Provided is a peripheral blood biomarker for predicting the long-term survival/need for therapeutic intervention in cancer immunotherapy. The present invention provides a method that uses a composition of a cell subpopulation in a sample obtained from a subject as an indicator to predict the long-term survival of the subject in cancer immunotherapy. The long-term survival/need for therapeutic intervention in a subject in cancer immunotherapy can be predicted by comparing the level of a CD4+ T cell subpopulation that correlates with dendritic cell stimulation in an antitumor immune response or a dendritic cell subpopulation that correlates with dendritic cell stimulation in an antitumor immune response with a reference standard.

Provided herein are methods and compositions for single cell characterization using affinity-oligonucleotide conjugates.

Provided herein, in one aspect, is a method of preventing or delaying the onset of clinical type 1 diabetes (T1D), comprising: providing a non-diabetic subject who is at risk for T1D; administering a prophylactically effective amount of an anti-CD3 antibody to the non-diabetic subject; and determining, prior to or after the administering step, that the non-diabetic subject has more than about 5% to more than about 10% TIGIT+KLRG1+CD8+ T-cells in all CD3+ T cells, which is indicative of successful prevention or delay of the onset of clinical T1D.

Provided herein are methods and compositions for single cell characterization using affinity-oligonucleotide conjugates. In some aspects, such methods may comprise attaching a first vessel barcoded polynucleotide to an oligonucleotide portion of an affinity-oligonucleotide conjugate, which binds to a target antigen expressed by a single cell that is isolated in a single vessel. In some aspects, the oligonucleotide portion of the affinity-oligonucleotide conjugate may comprise an antigen identification sequence (AID). In some aspects, the oligonucleotide portion of the affinity-oligonucleotide conjugate may further comprise an affinity molecular barcode (AMB) sequence. In some aspects, such methods may further comprise lysing the single cell and attaching a second vessel barcoded polynucleotide to a cell polynucleotide from the single cell.

A method for the evaluation of the efficacy of a drug aiming to eradicate a cellular reservoir of mammalian cells infected with a mammalian immunodeficiency virus, the method including: a) quantifying, the presence of lymphocyte cells expressing a CD89 differentiation marker on their surface; and b) concluding that the drug is efficient to eradicate the cellular reservoir of mammalian cells infected with the mammalian immunodeficiency virus when lymphocyte cells expressing a CD89 differentiation marker are absent.

This disclosure describes methods, kits, and systems for scoring the immune response to cancer through examination of tissue infiltrating lymphocytes (TILs). Methods of scoring the immune response in cancer using tissue infiltrating lymphocytes include detecting CD3, CD8, CD20, and FoxP3 within the sample and scoring the detection manually or scoring the digital images of the staining with the aid of image analysis and algorithms.

The subject matter disclosed herein is generally directed to novel CD8+ and CD4+ T cell subtypes associated with effector, suppressive or regulatory T cell functions. Moreover, the subject matter disclosed herein is generally directed to methods and compositions for use of the subtype. Also, disclosed herein are gene signatures and markers associated with the subtype and use of said signatures and markers. Further disclosed are therapeutic methods of using said gene signatures and immune cell subtype. Further disclosed are pharmaceutical compositions comprising populations of CD4+ and/or CD8+ TILs or populations of immune cells depleted for a specific subtype. Further disclosed are interactions with other T cell subtypes.

In certain embodiments methods of identifying T cell receptors that respond to specific target cell antigens are provided, where the methods comprise providing a substrate bearing a plurality of target cells (e.g., mammalian cells); contacting the target cells on the substrate with CD8+ T cells; and using label-free optical imaging to identify an increase in mass of a T-cell and/or a decrease in mass of a target cell, where an increase in mass of a T cell and/or a decrease in mass of a target cell is an indicator that said T cell bears a T cell receptor activated by antigens presented on said target cell.

The present invention relates to the use of a nucleic acid molecule encoding a first reporter gene, bordered by at least one first pair and one second pair of sequences targeting a site-specific recombinase in order to detect cells of a mammal infected with a virus responsible for an immunodeficiency.

This disclosure describes methods, kits, and systems for scoring the immune response to cancer through examination of tissue infiltrating lymphocytes (TILs). Methods of scoring the immune response in cancer using tissue infiltrating lymphocytes include detecting CD3, CD8, CD20, and FoxP3 within the sample and scoring the detection manually or scoring the digital images of the staining with the aid of image analysis and algorithms.