GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data

BACKGROUND

Characterizing and quantifying cell types within glioblastoma (GBM) tumors at scale will facilitate a better understanding of the association between the cellular landscape and tumor phenotypes or clinical correlates. We aimed to develop a tool that deconvolutes immune and neoplastic cells within the GBM tumor microenvironment from bulk RNA sequencing data.

METHODS

We developed an IDH wild-type (IDHwt) GBM-specific single immune cell reference consisting of B cells, T-cells, NK-cells, microglia, tumor associated macrophages, monocytes, mast and DC cells. We used this alongside an existing neoplastic single cell-type reference for astrocyte-like, oligodendrocyte- and neuronal progenitor-like and mesenchymal GBM cancer cells to create both marker and gene signature matrix-based deconvolution tools. We applied single-cell resolution imaging mass cytometry (IMC) to ten IDHwt GBM samples, five paired primary and recurrent tumors, to determine which deconvolution approach performed best.

RESULTS

Marker-based deconvolution using GBM-tissue specific markers was most accurate for both immune cells and cancer cells, so we packaged this approach as GBMdeconvoluteR. We applied GBMdeconvoluteR to bulk GBM RNAseq data from The Cancer Genome Atlas and recapitulated recent findings from multi-omics single cell studies with regards associations between mesenchymal GBM cancer cells and both lymphoid and myeloid cells. Furthermore, we expanded upon this to show that these associations are stronger in patients with worse prognosis.

CONCLUSIONS

GBMdeconvoluteR accurately quantifies immune and neoplastic cell proportions in IDHwt GBM bulk RNA sequencing data and is accessible here: https://gbmdeconvoluter.leeds.ac.uk.

Notizen: Electrical Conduction in Thiantrene

Electrical conductivity of thiantrene monocrystals was observed. The experimental results were interpreted as a “hopping” mechanism between the molecules of crystal.

Electrical Characterization of Ion Imiplanted, Thermally Annealed TiN Films Acting as Diffusion Barriers on Shallow Junction Silicon Devices

TiN films prepared by implantation onto evaporated Ti layers are tested as diffusion barriers in contact with a thick Al overlayer. Both the TiN/Al and TiSi2/TiN/Al contact structures are evaluated, after thermal treatments up to 600 C, on shallow junction diodes and four terminal resistor test patterns for contact resistance measurements. It is shown that, upon annealing at 600 C, the TiSi2/TiN/Al contact system still exhibits excellent electrical performances. The degradation is found to depend on TiSi2 thickness and contact area.