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

• Published in: Nature (London) 2022-03, Vol.603 (7902), p.728-735
• Main Authors: Legut, Mateusz, Gajic, Zoran, Guarino, Maria, Daniloski, Zharko, Rahman, Jahan A., Xue, Xinhe, Lu, Congyi, Lu, Lu, Mimitou, Eleni P., Hao, Stephanie, Davoli, Teresa, Diefenbach, Catherine, Smibert, Peter, Sanjana, Neville E.
• Format: Article
• Language: English
• Subjects: 38; 38/91; 42/44; 631/250/1619/554; 631/250/248; 631/61/191; 631/67/580; 96; 96/106; 96/31; Antigens; CD19 antigen; CD28 antigen; CD3 antigen; CD4 antigen; CD4-Positive T-Lymphocytes; CD8 antigen; CD8-Positive T-Lymphocytes; Cell cycle; Cell growth; Cell Proliferation; CRISPR; Cytokines; Cytotoxicity; Gene expression; Genomes; Genomics; Humanities and Social Sciences; Humans; Immunotherapy, Adoptive; Interleukin 1; Interleukin 2; Lymphocyte Activation - genetics; Lymphocytes; Lymphocytes T; multidisciplinary; Neoplasms; Science; Science (multidisciplinary); T cell receptors; Toxicity; Tumors
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-022-04494-7

The engineering of autologous patient T cells for adoptive cell therapies has revolutionized the treatment of several types of cancer 1 . 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 2 – 4 and raise safety concerns owing to the permanent modification of the genome. Here we identify positive regulators of T cell functions through overexpression of around 12,000 barcoded human open reading frames (ORFs). The top-ranked genes increased the proliferation and activation of primary human CD4 + and CD8 + T cells and their secretion of key cytokines such as interleukin-2 and interferon-γ. In addition, we developed the 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-β receptor (LTBR)—is typically expressed in myeloid cells but absent in lymphocytes. When overexpressed in T cells, LTBR induced profound transcriptional and epigenomic remodelling, leading to increased T cell effector functions and resistance to exhaustion in chronic stimulation settings through constitutive activation of the canonical NF-κB pathway. LTBR and other highly ranked genes improved the antigen-specific responses of chimeric antigen receptor T cells and γδ T cells, highlighting their potential for future cancer-agnostic therapies 5 . Our results provide several strategies for improving next-generation T cell therapies by the induction of synthetic cell programmes. A genome-scale gain-of-function screen using overexpression of nearly 12,000 open reading frames (ORFs) identifies positive regulators of human T cell function and suggests that ORF-based screens could be applied clinically to improve T cell therapies.