The invention described herein provides biological markers for the diagnosis, prognosis, and monitoring of prostate cancer.

This disclosure describes the characteristics of the “energetic” cancer stem cell (e-CSC) phenotype. This distinct sub-population of cancer stem cells (CSCs) has a unique energetic profile compared to bulk CSCs, being more glycolitic, having higher mitochondrial mass and elevated oxidative metabolism. e-CSCs also show an increased capacity to undergo cell cycle progression, enhanced anchorage-independent growth, and ALDH-positivity. The e-CSC phenotype presents new targets for cancer therapeutics, and in particular the anti-oxidant response, mitochondrial energy production, and mitochondrial biogenesis of e-CSCs makes them highly susceptible to mitochondrial inhibitors that target e-CSC anti-oxidant response, mitochondrial energy production, and mitochondrial biogenesis. Gene products for e-CSCs are disclosed, as well as classes of mitochondrial inhibiting therapeutic agents. Also disclosed are methods for identifying and separating e-CSCs front bulk cell populations.

Methods of diagnosing and predicting cancer relapse comprising measuring soluble CD28 levels in a subject, wherein an increase in soluble CD28 is indicative of cancer relapse or imminent cancer relapse, are provided. Methods of determining response to PD-1/PD-L1 based immunotherapy in a subject in need thereof, comprising measuring sCD28 levels in a subject undergoing PD-1/PD-L1 based immunotherapy at at least two time points wherein a decrease indicates response and an increase indicates lack of response, are also provided.

The present invention relates to a method of using Focal Adhesion Kinase (FAX) as a predictive marker to identify patients with early-stage colorectal cancer (CRC) at risk for recurrence. In particular, the present invention is a prognostic assay using FAK protein expression to predict those CRC patients with Stage I disease who may recur. The present invention will allow for quantitative measurement of the expression of FAK in tumor tissue of patients with early-stage CRC. As patients with stage I CRC are typically only treated with surgical resection, the present invention will uniquely facilitate the identification of those early-stage CRC patients who are at risk of recurrence and who may benefit from adjuvant therapy after resection of the primary cancer. This invention is not limited to patients with CRC and may be utilized for any condition that is caused by or causes FAK overexpression or dysfunction.

Methods of using T cell frequency (TCFR) in melanoma, e.g., as determined by high throughput DNA sequencing of the TCRB gene, as a predictor of disease progression and survival in patients with primary melanoma, and to select and treat subjects.

A method for predicting whether an early stage (IA, IB) non-small-cell lung cancer (NSCLC) patient is at a high risk of recurrence of the cancer following surgery involves subjecting a blood-based sample from the patient (obtained prior to, at, or after the surgery) to mass spectrometry and classification with a computer implementing a classifier. If the patients blood sample is classified as “high risk”, highest risk“or the equivalent, the patient can be guided to more aggressive treatment post-surgery. The classifier, or combination of classifiers, can be arranged in a hierarchical manner to make intermediate classifications, such as intermediate/high or intermediate/low, as well as low risk” or “lowest risk” classifications. Such additional classifications may guide clinical decisions as well.

Systemic Lupus Erythematosus is marked by altered immune regulation linked to waxing and waning clinical disease. Embodiments described herein identify sets of biomarkers/mediators and their use for informing and/or predicting a future SLE disease activity event such as an impending SLE flare or SLE-related organ inflammation. Such an approach can be beneficial in the management of lupus.

Assays and methods for diagnosing and treating autoimmune diseases. Particularly, the invention provides methods for differential diagnosis of specific autoimmune diseases, including autoimmune rheumatic disorders.

Provided by the present disclosure are fluorescent proteins that can detect kinase activity. The fluorescent proteins of the present disclosure have us in, for example, detecting kinase activity in any eukaryotic cell.

Provided is a method for evaluating the progression of glioma in an individual comprising monitoring the levels of circulating exosomes that are positive for survivin and a glial marker (such as glial fibrillary acidic protein). An increase in the level of such exosomes is indicative of poor prognosis. Levels of circulating exosomes that are positive for survivin and glial marker can also be used for evaluating the efficacy of a therapy for glioma in an individual, and modifying the therapy or introducing additional therapy if levels of such exosomes are found to be increasing.