van Amerongen Lab - Developmental, Stem Cell & Cancer Biology

        Swammerdam Institute for Life Sciences - University of Amsterdam         
lab milestones    social    science    teaching    communication & outreach   

News


Paper accepted

Our paper "How to use online tools to generate new hypotheses for mammary gland biology research: a case study for Wnt7b", previously available as a pre-print, has found a permanent home in the Journal of Mammary Gland Biology and Neoplasia.

Congratulations to Yorick and Nika!

25 November, 2020


Review accepted

Today we celebrated that Tanne’s review article on the dual function of CTNNB1 in cell adhesion and WNT signaling was accepted for publication in Open Biology.

Scientific details will follow as soon as the link to the final PDF is available. For now, we are happily awaiting the proofs and enjoying this bit of tangible output of working from home in the midst of a pandemic.

Congratulations Tanne!

19 November, 2020


Recruiting a staff scientist

We are recruiting a staff scientist (UD level, assistant professor). This is a non-tenure track position (50/50 teaching/research).

For details, see the official vacancy at the UvA website or over at Academic Transfer.

The deadline for applying is 7 December 2020 and we hope to still interview candidates before the Christmas break. You can contact Renée for more information.

9 November, 2020


The lab gets an official name

Amidst all of the COVID-19 craziness, 2020 also brought an exciting highlight:

The lab got an official name and now forms the Developmental, Stem Cell and Cancer Biology (DSCCB) research group in the Cell & Systems Biology cluster of the Swammerdam Institute for Life Sciences.

We still refer to ourselves as "the Wntlab" because it rolls off the tongue a bit easier.

24 October, 2020


Celebrating things worth celebrating - COVID style

We had planned to celebrate the start of Ingeborg’s appointment with a lab lunch in the Polder, but the Dutch Coronvirus measures got tightened - so those plans had to be cancelled and we had to improvise.

Our N=6 was just small enough to fit into the SILS common room at a safe social distance and all snacks were safely and properly aliquoted into individual portions.

Shortly after, the Corona protocol got updated and the rules got tightened even further, so we can now only do social experiments with a max. of N=4, unfortunately. Which only goes to show that you have to seize an opportunity when it presents itself!

8 October, 2020


Tanne and Renée talk about breasts on Radio Swammerdam

October is breast cancer awareness month - a very good reason for Radio Swammerdam to focus their weekly hour of science radio on the breast.
Tanne hosted the broadcast on Sunday morning 4 October and Renée joined as a guest. If you missed it, you can listen to the Radio Swammerdam podcast:

4 October, 2020


Ingeborg joins the lab as a new technician

We welcome Ingeborg Hooijkaas, who joined the lab on 1 October as our new technician.

Despite the pandemic, and with lots of us still spending considerable amounts of our time working from home, we hope that Ingeborg will quickly feel at home and be able to get up and running in the lab. Hopefully it will not be too long before she can get to meet all of her SILS colleagues face to face.

1 October, 2020


New pre-print: How to use online tools to generate new hypotheses for mammary gland biology research

We are excited to announce a new pre-print, "How to use online tools to generate new hypotheses for mammary gland biology research: a case study for Wnt7b", which is now available via Biorxiv.

Born out of necessity during the working from home phase of the pandemic in the spring of 2020, we (well, Yorick) finally had some time to thoroughly explore a bunch of online tools and datasets. After combining this online discovery tour with some existing work by Nika, we wrote this paper.

We are happy that the pre-print quickly got recognized on Twitter as an opportunity for dry-lab student projects:



In fact, we are crafting some of our own internship positions for the 2020-2021 academic year around this idea as well. We cannot possibly host all of the students that have applied for an internship position in our lab, but at least in this way we can give multiple students the option of joining our lab even when wet lab internship positions are scarce.

Hopefully, the students can also contribute to the start of our lab Wiki.

22 September, 2020


Hybrid lab meeting

All of our lab meetings are still held via Zoom, but today we succumbed to the temptation and held the lab meeting in a hybrid format (at a safe distance and sticking to the maximum occupancy of the meeting room): Only Saskia was working from home.

Tanne and Yorick had experiments to perform in the lab and Renée was on campus for one of only two live lectures with the Frontiers in Medical Biology BSc students (which was also hybrid, running via Zoom with an owl so two students who could not make it to campus could attend).

