Yunju Jeong, PhD
Pulmonary and Clinical Care Medicine
Yunju Jeong*, Hung N. Nguyen*, Merriam T. Louis, Yaunghyun H Kim, Humra Athar, Patrick G. Gavin, Ilya Korsunsky, Muhammad D. Sheikh, Reshmi Manandhar, Anthony Maeda, Steven J. Mentzer, Ivan O. Rosas, Lynette M. Sholl, Marina Vivero, G. Matt Hunninghake, Andreas P. Frei, Kara Lassen, Soumya Raychaudhuri, Michael B. Brenner, Edy Y. Kim
Edy Y. Kim
Rationale: To define molecular mechanisms in early ILD, we first applied single-cell RNA sequencing (scRNA-seq) to surgical lung biopsies from patients with earlier stage of ILD and validated mechanisms in lung fibroblasts from patients with early ILD.
Methods: We obtained lung tissues from patients with early ILD (N=7, VATS biopsies), late-stage Idiopathic Pulmonary Fibrosis (IPF, N=4, explant), or from donor controls (N=4). We applied scRNA-seq to disaggregated lung tissue, and analyzed data. For in vitro validation, we cultured primary lung fibroblasts from early ILD and healthy lung tissues. We profiled those primary lung fibroblasts in vitro by Q-PCR, ELISA, and ultra-low input(ULI)-RNA-seq.
Results: ScRNA-seq data demonstrated that T cells were expanded in early ILD lung compared to control or late-stage IPF. Interactome analysis suggested that fibroblasts produce CXCL12 to recruit CXCR4+ T cells to early ILD lung. We validated this axis with in vitro migration assays. Moreover, primary lung fibroblasts from ILD patients exhibit an autocrine LIF-LIFR loop that drives expression of CXCL12. In differential gene expression analysis, CXCR4+ T cells in early ILD had increased expression of granzyme K (GZMK), IFNG, and TNF. To understand the effector role of the CXCR4+ T cells, we treated primary early ILD fibroblasts in vitro with combinations of GzmK, IFNg and TNFa for analysis by ULI-RNA-seq. GzmK synergized with IFNg and TNFa to drive a specific inflammatory program including IL-33 in early ILD fibroblasts which is inhibited in vitro by baricitinib and ruxolitinib, two oral JAK inhibitors in wide clinical use for other diseases.
Conclusion: Our study defines the global transcriptome of earlier stage ILD lung at single-cell resolution. Autocrine LIF drives CXCL12 expression by fibroblasts, which recruit CXCR4+/GZMK+ T cells. GzmK synergizes with IFNg and TNFa to drive a gene signature that may inform biomarkers and therapeutic targets for early ILD.
This study provides insight into the mechanisms involved in the early stages of ILD, which have been poorly understood, and suggests potential clinical biomarkers such as IL-33 for early ILD and targeted therapies, such as targeting GzmK, IL-33, CXCR4, CXCL12, and LIFR. In particular, the inhibition of the GzmK-dependent inflammatory program by JAK inhibitors suggests that these drugs could be repurposed for the treatment of early ILD. The proposal of JAK inhibitors as potential treatments for early ILD is particularly noteworthy because these drugs are already in clinical use for other conditions and could be repurposed to target this new indication.