Deciphering HTLV-1-associated Lung Pathology through Integrated in vitro and Multi-cohort Multi-omics Analysis: Inflammation, Monocyte Recruitment and Differentiation Triggered by HTLV-1-exposed Alveolar Epithelial Cells

Background Human T-lymphotropic virus type 1 (HTLV-1) infects up to ten million people worldwide, and causes severe diseases, including adult T-cell leukemia/lymphoma and HTLV-1–associated myelopathy/tropical spastic paraparesis (HAM/TSP). Individuals with HAM/TSP are prone to pulmonary complications (e.g., bronchiectasis). Their bronchoalveolar lavage fluid typically shows increased levels of inflammatory cytokines, chemokines and cell adhesion molecules contributing to chronic inflammation. Results This study assessed the impact of HTLV-1 infection on lung inflammation by analyzing the alveolar transcriptome of A549 epithelial cells following exposure to HTLV-1. Co-culture with HTLV-1-infected MT-2 cells caused transcriptomic changes related to viral response, NF-κB activation, and inflammation. RT-qPCR confirmed elevated expression of the chemokine monocyte chemotactic protein-1 (MCP-1/CCL2) and colony stimulating factor 1 (CSF-1) in A549 MT-2 co-cultures. Increased CSF-1 expression was mechanistically linked to NF-κB signaling, using CRISPR/Cas9 RELA knockout. Supernatant from A549 MT-2 co-cultures triggered chemotaxis and macrophage differentiation of THP-1 and primary monocytes. Systems biology analysis revealed enrichment in pathways associated with monocyte infiltration and bronchiectasis. Finally, we validate the in vivo relevance of our in vitro model through multi-cohort multi-omics analysis combining bulk and single-cell transcriptomics, viral interactomics and multi-ancestry GWAS. Conclusions We describe an in vitro co-culture model that recapitulates HTLV-1-triggered lung inflammation, through RELA/NF-kB-dependent release of pro-inflammatory cytokines and chemokines resulting in monocyte chemotaxis, activation and differentiation. Integrated multi-omics analysis confirmed the in vivo relevance of our in vitro model.