2 September, 2020


Paper published in Genesis

The first mouse model generated in the lab has now been published as an open access paper in Genesis. You can get the PDF here if you want something that looks a bit prettier than the original preprint.

Congrats to all authors!

9 July, 2020


Paper accepted!

Our study "A novel Axin2 knock-in mouse model for visualization and lineage tracing of WNT/CTNNB1 responsive cells" by van de Moosdijk & van de Grift et al. was accepted for publication in genesis.

25 June, 2020


Fulbright Scholarship and Nijbakker-Morra fellowship awarded to Saskia de Man

In the spring of 2020, Saskia was awarded a Fulbright scholarship as well as a fellowship from the Nijbakker-Morra foundation. These funds will allow a short research visit to the United States.
A really cool collaboration is ready for take-off and we hope that the COVID-19 pandemic and travel restrictions will soon be lifted so Saskia can embark on this exciting scientific adventure.

20 June, 2020


New pre-print: Quantitative live cell imaging of WNT/CTNNB1 signaling dynamics

We are really excited to announce that we just posted a new pre-print on Biorxiv

PhD student Saskia de Man is first author on (and very much the driving force behind) this story, which combines CRISPR/Cas9-mediated genome editing in haploid cells, with quantitative live-cell imaging and computational modeling. This work is a collaboration with Mark Hink and Gooitzen Zwanenburg, both also from the Swammerdam Institute for Life Sciences (SILS).

Using CRISPR/Cas9, Saskia generated a scarless knock-in of SGFP2 into the endogenous CTNNB1 locus, resulting in the expression of a fully functional fluorescent CTNNB1 fusion protein. By using haploid cells, we ensured that all tagging events were homozygous. She then performed quantitative microscopy analysis using confocal time-lapse imaging, fluorescence correlation spectroscopy and number & brightness analysis to investigate the different functional pools of CTNNB1 in the cytoplasm and nucleus in the absence and presence of a WNT stimulus.

Check out the paper if you want to know all about the distribution of CTNNB1 across a fast diffusing, monomeric pool and a slow diffusing complex-associated pool, or if you are curious about the first ever in cellulo measurements of the absolute concentration of CTNNB1 in each of these different fractions, which we have also used to build a computational model for WNT/CTNNB1 signaling that reveals three critical nodes of regulation in our favorite signal transduction pathway. And there are really pretty movies too!



Congratulations to Saskia on this fine piece of work, which cost blood, sweat and multiple years. The feedback we got at the 2019 Gordon Research Conference on WNT signaling has really inspired us to whip this story into it’s final shape and we are happy that it is now ready to meet the world.

28 May, 2020


Playing with Science

ARTEZ students Iris Beek and Moritz Brill presented the outcome of their residency at Filip Studios in Arnhem, where they worked on the case study "Playing with Science", for which Renée was the case holder.

As always, it was inspiring and informative to witness how artists approach a scientific question, with exciting potential for future developments (of the project and the collaboration).


image by Iris Beek and Moritz Brill

21 May, 2020


Comment in Bionieuws

Renée was featured in the latest issue of Bionieuws, where she was asked to comment on a recent paper by Caleb Dawson and colleagues from the lab of Jane Visvader. The paper describes the discovery and characterization of a population of macrophages (a specific type of immune cell) in the mammary gland. What is really cool is that you can see this population sandwiched in between the basal and luminal epithelial cells of the mammary epithelium.

It is always really nice to be able to provide some background, context and perspective for journalists and the broader public. In this case, it also meant doing a bit of background reading and discovering two related papers published by the labs of Felicity Davis and Christine Watson.
Thanks to the author, Nina Wubben, for making sure that this is a balanced piece that also does not over promise an immediate therapeutic benefit of this basic finding.

The piece (in Dutch) is pasted below.

Those interested in the details should check out the following papers:
Dawson et al. (2020), Nature Cell Biology: https://doi.org/10.1038/s41556-020-0505-0
Hitchcock et al. (2020). The FEBS Journal: doi:10.1111/febs.15126
Stewart et al. (2019), Frontiers in Cell and Developmental Biology: doi: 10.3389/fcell.2019.00250

16 May, 2020


Did you catch the easter egg?

The April 30 issue of Cell is out, which means that the perspective that Renée wrote in honor of Roel Nusse winning one of the 2020 International Gairder Awards is now officially published.

