Lightnews — Scholar-powered news

Reposted by Junhong Choi

Memorial Sloan Kettering Cancer Center @mskcancercenter.bsky.social · Jun 24

🎉 Congrats to MSK postdoc research scholar Dr. Brendan Camellato for being named a 2025 @jcchildsfund.bsky.social ‬ Research Fellow! His work will focus on how cell signaling drives #stemcell differentiation with single-cell resolution. #JCCFellow

Jane Coffin Childs Fund for Medical Research @jcchildsfund.bsky.social · Jun 24

We're thrilled to announce the 2025 class of Jane Coffin Childs Fellows!

See our latest blog post and "look book" to learn more about our newest Fellows and their exciting research!

www.jccfund.org/blog/the-jan...

www.jccfund.org/wp-content/u...

www.jccfund.org

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Junhong Choi @choijunhong.bsky.social · Jun 24

Congrats Brendan Camellato for his Jane Coffin Childs Fellowship!! 🎉🎉

Jane Coffin Childs Fund for Medical Research @jcchildsfund.bsky.social · Jun 24

We're thrilled to announce the 2025 class of Jane Coffin Childs Fellows!

See our latest blog post and "look book" to learn more about our newest Fellows and their exciting research!

www.jccfund.org/blog/the-jan...

www.jccfund.org/wp-content/u...

www.jccfund.org

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Reposted by Junhong Choi

Sternberg Lab @sternberglab.bsky.social · May 28

We're thrilled to share the published version of our DRT9 story, online today @nature.com! Congratulations to all authors!

www.nature.com/articles/s41...

Sternberg Lab @sternberglab.bsky.social · Mar 26

Hello BlueSky! Inaugural post here from the Sternberg Lab. We're excited to share our latest work, in which we teamed up with the @WiedenheftLab to study how DRT9 reverse transcriptases provide antiviral immunity. Here’s what we found: www.biorxiv.org/content/10.1...

Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase

Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide...

www.biorxiv.org

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Junhong Choi @choijunhong.bsky.social · May 28

Thank you, Emma!!

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Junhong Choi @choijunhong.bsky.social · May 27

We’re still thinking about what this means for actual embryonic development, but it’s exciting to observe such effects in a tractable stem-cell-derived model! Huge thanks to everyone in the @jshendure.bsky.social lab—especially Jay—for supporting this project from start to finish! (13/13)

Junhong Choi @choijunhong.bsky.social · May 27

This reminds us of “transiently heritable” traits seen in other contexts, such as cellular reprogramming (doi.org/10.1038/s415...) and drug resistance in cancer (doi.org/10.1016/j.ce... the clonal bias can shape their fate decisions and cellular phenotypes. (12/13)

Single-cell mapping of lineage and identity in direct reprogramming - Nature

Combinatorial tagging of single cells using expressed DNA barcodes, delivered by a lentiviral vector, is used to track individual cells and reconstruct their lineages and trajectories during cell fate...

doi.org

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Junhong Choi @choijunhong.bsky.social · May 27

Even after resetting spatial context, we saw persistent clonal biases—suggesting an intrinsic, heritable factor shaping fate decisions, independent of spatial cues like Wnt signaling. (11/13)

Part of Image5 in the preprint, describing how major clades share similar cell-type compositions and cell numbers within each gastruloids.

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Junhong Choi @choijunhong.bsky.social · May 27

In this “tree-of-trees” experiment, we dissociated a monoclonal colony into single cells (resetting spatial context) and used them to generate separate gastruloids. (10/13)

Image describing two-epoch experiment, where we first start with single cell that makes a cell colony, which is dissociated in the second epoch and each made into a monoclonal gastruloid.

