Spatial transcriptomics of glioblastoma second surgery samples to compare progression and pseudoprogression. Spatial transcriptomics of glioblastoma second surgery samples to compare progression and pseudoprogression

We performed spatial transcriptomics on a case series of different clinical subtypes of glioblastoma second surgery samples due to novel enhancement following chemoradiation that were confirmed based on clinico-pathologic outcome as disease progression (PD) or pseudoprogression (psPD). All samples showed mixed histologic presentation (Control, Inflammatory, or Hypercellular) which complicated disease interpretation by pathology. Our goals were to (1) determine if spatial transcriptomics could better distinguish between PD and psPD than bulk RNA approaches in mixed samples, (2) determine which differentially expressed genes (DEGs) and estimated immune cell populations distinguish PD and psPD in similar histologic sites, and (3) identify varying molcular processes through gene ontology that separate PD and psPD in similar presenting areas. Overall design: NanoString Digital Spatial Profiling (DSP) with human Whole Transcriptome Atlas (WTA) was performed on glioblastoma samples with 4 showing progression (PD) and 4 showing pseudoprogression (psPD) taken from brain resection at second surgery.

本研究针对放化疗后出现新增强化灶的不同临床亚型胶质母细胞瘤（glioblastoma）二次手术样本开展空间转录组学（spatial transcriptomics）分析，此类样本经临床病理结局确认分为疾病进展（disease progression, PD）与假进展（pseudoprogression, psPD）两类。所有样本均呈现混合组织学表型（分为对照、炎症性或高细胞性），该特征使得病理诊断的判读难度显著增加。本研究的核心目标包括：(1) 探究在混合组织学样本中，空间转录组学是否较批量RNA（bulk RNA）测序方法更能有效区分PD与psPD；(2) 明确在相似组织学部位中，哪些差异表达基因（differentially expressed genes, DEGs）以及预测的免疫细胞群可作为区分PD与psPD的标志物；(3) 通过基因本体论（gene ontology, GO）分析，鉴定在相似临床表现区域中区分PD与psPD的不同分子过程。总体实验设计：针对二次手术切除的胶质母细胞瘤样本，采用搭载人类全转录组图谱（Whole Transcriptome Atlas, WTA）的NanoString数字空间分析（Digital Spatial Profiling, DSP）技术进行检测，其中4例为PD样本，4例为psPD样本。