Knocking down CAVIN1 in a 3D model reveals its connection with tumour invasiveness. Hybrid-DIA based phosphoproteomics profiling reveals an intriguing link between mTOR-signalling and its potential association to CAVIN1.

The mesenchymal-like subtype was shown to be marked by increased CAVIN1 and PRELP. Higher CAVIN1 correlates with higher relapse risk in two independent cohorts. We confirmed this in a second cohort and were able to link this to Epithelial to Mesenchymal Transition.

We stratified 412 CRC tumors into 4 distinct subtypes using quantitative proteomics. Our results show clear links to transcriptomics CMS, immune infiltration, tumor purity, and relapse.

🚨 Check out our new study on proteomic profiling in premetastatic colorectal cancer! Accross 412 tumors, we define molecular subtypes with distinct functional landscapes and revealed CAVIN1 as novel biomarkers for relapse risk.

We confirmed this observation and exploited it to compare different modalities of cell division arrest in human foreskin fibroblasts.

Histone turnover enables distinguishing between dividing cells from slow/non-dividing ones, due to the extremely slow core histone turnover in non-dividing cells.

Protein turnover provides an orthogonal measurement to abundance, revealing functional differences between cell types and states, and improving protein co-regulation analysis to determine members of protein complexes.

We then performed large-scale SC-pSILAC to study the undirected differentiation of human induced pluripotent stem cells through embryoid body induction in >1000 individual single cells. Our dataset shows protein turnover dynamics during cell differentiation over 2 months.

We studied treatments altering global protein turnover including proteasome(bortezomib), protein translation (cycloheximide), and B-cathenin inhibitions for altered turnover of a specific protein (GSK3 inhibitor). SC-pSILAC revealed treatment-related changes in single cells.

🚀 Excited to share our latest article in #singlecell proteomics published in Cell!.SC-pSILAC allows to simultaneously measure protein turnover and abundance in single cells, unlocking the first large-scale, 2D proteomic insights at single-cell resolution!.

RT @FranklinSystems: First announcement! The Brixen Summer School is back and is, as usual, building up a strong speaker list. Thank you @….

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🚨 More research on single-cell proteomics! We evaluated how formaldehyde fixation preserve proteome state, drug response and cell integrity. Cell fixation can facilitate access to #singlecell by enabeling sample shiping and prolonged sorting 📦.

Follow us on Bluesky! @jesperolsenlab.bsky.social🦉🦋.

Lastly we applied the workflow to analyse undirected stem cell differentiation enabling the accurate quantification of stem cells and lineage markers.

We further investigated the effect of 5-FU treatments on spheroids with the whisper 80SPD gradient, highlighting differential regulation of some 5-FU targets.

The improved sensitivity and peptide coverage allows for the detection of abundance PTM sites harboring phosphorylations and glycosylation without prior enrichment, opening new opportunities for SCP analysis.

We benchmarked the SCP workflow using Spectronaut and DIA-NN including  estimation of the error rate of identifications using a shuffled human mimic protein database.

Using the FAIMS Pro Duo coupled to the Vanquish Neo, we even reached >6000 proteins quantified in single HeLa cells at 80 SPD throughput.

Throughput is crucial in LFQ-SCP! We tested the recently introduced Whisper Zoom 80 and 120 SPD providing impressive proteome coverage at up to 3x increased throughput.