Sendoel Lab

Time for some fun!
A lovely paper on mathematical oncology.

🧪

#Math
#Cancer
#CANsky

www.biorxiv.org/content/10.6...

UZH: Postdoc in Bioinformatics or Bioinformatician Our lab at the University of Zurich studies the regulation of gene expression in stem cells and cancer. We are seeking a highly motivated and independent bioinformatician or postdoctoral researcher to...

Interested in gene expression analysis, single-cell biology or CRISPR screenings? We are looking for a skilled bioinformatician to join our collaborative and fun team.

If interested, get in touch here:

jobs.uzh.ch/job-vacancie...

I go away for a short walk and come back to this.

Flags flying at half-mast at the lake during the period of national mourning for all the victims of the Crans-Montana tragedy in Switzerland

On this national day of mourning across Switzerland for the victims of the Crans-Montana tragedy, we remember all those who were lost, all who are gravely injured, their families and loved ones, the rescuers, and medical teams caring for them

Such a heartbreaking loss of young lives in our region 💔

Nanopore sequencing of peptides, exciting possibilities ahead also for the microprotein field.

Very interesting.

Recent discoveries on the acquisition of the highest levels of human performance Scientists have long debated the origins of exceptional human achievements. This literature review summarizes recent evidence from multiple domains on the acquisition of world-class performance. We re...

Multidisciplinary training, over time, produces the highest impact people

www.science.org/doi/10.1126/...

"This promise of an AI future, is really just a collective anxiety that wealthy people have about how well they're gonna be able to control us in the future."

- @tressiemcphd.bsky.social with an absolute mic drop moment about AI bullshit.

Incredible words.
Listen to all of it!

Interesting.

We wrote two reviews on cell migration, published today in Nature Methods.

They provides practical guidelines how to select a cell-migration assay and how to analyze cell-migration data

Review 1: nature.com/articles/s41...

Review 2: nature.com/articles/s41...

There's still white space, reject;)

Validate using RT-qPCR.

Many thanks!

Thank you! ;)

Thank you @erc.europa.eu and the panel for supporting our project RIBOSCOPE! Above all, thank you to all past & present lab members whose dedication made this possible. We are excited to push single-cell technologies to map the translational landscape of cancer.

#ERCCoG

The summer of defenses comes to an end! Huge congratulations to David (@dadita.bsky.social ) on a brillant PhD and thank you for everything you have done to shape our lab community from day 1 on. We’re thrilled you’re staying in Zurich and wish you all the best in your next chapter!

Our first PhD generation is flying out of the nest. Thank you Merve and Clara for shaping our lab from day one on.

Wishing you all the best in your next chapters, we’re excited to see what comes next for you!

🔬✨ Join us this Saturday (September 6) | 16:00-23:00 at Nacht der Forschung 2025 at the University of Bern ✨ Come and check out our booth "RNA – Master of Versatility" 👩‍🔬

Meet our researchers & enjoy pipetted cocktails at the reproduzierBAR!
www.nachtderforschung.unibe.ch
#ndfunibern @unibe.ch

If you are interested in #DevBio, #organoids, #gastruloids or #CRISPR, check out the tweetorial to our new preprint on uncovering novel regulators of body plan formation in gastruloids using single cell CRISPR screens!

A big thank you to all co-authors that made this paper possible!

The authors report that all seven tested deep learning models failed to outperform simple baselines in predicting transcriptome changes after single or double perturbations.

I will duck for cover.

Genome-wide chromatin recording resolves dynamic cell state changes https://www.biorxiv.org/content/10.1101/2025.08.05.668773v1

Many thanks to all members of our lab and to our collaborators in the Lutolf and Zavolan labs!

In sum, our findings highlight polyadenylation-mediated control of transcript stability as a critical mechanism in shaping the mammalian body plan and position gastruloid-based single-cell CRISPR screening as a powerful platform for systematic discovery of developmental regulators.

Cells adopting notochord identity in Cnot8 KO gastruloids closely matched embryonic notochord cell profiles. This was accompanied by increased Nodal signaling and a profound loss of Hox gene expression, with a shift toward dorso-ventral and anterior primitive streak fates.

Single-cell RNA sequencing of Cnot8-deficient gastruloids demonstrated severely altered mesodermal patterning, with paraxial mesoderm largely absent and a bias toward axial mesoderm and notochord differentiation.

Intriguingly, Cnot8 KO organoids exhibited indeed transcript stabilization of Nodal along with multiple components and modulators of the TGF-β and Wnt signaling pathways, consistent with profoundly altered patterning cues.

Given the established role of the CCR4-NOT complex in mRNA deadenylation and turnover, we profiled the poly(A) landscape in Cnot8 knockout organoids and observed marked poly(A) tail elongation of key signaling transcripts, including Nodal.

Interestingly, transcriptomic analysis of these Brachyury-positive cells in Cnot8 KO organoids revealed signatures of notochord cells, a cell type usually absent in mammalian gastruloids.

Our screen revealed several novel regulators of germ layer differentiation, including a strong paraxial mesoderm-specific role of the CCR4-NOT component Cnot8. Loss of Cnot8 resulted in gastruloid patterning defects such as the formation of multiple Brachyury poles and aberrant growth.

Validation of our screen revealed strong global depletion of general depletion controls, while germ layer controls were selectively depleted in their respective germ layers, accompanied by the loss of characteristic transcriptomic markers.