Prostate tumour sections with hypoxic cores [Visium SD FFPE]
Year: 2026
Type: dataset
Abstract: Prostate Visium SD FFPE data associated with: Proteomics-constrained deconvolution reveals spatial cell-type programs in tumours Accurately resolving cell-type mixtures in spatial transcriptomics remains chal- lenging, particularly in heterogeneous tumours where cell populations are inter- mixed and matched single-cell references may be unavailable or poorly aligned. Current deconvolution approaches either require high-quality scRNA-seq priors, suffer from scalability limitations, or lack interpretability. We introduce PISTA- CHIO, a proteomics-informed spatial transcriptomics deconvolution framework based on constrained non-negative matrix factorization with a negative-binomial likelihood. Rather than using probabilistic priors, PISTACHIO incorporates hard spatial cell-type constraints derived from Imaging Mass Cytometry, enforcing biologically grounded sparsity and explicit spatial feasibility of cell-type pres- ence. PISTACHIO improved recovery of spatial cell-type distributions compared with Cell2location and STdeconvolve across synthetic and tumour datasets. Our approach remains robust under cell-type assignment errors, maintaining high cor- relation with ground truth under moderate noise, and achieves fast runtime on standard hardware, enabling practical large-scale deployment.
Source: DRYAD
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7172096002