van Amerongen Lab - Developmental, Stem Cell & Cancer Biology

- Swammerdam Institute for Life Sciences - University of Amsterdam -  
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New preprint: RNAseq story time!

We are happy to announce a new preprint, "Transcriptomic analysis of pubertal and adult virgin mouse mammary epithelial and stromal cell populations", which is now available on Biorxiv via this link or by scanning the QR code below.

The title tells you what you need to know, but there is always more to a story. So let’s dive in.

This work actually started a long time ago (we are talking 8 years or so...) when we were deciding which Wnt genes we should (or wanted to) work on in the context of mammary gland biology. There were some data out there as to which Wnts were expressed at different stages, but this was mainly based on Northern blotting and/or RT-PCR data. We lacked information on their expression in the different epithelial and stromal cell populations and we also lacked information on their expression dynamics - especially when we would compare puberty and adult virgin stages and, more importantly, during the different stages of the estrous cycle. After lots of back and forth we decided that this would become one of our first RNAseq experiments and that, if we were going to get such detailed information on the different mammary gland populations, we would do this for the different stages of the estrous cycle - as this is really a staple of our research program: to try and understand how cells communicate and how signaling works at endogenous levels.

Collecting the samples was a tremendous amount of work, since estrous cycle staging is quite labor intensive if you want to do it right. Then, all of the individual samples also needed to be processed (i.e. tissue digestion and FACS sorting) as soon as we had the right stage, so this was a major logistic effort with long days. Especially the yield of the basal cells was often lower than hoped, so we also having to end up to pool some samples that we would have liked to have kept as individual replicates just to get sufficient RNA yield, etcetera. All of the credit for that work goes to Nika and Katrin, obviously.

We did not have the possibility for RNAseq on site back then, so we collaborated with Jos Jonkers from the Netherlands Cancer Institute and got access to their genomics and sequencing facility. Katrin introduced the lab to bioinformatics analyses and Nika ultimately wrote up this work as a chapter for her PhD thesis.

A couple of things to note about this study:

First, we think these are really nice datasets that others can also use for re-analysis and to determine changes between pubertal and adult epithelial and stromal cell populations, for instance. They are available from NCBI Geo.
Second, we found that the Wnt gene expression landscape was complex, but perhaps slightly less dynamic than we had initially thought, with different Wnt genes being expressed in quite defined patterns across the different cell types in the tissue. That finding actually gave rise to an entire new line of research in the lab.
Third, we found that the physiological changes during the estrous cycle were not as big as we had expected (or hoped). We detected a proliferation response in the epithelial cells, but it’s really quite subtle. The more substantial changes seem to occur in the stromal cell populations - which might be interesting for follow up studies.

Altogether, we think this work adds useful information to what we already know about the developmental dynamics of the mammary gland. As always there are more questions than answers, but the work is now finally out there and we hope this is a useful resource for others! It has also been submitted to a journal, so we hope it will soon find a peer-reviewed home as well.

13 January, 2024

Now recruiting 2 PhD students

After this we will be out of money again for a while, so if you want to work with us you need to jump on this opportunity and apply to one of our two open PhD positions:

Early cell fate decisions using 3D cell culture models
Thanks to a starters grant from the Dutch government awarded to Thijs van Boxtel, we are recruiting a PhD candidate to study early cell fate decisions using 3D cell culture models for embryonic development.
This vacancy closes on 31 January 2024. See our jobs page for more info and a link to the vacancy.

Single-cell dynamics in mammary gland organoids
Do you want to be part of a unique collaboration between our group at SILS and the labs of Sander Tans and Jeroen van Zon at AMOLF (right across the street)? In this cross-disciplinary (physics and biology) project, you will follow individual cells as they grow, move, and differentiate to form branched duct architectures in mammary gland organoids.
AMOLF controls when the vacancy closes. See our jobs page for more info and a link to the vacancy.

12 January, 2024

Talk in San Francisco

Renée gave a talk in San Francisco, where she was invited and hosted by Dr. Laura van ’t Veer to present our work on WNT signaling and breast cancer in the UCSF Breast Oncology Program seminar series.

It was a webinar (we actually hosted our host at the UvA for the occasion), so there was no actual trip to California involved this time, alas. Still, it was a pleasure and an honor to share our work with this renowned group of expert basic and translational researchers.

10 January, 2024

Welcome to our new internship students

It is the time of year again where we welcome our new MSc internship students.

Welcome to Rasmus (who will be working under the supervision of Thijs on our breast cancer research line) and Thomas (who will be working under the supervision of Marleen and Ingeborg on our gene regulation research line).

They join Gwendolyn, who already started on a collaborative image data analysis project under the co-supervision of Marten Postma and Tanne.

