While deep learning (DL) is used in patients’ outcome predictions, the insufficiency of patient samples limits the accuracy. In this study, we investigated how transfer learning (TL) alleviates the small sample size problem. A 2-step TL framework was constructed for a difficult task: predicting the response of the drug temozolomide (TMZ) in glioblastoma (GBM) cell cultures. The GBM is aggressive, and most patients do not benefit from the only approved chemotherapeutic agent TMZ. O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status is the only biomarker for TMZ responsiveness but has shown limited predictive power. The 2-step TL framework was built on 3 datasets: (1) the subset of the Genomics of Drug Sensitivity in Cancer (GDSC) dataset, including miscellaneous cell cultures treated by TMZ, cyclophosphamide, bortezomib, and oxaliplatin, as the source dataset; (2) the Human Glioblastoma Cell Culture (HGCC) dataset, for fine-tuning; and (3) a small target dataset GSE232173, for validation. The latter two included specifically TMZ-treated GBM cell cultures. The DL models were pretrained on the cell cultures treated by each of the 4 drugs from GDSC, respectively. Then, the DL models were refined on HGCC, where the best source drug was identified. Finally, the DL model was validated on GSE232173. Using 2-step TL with pretraining on oxaliplatin was not only superior to those without TL and with 1-step TL but also better than 3 benchmark methods, including MGMT. The oxaliplatin-based TL improved the performance probably by increasing the weights of cell cycle-related genes, which relates to the TMZ response processes. Our findings support the potential of oxaliplatin being an alternative therapy for patients with GBM and TL facilitating drug repurposing research. We recommend that following our methodology, using mixed cancers and a related drug as the source and then fine-tuning the model with the target cancer and the target drug will enhance drug response prediction. ... Read more

A major challenge for treating patients with pancreatic ductal adenocarcinoma (PDAC) is the unpredictability of their prognoses due to high heterogeneity. We present Multi-Omics DEep Learning for Prognosis-correlated subtyping (MODEL-P) to identify PDAC subtypes and to predict prognoses of new patients. MODEL-P was trained on autoencoder integrated multi-omics of 146 patients with PDAC together with their survival outcome. Using MODEL-P, we identified two PDAC subtypes with distinct survival outcomes (median survival 10.1 and 22.7 months, respectively, log rank p = 1 × 10 ⁻⁶), which correspond to DNA damage repair and immune response. We rigorously validated MODEL-P by stratifying patients in five independent datasets into these two survival groups and achieved significant survival difference, which is superior to current practice and other subtyping schemas. We believe the subtype-specific signatures would facilitate PDAC pathogenesis discovery, and MODEL-P can provide clinicians the prognoses information in the treatment decision-making to better gauge the benefits versus the risks. ... Read more