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a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
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kidney transplant needle-core biopsies  (Radboud University)
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a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
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a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded (FFPE) pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).

Journal: medRxiv

Article Title: Distinct Sarcoma Microenvironments Predict Benefit from Addition of Pembrolizumab to Preoperative Radiotherapy and Surgery in SU2C-SARC032

doi: 10.1101/2025.11.01.25339299

Figure Lengend Snippet: a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded (FFPE) pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).

Article Snippet: RNA was extracted from FFPE pre-treatment core needle biopsies and surgically resected tumors using RNAstorm FFPE RNA Extraction Kits (Cell Data Sciences).

Techniques: Control, Adjuvant, Isolation, Formalin-fixed Paraffin-Embedded, Next-Generation Sequencing, Cytometry, Flow Cytometry

a , UMAP plots showing the different non-malignant and malignant cell states identified for each major cell type in the STS scRNA-seq reference atlas, including endothelial cells, cancer associated fibroblasts (CAFs), B cells, lymphoid, and myeloid cells. b , Scatter plots showing the correlation between the abundance of cell types recovered in bulk RNA-seq of post-treatment formalin-fixed paraffin embedded (FFPE) samples using CIBERSORTx and measured through flow cytometry in the matched dissociated fresh tumor samples. Spearman’s correlation coefficients and two-sided P-values are displayed on the graph. The line of best fit by linear regression and 95% confidence intervals are shown on the graph.

Journal: medRxiv

Article Title: Distinct Sarcoma Microenvironments Predict Benefit from Addition of Pembrolizumab to Preoperative Radiotherapy and Surgery in SU2C-SARC032

doi: 10.1101/2025.11.01.25339299

Figure Lengend Snippet: a , UMAP plots showing the different non-malignant and malignant cell states identified for each major cell type in the STS scRNA-seq reference atlas, including endothelial cells, cancer associated fibroblasts (CAFs), B cells, lymphoid, and myeloid cells. b , Scatter plots showing the correlation between the abundance of cell types recovered in bulk RNA-seq of post-treatment formalin-fixed paraffin embedded (FFPE) samples using CIBERSORTx and measured through flow cytometry in the matched dissociated fresh tumor samples. Spearman’s correlation coefficients and two-sided P-values are displayed on the graph. The line of best fit by linear regression and 95% confidence intervals are shown on the graph.

Article Snippet: RNA was extracted from FFPE pre-treatment core needle biopsies and surgically resected tumors using RNAstorm FFPE RNA Extraction Kits (Cell Data Sciences).

Techniques: RNA Sequencing, Formalin-fixed Paraffin-Embedded, Flow Cytometry