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timcoorens.bsky.social
Tim Coorens
@timcoorens.bsky.social
560 followers 140 following 31 posts
Research Group Leader at EMBL-EBI | Former postdoc at Broad Institute | Former PhD student at Sanger Institute | Lineage tracing, cancer genomics, human development
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Reposted by Tim Coorens
ebi.embl.org
EMBL-EBI @ebi.embl.org · Aug 12
Welcome @timcoorens.bsky.social ‪ ‬🇳🇱, our new Research Group Leader.

Find out how Tim’s group is exploring using large-scale single-cell and spatial data to trace cell lineages, understand cancer origins, and uncover how mutations drive disease.

www.ebi.ac.uk/about/news/p...
🖥️🧬
Welcome: Tim Coorens
EMBL-EBI’s newest Research Group Leader is investigating how somatic mutations reveal the hidden histories of human cells.
www.ebi.ac.uk
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Tim Coorens @timcoorens.bsky.social · Jul 3
Last but not least, if you're interested in somatic mutations, new technologies and computational genomics - we're hiring a postdoc in my brand new lab
@emblebi.bsky.social!

Reach out if interested or you have any questions, and apply here: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Postdoctoral Fellow in Coorens Group
We are looking for a motivated and talented postdoctoral-level researcher with experience in genomic analyses to join the newly established Coorens group at EMBL-EBI. We study how normal cells in diff...
embl.wd103.myworkdayjobs.com
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Tim Coorens @timcoorens.bsky.social · Jul 3
This effort would be impossible without the work of many hundreds of people, including the scientists, the NIH staff, and - of course - the donors and their family. A very exciting time to study somatic evolution and I can't wait to see what the next years bring.
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Tim Coorens @timcoorens.bsky.social · Jul 3
SMaHT will generate massive amounts of data, including short-read, long-read, duplex, single cell DNA, and donor specific assemblies, and much more. Check out our stellar data platform (data.smaht.org), courtesy of our Data Analysis Center in Peter Park's lab - watch this space for future data!
SMaHT Data Portal
data.smaht.org
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Tim Coorens @timcoorens.bsky.social · Jul 3
Underpinning the efforts of the Network is a set of 150 donors from across the US and age range, collected by the NDRI, with many tissues samples for each donor - an absolutely unique collection and momentous effort. Also more info at our consortium website: smaht.org
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Tim Coorens @timcoorens.bsky.social · Jul 3
The SMaHT Network, funded by the NIH Common Fund, has over 300 members from over 50 different institutions all working together on developing new tools and technologies to detect somatic variation, analysing the data in the best way possible, and generating a reference catalog of mosaicism
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Tim Coorens @timcoorens.bsky.social · Jul 3
The cells in our bodies constantly acquire mutations. But what are the patterns of mutations across tissues? How do mutations in normal cells lead to cancer and disease? These are questions we will tackle within the Somatic Mosaicism across Human Tissues (SMaHT) Network, now described in @nature.com
The Somatic Mosaicism across Human Tissues Network - Nature
The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.
www.nature.com
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Reposted by Tim Coorens
cimususc.bsky.social
CiMUS @cimususc.bsky.social · Jun 27
Upcoming #CiMUSseminar on Monday ⤵️

🗣 Dr. @timcoorens.bsky.social from @ebi.embl.org :

🧪 "Somatic mutations across normal tissues: past, present, future"

📅 June 30, 1 PM
📍 Theatre room, CiMUS

#RedeCiGUS #FondosEuropeos
‪@mobilegenomes.bsky.social‬ @usc.gal ‪
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Reposted by Tim Coorens
gmaci.bsky.social
Geoff Macintyre @gmaci.bsky.social · Jun 23
🚨Chemo treatment upgrade!🚨

Check out our approach to modernise chemotherapy treatment published today in @natgenet.nature.com. From @cniostopcancer.bsky.social #TailorBio @cruk-ci.bsky.social www.nature.com/articles/s41... More details 👇
www.nature.com
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Reposted by Tim Coorens
naxerova.bsky.social
Kamila Naxerova @naxerova.bsky.social · May 21
Social media grump Kamila has finally made it onto Bluesky!

Please check out my new perspective on metastasis evolution in @natrevcancer.nature.com if you need a reprieve from the news.

I tried my best to develop some new conceptual thoughts here, you be the judge whether I succeeded.
natrevcancer.nature.com
Nature Reviews Cancer @natrevcancer.nature.com · Apr 30
🚨 PERSEPCTIVE

Naxerova explains how genetic analysis of primary tumors & metastases can distinguish competing metastasis models, arguing that quantifying whether metastasis occurs through nonrandom lineage selection could offer insights into metastasis biology.

