Abstract: The present invention features a knock-in mouse comprising a mutation in an endogenous CRBN locus and methods of use thereof.

Abstract: The subject matter disclosed herein is generally directed to epitopes that specifically bind to subject specific HLA class I molecules in MCC. The epitope identified is specific for MCC and is encoded for in the Merkel Cell Polyomavirus (MCPyV) large T antigen (MCPyV LT).

Abstract: Methods disclosed herein concern cancer proteogenomics, which integrates genomics, transcriptomics and mass spectrometry (MS)-based proteomics to gain insights into cancer biology and treatment efficacy. To promote clinical utility of embodiments herein, proteogenomics approaches were developed for frozen core needle biopsies using tissue-sparing specimen processing with or without a microscaled proteomics workflow.

Abstract: Immunogenic compositions comprising one or more polypeptides, wherein the one or more polypeptides: is capable of binding to Major Histocompatibility Complex (MHC) class I, and is derived from one or more proteins of SARS-CoV-2. Also provided include methods of treating and preventing diseases using the immunogenic compositions.

Abstract: Disclosed herein are polypeptides and compositions comprising one or more neoantigens, methods of identifying neoantigens, and methods for preparing a neoantigen for an immunogenic pharmaceutical composition. The neoantigen can be specific to a subject that has a cancer, disease, or other disorder.

Abstract: Adaptive immune responses rely on the ability of cytotoxic T cells to identify and eliminate cells displaying disease-specific antigens on human leukocyte antigen (HLA) class I molecules. Investigations into antigen processing and display have immense implications in human health, disease and therapy. To extend understanding of the rules governing antigen processing and presentation, immunopurified peptides from B cells, each expressing a single HLA class I allele, were profiled. A resource dataset containing thousands of peptides bound to distinct class I HLA-A, -B, and -C alleles was generated by implementing a novel allele-specific database search strategy. Applicants discovered new binding motifs, established the role of gene expression in peptide presentation and improved prediction of HLA-peptide binding by using these data to train machine-learning models. These streamlined experimental and analytic workflows enable direct identification and analysis of endogenously processed and presented antigens.

Abstract: The present disclosure provides for compositions and methods of treating cancer. In some embodiments, PTPN11 is targeted with and anti-PTPN11 drug, such as a Shp2 inhibitor (e.g., SHP099). In some embodiments, other upregulated, hyperphosphorylated, or hyperacetylated target proteins are inhibited or targeted.

Abstract: Adaptive immune responses rely on the ability of cytotoxic T cells to identify and eliminate cells displaying disease-specific antigens on human leukocyte antigen (HLA) class I molecules. Investigations into antigen processing and display have immense implications in human health, disease and therapy. To extend understanding of the rules governing antigen processing and presentation, immunopurified peptides from B cells, each expressing a single HLA class I allele, were profiled using accurate mass, high-resolution liquid chromatography-mass spectrometry (LC-MS/MS). A resource dataset containing thousands of peptides bound to 28 distinct class I HLA-A, -B, and -C alleles was generated by implementing a novel allele-specific database search strategy. Applicants discovered new binding motifs, established the role of gene expression in peptide presentation and improved prediction of HLA-peptide binding by using these data to train machine-learning models.

Abstract: The present invention features a knock-in mouse comprising a mutation in an endogenous CRBN locus and methods of use thereof.

Abstract: The present invention provides fusion proteins, polynucleotides, kits, as well as TALE- or CRISPR-Cas based systems and methods. The present invention relies on proximity-dependent biotinylation, which allows site-directed protein or DNA purification and identification. The present invention provides tools for delineating the genetics of disease mechanism and for the identification of therapeutic targets and markers.

Abstract: The present invention features a knock-in mouse comprising a mutation in an endogenous CRBN locus and methods of use thereof.

Abstract: The present invention features a knock-in mouse comprising a mutation in an endogenous CRBN locus and methods of use thereof.

Abstract: Proteomic methods for identifying cancer related proteins and related products and kits are provided. The cancer specific proteins are extracellular matrix proteins that are associated with various aspects of cancer. Panels or signature sets of proteins useful in the detection, diagnosis and treatment of cancers as well as monitoring therapeutic progress in a cancer patient are provided herein along with methods for their detection and for their use in targeting imaging and/or therapeutic agents to the tumors via binding to the specified proteins. The proteins were identified using proteomics analyzes of tissue samples taken from cancer patients. In certain aspects the proteins are particularly useful in colon cancer patients.

Abstract: The present invention features a knock-in mouse comprising a mutation in an endogenous CRBN locus and methods of use thereof.

Abstract: Proteomic methods for identifying cancer related proteins and related products and kits are provided. The cancer specific proteins are extracellular matrix proteins that are associated with various aspects of cancer. Panels or signature sets of proteins useful in the detection, diagnosis and treatment of cancers as well as monitoring therapeutic progress in a cancer patient are provided herein along with methods for their detection and for their use in targeting imaging and/or therapeutic agents to the tumors via binding to the specified proteins. The proteins were identified using proteomics analyses of tissue samples taken from cancer patients. In certain aspects the proteins are particularly useful in colon cancer patients.

Abstract: The invention relates to tuberculosis diagnostic methods and devices that measure particular biomarker profiles in subjects and identify a subject having tuberculosis based on such profiles.

Abstract: Proteomic methods for identifying cancer related proteins and related products and kits are provided. The cancer specific proteins are extracellular matrix proteins that are associated with various aspects of cancer. Panels or signature sets of proteins useful in the detection, diagnosis and treatment of cancers as well as monitoring therapeutic progress in a cancer patient are provided herein along with methods for their detection and for their use in targeting imaging and/or therapeutic agents to the tumors via binding to the specified proteins. The proteins were identified using proteomics analyses of tissue samples taken from cancer patients. In certain aspects the proteins are particularly useful in colon cancer patients.

Abstract: Proteomic methods for identifying cancer related proteins and related products and kits are provided. The cancer specific proteins are extracellular matrix proteins that are associated with various aspects of cancer. Panels or signature sets of proteins useful in the detection, diagnosis and treatment of cancers as well as monitoring therapeutic progress in a cancer patient are provided herein along with methods for their detection and for their use in targeting imaging and/or therapeutic agents to the tumors via binding to the specified proteins. The proteins were identified using proteomics analyzes of tissue samples taken from cancer patients. In certain aspects the proteins are particularly useful in colon cancer patients.

Abstract: The present invention features a knock-in mouse comprising a mutation in an endogenous CRBN locus and methods of use thereof.

Abstract: The present invention features compositions and methods for identifying a subject having a B cell neoplasia or related condition responsive to treatment with lenalidomide and lenalidoinide-related compounds.