T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes

AbstractChimeric antigen receptor (CAR) T cells still have limited effects in cancer, and especially in solid tumors, due to T cell dysfunction and exhaustion. CAR T cells overexpressing c-Jun (JUN CAR T cells) have been introduced to solve this problem. In this paper, we analyze JUN CAR T cells scRNA-seq data in solid tumors, by applying a genome-wide signature of T cell dysfunction, TID. This signature comes from the bulk RNA-seq signature TIDE, introduced to predict immune checkpoint inhibitor response. Our analysis confirms that on average, JUN CAR T cells are less dysfunctional than non-JUN CAR T cells. However, it also shows heterogeneity within JUN CAR T cells, which brings uncertainty about possible tumor resistance. We conclude that genome-wide dysfunction signature TID helps de-risking CAR T cell therapy for solid tumors.

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A genome-wide screen in macrophages identifies new regulators of IFNγ-inducible MHCII that contribute to T cell activation

10.1101/2020.08.12.248252 ◽

2020 ◽

Cited By ~ 1

Author(s):

Michael C. Kiritsy ◽

Laurisa M. Ankley ◽

Justin D. Trombley ◽

Gabrielle P. Huizinga ◽

Audrey E. Lord ◽

...

Keyword(s):

T Cell ◽

T Cell Activation ◽

Cell Activation ◽

Glycogen Synthase ◽

Surface Expression ◽

Host Immunity ◽

Dynamic Regulation ◽

Genome Wide ◽

A Genome ◽

Mhcii Expression

AbstractCytokine-mediated activation of host immunity is central to the control of pathogens. A key cytokine in protective immunity is interferon-gamma (IFNγ), which is a potent activator of antimicrobial and immunomodulatory effectors within the host. A major role of IFNγ is to induce major histocompatibility complex class II molecules (MHCII) on the surface of cells, which is required for CD4+ T cell activation. Despite its central role in host immunity, the complex and dynamic regulation of IFNγ-induced MHCII is not well understood. Here, we integrated functional genomics and transcriptomics to comprehensively define the genetic control of IFNγ-mediated MHCII surface expression in macrophages. Using a genome-wide CRISPR-Cas9 library we identified genes that control MHCII surface expression, many of which have yet to be associated with MHCII. Mechanistic studies uncovered two parallel pathways of IFNγ-mediated MHCII control that require the multifunctional glycogen synthase kinase 3 beta (GSK3β) or the mediator complex subunit MED16. Both pathways are necessary for IFNγ-mediated induction of the MHCII transactivator CIITA, MHCII expression, and CD4+ T cell activation. Using transcriptomic analysis, we defined the regulons controlled by GSK3β and MED16 in the presence and absence of IFNγ and identified unique networks of the IFNγ-mediated transcriptional landscape that are controlled by each gene. Our analysis suggests GSK3β and MED16 control distinct aspects of the IFNγ-response and are critical for macrophages to respond appropriately to IFNγ. Our results define previously unappreciated regulation of MHCII expression that is required to control CD4+ T cell responses by macrophages. These discoveries will aid in our basic understanding of macrophage-mediated immunity and will shed light on mechanisms of failed adaptive responses pervasive in infectious disease, autoimmunity, and cancer.

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Genome-wide CRISPR screen identifies FAM49B as a key regulator of actin dynamics and T cell activation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1801340115 ◽

2018 ◽

Vol 115 (17) ◽

pp. E4051-E4060 ◽

Cited By ~ 30

Author(s):

Wanjing Shang ◽

Yong Jiang ◽

Michael Boettcher ◽

Kang Ding ◽

Marianne Mollenauer ◽

...

Keyword(s):

T Cell ◽

T Cell Receptor ◽

T Cell Activation ◽

Cell Activation ◽

Active Form ◽

Cell Receptor ◽

Small Gtpase ◽

Genome Wide ◽

A Genome ◽

Crispr Screen

Despite decades of research, mechanisms controlling T cell activation remain only partially understood, which hampers T cell-based immune cancer therapies. Here, we performed a genome-wide CRISPR screen to search for genes that regulate T cell activation. Our screen confirmed many of the known regulators in proximal T cell receptor signaling and, importantly, also uncovered a previously uncharacterized regulator, FAM49B (family with sequence similarity 49 member B). FAM49B deficiency led to hyperactivation of Jurkat T cells following T cell receptor stimulation, as indicated by enhancement of CD69 induction, PAK phosphorylation, and actin assembly. FAM49B directly interacted with the active form of the small GTPase Rac, and genetic disruption of the FAM49B–Rac interaction compromised FAM49B function. Thus, FAM49B inhibits T cell activation by repressing Rac activity and modulating cytoskeleton reorganization.

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