Manipulation of Alternative Splicing of IKZF1 Elicits Distinct Gene Regulatory Responses in T Cells

TL;DR

This study shows that changes in how the IKZF1 gene is spliced in T cells can significantly affect gene activity and may contribute to autoimmune diseases.

Contribution

The study reveals that alternative splicing of IKZF1 has functional consequences in T cells and may influence autoimmune disease risk.

Findings

Alternative splicing of IKZF1 affects gene expression, chromatin accessibility, and protein production in T cells.

Modest splicing changes in IKZF1 lead to compensatory responses in other IKAROS family members and impact autoimmunity-related genes.

IKZF1 splicing alterations may contribute to autoimmune disease risk by affecting gene regulation in T cells.

Abstract

What are the main findings?
Alternative splicing of IKZF1 in human T cells strongly influences gene expression, chromatin accessibility, and protein production.Even modest perturbations of IKZF1 splicing elicit compensatory responses in other IKAROS family members and impact autoimmunity-associated genes.

Alternative splicing of IKZF1 in human T cells strongly influences gene expression, chromatin accessibility, and protein production.

Even modest perturbations of IKZF1 splicing elicit compensatory responses in other IKAROS family members and impact autoimmunity-associated genes.

What are the implications of the main findings?
Alternative transcripts generated by splicing are not simply transcriptional “noise,” but have clear functional roles in mature T cells.Dysregulation of IKZF1 splicing may contribute to autoimmune disease risk, highlighting splicing isoforms as potential therapeutic targets.

Alternative transcripts generated by splicing are not simply transcriptional “noise,” but have clear functional roles in mature T cells.

Dysregulation of IKZF1 splicing may contribute to autoimmune disease risk, highlighting splicing isoforms as potential therapeutic targets.

Genome-wide studies have identified significant allelic associations between genetic variants in or near the IKZF1 gene and multiple autoimmune disorders. IKZF1, encoding the transcription factor IKAROS, produces at least 10 distinct transcripts. To explore the impact of alternative splicing of IKZF1 on the function of mature T cells and the risk of autoimmunity, we generated a panel of human T-cell clones with truncating mutations in IKZF1 exons 4, 6, or both. Differences in gene expression, chromatin accessibility, and protein abundance among clones were assessed by RNA-seq, ATAC-seq, and immunoblotting. Clones with single targeting events clustered separately from double-targeted clones on multiple parameters, but overall, clone responses were highly heterogeneous. Perturbation of IKZF1 splicing resulted in significant differences in expression and chromatin accessibility of other autoimmunity-associated genes and elicited compensatory expression changes in other IKAROS family members. Our results suggest that even modest alterations of IKZF1 splicing can have significant effects on gene expression and function in mature T cells, potentially contributing to autoimmunity in susceptible individuals.

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