Abstract: . There is great interest in developing strategies to identify proteolytic substrates. Synthetic peptide libraries are among the most widely used to screen substrates-based activity, however, this technique is limited by the size of libraries and is time-consuming. Several combinatorial library-based display technologies such as phage, bacteria and yeast display, can identify better substrates for protease activity with higher-throughput sequencing and enrichment of specific substrates over multiple rounds of selection. Even though these profiling techniques provide greater coverage of protease cleavable substrates, such cells are less capable of accessing difficult to deliver sites, pose immunogenicity concerns, and have not been applied to discriminate on-from off-target activity in vivo. Disclosed herein are in vitro and in vivo methods for screening protease substrates.

Abstract: Disclosed herein are bacterial protease-activated prodrug compositions and methods of their use for the treatment and prevention of bacterial infection. Also disclosed are methods of reducing or eliminating defiant bacterial populations. An exemplary prodrug composition includes a cationic antimicrobial peptide conjugated to an anionic peptide with a protease-cleavable linker substrate, wherein the antimicrobial peptide is inactive while it is in conjugation with the anionic peptide. Upon cleavage by the protease, the cationic AMP is released from the anionic peptide and can act upon bacteria. The protease is specific to the bacteria that are present in the sample or the subject, creating an auto-titrating mechanism wherein the AMP is released from the peptide only when there is bacteria present.

Abstract: The present disclosure relates to nanoparticle compositions for modifying antigen-specific T cells and uses thereof.

Abstract: The present disclosure relates to promoter constructs comprising: one or more heat shock elements: a core promoter; and a gene of interest: vectors comprising the promoter constructs, and immune cells modified to include the promoter constructs. The promoter constructs provide the ability to remotely control immune cell therapies by thermal targeting. The present disclosure also provides methods of use for the promoter constructs.

Abstract: Disclosed herein are bacterial protease-activated prodrug compositions and methods of their use for the treatment and prevention of bacterial infection. Also disclosed are methods of reducing or eliminating defiant bacterial populations. An exemplary prodrug composition includes a cationic antimicrobial peptide conjugated to an anionic peptide with a protease cleavable linker substrate, wherein the antimicrobial peptide is inactive while it is in conjugation with the anionic peptide. Upon cleavage by the protease, the cationic AMP is released from the anionic peptide and can act upon bacteria. The protease is specific to the bacteria that are present in the sample or the subject, creating an auto-titrating mechanism wherein the AMP is released from the peptide only when there is bacteria present.

Abstract: The invention relates to methods and products associated with in vivo enzyme profiling. In particular, biomarker nanoparticles capable of quantitatively detecting enzymatic activity in vivo are described. These nanoparticles can be used to detect in vivo enzyme activity. The invention also relates to products, kits, and databases for use in the methods of the invention.

Abstract: Disclosed are synthetic antigen chimeric antigen receptor systems and methods of their use for the treatment of cancer.

Abstract: Systems and methods for multiplexed cell sorting are provided herein. The disclosed cell sorting system is referred to as DNA gated sorting (DGS). An exemplary system provides a set of orthogonal sorting probes and release probes for sorting cells of one or more different cell types from a biological specimen.

Abstract: A nanoparticle activity sensor containing a reporter and at least one tuning domain that modifies a distribution or residence time of the activity sensor when administered to a patient. When administered to the patient, the activity sensor enters cells or tissue where it is cleaved by enzymes specific to a physiological state such as a disease to release a detectable analyte. The tuning domains include molecular structures that modulate distribution or decay by protecting the particle from premature cleavage and indiscriminate hydrolysis, shielding the particle from immune detection and clearance, or by targeting the particle to specific tissue, bodily fluids, or cell types.

Abstract: The present invention relates to methods and products associated with in vivo enzyme profiling. In particular, the invention relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. The invention also relates to products, kits, and databases for use in the methods of the invention.

