The impact of clinical irradiation on tumour cells and the microenvironment of undifferentiated pleomorphic sarcoma
Creators: name: Brown, Samuel
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Sarcoma
subject: Spatial Transcriptomics
subject: Neoadjuvant
subject: Radiotherapy
subject: Tumour Microenvironment
subject: Leukocytes
subject: Cancer
subject: Undifferentiated Pleomorphic Sarcoma
subject: Machine Learning
subject: Multi-Omics
subject: Non-negative Matrix Factorization
subject: Proteomics
subject: Oncology
subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: Biology--Cell
subject: Biology--Molecular
subject: Immunology
subject: FOS: Clinical medicine
subject: Chemistry--Radiation

description: Introduction: Immunotherapy resistance and tumour heterogeneity in undifferentiated pleomorphic sarcoma (UPS) are driven by an immune-cold tumour microenvironment (TME) with abundant pro-tumour macrophages and low lymphocyte infiltration. While external beam radiation (EBR) can stimulate an immune-hot phenotype in certain contexts, the effects of EBR in UPS remain poorly defined. In Alberta, neoadjuvant protocols can differ between patients. One group undergoes high-dose EBR (50 Gray EBR or low-dose doxorubicin combined with 30 Gray EBR), while another group will not receive neoadjuvant therapy. Pre-treating intends to locally control disease, however, consequences on the TME remain unknown. Here, I quantify the effects of neoadjuvant EBR on both tumour and immune cells using clinical samples. Approach: We profiled transcriptomes from 19 UPS patients, treated with either surgery only, the Edmonton, or the Calgary neoadjuvant protocols. To improve coverage of intra-tumoural TME heterogeneity, we separately sampled multiple regions within each tumour. Immune and tumour cell transcriptomes were collected individually using the NanoString GeoMx digital spatial profiling (DSP) platform. To support these results we further generated global proteomics data from the same samples and integrated these with a large external bulk RNAseq cohort. Results: I systematically evaluated the impact of high-dose radiotherapy on surgical UPS samples with high spatial resolution across histologically-distinct tumour regions. In Aim 1, differential expression analysis identified radiation-associated genes in both tumour and TME cells with significant changes most dramatic in the tumour margin. In Aim 2, I identified gene expression programs and their usage across samples in the 2 treatment groups. Expression programs altered by radiation represented activities related to enhanced antigen presentation and upregulation of cytokine secretion. In Aim 3, data integration revealed that radiation is positively associated with a phenotype that improves patient survival. Conclusion: This study broadens our understanding of how radiation impacts UPS biology. I identify prognostic expression programs that cells alter in response to high-dose radiation and show that the tumour margin is a key region in need of additional research. This work paves the way toward the identification of combination therapies that synergize with radiation to optimize the immune response in UPS.