Epigenetic lockdown of type I interferon sensing and signalling in human pluripotent cells

The Human Silencing Hub (HUSH) complex safeguards genome integrity in human somatic cells by repressing transposable elements and regulating type I interferon (IFN-I) induction. In early development, the IFN-I pathway is inactive, yet its underlying regulation is poorly understood. Here, we use depletion of the HUSH complex in human induced pluripotent stem cells (iPSCs) as a tool to investigate epigenetic control of the IFN-I system in early development. We confirmed that human iPSCs display an attenuated IFN-I pathway, whereas iPSC-derived neural progenitor cells (NPCs) respond robustly to IFN-I pathway agonists. We found that, in iPSCs, depletion of MPP8, a core component of all HUSH complexes, was sufficient to induce both expression of young LINE-1 elements and genes linked to the IFN system including double-stranded RNA sensors and interferon-stimulated genes (ISGs). ISG upregulation had little effect on pluripotency markers and occurred without IFN signalling, suggesting that, in contrast to differentiated cells, these ISGs are direct transcriptional targets of the HUSH complex in early development. Chromatin profiling by CUT&Tag confirmed MPP8 enrichment at HUSH-regulated ISGs and revealed a bimodal binding profile of MPP8 to both ISGs and non-ISGs, the latter largely driven by young LINE-1 elements. We propose that shutdown of the IFN-I system in pluripotent stem cells is essential to prevent lethality from unwarranted self-nucleic acid sensing. This shutdown is achieved through a triple-layer of epigenetic lockdown acting on ligands, sensors, and effectors across the IFN-I pathway. Pluripotent cells, therefore, represent a ground state of immune evasion that cancer cells may evolve towards through increasing expression of MPP8.