Single-cell spatial transcriptomics uncovers niches that govern response to PD-1/PD-L1 blockade in cutaneous squamous cell carcinoma

Neoadjuvant PD-1/PD-L1 blockade demonstrates robust efficacy in cutaneous squamous cell carcinoma, yet a significant proportion of patients do not achieve a major pathological response for unclear reasons. Here, we characterize spatially resolved gene expression profiles before, during, and after treatment in cutaneous squamous cell carcinoma (cSCC) patients enrolled on two pivotal phase II clinical trials of neoadjuvant PD-1/PD-L1 blockade. Using single-cell RNA-based spatial molecular imaging, we profiled more than 56 million transcripts from over 250,000 cells across 27 patients. Traditional cell type clustering uncovered five broad cell types (keratinocytes, fibroblasts, B-lineage cells, myeloid cells, and a mixed dendritic/T/NK compartment). Genes associated with interferon signaling and metabolic pathways were significantly upregulated in responders, but bulk gene expression alone did not fully distinguish responders from non-responders. We then applied a spatial clustering approa..., , # Single-cell spatial transcriptomics uncovers niches that govern response to PD-1/PD-L1 blockade in cutaneous squamous cell carcinoma Dataset DOI: [10.5061/dryad.s4mw6m9jh](10.5061/dryad.s4mw6m9jh) ## Description of the data and file structure This repository contains a Seurat object (named “seurat_object”) generated from CosMx SMI using the manufacturer's 1000 plex panel. The object enables researchers to reproduce or extend the analyses performed in our study. All cell metadata has been de-identified according to our IRB-approved protocol, and no personally identifiable information (PII) is included. The data comes from 2 tissue microarrays of formalin fixed paraffin embedded tissue of human cutaneous SCC specimens taken before, during, or after immunotherapy. ### Files and variables #### Seurat_Object_cSCC.RDS ``` – A serialized R object in Seurat format, which includes: – Filtered and normalized gene expression data. – Cell-level metadata (excluding direct identifie..., All patient data used in this study were de-identified in accordance with institutional review board (IRB) requirements and relevant data privacy regulations (e.g., HIPAA). Specifically, the research team removed or replaced all direct and indirect identifiers, including names, dates of birth, addresses, and medical record numbers, with coded pseudonyms or aggregated values. No link to identifiable personal information was retained, ensuring that the data cannot be traced back to individual participants. All de-identified data were stored in secure, access-controlled repositories with strict oversight, and were only used for the purposes of this study.新辅助PD-1/PD-L1阻断治疗在皮肤鳞状细胞癌中展现出显著疗效，但仍有相当比例的患者未获得主要病理缓解，其背后机制尚不明确。本研究针对两项新辅助PD-1/PD-L1阻断治疗的关键II期临床试验中入组的皮肤鳞状细胞癌（cutaneous squamous cell carcinoma, cSCC）患者，刻画了治疗前、治疗期间及治疗后的空间分辨基因表达谱特征。本研究采用基于单细胞RNA的空间分子成像技术，对27例患者的超过25万个细胞中的5600余万个转录本进行了转录组分析。传统细胞类型聚类分析揭示了五类宽泛的细胞群：角质形成细胞、成纤维细胞、B系细胞、髓系细胞以及树突状细胞/T细胞/NK细胞混合群。应答患者中与干扰素信号通路及代谢通路相关的基因显著上调，但仅依靠整体基因表达谱无法完全区分应答者与无应答者。随后本研究采用空间聚类分析方法……# 单细胞空间转录组学揭示调控皮肤鳞状细胞癌PD-1/PD-L1阻断治疗应答的微环境生态位 数据集DOI: [10.5061/dryad.s4mw6m9jh](10.5061/dryad.s4mw6m9jh) ## 数据与文件结构说明 本仓库包含一个通过CosMx空间分子成像（CosMx SMI）结合厂商1000重检测panel构建的Seurat对象（命名为"seurat_object"）。该对象可供研究人员复现或拓展本研究中的分析流程。所有细胞元数据均已按照机构审查委员会（Institutional Review Board, IRB）批准的方案完成去标识化处理，未包含任何个人可识别信息（Personally Identifiable Information, PII）。本数据集来源于2个组织微阵列，其样本为免疫治疗前、治疗期间或治疗后获取的人皮肤鳞状细胞癌福尔马林固定石蜡包埋组织标本。 ### 文件与变量 #### Seurat_Object_cSCC.RDS —— 一个Seurat格式的序列化R对象，包含以下内容：—— 经过过滤与标准化的基因表达数据；—— 细胞级元数据（不含直接标识信息……）。本研究中使用的所有患者数据均已按照机构审查委员会（IRB）要求及相关数据隐私法规（如美国健康保险流通与责任法案HIPAA）完成去标识化处理。具体而言，研究团队已将所有直接及间接标识符（包括姓名、出生日期、住址及病历号）替换为编码化名或聚合值，未保留任何可关联至可识别个人信息的链接，确保本数据集无法追溯至单个受试者。所有去标识化数据均存储于经过严格监管、受访问控制的安全仓库中，且仅用于本研究相关分析。