Work

Analysis code for: Zhao et al 2026

Year: 2026

Type: software

Abstract: This repository contains the R analysis code used in Zhao et al. (2026), "Spatial remodeling of the tumor microenvironment after anti-PD-1 underlying clinical response to anti-VEGFR2 therapy". The code covers three analysis modules: (1) clinical outcome analyses including Kaplan–Meier survival, Cox proportional hazards modeling, and propensity score matching; (2) single-cell spatial proteomics (Canopy MxIF) including cell typing, cellular neighborhood analysis, permutation-based cell–cell interaction testing, microvessel density quantification, and spatial proximity analysis; and (3) single-cell RNA sequencing including preprocessing, cell annotation, VEGF expression dynamics, and gene set enrichment analysis. Scripts for reproducing all main figures are included. Data are available via GEO (GSE316380) and upon reasonable request to the corresponding author ([email protected]).

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.20859484

Authors: Teske, Jacob, Zhao, Xianda, Shi, Qian, Kour, Oudom, Yoon, Harry

Institution: Mayo Clinic

Language: English

Topic: Cancer Immunotherapy and Biomarkers

Subfield: Oncology

Field: Medicine

Domain: Health Sciences

SDG: Good health and well-being

Open Access status: green

Funders: National Institutes of Health, National Cancer Institute