Provided herein are methods and compositions for generating engineered cells, such as cells expressing a recombinant receptor, including methods involving stimulation and/or engineering of an input composition having a defined ratio of naive-like CD4+ T cells to naive-like CD8+ T cells. In particular, the methods can be used to engineer T cells with genetically engineered receptors, such as genetically engineered antigen receptors such as engineered (recombinant) TCRs and chimeric antigen receptors (CARs), or other recombinant chimeric receptors. Features of the methods include producing a more consistent and/or predictable T cell product and/or a product with lower toxicity compared with other methods.

Fibronectin type III domains (FN3) that specifically bind to CD8A, related polynucleotides capable of encoding CD8A-specific FN3 domains, cells expressing the FN3 domains, as well as associated vectors, and detectably labeled FN3 domains are useful in therapeutic and diagnostic applications.

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

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.

In the present invention, inventors investigate the representation of T cell subsets in Toxic epidermal necrolysis (TEN) a life-threatening cutaneous adverse drug reaction (cADR), characterized by massive epidermal necrosis. To better understand why skin symptoms are so severe in TEN disease, inventors conducted a prospective immunophenotyping study on skin samples and blood from 18 TEN patients, using mass cytometry and next generation TCR sequencing. Deep sequencing of the T cell receptor CDR3 repertoire revealed massive expansion of unique CDR3 clonotypes in blister cells. Over-represented clonotypes were mainly effector memory CD8+CD45RACCR7 T cells, and expressed high levels of cytotoxic (Granulysin and Granzymes A & B) and activation (CD38) markers. Thus present invention relates to non-invasive, specific and rapid methods for diagnostic and monitoring Toxic Epidermal Necrolysis. More specifically present invention relates to methods for diagnosis and/or monitoring of Toxic Epidermal Necrolysis through detection of a specific population of T lymphocytes in a subject. The present invention also relates to a method of preventing or treating a Toxic Epidermal Necrolysis in a subject in need thereof.

There is provided methods of determining tuberculosis (TB) infection status in an individual comprising: (i) providing a sample comprising T-cells; (ii) exposing the sample of (i) to one or more TB antigens; (iii) identifying T-cells in the sample that are CD4 positive and (a) secrete TNF- without secreting IFN-; or (b) secrete IFN- without secreting TNF-; (iv) identifying those cells of (iii) which are also CCR7 and, CD127 negative; and optionally (v) calculating the cells identified in (iv) as a percentage of those identified in (iii); wherein the identification of cells in (iv) and/or the percentage of T-cells calculated in (v) correlates to TB infection status of the individual, and wherein steps (iii) and (iv) can be carried out either sequentially or simultaneously. There are also provided compositions and kits for use in such methods.

Methods and systems for diagnosing, providing prophylaxis, and treating one or more age-related neurodegeneration or pathological cognitive impairment are provided. An increased presence of CD103+ resident memory CD8+ T cells (CD8+ T.sub.RM) can be detected in blood sample obtained from the human subjects with one or more symptoms of loss of short-term or long-term memory, decreased ability to maintain focus, and decreased problem-solving capacity. An increased presence of CD103+ CD8+ T.sub.RM can be compared to a value obtained from one or a pool of healthy human subjects with none of the one or more symptoms. One or more of a therapeutically effective amount of: an inhibitor of cluster of differentiation (CD103), an inhibitor of perforin-1, and an inhibitor of interferon gamma (IFN) can be administered as treatment of age-related neurodegeneration or pathological cognitive impairment. Pathological neurodegeneration can include Parkinson's disease, multiple sclerosis, or Alzheimer' s disease.

The invention provides methods for treating pathological conditions associated with an undesirable inflammatory component. The invention is generally directed to reducing inflammation by administering cells that have one or more of the following effects in an injured subject: interact with splenocytes, preserve splenic mass, increase proliferation of CD4.sup.+ and CD8.sup.+ T-cells, increase IL-4 and IL-10, decrease IL-6 and IL-1, and increase M2:M1 macrophage ratio at the site of injury. The invention is also directed to drug discovery methods to screen for agents that modulate the ability of the cells to have these effects. The invention is also directed to cell banks that can be used to provide cells for administration to a subject, the banks comprising cells having desired potency for achieving these effects.

The present disclosure provides a method of treating cancer by immune checkpoint blockade, or selecting patients for treatment with immune checkpoint blockers, by detecting tumors with high levels of T-lymphocytes with low levels of activation and proliferation. In various embodiments the tissue sample may be from a conventional biopsy. In various embodiments the cancer may be non-small cell lung cancer.

The present invention relates to a kit for detecting a subset of a human regulatory T cell, and a detection method thereof, and belongs to the technical field of cell subset detection. The present invention provides a kit which includes the following components: a blood dilution solution, a mononuclear cell isolation solution, a cell culture solution, a lymphocyte activation liquid, a dead-cell-removing dye, an FcR blocking agent, fluorescence-labeled antibodies against human cell-surface markers, fluorescence-labeled antibodies against human intracellular molecules, a PBS buffer, lipopolysaccharide, a washing buffer, a cell staining buffer, a cell fixing solution, and a membrane-permeable wash buffer. At the time of detection, firstly mononuclear cells are isolated from whole blood, secondly human peripheral blood mononuclear cells are stimulated, and finally the subsets of the regulatory T cells can be detected just by fluorescent antibody staining. Use of the kit and detection method of the present invention can identify 2-6 subsets of regulatory T cells quickly and easily.