Protocol for using scCURE to construct an immunotherapy outcome prediction model

It is challenging to predict the immunotherapy outcome from the baseline status of patients with cancer. Here, we introduce a protocol for constructing an immunotherapy prediction model utilizing single-cell RNA sequencing (scRNA-seq)-based changed and unchanged cell recognition during immunotherapy (scCURE). Initially, we describe the steps for using scCURE to discriminate unchanged cells with similar cellular and molecular functions from whole scRNA-seq data. Subsequently, we demonstrate ways to construct immunotherapy outcome prediction models using either scRNA-seq or bulk RNA sequencing (RNA-seq) data, predicated on the unchanged cells identified by scCURE. For complete details on the use and execution of this protocol, please refer to Zou et al.¹