8 January, 2024

New publication: A molecular toolbox to study progesterone receptor signaling

Our paper "A molecular toolbox to study progesterone receptor signaling" has been published in the Journal of Mammary Gland Biology and Neoplasia.
This is Marleen’s first first-author paper, with other contributions from our former MSc student, Muriel Wagner, as well as Tanne, Thijs and Renée. Congrats!
Read it here and if you like what you see, you can get the plasmids from Addgene (#206159 through #206171).

29 November, 2023

Now recruiting a new staff scientist with a focus on 3D tissue organoids (UD/assistant professor level)

We are excited to announce this rare opportunity, thanks to the recent sectorplangelden: We are looking for a new colleague to join our scientific staff with a focus on 3D tissue organoids (mainly breast and mammary gland, but with some room for intestine).

The full advertisement can be found by clicking on this link right here, but in brief: You will consolidate and expand our research line on mouse and, predominantly, human tissue organoids for breast and intestine. The main focus will be on the mammary gland, where you will join ongoing international efforts in human breast organoid technology development with strong connections to the European mammary gland research community and links to both breast cancer and breast milk research.

The vacancy closes on 31 December 2023 and all applications must be submitted via the official vacancy website in order to end up in the system. We are looking for the best fit for our team and interested candidates should not hesitate to reach out to Renée for further details.

21 November, 2023

20th Dutch Chromatin meeting

At the initiative of Maike Stam, the 20th edition of the Dutch Chromatin meeting returned to Amsterdam. Together with Maike, Renée, Thijs, Frank Jacobs and Rutger Gjaltema turned it into an all SILS organised event.

It was a great day full of science, with an interesting line up of (invited) speakers and an interactive poster session.
Unfortunately the event had to be held off campus because we could not reserve an auditorium big enough for the 200 attendees at Science Park. Thanks to NWO and the Amsterdams Universiteitsfonds and our commercial sponsors we were able to host everyone at hotel Casa, near the Amstel station.

More details on the meeting website.

from left to right: Marleen presenting her poster, poster awards and goodie bags waiting to be handed out to speakers and poster prize winners, Thijs and Rutger looking pretty happy with how things are progressing so far.

3 November, 2023

FNWI Pubquiz

Since our enthusiasm was bigger than the maximum allowed team size at the annual FNWI Pubquiz, we had to divide ourselves into two teams of three. Strategically not the smartest move, and we did not win, but it looks like we had fun!

31 October, 2023

PhD defense: Yorick becomes dr. Van de Grift

On 18 October 2023, Yorick was the fourth PhD student from the lab to successfully defend a PhD thesis. We gathered in the Agnietenkapel for the occasion and the questions from the committee beautifully covered all of the various aspects of the work described in the thesis.

Congratulations Yorick!

We were especially happy that Claudio Cantu could join us from Sweden to take part in the defense ceremony (and give a seminar the next day). This ensured a proper hand over as Yorick wil be joining his lab in Linköping for a postdoc.

18 October, 2023

Keynote talk in Groningen

Renée gave a keynote talk at the annual CRCG PhD day of the Cancer Research Center in Groningen. Thanks for the wonderful invitation and the opportunity to talk to early career scientists about the different academic and life choices in our line of work!

12 October, 2023

Theatercollegetour kick off

Renée played/gave (not sure what verb to use with a theatercollege) her first theatercollege during a matinee in Venlo. Thanks to the interactive, friendly and interested audience for the warm welcome! It was a pleasure to be part of a line up with two other theatercolleges on free will (or the lack thereof) and inheritance tax with comedian Fuad Hassen functioning as excellent glue and a light note in between the different performances.

Next up is Amsterdam on 28 November!

8 October, 2023

Weekend van de Wetenschap 2023

Thijs and Renée spent all Saturday at Science Park during the annual open day (part of the national "Weekend of Science"), to share the fascinating biology of the mammary gland, or breast. Join us next year if you too are curious about the extra nipples of Harry Styles!

7 October, 2023

Radio 1

Renée was interviewed on Radio 1, as a studio guest in Villa VdB, about the upcoming theatercollegetour of the Universiteit van Nederland.

Together with 13 other scientists from the different Dutch universities, Renée will perform in theaters all across the Netherlands during the 2023-2024 theater season.

You can catch Renée in Venlo (8 Oct 2023), Amsterdam (28 Nov 2023) and Enschede (31 Jan 2024), and after that in Sneek, Tilburg and Hoofddorp if you want to learn more about stem cells and how they might one day be able to prevent our bodies from ageing. Check out the website of the Universiteit van Nederland for all the details.

2 October, 2023

Joëlle starts as a PhD student

Joëlle started her PhD thesis research. Supervised by Thijs and Renée), Joëlle will join Anna on the NWO-XL project and use gastruloids as a model system for early mammalian development to study if and how developmental signals (mainly WNT and BMP/Nodal) are interpreted differently depending on the cellular chromatin state. She will be co-supervised by Marten Postma, who also recently joined our NWO-XL consortium and with whom we are collaborating on cell based models and quantitative image analysis

And with that, the lab’s research line on early embryogenesis is officially alive and kicking. Welcome Joëlle!

