The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

The present invention provides methods for detecting and/or monitoring the function a donor cell in a recipient by detecting specific isoforms of one or more polypeptides in the sample; wherein the donor cell and the recipient express different specific isoforms of each of the one or more polypeptides. In some embodiments, the specific isoforms are detected by mass spectrometry. The invention also provides methods of treatment with donor cells where the donor cells are monitored by the methods described herein.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., clocking), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

The presently disclosed subject matter provides methods and compositions for treating myeloid disorders (e.g., acute myeloid leukemia (AML)). It relates to immunoresponsive cells bearing antigen recognizing receptors (e.g., chimeric antigen receptors (CARs)) targeting AML-specific antigens.

The present invention provides compositions and methods that can be used to determine a peptide signature for an antibody repertoire in a sample comprising multiple antibodies. The method can be used to characterize a phenotype in a sample, such as providing a diagnosis, prognosis or theranosis of a medical condition.

The present disclosure relates generally to biological entity-protein (e.g. protein-protein) interactions for potential therapeutic applications, and more specifically to high-throughput methods for identifying bridging molecules that induce the formation of recruited biological entity-bridging molecule-target protein complexes to effect said biological entity-protein interactions. The present disclosure also provides methods for using said bridging molecules for treatment of disorders mediated by the target protein of the recruited biological entity-molecule-target protein complex.

The present disclosure provides methods and reagents useful for analyzing protein-protein interfaces such as interfaces between a presenter protein (e.g., a member of the FKBP family, a member of the cyclophilin family, or PIN1) and a target protein. In some embodiments, the target and/or presenter proteins are intracellular proteins. In some embodiments, the target and/or presenter proteins are mammalian proteins.

Protein scaffolds and scaffold libraries based on a fibronectin type III (FN3) domain with an alternative binding surface design, isolated nucleic acids encoding the protein scaffolds, vectors, host cells, methods of making thereof, and uses as therapeutic molecules for treatment and diagnosis of diseases and disorders.

The disclosure provides for methods and systems for detecting antibody protein product self-association comprising inducing co-agglutination of nanoparticles and solid supports to capture the nanoparticles, each coated with a ligand specific for immunoglobulins, and utilizing a fluidic device to detect co-agglutination and antibody protein product self-association.