Characterising the transcriptomic response of peripheral blood mononuclear cells to very low pH at single-cell resolution

Thesis

The tumour microenvironment (TME) is characterised by being acidic with pH as low as 6, which is accompanied by hypoxia, lactic acid accumulation and increased glycolysis levels. While previous studies have focused on the association between TME acidity and tumour development, our understanding of the transcriptomic response to environmental acidosis among immune cells is incomplete. Here, we have performed the first single-cell transcriptomic profiling of cultured peripheral blood mononuclear cells (PBMCs) in acidic environments, investigating molecular mechanisms underlying immune response to extracellular acidification. I have found that low pH is associated with distinct gene expression features, describing a conserved low pH-specific signature of 34 genes that was identified with differential expression (DE) analysis and high-dimensional weighted gene co-expression network analysis (hdWGCNA). Further, I described the cell types most transcriptomically affected by low pH, peforming UMAP visualization to identify pH-sensitive cell types, including normal and low pH-specific clusters. Subsequent transcription factor (TF) analysis using the package SCENIC, identified TF regulons in response to low pH, including CREM and FOXO3. Finally I explored the effect of single nucleotide variation at the gene GPR65 that encodes a pH-sensitive G protein coupled receptor (GPCR) implicated in autoimmunity, describing genetically determined heterogeneity in acidity response. In summary, this project provides a novel transcriptomic reference to study the impact of acidity on transcriptomic response to low pH, which might be helpful for discovering novel targets associated with acidic TME.

Authors: Sun, X

• DOI: 10.5287/ora-0zp4gnyv7
• Type of award: MSc by Research
• Level of award: Masters
• Awarding institution: University of Oxford
• Language: English
• Keywords: tumour microenvironment; environmental acidity; low pH; single-cell RNA sequencing; peripheral blood mononuclear cells