Altered AP-1, RUNX, and EGR chromatin dynamics drive human fibrotic lung disease

Area of Science:

• Pulmonary medicine
• Molecular biology
• Genomics

Background:

• Pulmonary fibrosis, including systemic sclerosis-associated interstitial lung disease (SSc-ILD), involves myofibroblasts and macrophages.
• Understanding the transcriptional control of profibrotic gene programs is crucial for SSc-ILD.
• Previous single-cell RNA-sequencing provided limited insight into transcriptional regulation.

Purpose of the Study:

• To determine chromatin accessibility dynamics and transcription factors driving profibrotic gene programs in human SSc-ILD.
• To elucidate transcription factor-regulatory element-gene networks in pulmonary fibrosis.

Main Methods:

• Multiomic single-nucleus assay for transposase-accessible (ATAC)/RNA-sequencing on SSc-ILD and control lungs.
• Chromatin accessibility analysis using ChromBPNet to infer transcription factor binding dynamics.
• Hierarchical causal modeling for single-cell multiomics data (HALO) to reveal regulatory networks.

Main Results:

• Increased transcription factor binding to profibrotic genes (CTHRC1, ADAM12, SPP1, CCL18) was inferred.
• SSc-ILD fibroblasts showed enhanced binding and enhancer activity by AP-1, RUNX, and EGR transcription factors.
• Macrophages displayed enhanced binding of AP-1 and basic helix-loop-helix (bHLH)-ZIP transcription factors to SPP1^hi phenotype genes.

Conclusions:

• Specific AP-1, RUNX, and EGR enhancers control profibrotic gene programs in SSc-ILD fibroblasts.
• A bHLH-ZIP enhancer was identified in SPP1^hi macrophages.
• These findings offer comprehensive insights into the transcriptional control of SSc-ILD gene expression.