SUPR
Single cell RNAseq of microenvironmental cell types in tumors
Dnr:

NAISS 2025/22-908

Type:

NAISS Small Compute

Principal Investigator:

Kristian Pietras

Affiliation:

Lunds universitet

Start Date:

2025-09-15

End Date:

2026-10-01

Primary Classification:

30108: Cell and Molecular Biology

Webpage:

Allocation

Abstract

Cancer is a complex disease and an evolutionary phenomenon in which malignant cells and the tumor microenvironment (TME) co-evolve over time. High-grade gliomas (HGG) are aggressive tumors of the brain. They infiltrate adjacent brain areas, precluding surgery and inevitably causing death. The dismal prognosis results from intrinsic features including intra-tumoral heterogeneity, phenotypic plasticity and tumor microenvironment (TME) cues: in the current perception of HGG, tumor cells dwell in interconnected, but functionally and spatially segregated regions that form complex niches. The main types of such tumor niches are the perivascular niche (PVN), localized around blood capillaries, the hypoxic, and the invasive niche at the tumor border, where glioma cells infiltrate physiologic tissue. Our previous investigations demonstrated the presence and impact of CAFs and pericytes in HGG progression. However, they have not been sufficient to deeply characterize their role in the distinct spatial niches. This holds particularly for the invasive niche, where glioma cells are sparser and infiltrate physiologic tissue. To overcome this knowledge gap, this project aims to utilize Xenium and Visium HD technologies on tumors from two established mouse models that faithfully recapitulate HGG (n-tva and pax-tva). The combination of these two technologies will allow us to analyze the expression and co-expression patterns of hundreds of transcripts at a sub-cellular level, providing a much richer view the structure, composition and interaction of these niches both in adult and pediatric HGG. We will be mainly focusing on cancer associated fibroblasts (CAFs) and pericytes and the characterization of their role in the tumor niches and effects on tumor infiltration. Moreover, by sampling tumors before and in several time points after radiotherapy treatment, we will enrich our understanding of biological response to treatment. We also hope to be able to analyze human samples in the future. Our study is currently developing, and we expect to get raw data for analyses in September 2025. We are asking for renovation of this project, both the computational and storage resources, as we anticipate the need for computational resources specially in the first stages of the project. The resources and support provided by National Academic Infrastructure for Supercomputing in Sweden (NAISS) and PDC will be vital for the realization of this project and we would be grateful to be granted a continuation.