Lightnews — Scholar-powered news

JesperOlsenLab @jesperolsenlab.bsky.social · Sep 5

We made a short video for the ERA PerMed video competition 🎬
We present our collaborative project on “personalising clinical decisions in ovarian cancer through patient-derived in vitro models”.
Have a look at it 👇🏼 and don’t forget to suport us by putting like on Youtube 👍🏼

youtu.be/J4bc1MPqIqE?...

OVA-PDM - Personalising clinical decisions in ovarian cancer through patient-derived in vitro models

YouTube video by European Partnership for Personalised Medicine

youtu.be

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JesperOlsenLab @jesperolsenlab.bsky.social · Jul 19

With a 40% reduction in analysis time and >12,000 proteins covered in 2.7 hours, it's setting new benchmarks for proteome studies.

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JesperOlsenLab @jesperolsenlab.bsky.social · Jul 19

The new Astral Zoom MS overcomes previous MS limitations and is now achieving ultra-fast scans up to 270 Hz. It allows to identity > 100,000 peptides with short LC gradients.

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JesperOlsenLab @jesperolsenlab.bsky.social · Jul 19

🚀 Check out our preprint on the new Thermo Scientific Orbitrap Astral Zoom MS 💫👇🏼

www.biorxiv.org/content/10.1...

Higher-Throughput Proteome Profiling Enabled by Parallelized Pre-Accumulation and Optimized Ion Processing in the Orbitrap Astral Zoom Mass Spectrometer

High-throughput proteomics is critical for understanding biological processes, enabling large-scale studies such as biomarker discovery and systems biology. However, current mass spectrometry technolo...

www.biorxiv.org

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JesperOlsenLab @jesperolsenlab.bsky.social · Jul 1

The combination of pre accumulation and faster scans significantly improves peptide/protein IDs on short LC gradients and boosts sensitivity for high-throughput workflows 📈
The benefits are even higher with ΦSDM, especially in fast, low-resolution Orbitrap runs.

JesperOlsenLab @jesperolsenlab.bsky.social · Jul 1

Florian Harking & Ulises H. Guzman made it happen by preaccumulating ions in the bent flatapole and applying phase-constrained spectrum deconvolution method (ΦSDM).

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JesperOlsenLab @jesperolsenlab.bsky.social · Jul 1

Boosting Orbitrap MS/MS speed to ∼70 Hz? 🚀

Read how we did it in our latest paper 👇

pubs.acs.org/doi/10.1021/...

Enhancing Tandem MS Sensitivity and Peptide Identification via Ion Preaccumulation in an Orbitrap Mass Spectrometer

High-throughput mass spectrometry-based proteomics has gained increasing interest for both academic and industrial applications. As implementation of faster gradients has facilitated higher sample thr...

pubs.acs.org

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JesperOlsenLab @jesperolsenlab.bsky.social · May 31

🦷 Excited to share how proteomics is pushing the boundaries of palaeoanthropology!
We used proteomics on Paranthropus robustus fossils from South Africa (~2 million years old) to get insights into biological sex and variation.
A great example of how LC-MS/MS can uncover new transformative info👇

Palesa @palaeoprotpalesa.bsky.social · May 29

Hello,

Our paper on enamel proteins from Paranthropus robustus has finally been peer reviewed, please have a read here: www.science.org/doi/10.1126/...

Paranthropus robustus has been puzzling scientists since its discovery in 1938 in South Africa, where a high number of fossils have been found.

Enamel proteins reveal biological sex and genetic variability in southern African Paranthropus

Paranthropus robustus is a morphologically well-documented Early Pleistocene hominin species from southern Africa with no genetic evidence reported so far. In this work, we describe the mass spectrome...

doi.org

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JesperOlsenLab @jesperolsenlab.bsky.social · Apr 25

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.

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JesperOlsenLab @jesperolsenlab.bsky.social · Apr 25

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.

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JesperOlsenLab @jesperolsenlab.bsky.social · Apr 25

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.

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JesperOlsenLab @jesperolsenlab.bsky.social · Apr 25

🚨 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.
www.embopress.org/doi/full/10....

Proteomics of colorectal tumors identifies the role of CAVIN1 in tumor relapse | Molecular Systems Biology

imageimageProteomics profiling of a pre-metastatic colorectal cancer cohort identifies four proteomics-based subtypes and highlights the role of CAVIN1 in relapse in EMT-like tumors. Mass-spectrometr...

www.embopress.org

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JesperOlsenLab @jesperolsenlab.bsky.social · Apr 24

We also identified aberrant PDGF receptor (PDGFR) activation as a key feature of OCSCs.
When we treated patient-derived ovarian cancer cells with a PDGFR inhibitor, their stemness potential dropped (sphere formation ↓).

JesperOlsenLab @jesperolsenlab.bsky.social · Apr 24

Our stemness signature correlates with chemo-refractoriness in clinical proteomics data.
That’s huge: it means this signature might help predict therapy resistance.

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JesperOlsenLab @jesperolsenlab.bsky.social · Apr 24

Stemness-associated proteins were involved in extracellular matrix remodeling.
This points to a link between the stem-like state and the tumor microenvironment.

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JesperOlsenLab @jesperolsenlab.bsky.social · Apr 24

To validate our stemness signature, we used single-sample GSEA on published proteomics data from embryonic stem cell differentiation.

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JesperOlsenLab @jesperolsenlab.bsky.social · Apr 24

We profiled the proteome and phosphoproteome of 3D spheres enriched for OCSCs from 10 treatment-naive patient-derived lines.
This revealed a shared stemness-related signature across patients, despite high inter-patient heterogeneity.

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JesperOlsenLab @jesperolsenlab.bsky.social · Apr 24

Our new study is out! 🚨
We used mass spectrometry to uncover a conserved stemness signature in ovarian cancer stem cells (OCSCs).
Check what we found and why it matters. 👇
#OvarianCancer #CancerStemCells #MassSpec #proteomics
www.mcponline.org/article/S153...

Quantitative proteomics and phosphoproteomics analysis of patient-derived ovarian cancer stem cells

High-grade serous ovarian carcinoma (HGSOC) is the deadliest gynecologic cancer. Key to the progression and ultimate lethality of this subtype is the intra-tumoral heterogeneity (ITH), which is define...

www.mcponline.org

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JesperOlsenLab @jesperolsenlab.bsky.social · Mar 31

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

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JesperOlsenLab @jesperolsenlab.bsky.social · Mar 31

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

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JesperOlsenLab @jesperolsenlab.bsky.social · Mar 31

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

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JesperOlsenLab @jesperolsenlab.bsky.social · Mar 31

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

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JesperOlsenLab @jesperolsenlab.bsky.social · Mar 31

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

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JesperOlsenLab @jesperolsenlab.bsky.social · Mar 31

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

www.cell.com/cell/fulltex...

Global analysis of protein turnover dynamics in single cells

The SC-pSILAC method enables single-cell measurement of both protein abundance and turnover, providing notable advances in the depth and versatility of proteomic technologies.

eur02.safelinks.protection.outlook.com

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JesperOlsenLab @jesperolsenlab.bsky.social · Feb 4

Finally fixed cells showed altered morphology vs. non fixed cells. Yet, after freezing the morphological changes in fixed cells are reduced compared to non fixed cells. Fixed frozen single cells have significantly lower CVs than non fixed frozen cells, enhancing data quality and reproducibility.