Defining and targeting patterns of T cell dysfunction in inborn errors of immunity

Abstract

Inborn errors of immunity (IEIs) are a group of more than 450 monogenic disorders that impair immune development and function. A subset of IEIs blend increased susceptibility to infection, autoimmunity, and malignancy and are known collectively as primary immune regulatory disorders (PIRDs). While many aspects of immune function are altered in PIRDs, one key impact is on T-cell function. By their nature, PIRDs provide unique insights into human T-cell signaling; alterations in individual signaling molecules tune downstream signaling pathways and effector function. Quantifying T-cell dysfunction in PIRDs and the underlying causative mechanisms is critical to identifying existing therapies and potential novel therapeutic targets to treat our rare patients and gain deeper insight into the basic mechanisms of T-cell function. Though there are many types of T-cell dysfunction, here we will focus on T-cell exhaustion, a key pathophysiological state. Exhaustion has been described in both human and mouse models of disease, where the chronic presence of antigen and inflammation (e.g., chronic infection or malignancy) induces a state of altered immune profile, transcriptional and epigenetic states, as well as impaired T-cell function. Since a subset of PIRDs amplify T-cell receptor (TCR) signaling and/or inflammatory cytokine signaling cascades, it is possible that they could induce T-cell exhaustion by genetically mimicking chronic infection. Here, we review the fundamentals of T-cell exhaustion and its possible role in IEIs in which genetic mutations mimic prolonged or amplified T-cell receptor and/or cytokine signaling. Given the potential insight from the many forms of PIRDs in understanding T-cell function and the challenges in obtaining primary cells from these rare disorders, we also discuss advances in CRISPR-Cas9 genome-editing technologies and potential applications to edit healthy donor T cells that could facilitate further study of mechanisms of immune dysfunctions in PIRDs. Editing T cells to match PIRD patient genetic variants will allow investigations into the mechanisms underpinning states of dysregulated T-cell function, including T-cell exhaustion.

Keywords: CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 (CRISPR associated protein 9)-mediated genome editing; human immunology; inborn error of immunity (IEI); precision medicine; t cell exhaustion.

Figure 1

Canonical three-signal activation model for T cells. Activation is dependent on integration of three signals: 1) recognition by the T-cell receptor (TCR) of an antigen presented as a peptide by the major histocompatibility complex (pMHC) on antigen-presenting cells (APCs); 2) costimulation, which lowers the stimulation threshold of naïve T cells, prevents anergy, and enhances cytokine production; and 3) cytokine signaling along the JAK-STAT pathway, which amplifies the clonal expansion, survival, and differentiation of T cells. These converging cellular signaling cascades influence the activation and differentiation status of T lymphocytes, in this case, CD8+ T cells. Adapted from “Three Signals Required for T cell Activation”, by BioRender.com (2022). Retrieved from https://app.biorender.com/biorender-templates/t-5f7c7b883b9a9000abcf98e4-three-signals-required-for-t-cell-activation.

Figure 2

Differential T-cell responses to short-term (acute) and long-term (chronic) infections. (A) In acute infections (solid black line), T-cell response spikes are marked by acquisition of effector function (e.g., cytokine production) and upregulation of activation markers and clonal expansion. When an infection or antigen is cleared, a small subset of effector T cells differentiate into memory cells, poised to reactivate upon re-infection, while most cells die. However, if the antigen level or inflammation persists as in the case during chronic infections, T cells develop into a distinct subset, termed “exhausted” T cells (solid red line). (B) Among the characteristics that define exhausted T cells are 1) coordinate expression of multiple immunoregulatory receptors, 2) decreased effector function, 3) altered metabolic function, and 4) altered transcriptional and epigenetic status.

Figure 3

CRISPR-Cas9 gene editing to model IEIs/PIRDs. The CRISPR-Cas9 system consists of the Cas9 protein in complex with a targeting gRNA, forming a ribonucleoprotein (RNP). Specificity is conferred through various mechanisms including the sgRNA and presence of the PAM sequence. The Cas9 opens and cuts the targeted sequence on both strands to generate double-strand breaks (DSBs). This activates DNA repair pathways (NHEJ and HDR) in cells and results in modifications at a target locus. The NHEJ pathway can be used for scenarios in which genetic variants result in the loss of expression of an encoded protein, while HDR can be employed for introduction of missense mutations. IEIs, inborn errors of immunity; PIRDs, primary immune regulatory disorders; sgRNA, single-guide RNA; PAM, protospacer adjacent motif; NHEJ, non-homologous end joining; HDR, homology-directed repair. Adapted from “CRISPR/Cas9 Gene Editing”, by BioRender.com (2022). Retrieved from https://app.biorender.com/biorender-templates/t-5f873df466346900a43c6db1-crisprcas9-gene-editing.

Figure 4

Retuning altered pathways to improve function. CRISPR-Cas9 can be used to edit healthy donor primary T cells to match the patient variant to overcome paucity of patient cells, especially those prior to immune-relevant therapy. Testing of treatment options (both preexisting and novel) can be exploited using high-throughput screening strategies to study the impact of blocking and/or stimulating identified dysfunctional pathways. This will allow us to identify and target common states of dysfunction across monogenic diseases.