📖 👇
Evolutionary paths towards metastasis - Nature Reviews Cancer
In this Perspective, Kamila Naxerova discusses how genetic analyses of primary tumours and matched metastases can distinguish between competing metastasis evolution models, arguing that further insights into human metastasis biology could be enabled by a framework that rigorously quantifies whether metastases descend from a nonrandom selection of primary tumour lineages.
bit.ly
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Reposted by Tim Coorens
kelleyharris.bsky.social
Kelley Harris @kelleyharris.bsky.social · May 20
If you’ve ever wondered about the statistical significance of differences among mutational signature profiles, check out our new Aggregate Mutation Spectrum Distance (AMSD) preprint co-led by Sam Hart and @alisonfeder.bsky.social with @nalcala.bsky.social www.biorxiv.org/cgi/content/...
A signature-agnostic test for differences between tumor mutation spectra reveals carcinogen and ancestry effects
Mutational signatures contain valuable information about the mutational processes shaping cancer genomes. However, despite dozens of tools to identify signatures in cancer samples, there is not an est...
www.biorxiv.org
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Reposted by Tim Coorens
smahtnetwrk.bsky.social
smahtnetwrk.bsky.social @smahtnetwrk.bsky.social · May 16
Keeping you in the loop! ➰
Our Linktree includes all SMaHT websites and social media accounts for easy and consistent access.

Find all our social media accounts in one place:
linktr.ee/smahtnetwork
SMaHT Network | Instagram, Facebook | Linktree
Aiming to transform our understanding of somatic mosaicism.
linktr.ee
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Reposted by Tim Coorens
bloodgenes.bsky.social
Vijay G. Sankaran @bloodgenes.bsky.social · May 1
Thrilled to see my #MITS25 talk brought to life by the brilliant 🎨 @atjcagan.bsky.social! Dive into the stellar science from @g-agarwal.bsky.social & co - fresh on bioRxiv: www.biorxiv.org/content/10.1...
#Genomics #SomaticEvolution
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timcoorens.bsky.social
Tim Coorens @timcoorens.bsky.social · Apr 27
Thanks again for coming over to speak! It was an amazing talk
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Tim Coorens @timcoorens.bsky.social · Mar 21
Thanks very much, Daniel!
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Reposted by Tim Coorens
sangerinstitute.bsky.social
Wellcome Sanger Institute @sangerinstitute.bsky.social · Mar 20
Read ‘The somatic mutation landscape of normal gastric epithelium’ from @sangerinstitute.bsky.social, @broadinstitute.org, The University of Hong Kong & others in @nature.com ⤵️

www.nature.com/articles/s41...
The somatic mutation landscape of normal gastric epithelium - Nature
Whole-gene sequencing of microdissected gastric glands from individuals with and without gastric cancer reveals distinct patterns of somatic mutations and provides insights into influen...
www.nature.com
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Tim Coorens @timcoorens.bsky.social · Mar 20
Thanks to all the donors and their families for making this study possible. And many thanks to Grace Collord, Peter Campbell, @imartincorena.bsky.social , SY Leung, Mike Stratton and all other co-authors. @broadinstitute.org @sangerinstitute.bsky.social
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Tim Coorens @timcoorens.bsky.social · Mar 20
In short, the normal stomach shows a landscape of somatic mutations with many differences from those of other organs. Our findings provide insights into intrinsic and extrinsic influences on somatic evolution in the gastric epithelium in healthy, precancerous and malignant states
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Tim Coorens @timcoorens.bsky.social · Mar 20
Because we used the LCM approach, we can map these driver clones to their location in tissues, which reveals expansions of mutant clones and local selective pressures. We find three CTNNB1 mutant clones right next to one another, rather than evenly distributed.
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Tim Coorens @timcoorens.bsky.social · Mar 20
Lastly, the stomach also shows a rich landscape of driver mutations, most notably in epigenetic modifiers (ARID1A, ARID1B, KDM6A) and surprisingly inactivating mutations in CTNNB1 (unlike the activating ones observed in cancer).
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Tim Coorens @timcoorens.bsky.social · Mar 20
Glands with trisomies were not associated with a specific stomach region, and their incidence does not linearly increase with age, but are associated with severe chronic inflammation. It's plausible these are a consequence of an exposure, a pathogen or otherwise, long before the time of sampling.
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Tim Coorens @timcoorens.bsky.social · Mar 20
Intriguingly, these trisomies happen multiple times in the same donor, with different alleles amplified. In one case, we found trisomies in 9 of 12 glands sampled. Timing analysis shows these all happened around the same time, suggesting a sudden burst or selective advantage.
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Tim Coorens @timcoorens.bsky.social · Mar 20
The most surprising finding, however, comes from the CNVs in the stomach. We find extraordinarily high rates of somatic whole-chromosome gains/trisomies in the stomach, mostly of chrs 20 and 13, highly concentrated in a few patients.
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Tim Coorens @timcoorens.bsky.social · Mar 20
While SBS17 is very common in gastric cancer, we only find it very rarely in normal glands, and only in very low proportions. So while stomach cells can get exposed to SBS17, high levels of SBS17 seem to be exclusive to overt cancer.
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Tim Coorens @timcoorens.bsky.social · Mar 20
The mutational signatures are mostly SBS1, SBS5 and SBS18, like other epithelial tissues. Metaplastic glands have much more SBS1 and SBS18 (ROS), and indels linked to polymerase slippage. These are also dominant in intestinal glands, so may suggest a “rewiring” of the mutation rate.
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