The present disclosure provides methods of processing or analyzing a sample. A method for processing a sample may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule), barcoding the probe-nucleic acid molecule complex, and performing extension, denaturation, and amplification processes. A method for processing a sample may comprise hybridizing first and second probes to adjacent or non-adjacent target regions of a nucleic acid molecule (e.g., an RNA molecule), linking the first and second probes to provide a probe-linked nucleic acid molecule, and barcoding the probe-linked nucleic acid molecule. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well. One or more processes of the methods described herein may be performed on a cell, such as a permeabilized cell.

Disclosed are compositions and methods for ex vivo expansion of tumor-infiltrating lymphocytes for use in adoptive cell therapy (ACT). Also disclosed are compositions and method for identifying an agent for ex vivo expansion of tumor-infiltrating lymphocytes for use in ACT. Also disclosed are methods for treating cancer using tumor-infiltrating lymphocytes expanded by the disclosed methods.

A method of predicting the likelihood of success of a gene therapy procedure includes inducing DNA damage in a cell sample from an individual. The ability of the individual's cells in the sample to repair the DNA damage is then assessed to determine whether the individual could tolerate DNA damage caused by a gene therapy vector. In preferred embodiments, the ability of the individual's cells to repair DNA damage is assessed by detecting, and monitoring the subsequent disappearance of, a marker of DNA damage repair (such as gamma H2AX or phosphorylated 53BP1) in the sample.

A method for detecting and quantifying of the frequency of T cells to multiple antigenic peptide epitopes comprising: measuring intracellular Ca2+ signaling in individual T cells that are labeled with Ca2+ sensitive fluorophore; wherein said T cells are placed on the glass bottom of a well-covered with antibodies or other capturing proteins specific for non-stimulatory T cells' surface receptors and wherein a peptide antigens are injected into the well and the peptide binds to MHC molecules on the T-cell surface, wherein an increase in the intracellular concentration of Ca2+ in responding T cells leads to rise in intracellular fluorescence that is detected by fluorescent microscope and wherein the response rate of said detected fluorescence can be utilized to determine the quantity of responding T cells and the efficiency of said cells.

The present disclosure provides, inter alia, compositions and methods for harnessing the immune system (e.g., T cells) as a detection tool to diagnose and predict cancer patient treatment outcomes and for monitoring the persistence of functional, non-genetically modified, T cell therapies in vivo after administration to a subject.

Provided is a method for diagnosing a subject having or at risk of having mild cognitive impairment (MCI), including stimulating T cells in a biological sample obtained from the subject with an amyloid β peptide or a fragment thereof and evaluating a magnitude of a T cell response toward the amyloid β peptide or the fragment thereof. Also provided is a kit for diagnosing MCI by using the method.

The invention relates to a new potency assay for characterizing the quality and activity of an immune cell expressing a chimeric antigen receptor, the kit to carry out this assay and uses thereof.

Compositions and methods are provided for inhibiting T cell mediated destruction of virally transduced, trangene containing cells.

The present invention relates to peptides, proteins, nucleic acids and cells for use in immunotherapeutic methods. In particular, the present invention relates to the immunotherapy of cancer. The present invention furthermore relates to tumor-associated T-cell peptide epitopes, alone or in combination with other tumor-associated peptides that can for example serve as active pharmaceutical ingredients of vaccine compositions that stimulate anti-tumor immune responses, or to stimulate T cells ex vivo and transfer into patients. Peptides bound to molecules of the major histocompatibility complex (MHC), or peptides as such, can also be targets of antibodies, soluble T-cell receptors, and other binding molecules.

The invention relates to a method of isolating a T cell that expresses a T cell receptor capable of binding specifically to an antigen presented by a cancer cell in association with an MR1 molecule. The method comprises the steps of (a) providing a preparation of T cells, (b) contacting the preparation with cancer cells expressing MR1 protein; (c) isolating a T cell that is specifically reactive to said cancer cells. The invention further relates to a method of preparing a T cell preparation expressing select MR1 recognizing T cell receptors from transgene expression vectors, the use of such T cell preparations in treatment of cancer, and to collections of MR1 reactive T cell receptor encoding nucleic acids and cells.