Compositions and methods for screening for a disease or a disorder associated with a deficiency in frataxin in a subject using biomarkers for diseases or disorders associated with a deficiency in frataxin are disclosed. The compositions and methods include determining the acetylation status of mitochondrial proteins. Also disclosed are methods of detecting progression of a disease or a disorder associated with a deficiency in frataxin in a subject and methods of monitoring effectiveness of a therapy for diseases or disorders associated with a deficiency in frataxin.

The present invention relates to a compound for use in detecting “reader” and “eraser” proteins of lysine lipoylation. The present invention provides an affinity-based probe, referred to herein as “KPlip”, capable of interrogating the lipoylated peptide/protein interactions under native cellular environments. The chemical probe allows for the identification of potential regulators of lysine lipoylation, thus uncovering new biology related to lipoylation. There is also provided a method of using the compound to identifying proteins that interact with lipoylated proteins.

The invention provides an isolated peptide comprising a lysine 2-hydroxyisobutyrylation site, a lysine 2-hydroxyisobutyrylation specific affinity reagent that specifically binds to the peptide, and a method for detecting protein lysine 2-hydroxyisobutyrylation in a sample using the reagent.

Noninvasive methods of determining breast cancer subtype in a subject are provided that employ newly identified biomarkers. Said methods comprise isolating a population of extracellular vehicles in a biofluid sample of a subject and detecting differential expression in one or more proteins or peptides therein. Such differential expression is compared to one or more expression profiles within a panel of biomarkers, with each expression profile in the panel associated with a subtype of breast cancer. Also provided are kits for detecting a subtype of breast cancer and/or identifying the recurrence thereof, each comprising an antibody, aptamer, or other detection means against the aforesaid biomarkers. Methods for monitoring treatment efficacy in a subject experiencing breast cancer using the same platforms are also provided.

The subject invention pertains to biomarkers for identifying a subject as having high risk of the development PE. The biomarkers presented herein include miRNAs, post-translational modification of histone proteins, amount, expression and/or activity of histone or DNA modifying enzymes and methylation of sites in the genomic DNA. In certain embodiments, increased miR-17, increased acetylation of H4 histone protein, decreased amount, expression and/or activity of HDACS mRNA or protein or increased methylation of DNA at the genomic site CYP19A1 in the blood, serum or plasma of a subject compared to that of a control subject is used to predict the development of PE in the subject. The invention also provides kits and reagents to conduct assays to quantify biomarkers described herein. The invention further provides the methods of treating and/or managing PE in a subject identified as having a high risk of the development of PE.

This disclosure relates generally to methods and agents for assessing T-cell function and for predicting responses to therapy. More particularly, the present invention relates to methods and agents for detecting different forms of Eomesodermin (EOMES) in T-cells, which are useful for assessing the function of a T-cell, for assessing the immune function of a subject, for predicting the likelihood of response of a cancer patient to therapy including immunotherapy, for stratifying a cancer patient as a likely responder or non-responder to a therapy, and for managing treatment of a cancer patient.

The present application provides methods for preparing soluble lipidated ligand agents comprising a ligand entity and a lipid entity, and in some embodiments, provides relevant parameters of each of these components, thereby enabling appropriate selection of components to assemble active agents for any given target of interest.

Provided herein are turn-on fluorescent chemical probes useful for monitoring and/or detecting lysine delipoylation activity in a sample including or suspected of including a delipoylation enzyme.

Methods for identifying viral protein constituents and quantifying the relative abundance of such viral protein constituents in a sample of viral particles are disclosed. In embodiments, the methods include first-dimension chromatography to separate intact viral capsid components of the sample, online denaturation of the viral capsid components to produce intact viral proteins, second-dimension chromatography to separate the viral proteins, and mass spectrometry to determine the masses of the viral proteins and identify the viral protein constituents of the sample.

The invention provides an isolated peptide comprising a lysine 3-hydroxybutyrylation site, a lysine 3-hydroxybutyrylation specific affinity reagent that specifically binds to the peptide, and a method for detecting protein lysine 3-hydroxybutyrylation in a sample using the reagent.