Genome-wide Specificity of Highly Efficient TALENs and CRISPR/Cas9 for T Cell Receptor Modification

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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Faculty Opinions recommendation of Highly efficient NMR assignment of intrinsically disordered proteins: application to B- and T cell receptor domains.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718013250.793477317 ◽

2013 ◽

Author(s):

Vladimir Uversky

Keyword(s):

T Cell ◽

T Cell Receptor ◽

Nmr Assignment ◽

Intrinsically Disordered Proteins ◽

Cell Receptor ◽

Disordered Proteins ◽

Intrinsically Disordered ◽

Highly Efficient

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Ets1 Promotes the Differentiation of Post-Selected iNKT Cells through Regulation of the Expression of Vα14Jα18 T Cell Receptor and PLZF

International Journal of Molecular Sciences ◽

10.3390/ijms222212199 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12199

Author(s):

Ya-Ting Chuang ◽

Wan-Chu Chuang ◽

Chih-Chun Liu ◽

Chia-Wei Liu ◽

Yu-Wen Huang ◽

...

Keyword(s):

T Cell ◽

T Cell Receptor ◽

Target Genes ◽

Cell Receptor ◽

Mechanisms Of Action ◽

Inkt Cells ◽

Genome Wide ◽

Invariant Natural Killer ◽

Multiple Stages ◽

Molecular Picture

The transcription factor Ets1 is essential for the development/differentiation of invariant Natural Killer T (iNKT) cells at multiple stages. However, its mechanisms of action and target genes in iNKT cells are still elusive. Here, we show that Ets1 is required for the optimal expression of the Vα14Jα18 T cell receptor (TCR) in post-selected thymic iNKT cells and their immediate differentiation. Ets1 is also critical for maintaining the peripheral homeostasis of iNKT cells, which is a role independent of the expression of the Vα14Jα18 TCR. Genome-wide transcriptomic analyses of post-selected iNKT cells further reveal that Ets1 controls leukocytes activation, proliferation differentiation, and leukocyte-mediated immunity. In addition, Ets1 regulates the expression of ICOS and PLZF in iNKT cells. More importantly, restoring the expression of PLZF and the Vα14Jα18 TCR partially rescues the differentiation of iNKT cells in the absence of Ets1. Taken together, our results establish a detailed molecular picture of how Ets1 regulates the stepwise differentiation of iNKT cells.

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Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities

10.1101/2021.09.17.460747 ◽

2021 ◽

Author(s):

Magdalena L Russell ◽

Aisha Souquette ◽

David M Levine ◽

E Kaitlynn Allen ◽

Guillermina Kuan ◽

...

Keyword(s):

T Cell ◽

T Cell Receptor ◽

Selection Process ◽

Cell Receptor ◽

Genetic Loci ◽

Genome Wide ◽

Tcr Repertoire ◽

Genes Encoding ◽

Gene Usage ◽

Genetically Determined

Every T cell receptor (TCR) repertoire is shaped by a complex probabilistic tangle of genetically determined biases and immune exposures. T cells combine a random V(D)J recombination process with a selection process to generate highly diverse and functional TCRs. The extent to which an individual's genetic background is associated with their resulting TCR repertoire diversity has yet to be fully explored. Using a previously published repertoire sequencing dataset paired with high-resolution genome-wide genotyping from a large human cohort, we infer specific genetic loci associated with V(D)J recombination probabilities using genome-wide association inference. We show that V(D)J gene usage profiles are associated with variation in the TCRB locus and, specifically for the functional TCR repertoire, variation in the major histocompatibility complex locus. Further, we identify specific variations in the genes encoding the Artemis protein and the TdT protein to be associated with biasing junctional nucleotide deletion and N-insertion, respectively. These results refine our understanding of genetically-determined TCR repertoire biases by confirming and extending previous studies on the genetic determinants of V(D)J gene usage and providing the first examples of trans genetic variants which are associated with modifying junctional diversity. Together, these insights lay the groundwork for further explorations into how immune responses vary between individuals.

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