The present invention provides systems and methods for performing forward genetic screens in cells and methods of treating disease through inhibiting targets identified in a forward genetic screen as involved in a pathway associated with the disease. The invention involves the use of multiple tandem fluorescent reporter molecules separated by cleavage sites under the control of a single promoter to enhance the fluorescent readout from a cell screen.

Disclosed is using a TEV protease (wild type or mutant) suited for removal from a reaction mixture, wherein the TEV protease displays a dual affinity tag including a chitin binding domain (CBD) tag and a histidine tag, preferably where the CBD tag precedes the N-terminus of the protease and the CBD tag is preceded by the histidine tag, which is preferably a 6-mer histidine tag; and optionally further including linkers, preferably Gly-Ser linkers, and more preferably a 6-mer Gly-Ser linker, between the tags. A linker, also preferably a Gly-Ser linker, can also follow the CBD tag and precede the protease portion. In certain embodiments, no such linkers are present and in other embodiments, only one such linker is present.

The present disclosure provides methods in which adherent cells are treated with small molecules, cultured, lysed, and then analyzed by mass spectrometry to measure the activities of endogenous enzymes. The implementation of this method relies on the use of surfaces that are nanopatterned with cell adhesion ligands to mediate cell attachment and a peptide that is a substrate for the desired enzyme activity in the lysate.

The present disclosure, in some aspects, provides mutant TEV proteases that exhibit improved activity, where the mutant TEV exhibits increase efficiency and/or an increased Kcat for cleavage of an amino acid sequence, and TEV proteases are commonly used for laboratory methods including cleaving fusion proteins and removing a purification tag, such as a maltose binding protein or a poly-histidine tag, from a fusion protein or an antibody.

Disclosed are cluster CAR and therapeutic payload nucleic acids, immune cells containing them, and uses thereof for controllable adoptive cell therapy and killing CAR T-cell resistant tumor cells.

Disclosed herein include methods, compositions, and kits suitable for robust and tunable control of payload gene expression. Some embodiments provide rationally designed circuits, including miRNA-level and/or protein-level incoherent feed-forward loop circuits, that maintain the expression of a payload at an efficacious level. The circuit can comprise a promoter operably linked to a polynucleotide encoding a fusion protein comprising a payload protein, a protease, and one or more self-cleaving peptide sequences. The payload protein can comprise a degron and a cut site the protease is capable of cutting to expose the degron. The circuit can comprise a promoter operably linked to a polynucleotide comprising a payload gene, a silencer effector cassette, and one or more silencer effector binding sequences.

Tobacco etch virus protease (TEV) is one of the most widely used proteases in biotechnology because of its exquisite sequence-specificity. A limitation of TEV is its slow catalytic rate, which limits product generation and therefore signal output. Provided is a generalizable yeast-based platform for directed evolution of protease catalytic properties. Protease activity is determined via proteolytic release of a membrane-anchored transcription factor, and access to TEV's cleavage site is temporally regulated using a photosensory LOV domain. By gradually decreasing light exposure time, faster variants of TEV were selected over multiple rounds of selection. The mutant TEV proteases and the directed evolution platform are useful in a wide range of biotechnology applications, such as FLARE and SPARK tools.