A Non-Canonical Effector Transcriptional Programme Characterises IFN-γ– Mediated Hyperinflammation in MIS-C

<title>Abstract</title> <p>Background Multisystem inflammatory syndrome in children (MIS-C) is a severe hyperinflammatory disorder that develops weeks after SARS-CoV-2 infection. IFN-γ is consistently implicated as a central mediator, yet the transcriptional programme and upstream signalling axis that sustain IFN-γ production in MIS-C remain poorly defined, and it is unclear whether they engage the canonical IL-12/STAT4/T-bet pathway or proceed through alternative effector routes. Methods We studied paired flare and remission samples from paediatric patients with MIS-C using an integrated multi-omic approach: single-cell multiome profiling (simultaneous single-cell RNA sequencing and chromatin accessibility profiling by ATAC-seq), bulk RNA sequencing in a discovery and an independent validation cohort, plasma cytokine profiling, and whole-exome sequencing. Within-patient flare–remission comparisons and cross-cohort replication were used to identify reproducible transcriptional and chromatin-level features. Results We characterise a non-canonical IFN-γ effector programme in MIS-C. CD8⁺ effector-memory T cells and natural killer cells showed IFNG upregulation alongside coordinated induction of BATF, STAT1, and PRDM1, confirmed in per-patient analyses across CD8⁺ effector-memory T, natural killer, and γδ T cells, with broader lymphoid engagement extending to naive populations. STAT4 was downregulated across both bulk cohorts and in natural killer cells, and plasma IL-12p70 was not elevated, indicating limited engagement of the classical IL-12/STAT4 axis, whereas IL6ST (gp130) was upregulated, consistent with a gp130-associated programme converging on the BATF/STAT1 axis. The IFN-γ–regulatory long non-coding RNA IFNG-AS1 was downregulated despite sustained IFNG transcription, indicating chromatin-level decoupling. Checkpoint receptors (CTLA4, HAVCR2) were upregulated without induction of canonical exhaustion factors (NR4A2, NR4A3), indicating a persistent effector state distinct from exhaustion. CD8⁺ effector-memory and γδ T cells converged on this output through distinct regulatory architectures. No monogenic predisposition was identified. Conclusions These observations associate MIS-C with a gp130-linked, BATF/STAT1/PRDM1-anchored non-canonical IFN-γ effector programme, consistent with acquired post-viral transcriptional reprogramming rather than monogenic predisposition. The findings nominate gp130-associated signalling, JAK1/2 inhibition, and IFN-γ–directed therapy as candidate avenues for preclinical investigation in MIS-C and broader post-viral hyperinflammation.</p>