Project Title
Single-Cell Multi-Omics Landscape of Basal Cell Carcinoma Reveals Immune and Regulatory Remodeling During PD-1 Blockade Therapy
Overview
This repository contains the full computational workflow, scripts, visualization code, and processed data objects for our study profiling the single-cell transcriptomic (scRNA-seq) and chromatin accessibility (scATAC-seq) landscapes of Basal Cell Carcinoma (BCC) patients before and after anti–PD-1 immunotherapy. The analysis integrates cell states, regulatory programs, trajectory remodeling, and chromatin–gene regulatory networks, revealing how PD-1 blockade reshapes the tumor microenvironment and reactivates anti-tumor immunity. This repository is designed to be fully reproducible, modular, and extensible, enabling other researchers to apply the pipeline to their own datasets.
Key Objectives
• Characterize immune ecosystem remodeling in BCC following PD-1 therapy.
• Identify transcriptional states and signaling pathways associated with treatment response.
• Reconstruct regulatory networks driving CD8⁺ T cell activation, exhaustion, and transition.
• Integrate scRNA + scATAC to map enhancer–gene interactions and cell-type–specific accessibility.
• Highlight gene programs associated with response durability and therapy sensitivity.
Data Summary
• scRNA-seq: Matched pre-/post-PD-1 treatment tumor biopsies
• scATAC-seq: High-resolution chromatin accessibility profiles from the same patients
• Metadata: Clinical annotations, response categories, QC metrics
• Gene sets: Marker genes, curated immune signatures, TF target sets