Did you catch the easter egg that is hidden in the figure?



WNT proteins are morphogens, which means that they are produced by specific cells and then diffuse (i.e. dilute) as they spread in the nearby surroundings. This spreading occurs in a gradient. As a result, cells that are closer or further removed from the source are exposed to different concentrations of WNT proteins and they are also wired to respond (i.e. activate specific genes) differently to specific concentrations of the protein.
In the textbook, this principle is typically depicted as the "French Flag model" (with blue, white and red zones depicting zones of low, medium and high concentrations of the morphogen). For the occasion, Renée and Tanne (who drew the figure) changed this into a "Dutch Flag model". It still looks the same and just required a bit of tweaking: changing the order to red, white and blue and adding a dash of orange - the Dutch national color- on top.

May this model live long and prosper!

1 May, 2020


Blog post on collaboration between artists and scientists

Renée was featured on the LSE impact blog in a post titled "To drive innovation, scientists should open their doors to more equitable relations with the arts". Written by Paige Jarreau, the piece highlights the unexpected spin offs that can occur from collaborations between artists and scientists.

30 April, 2020


Lab life in times of the COVID-19 pandemic

Like everyone else on the planet, we are dealing with the effects of the COVID-19 pandemic as best as we can. We went into work-from-home mode on 16 March with only a few critical experiments continuing and are staying in touch via Zoom (for group meetings) and Skype (for 1-on-1 meetings).

The most important thing right now is that everybody tries to stay healthy and sane as we are mostly cooped up inside to #FlattenTheCurve.
Working from home under these conditions is definitely not your average working-from-home day where you can quietly focus and concentrate on the work at hand. The news and a surreal "new normal" are a constant distraction - as are the questions and uncertainties about how all of this is affecting the progress of PhD trajectories.

Two new internships students, Femke and Zino, joined our lab for their BSc and MSc internships earlier this year. Their practical training was brutally interrupted, but official arrangements are now in place from the Biomedical Sciences program to deal with this situation. Femke is developing some CellProfiler skills under the supervision of Tanne using an existing dataset from Saskia and Zino is interrupting his internship on Wnt reporters in 3D organoid cultures under the supervision of Yorick to first write his literature thesis.

So far, everyone else has also made great efforts to be as productive as possible under the circumstances. Renee is still making her way through the original to do list and is finding out that Zoom meetings are much more tiring than meeting people in person. Larissa, Saskia, Tanne and Yorick are all writing drafts of papers/reviews/thesis chapters. While everyone can keep themselves busy for a couple of weeks in this way, we have also begun thinking about how we can potentially pick up our experimental work again in the longer term.

Hang in there everyone!


Our 2020 lab picture is a screenshot from one of our zoom meetings

9 April, 2020


New pre-print

We are happy to share a pre-print describing the generation and characterization of the first mouse model we built in the lab. Read it here.

Former PhD student Anoeska van de Moosdijk and current PhD student Yorick van de Grift are joint first authors, with other important contributions by PhD student Saskia de Man and technician Amber Zeeman. This work was funded by a 2015 grant from KWF Kankerbestrijding/Alpe d’HuZes. With a special thanks to the patient advocate on the interview selection committee who understood and supported the basic research that is required for long-term progress and stepwise innovation as we try to build better models for cancer research.

For those interested in the details: We generated a new 3’ knock-in in the Axin2 locus to allow both direct visualization (3xNLS-SGFP2 reporter) and lineage tracing (using a doxycycline inducible rtTA3) of WNT/CTNNB1 responsive cells. The strain can be combined with a tetO- and/or lineage-tracing reporter of interest. We are in the process of submitting this strain to an international repository so we can share it as broadly and quickly as possible with the rest of the scientific community.

4 April, 2020


Essay on the contributions of Roel Nusse to the Wnt signaling field

Today it was announced that Roel Nusse is one of the winners of the 2020 Gairdner Award. In honor of his contributions to the field of Wnt signaling and its broader implications in cancer and stem cell biology, Renée wrote an invited essay for Cell.
Thanks to Tanne for designing the figure!

The piece is available as Open Access publication here and can also be downloaded as a PDF file here.

