Project description:Functional discovery of tumor-reactive T cell receptors by massively parallel library synthesis and screening: NKIRTIL063 titration screen
| PRJNA1068301 | ENA
Project description:Functional discovery of tumor-reactive T cell receptors by massively parallel library synthesis and screening: validation in CD8 T cells
| PRJNA1068078 | ENA
Project description:Functional discovery of tumor-reactive T cell receptors by massively parallel library synthesis and screening: validation in CD4 T cells and OVC190 TCR screen
Project description:The screening of a previously reported fluorescein labelled 10,000 member PNA encoded peptide library allowed information on the interaction between the peptide-ligands and the cell surface receptors to be extracted, identified new peptide ligands for cell surface receptors, and gave crucial information about consensus sequences. A novel indirect amplification of the PNA signal by amplification of the PNA-complementary DNA library was developed to screen PNA-encoded peptide library against D54, HEK293T, and HEK293T-CCR6 cells. This work generates a new approach to biological discovery and an expansion of modern microarray techniques. In addition, the microarray approach facilitates screening for differences in surface-receptor ligands and/or receptor expression between various cell types including diseased and normal cells.
Project description:Neoantigen-reactive cytotoxic T lymphocytes play a vital role in precise cancer cell elimination. In this study, we demonstrate the effectiveness of personalized neoantigen-based T cell therapy in inducing tumor regression in two patients suffering from heavily-burdened metastatic ovarian cancer. Our approach involved the development of a robust pipeline for ex vivo expansion of neoantigen-reactive T lymphocytes. Neoantigen peptides were designed and synthesized based on the somatic mutations of the tumors and their predicted HLA binding affinities. These peptides were then presented to T lymphocytes through co-culture with neoantigen-loaded dendritic cells for ex vivo expansion. Subsequent to cell therapy, both patients exhibited significant reductions in tumor marker levels and experienced substantial tumor regression. One patient achieved repeated cancer regression through infusions of T cell products generated from newly identified neoantigens. Transcriptomic analyses revealed a remarkable increase in neoantigen-reactive cytotoxic lymphocytes in the peripheral blood of the patients following cell therapy. These cytotoxic T lymphocytes expressed polyclonal T cell receptors (TCR) against neoantigens, along with abundant cytotoxic proteins and pro-inflammatory cytokines. The efficacy of neoantigen targeting was significantly associated with the immunogenicity and TCR polyclonality. Notably, the neoantigen-specific TCR clonotypes persisted in the peripheral blood after cell therapy. Our findings indicate that personalized neoantigen-based T cell therapy triggers cytotoxic lymphocytes expressing polyclonal TCR against ovarian cancer, suggesting its promising potential in cancer immunotherapy.
2023-12-01 | GSE248401 | GEO
Project description:Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies
Project description:Here we developed a massively parallel in-library ligation methodology to simultaneously perturb four pre-designed targets in CRISPR/Cas9 screening. Thousands of pairs of sequences precisely ligated with their counterparts in library, which enabled simultaneous expression of four gRNAs from each single vector. We demonstrated this novel method with 6,236 4-gene combinations targeting 1,599 immune response related genes, and generated a plasmid library with 1,400x coverage. The library performance was evaluated in a canonical T cell activation experiment, and combinations involved in TCR signaling pathway or TCR complex were successfully identified as positive regulators. Novel combination that is reflecting a potential pathway crosstalk was also verified. This new methodology expands the capacity of the perturbation in CRISPR screening and provided a powerful tool for researches in broad fields to study the combinatorial outcomes from coordinated gene behaviors.
Project description:The goal of this study is to demonstrate the ability of a novel platform to screen, identify and characterize neoantigen-specific T-cells and their receptors by combining targeted RNA-seq data on subset of T-cell specific genes and T-cell Receptor sequencing
Project description:Here we describe our work on the development of an ABPP screening platform for cysteine reactive covalent fragments against deubiquitinating enzymes (DUBs) on 96 well plate format. Within this targeted workflow, we profile cysteine reactive fragments by competition with biotinylated ubiquitin probe in cell lysates and employ label free data independent acquisition (DIA) MS method. The platform was used to screen a library of 138 Cys-reactive covalent fragments against DUBome in HEK293T cell lysate, identifying functionally relevant hit fragments for numerous DUBs and demonstrating the utility of the approach in expanding the liganded proteome.