The present disclosure provides methods, systems, and kits for processing nucleic acid molecules. A method may comprise providing a template nucleic acid fragment (e.g., within a cell, cell bead, or cell nucleus) within a partition (e.g., a droplet or well) and subjecting the template nucleic acid fragment to one or more processes including a barcoding process and a single primer extension or amplification process. The processed template nucleic acid fragment may then be recovered from the partition and subjected to further amplification to provide material for subsequent sequencing analysis. The methods provided herein may permit simultaneous processing and analysis of both DNA and RNA molecules originating from the same cell, cell bead, or cell nucleus.

A purpose of the present invention is to provide a composition for preserving a sample, in particular, a composition able to preserve cells or a tissue without causing a change in the state of cells. Another purpose of the present invention is to provide a sample preservation method for preparing a suspension containing a target object from a preserved sample, and a method for analyzing a target object in a sample. The present disclosure provides a sample preservation composition containing albumin and lactic acid or a salt thereof. The concentration of sodium ions in the composition is 50-300 mmol/L. Further provided are a method for preserving a sample using the composition, a method for preparing a sample suspension, and a method for analyzing a target object in the sample suspension.

The present disclosure relates to novel epitope-based compositions, including vaccines, against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and diseases caused by SARS-CoV-2, including the highly contagious coronavirus disease 2019. The disclosure relates to immunogenic polypeptides (including concatemeric polypeptides, hybrid Ii-key constructs, and chimeric or fusion polypeptides as disclosed herein) and the uses thereof, particularly in vaccine compositions. The disclosure also relates to nucleic acids, vectors, and cells which express the polypeptides and the uses thereof. The polypeptides of the invention more specifically comprise an agretope predicted to be a ligand of HLA class I and/or HLA class II MHC molecules, as well as an epitope that is predicted to be recognized by T-cells in the context of MHC class I and/or class II molecules. The compositions are particularly suited to produce vaccines, particularly for vaccinating against SARS-CoV-2 infection and related diseases caused by SARS-CoV-2, including COVID-19.

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 disclosure relates to compositions and methods for inducing an immune response to a composition of the invention in a subject. Additionally, the present disclosure generally relates to methods for screening for immune response to a composition of the invention.

A pharmaceutical composition contains an antibody or a fragment thereof specific for COL6A3 for the treatment of a cancer. A method of treating a cancer includes administering to a subject in need thereof the pharmaceutical composition. A kit includes a container that contains the pharmaceutical composition. A method of producing an antibody or a fragment thereof against a peptide or a MHC/peptide complex. A method for detecting a diseased tissue includes administering to a subject in need thereof an antibody or a fragment thereof conjugated to a radioisotope and detecting a signal from the radioisotope in the subject. A method for treating a diseased tissue includes administering to a subject in need thereof an antibody or a fragment thereof conjugated to a toxin.

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.

A method of treating a patient who has hepatocellular carcinoma (HCC), colorectal carcinoma (CRC), glioblastoma (GB), gastric cancer (GC), esophageal cancer, NSCLC, pancreatic cancer (PC), renal cell carcinoma (RCC), benign prostate hyperplasia (BPH), prostate cancer (PCA), ovarian cancer (OC), melanoma, breast cancer (BRCA), CLL, Merkel cell carcinoma (MCC), SCLC, Non-Hodgkin lymphoma (NHL), AML, gallbladder cancer and cholangiocarcinoma (GBC, CCC), urinary bladder cancer (UBC), and uterine cancer (UEC) includes administering to said patient a composition containing a population of activated T cells that selectively recognize cells in the patient that aberrantly express a peptide. A pharmaceutical composition contains activated T cells that selectively recognize cells in a patient that aberrantly express a peptide, and a pharmaceutically acceptable carrier, in which the T cells bind to the peptide in a complex with an MHC class I molecule, and the composition is for treating the patient who has HCC, CRC, GB, GC, esophageal cancer, NSCLC, PC, RCC, BPH, PCA, OC, melanoma, BRCA, CLL, MCC, SCLC, NHL, AML, GBC, CCC, UBC, and/or UEC. A method of treating a patient who has HCC, CRC, GB, GC, esophageal cancer, NSCLC, PC, RCC, BPH, PCA, OC, melanoma, BRCA, CLL, MCC, SCLC, NHL, AML, GBC, CCC, UBC, and/or UEC includes administering to said patient a composition comprising a peptide in the form of a pharmaceutically acceptable salt, thereby inducing a T-cell response to the HCC, CRC, GB, GC, esophageal cancer, NSCLC, PC, RCC, BPH, PCA, OC, melanoma, BRCA, CLL, MCC, SCLC, NHL, AML, GBC, CCC, UBC, and/or UEC.

The invention relates to a method for determination of the frequency of regulatory T-cells in samples obtained from human blood and to methods for the preparation of compositions comprising predetermined amount of regulatory T-cells. The invention is based on the conception that a large fraction of regulatory T-cells present in human peripheral blood do not express detectable amounts of Foxp3, the master transcription factor used for identification of regulatory T-cells, as a result of cytokine deprivation outside of the tissue context.

Polypeptides which may be used for preventing or treating allergy to moulds of the Cladosporium and/or Alternaria genus, have up to 30 amino acids in length and comprise: (I) the amino acid sequence: (a) GGYKAAVRPTMLE (SEQ ID NO: 35; Cla35), (b) AE V YQKLK SLTKK (SEQ ID NO: 31; Cla16), (c) VAITYASRAQGAE (SEQ ID NO: 32; Cla25), (d) GHHFKERGT-GSLVIT (SEQ ID NO: 33; Cla26), or (e) ANYTQTKTVSIRL (SEQ ID NO: 34; Cla29); or (II) a T cell epitope-containing variant sequence which is a said amino acid sequence (I) having up to six amino acid modifications, each of which is independently a deletion, substitution or insertion.