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: 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: Embodiments of the present disclosure relate generally to compositions and methods for the design of remote controlled biological systems, and more specifically to synthetic bioswitches that provide the ability to non-invasively and remotely control the function and activity of live cells, such as for example and not limitation, the expression of biologically active proteins or biological therapeutics, and the manipulation of physiologic or genetic processes and/or protein expression in live cells, in vivo (including, e.g., at desired anatomical sites) or ex vivo.

Abstract: The disclosure provides methods and compositions to digitally profile biological activity by detecting the activity of at least two biomarkers using protease activity sensors or biocomparators.

Abstract: The present invention provides method for longitudinal monitoring of disease changes and/or drug response. At multiple time points, a composition is introduced into a body of a subject (the composition includes an activity sensor comprising a plurality of reporters liberated through enzymatic cleavage, which occurs in a tissue of the body when enzymes associated with known activity of a therapeutic intervention are present in the body) and reporters are detected to determine activity levels of disease-associated enzymes in the subject, which is correlated to changes in disease state and/or drug response. A report or therapeutic response profile may further be used to support a clinical trial and for longitudinal monitoring of disease progression or regression in a subject. A prospective or active clinical trial participant, or patient undergoing treatment, may be qualified, stratified or staged based on the determined activity levels.

Abstract: Methods of the present invention predict a physiological state of a subject. A composition comprising activity sensors is introduced into a body of a subject. The activity sensors comprise a plurality of reporters susceptible to cleavage when processed by the body during extracellular matrix remodeling. Cleavage may be indicative of enzymatic activity in the extracellular matrix. Signals detected by the activity sensors may be predictive of a physiological state. A sample is collected from the subject, and liberated reporters are detected in the sample. An onset of the physiological state of the subject, which may be a disease characterized by inflammation or atrophy, may be diagnosed based on the liberated reporters detected.

Abstract: The invention provides methods and compositions that use a process in the body to deliver an active form of the activity sensor to a target site within the body. The activity sensors, which release detectable reporters when acted on by certain enzymes within the body, are provided as pro-analytes. Processes within the body deliver the activity sensors in active form to a target site of interest. For example, enzymes or a chemical environment within the body may cleave blocking groups from the activity sensors, or the body's tissues and organs may collect the activity sensors at the target site based on size or composition of the activity sensors.

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: 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: 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: An engineered cyclic peptide provides structural constraints to resist non-specific degradation in the human body and includes environment-specific cleavage sites to allow release of a linearized peptide upon reaching a target environment. The linearized peptide can include a reporter molecule or a bioactive therapeutic such that the cyclic peptide is essentially inactive at administration and in circulation but becomes reactive only upon exposure to target-specific environmental factors such as a specific combination of differentially-expressed proteases associated with a target tissue or disease state. The peptides can include tuning that modulate distribution by targeting the particle to specific tissue, bodily fluids, or cell types.

Abstract: An engineered cyclic peptide provides structural constraints to resist non-specific degradation in the human body and includes environment-specific cleavage sites to allow release of a linearized peptide upon reaching a target environment. The linearized peptide can include a reporter molecule or a bioactive therapeutic such that the cyclic peptide is essentially inactive at administration and in circulation but becomes reactive only upon exposure to target-specific environmental factors such as a specific combination of differentially-expressed proteases associated with a target tissue or disease state. The peptides can include tuning that modulate distribution by targeting the particle to specific tissue, bodily fluids, or cell types.

Abstract: Methods and compositions for screening or diagnosis of liver disease are provided. The results may also indicate course and efficacy of treatment. The composition includes an activity sensor and a reporter releasably attached to the activity sensor. The method includes detecting the presence and/or amount of a reporter. The reporter is released from an activity sensor in the presence of diseased liver tissue but remains attached to the activity sensor in healthy tissue. The presence and/or amount of the reporter are used to characterize the liver disease. The liver disease may be nonalcoholic steatohepatitis (NASH) and results may further indicate staging of NASH.

Abstract: Methods of the disclosure provide an analytical pipeline for mapping activity in a disease-specific manner. Any of a variety of diseases or medical conditions may be mapped using the analytical pipeline. In preferred embodiments, the pipeline uses expression data (e.g., from RNA-Seq) to identify proteases that are active in disease tissue and subject to differential expression relative to normal tissue. A machine learning classifier selects a subset of the proteases that identify the disease with a threshold sensitivity and specificity, in which the subset is small enough that a corresponding set of protease substrates may be assembled into a nanoparticle activity sensor that, when administered to a patient, are cleaved in the presence of disease tissue to release detectable analytes signifying presence of the disease.

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

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: 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: 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.