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A genome-scale screen for synthetic drivers of T-cell proliferation

ABSTRACT: The engineering of patient T-cells for adoptive cell therapies has revolutionised the treatment of several cancer types. However, further improvements are needed to increase response and cure rates. CRISPR-based loss-of-function screens have been limited to negative regulators of T-cell functions and raise safety concerns due to permanent genome modification. Here we identify positive T-cell regulators via overexpression of ~12,000 barcoded human open reading frames (ORFs). The top-ranked genes increased primary human CD4+ and CD8+ T-cell proliferation, activation, and secretion of key cytokines like interleukin-2 and interferon-gamma. In addition, we developed a single-cell genomics method (OverCITE-seq) for high-throughput quantification of the transcriptome and surface antigens in ORF-engineered T-cells. The top-ranked ORF, lymphotoxin beta receptor (LTBR), is typically expressed in myeloid cells but absent in lymphocytes. When overexpressed in T-cells, LTBR induced profound transcriptional and epigenomic remodelling, increasing T-cell effector functions, as well as resistance to exhaustion in chronic stimulation settings, via constitutive activation of the canonical NF-kappaB pathway. LTBR and other top-ranked genes improved antigen-specific chimeric antigen receptor (CAR) T-cell and gamma delta T-cell responses, highlighting their potential for future cancer-agnostic therapies5. Our results provide several strategies for improving next generation T-cell therapies via induction of new synthetic cell programmes.

ORGANISM(S): Escherichia coli Homo sapiens

PROVIDER: GSE193736 | GEO | 2022/01/21

REPOSITORIES: GEO

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Project description:All nucleated mammalian cells express major histocompatibility complex (MHC) proteins that present peptides on cell surfaces for immune surveillance. These MHC-presented peptides (pMHC) can convey non-self antigens derived from pathogens or mutations to amount T-cell responses. Alterations in tumor-specific antigens – particularly mutation-bearing peptides (neoantigens) presented by MHC — can serve as potent substrates for anti-tumor immune responses. Here we employed an integrated genomic and proteomic antigen discovery strategy aimed at measuring interferon gamma (IFN-γ) induced alterations to antigen presentation, using a lymphoma cell line. IFN-γ treatment resulted in a set of differentially expressed proteins (2 % of all quantified proteins) including components of antigen presentation machinery or interferon signaling pathways. In addition, several proteasome subunits were found to be modulated, consistent with previous reports of immunoproteasome induction by IFN-γ exposure. This finding suggests that a modest proteomic response to IFN-γ could create larger alteration to cells antigen repertoires. Accordingly, by surveying immunopeptides, distinct peptide repertoires were exclusively observed in the IFN-γ induced samples. Furthermore, an additional set of presented peptides distinguished control and the IFN-γ samples by their altered relative abundances including neoantigens. Accordingly, we developed a classification system to distinguish peptides which are differentially presented due to altered expression from novel peptides resulting from changes in antigen processing. Taken together, these data demonstrate that IFN-γ can re-shape antigen repertoires by identity and by abundance. Extending this approach to models with greater clinical relevance should help develop strategies by which immunopeptide repertoires are intentionally reshaped to improve endogenous or vaccine-induced anti-tumor immune responses and potentially anti-viral immune responses.

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A genome-scale screen for synthetic drivers of T-cell proliferation

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