Abstract: The present invention relates to methods and products associated with in vivo enzyme profiling. In particular, the invention relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. The invention also relates to products, kits, and databases for use in the methods of the invention.

Abstract: It is an object of this disclosure to provide systems, devices, and methods for the direct use of fluorescent reporters that measure multiaxial and dynamic shear flows that occur invitro or in vivo across a surface of interest, where shear flows canbe measured, quantified and/or correlated to physiological changes in cells or tissues in real time. In certain embodiments, this disclosure contemplates imaging or visualizing the shear field applied to a surface, e.g., a surface of cells or inner lining of a blood vessel, the lumen of pumping lymphatics, within the bile duct, vessels with significant leakage, inflamed endothelium, tumor vasculature, or other systems.

Abstract: Some aspects of this invention provide reagents and methods for the sensitive, quantitative and simultaneous detection of target analytes in complex biological samples by liquid chromatography tandem mass spectrometry (LC MS/MS). Some aspects of this invention provide affinity reagents encoded with mass reporters for the sensitive and quantitative translation of an analyte of interest into a mass tag. The reagents and methods provided herein have general utility in analyte detection and encoding, for example, in biomolecular profiling, molecular diagnostics, and biochemical encoding.

Abstract: Some aspects of this invention provide reagents and methods for the sensitive, quantitative and simultaneous detection of target analytes in complex biological samples by liquid chromatography tandem mass spectrometry (LC MS/MS). Some aspects of this invention provide affinity reagents encoded with mass reporters for the sensitive and quantitative translation of an analyte of interest into a mass tag. The reagents and methods provided herein have general utility in analyte detection and encoding, for example, in biomolecular profiling, molecular diagnostics, and biochemical encoding.

Abstract: The present invention relates to methods and products associated with in vivo enzyme profiling. In particular, the invention relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. The invention also relates to products, kits, and databases for use in the methods of the invention.

Abstract: The present disclosure relates to methods and products associated with in vitro and in vivo protease activity measurements and enzyme profiling. Some aspects of the present disclosure relate to measuring remotely triggered protease activity. In particular, the disclosure relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence or absence of active enzymes associated with disease or conditions. The disclosure also relates to products, kits, and databases for use in the methods of the disclosure.

Abstract: CRISPR-based diagnostic methods and compositions are provided. One embodiment provides the use of DNA-barcoded antibodies or peptide-MHC (pMHC) tetramers (e.g., Kb-OVA257-264, Db-GP10025-33, Db-GP33-41) and CRISPR-Cas protein, and a guided DNA endonuclease, to achieve ultrasensitive detection of soluble and cell surface proteins. The disclosed embodiments can use type V: Cas12a; type VI: Cas13a, or Cas13b. Combining DNA encoding with CRISPR-Cas protein recognition is a sensitive system because barcodes can be isothermally amplified and Cas, for example Cas12a, enzymatically cleaves DNA reporters upon barcode detection, providing two rounds of amplification and enabling measurement of protein concentration by sample fluorescence or using by paper-based assays.

Abstract: The present disclosure relates to methods and products associated with in vitro and in vivo protease activity measurements and enzyme profiling. Some aspects of the present disclosure relate to measuring remotely triggered protease activity. In particular, the disclosure relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence or absence of active enzymes associated with disease or conditions. The disclosure also relates to products, kits, and databases for use in the methods of the disclosure.

Abstract: Disclosed herein are protease-based biological circuits for use in the diagnosis and treatment of disease and disorders characterized by aberrant protease signaling. An exemplary method of treating disease in a subject includes administering to the subject a plurality of therapeutic agent loaded-liposomes, wherein each of the liposomes comprises a different density of peptides surrounding the core and a different dose of the therapeutic agent, wherein the peptides comprise a cleavage site for a protease of interest, and wherein cleavage of the peptides open the liposome and release the therapeutic agent from within the liposome.

Abstract: An activity-based nanosensor composition for detecting protease activity comprising a cleavable detectable substrate and methods of use are disclosed.