1 October, 2023

Lab trip

We carved out some time for a lab trip in the forest near Maarn. Joëlle joined for the occasion, a couple of days before the official start of her contract.

The original goal was to go on a mushroom hike since it was the height of the fungal season. With that mission accomplished, we tried our hand at mini golf in the afternoon.

27 September, 2023

New PhD thesis from the lab

Yorick dropped off the printed copies of his PhD thesis. Another beautiful piece of work, albeit somewhat on the hefty side. One month to go before the defence!

22 September, 2023

2023 WNT meeting in Spain

Renée gave a talk and chaired a session at the 2023 GRC on WNT signaling, which was held just outside of Barcelona. It was great to catch up with old friends, be emerged in really cool science for a couple of days - and to see the continued influx of young investigators: a clear signal that the WNT field is very much alive and kicking.

31 July, 2023

New pre-print! Celebrating the first first author submission of Marleen

More cake? Well yes indeed!

We celebrated the Biorxiv and journal submission of Marleen’s first first-author paper, called "A molecular toolbox to study progesterone receptor signaling". Also the first shared senior author publication by Thijs and Renée, by the way, in case anyone is counting.

Quite some time ago already, we had the need to measure the effects of progesterone and progesterone receptor (PR) signaling in vitro. Long story short, this turned out to be really finicky and far from straightforward.
As our scientific interest in PR signaling continued to grow, at the start of her PhD Marleen set out to optimize the experimental conditions to obtain more robust readouts. Along the way we developed some new tools (mainly new PR reporter plasmids) that we hope will be useful for the wider research community.

So head on over to Biorxiv to get the ins and outs of measuring PR signaling responses in breast (cancer) cell lines: You can read the pre-print by clicking here or by scanning the QR code below.

We are of course interested to hear your feedback.

As we await the outcome of our journal submission we will take a well deserved holiday break and as soon as we get back we will finish submitting our DNA constructs to Addgene, to ensure that all of these tools will be available to everyone.


21 July, 2023

Two highlights in one

We are really excited to announce that our position paper, which is the outcome of the 2022 ENBDC Think Tank held in Amsterdam was published today.

In this review we discuss what are - according to the ENBDC organizing committee - the biggest breakthroughs in mammary gland biology and breast cancer research of the past decade, as well as the biggest challenges that lie ahead for the next then years. The paper should be available open access via this link or directly via the Journal of Mammary Gland Biology and Neoplasia website.

We hope that this will also be especially useful to newcomers in the field, and we will probably test this hypothesis on our new Frontiers students come September.

As promised, the second highlight contained within this news snippet is that this the first paper co-authored by Thijs and Renée.

14 July, 2023


We had cake to celebrate that we finally managed to get one of our permits approved.

Sometimes the biggest hurdles in academia are of the administrative type. Barring their removal, jumping over them should be celebrated so as to forget that grants and papers could, should and would have been written in that time instead. Plus, the weather was real nice out.

6 July, 2023

lab BBQ

Thijs hosted our lab BBQ this year, where we celebrated the start of summer, the upcoming completion of the BSc and MSc internships and other highlights - including the award of a starters grant to Thijs and the decision that one of the UD positions available from the sectorplangelden was awarded to our group.
It makes up for the negative grant funding decisions that we have been plagued with so far this year and it also means that exciting times lie ahead, with the opportunity to consolidate both our research lines on early mammalian development and 3D tissue organoids.

But more on that later, first: champagne (never mind Renée’s facial expression while popping the cork).

27 June, 2023

NWO Life conference

As one of the committee members of the NWO research community "From Genes To Organisms", Renée chaired a session at the 2023 NWO Life conference.

Due to other obligations she couldn’t stay for the whole meeting (first time that happened). There was time to attend the strategy evening that preceded the conference, with presentations during dinner on FAIR data.

Joining one of the NWO research communities is highly recommended for everyone who wants to get a better understanding of how NWO operates, not to mention to help build a better and stronger life sciences communities in the Netherlands. Who knows, maybe you can even have some impact on the development of science policy.

The conference itself started with a keynote talk by Frans de Waal, before breaking up into parallel sessions. As always, the production value was top notch, making the ambience in the auditorium more like a cross between a Taylor Swift concert and a Hollywood award show, but the more people show up, the more it will also become a place to run into people you know (either IRL or "only from Twitter") or want to get to know.

23 May, 2023

DSCCB Volleyball team

Despite the fact that some of us were clearly still hiding in the office, but we did compete in the FNWI Volleyball Tournament, with Yorick also dropping by as special reinforcement.