31 March, 2020


NWO Grant awarded

Renée was awarded a Klein1 grant in the NWO open competition. Using a combination of quantitative live cell imaging and fluorescent tagging of endogenous Wnt pathway components, we hope to achieve a better understanding of the central working mechanism of the WNT/CTNNB1 pathway.

This is the first funding we got for this new line of research in the lab, thanks in large part to all of the preliminary data that were carefully collected by Saskia over the past few years, in close collaboration with Mark Hink.

See the Dutch abstract below from the NWO website:.

26 March, 2020


Short review on WNT/CTNNB1 signaling in breast cancer

We published a short review article on the role of WNT/CTNNB1 signaling in human breast cancer in Frontiers in Cell and Developmental Biology, as part of the special topic on mammary gland biology (edited by Dr. Zuzana Koledova from Masryk University).

The review article was inspired by and based on an MSc literature thesis, written by Emma van Schie (who is first author on the paper). The best outcome of research based teaching! It also helped Renée organize her thoughts on the current knowledge gaps in the field.

2 February, 2020


First publication of 2020

We published our first paper in 2020! Previously out as a pre-print on BioRxiv we are happy that our study about the interaction between TMEM98 and FRAT2 found a peer-reviewed home in Plos One.

First author Tanne van der Wal just started her PhD in October, and this is earlier work from her BSc internship. Taking old data from Renée that had been accumulating since 2004, we wrapped up the characterization of the trafficking of this transmembrane protein and verified that 15 years after the start of this project across town at the Netherlands Cancer Institute this transmembrane protein still modulates FRAT2 protein levels, thereby reducing WNT/CTNNB1 signaling activity.

It was a nice bonus to see Figure 2 from the paper being highlighted on Twitter for #FluorescenceFriday.



24 January, 2020


Lecture about genome editing

On Monday evening 13 January, Renée gave a lecture for members and guests of the "Chemische Kring" (society of chemists) in Rotterdam about the ins and outs of gene editing. The lecture hall at the "Hogeschool Rotterdam" was filled with an exciting mixture of chemists, biologists (including some students who came to attend after working with CRISPR/Cas in the lab themselves) and the occasional philosopher.



We talked about bacterial immune systems, CRISPR babies and the history of cutting and pasting with DNA. Hopefully there was enough depth for the chemists and not too much detail for the less molecularly inclined!

13 January, 2020


NEMO Kinderlezing

Renee gave the last NEMO Kinderlezing of 2019 . This time the topic was aging. A lot of 8-12 year olds came to the NEMO Studio Theater and together we went searching for an answer to the question: "How old can I get?"

That took us on a journey deep inside our bodies, where we peaked into the cells to figure out how cells know what to do, to see how the DNA and mitochondria work, and to discover how little mistakes and malfunctions in these microscopically small components contribute to aging. We also talked about extending life span, and how new techniques like cutting-and-repairing our DNA might one day prevent us from getting old or sick.
But this crowd was not fooled very easily and the morning lecture essentially ended with a philosophical question from one of the younger kids: Why do we want to live forever? Can we just not accept the fact that life has an end to it? This was followed by a sobering conclusion from the first row that even if we were able to extend life into all eternity, the universe itself has a final lifespan. On that note, we all had a look at some cells under the microscope and went home. A little bit older, but also a little bit wiser.

Thanks to all the kids for asking such interesting questions, for offering your perspective and for making me need all of my science fiction and space knowledge to keep up with you! And of course thanks to everyone at NEMO and FNWI communication for the awesome help in prepping for this audience.


image credit: Marion Vetter

15 December, 2019


ENBDC Think Tank in Manchester

Renee travelled to Manchester, where she met up with the rest of the ENBDC organizing committee for a peptide hydrogel workshop (thanks to everyone involved!) and a full day talking about research gaps in breast (cancer) biology.


image credit: Leander Blaas (via Twitter).

Thank you to Rob Clarke for running such an entertaining and smoothly organized Think Tank and for taking us out to dinner in a former cotton exchange on the UK election evening to drown any Brexit-related sorrow in good conversation.

12 December, 2019


Seminar in Aberdeen

Renee gave a talk at the University of Aberdeen, the third oldest university in Scotland. She got to talk about science with loads of different and interesting people all day, which is always a bonus. Thank you to Stefan Hoppler for the invitation and for making this such an enjoyable visit, including the sampling of the local pub food and Indian cuisine!

28 November, 2019



older news items