Integrating AI/ML and multi-omics approaches to investigate the role of TNFRSF10A/TRAILR1 and its potential targets in pancreatic cancer

Abstract

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies, with a five-year survival of under 10 % despite current therapies. Aggressive tumor biology, a desmoplastic stroma that limits drug delivery and immune cell infiltration, and profound resistance to apoptosis make it more complex to treat. Here, we describe a multi-layered system biology and drug discovery pipeline that integrates bulk genomics, single-cell spatial transcriptomics, proteomics, competing endogenous RNA (ceRNA) network analysis, and deep learning-driven quantitative structure-activity relationship (QSAR) modeling. By implementing this pipeline, we predicted that TNFRSF10A encodes for the TRAILR1 death receptor as a potential therapeutic target in PDAC. Mutational and expressional analysis also confirmed TNFRSF10A as a putative target in PDAC. Cancer cells within the PDAC microenvironment exhibit aberrantly elevated TNFRSF10A expression. Immune-excluded tumor niches and pro-survival signaling link this elevated expression. Using an advanced transformer-based deep learning approach, SELFormer, combined with QSAR analysis-based virtual screening, we identified previously unexplored FDA-approved drugs and natural compounds, i.e., Temsirolimus, Ergotamine, and capivasertib, with potential TRAILR1 modulatory effects. During molecular dynamics simulations, these repurposed candidates showed the highest binding affinities against TNFRSF10A for 300 ns. These showed favorable binding energies (MM-PBSA), minimal RMSD drift, PCA, and SASA. We propose TNFRSF10A as a therapeutically important PDAC vulnerability nurtured by spatially resolved expression patterns and dynamic molecular modeling. This study has used a novel integration of AI-implemented chemical modeling, high-throughput screening, and a multi-omics approach to unravel and pharmacologically target a cancer compartment-specific weakness in a notoriously drug-resistant cancer.