12a-based assay as a proxy for protease activity. As proof-of-concept, we show activity-based, multiplexed detection of the SARS-CoV-2-associated protease, 3CL, and the apoptosis marker, caspase 3, with high sensitivity and selectivity. GPDs yield >25-fold turn-on signals, 100-fold improved response compared to commercial probes, and detection limits as low as 58 pM at room temperature. Moreover, nanomolar concentrations of proteases can be detected visually by leveraging the aggregation-dependent color change of the gold nanoparticles. We showcase the clinical potential of GPDs by detecting a colorectal cancer-associated protease, cathepsin B, in three different patient-derived cell lines. Taken together, GPDs detect physiologically relevant concentrations of active proteases in challenging biological samples, require minimal sample processing, and offer unmatched multiplexing capabilities (mediated by DNA), making them powerful chemical tools for biosensing and disease diagnostics.
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Affiliation(s)
- Subrata Pandit
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
| | - Mark Duchow
- Department of Oncology, Dell Medical School, The University of Texas at Austin, 1601 Trinity St., Austin, TX 78712, USA
| | - Wilson Chao
- Department of Biochemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
| | - Anna Capasso
- Department of Oncology, Dell Medical School, The University of Texas at Austin, 1601 Trinity St., Austin, TX 78712, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
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Holay N, Somma A, Duchow M, Soleimani M, Capasso A, Kottapalli S, Rios J, Giri U, Diamond J, Schreiber A, Piscopio AD, Van Den Berg C, Eckhardt SG, Triplett TA. Elucidating the direct effects of the novel HDAC inhibitor bocodepsin (OKI-179) on T cells to rationally design regimens for combining with immunotherapy. Front Immunol 2023; 14:1260545. [PMID: 37744352 PMCID: PMC10513502 DOI: 10.3389/fimmu.2023.1260545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Histone deacetylase inhibitors (HDACi) are currently being explored for the treatment of both solid and hematological malignancies. Although originally thought to exert cytotoxic responses through tumor-intrinsic mechanisms by increasing expression of tumor suppressor genes, several studies have demonstrated that therapeutic responses depend on an intact adaptive immune system: particularly CD8 T cells. It is therefore critical to understand how HDACi directly affects T cells in order to rationally design regimens for combining with immunotherapy. In this study, we evaluated T cell responses to a novel class-selective HDACi (OKI-179, bocodepsin) by assessing histone acetylation levels, which revealed rapid responsiveness accompanied by an increase in CD4 and CD8 T cell frequencies in the blood. However, these rapid responses were transient, as histone acetylation and frequencies waned within 24 hours. This contrasts with in vitro models where high acetylation was sustained and continuous exposure to HDACi suppressed cytokine production. In vivo comparisons demonstrated that stopping OKI-179 treatment during PD-1 blockade was superior to continuous treatment. These findings provide novel insight into the direct effects of HDAC inhibitors on T cells and that treatment schedules that take into account acute T cell effects should be considered when combined with immunotherapies in order to fully harness the tumor-specific T cell responses in patients.
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Affiliation(s)
- Nisha Holay
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, United States
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Alexander Somma
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Mark Duchow
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Milad Soleimani
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, United States
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Anna Capasso
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Srividya Kottapalli
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Joshua Rios
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Uma Giri
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Jennifer Diamond
- OnKure Therapeutics, Boulder, CO, United States
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Denver, CO, United States
| | - Anna Schreiber
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Denver, CO, United States
| | | | - Carla Van Den Berg
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, United States
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
- Division of Pharmacology and Toxicology, College of Pharmacy, University of Texas at Austin, Austin, TX, United States
| | - S. Gail Eckhardt
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, United States
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Todd A. Triplett
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
- Department of Immunotherapeutics & Biotechnology, School of Pharmacy, Texas Tech University Health Sciences Center, Abilene, TX, United States
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