While we did not win, from the looks of it, the team was in high spirits.

17 May, 2023

2023 ENBDC Weggis Workshop

Marleen, Tanne and Renée went to Switzerland for the ENBDC Weggis workshop. While the day train made it to Switzerland according to schedule, the NightJet got cancelled just prior to departure, which meant that Renée had to get a last minute airplane ticket after all. Luckily she was on the same flight as Jos Jonkers, which made for good travel company and time to catch up.

This year, Tanne was one of the PhD/postdoc organizers, which included a pre-meeting session for just the early career researchers on the day prior to the official start of the workshop. Marleen gave a talk here and both Tanne and Marleen presented posters at the workshop, while Renée gave a talk.

It is always good to be back in Weggis and see old and new faces so we are looking forward to next year already.

30 April, 2023

First OrganoidNL meeting

Together with colleagues from AMOLF and Utrecht (Hubrecht, UMC and Prinses Máxima), Renée organized the very first OrganoidNL symposium to highlight and celebrate all of the exciting organoid research that is going on in the Netherlands. On the evening prior, Thijs and Renée had the honor and pleasure of taking keynote speaker Jacob Hanna out for dinner.

The most heard comment at the meeting?
"Why didn ’t we have this yet?".

This means we will probably be back next year!

And with that it is on to organizing the next meetings as we have exciting things on the horizon for the Dutch chromatin biology and gastruloid research communities.

31 March, 2023

Our 2023 artist in residence arrives

French composer Julia Pajot is our 2023 artist in residence. She has developed her own system to represent various aspects of matter and will apply her system, including spatial orchestration, to our multi scale studies of mammary gland biology - meaning that we should get an orchestral piece of the developmental dynamics of the mammary gland at the molecular, cell and tissue level.

It never hurts to think big. More details on our artist in residency page, link in the menu.

24 March, 2023

Rosa performs at the InScience Festival

Renée tagged along with our 2021-2022 artist in residence Rosa Schogt to the InScience Festival in Nijmegen, where Rosa performed some of her science inspired poetry in the Amazing Discoveries tent.

Smart and perfect set up with silent disco headphones so everybody had clear sound.

18 March, 2023

Short lecture on stem cells and cancer for high school students and their parents

The Science Park Campus open day was held on Friday 17 March. This meant that lots of high school students and their parents visited us to get a feel for our university and to see if our Biomedical Sciences Program aligned with the interests and expectations.

Renée was happy to give a talk about stem cells and cancer again as part of this "studievoorlichting".

17 March, 2023

Review article on visualizing WNT signaling is out

The review article by Tanne and Renée on Visualizing WNT signaling in mammalian systems came out today. See our publications page for all relevant links.

16 March, 2023

PhD defense: Saskia becomes dr. De Man

Today Saskia defended her PhD thesis in De Agnietenkapel, which was filled to the brim with family, friends and (former) colleagues. This was also the first time that Renée acted in the formal capacity of promotor and used her ius promovendi to officially award Saskia the title of doctor.

Saskia did an excellent job in answering questions from the committee members with just the right combination of confident eloquence and critical scientific nuance. In 45 minutes the full scope of the thesis (which literally deserves the description from mouse to molecule) was covered: from functional imaging to computational modelling and genetic screens. We were especially happy that Andres Lebensohn was able to come over from the United States to join in the celebration. Chapter 6 of the thesis describes the results from Saskia’s stay in his lab at the NIH.

Congratulations Saskia - and thank you again for being the driving force behind setting up the lab’s research line on imaging WNT/CTNNB1 signaling!

13 March, 2023

EMBO course Techniques for Mammary Gland Research

Together with Maria Vivanco (Spain) and Martin Jechlinger (Germany) Renée organised an EMBO practical course at the EMBL campus in Heidelberg. This was the 4th time this course was organised, but the first time that Renée was involved.


We had participants from all across the world - from Argentina and Mexico to Finland and Poland. The week was filled with fun and useful science, from fat pad transplantations and carmine stainings to intraductal injections, FACS and 3D organoid cultures with a demonstration of the local lightsheet microscopy set up and imaging facilities to boot.

The EMBL facilities were amazing, as was the local support during the week - not to mention the food in the EMBL canteen...

If the course is evaluated favourably by those attending, we we hope to be back in 2025!

10 March, 2023

Why outreach should count towards valorisation and impact

In the fall, Renée gave a lecture for high school teachers (organised by BetaPartners). Today we learned that one of the teachers was inspired to use the topic of genome editing and the information provided in the lecture to generate new learning materials and assignments for their high school students!

Not only fun to hear, but also evidence that outreach counts towards societal impact and valorisation of our basic research: somewhere in the Netherlands, high school students will soon be repairing oncogenic CTNNB1 mutations (at least on paper or in silico).

10 March, 2023

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