Predicting Prognosis Outcomes of Primary Central Nervous System Lymphoma with High-Dose Methotrexate-Based Chemotherapeutic Treatment Using Lipidomics

Primary central nervous system lymphoma (PCNSL) is a rare extranodal lymphomatous malignancy which is commonly treated with high-dose methotrexate (HD-MTX)-based chemotherapy. However, the prognosis outcome of HD-MTX-based treatment cannot be accurately predicted using the current prognostic scoring systems, such as the Memorial Sloan Kettering Cancer Center (MSKCC) score. We studied two cohorts of patients with PCNSL and applied lipidomic analysis on their cerebrospinal fluid (CSF) samples. After removing the batch effects and features engineering, we applied and compared several classic machine-learning models based on lipidomic data of CSF to predict the relapse of PCNSL in patients who were treated with HD-MTX-based chemotherapy. We managed to remove the batch effects and got the optimum features of each model. Finally, we found that Cox regression had the best prediction performance (AUC = 0.711) on prognosis outcome. We developed a Cox regression model based on lipidomic data, which could effectively predict PCNSL patient prognosis before the HD-MTX-based chemotherapy treatments.