Democratised single cell proteomics uncovers tumor associated macrophage signature in CYLD cutaneous syndrome skin tumors

ABSTRACT: Single-cell proteomics (SCP) reveals heterogeneity and biological insights inaccessible to bulk analysis. Key limitations are cost, sample loss during processing, and accessibility to state-of-the-art instrumentation. We describe a label free SCP methodology in human tissue, combining fluorescence activated cell sorting (FACS), oil-immersion cell handling, mass-spectrometry, and neural-network derived spectral libraries which aims to improve user uptake. We tested this methodology in a skin tumor syndrome, CYLD cutaneous syndrome (CCS), assessing tumor heterogeneity. Using a Bruker timsTOF HT platform we quantified > 4000 proteins, averaging ~700 per cell, through a cost-effective pipeline without specialised liquid handling infrastructure. By utilising pre-existing bioinformatic tools from the scRNA-seq field we implemented a robust analysis methodology, discriminating between macrophages, dendritic cells and tumor keratinocytes, in an unbiased analysis of 419 CCS tumor cells. We confirmed the biological accuracy of cell annotations by cross referencing with each cell's FACS markers. Furthermore, we identified novel CCS tumor biology in a tumor associated macrophage population with a tumor microenvironment remodelling signature. Our findings demonstrate an accessible SCP technology capable of yielding novel biological discoveries in clinical tissue.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Monocyte, Dendritic Cell, Epithelial Cell, Keratinocyte, Skin, Macrophage

DISEASE(S): Brooke-spiegler Syndrome

SUBMITTER: Joseph Inns  

LAB HEAD: Joseph Inns

PROVIDER: PXD073250 | Pride | 2026-06-18

REPOSITORIES: Pride