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