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Junhong Choi @choijunhong.bsky.social · May 27

Previous works (e.g., by Michelle doi.org/10.1016/j.de... and by Harry doi.org/10.1038/s415...) suggested spatial context plays a big role in gastruloids fate decisions. So we designed a two-epoch experiment to test that… (9/13)

Recording morphogen signals reveals mechanisms underlying gastruloid symmetry breaking - Nature Cell Biology

Toettcher, McNamara and colleagues use synthetic ‘signal-recording’ gene circuits on mouse gastruloids and find that cell sorting rearranges patchy domains of Wnt activity into a single pole, which de...

doi.org

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Junhong Choi @choijunhong.bsky.social · May 27

Together, we found: Cell fates can diverge as early as the first cell division! Sister cells can follow drastically different paths—e.g., one lineage becomes mostly somites, another mostly neurons! (8/13)

Image showing early clonal bias from first, third and 12th cell division influencing cell fate decision between somitic vs. neural cell fate.

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Junhong Choi @choijunhong.bsky.social · May 27

Once we knew monoclonal lineage recording worked, we teamed up with @cxqiu.bsky.social—an amazing and generous computational biologist—to dive into the lineage trees. (7/13)

Image showing the lineage tree of monoclonal gastruloid.

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Junhong Choi @choijunhong.bsky.social · May 27

(Side note: Sam also used this approach to generate monoclonal embryoid bodies for perturbation screening with @sdomcke.bsky.social and @cxqiu.bsky.social.) bsky.app/profile/sdom... (6/13)

Silvia Domcke @sdomcke.bsky.social · May 25

Expanding Perturb-seq-like screens to multicellular systems also increases the complexity of confounding effects. We encountered this when we perturbed all TFs in mosaic embryoid bodies (EBs) and develop a scalable solution by barcoding monoclonal individuals. 🧵 www.biorxiv.org/content/10.1...

Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens

Genetic screens in organoids hold tremendous promise for accelerating discoveries at the intersection of genomics and developmental biology. Embryoid bodies (EBs) are self-organizing multicellular str...

www.biorxiv.org

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Junhong Choi @choijunhong.bsky.social · May 27

To solve this, Sam developed a robust protocol to create “monoclonal gastruloids”—gastruloids seeded from a single cell. These were ideal for DNA Typewriter lineage reconstruction! (5/13)

Image describing the monoclonal gastruloid induction protocol.

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Junhong Choi @choijunhong.bsky.social · May 27

However, conventional gastruloids start with 300–500 cells, and that’s a problem for us—lineage tracing from 500 cells gives you 500 independent trees, masking clonal info from earlier developmental events. (4/13)

Image describing conventional gastruloid induction protocol, which starts with 300-500 cells.

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Junhong Choi @choijunhong.bsky.social · May 27

Mouse 3D gastruloids seemed like the perfect testbed—they mimic key features of early mammalian development in both shape and cell types. (Image from Turner @gastruloids.bsky.social & Martinez Arias @amartinezarias.bsky.social : doi.org/10.1002/bies...) (3/13)

Image of 3D gastruloids, highlighting their morphological development and cell-type differentiations

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Junhong Choi @choijunhong.bsky.social · May 27

We previously showed that DNA Typewriter can record high-resolution lineage trees in cultured cells (HEK293T). www.nature.com/articles/s41... But could we use it to study how clonal memory shapes cell fate decisions during development? (2/13)

A time-resolved, multi-symbol molecular recorder via sequential genome editing - Nature

A DNA memory device, DNA Typewriter, uses sequential prime editing to record the order of multiple cellular events.

www.nature.com

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Junhong Choi @choijunhong.bsky.social · May 27

New preprint with the Shendure lab @jshendure.bsky.social ! We apply the DNA Typewriter lineage recorder to mouse 3D gastruloids, a powerful model of early mammalian development. Led by Sam Regalado and CX Qiu @cxqiu.bsky.social : www.biorxiv.org/content/10.1... (1/13)

Lineage recording in monoclonal gastruloids reveals heritable modes of early development

Mammalian stem cells possess a remarkable capacity for self-organization, a property that underlies increasingly sophisticated in vitro models of early development. However, even under carefully contr...

www.biorxiv.org

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Junhong Choi @choijunhong.bsky.social · May 7

Thank you for kind words!!

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Junhong Choi @choijunhong.bsky.social · May 7

Thanks, Eric!

Junhong Choi @choijunhong.bsky.social · May 6

Very grateful to receive the Searle Scholars Award, especially during this challenging time! This support will help our lab realize our vision of genomic recording for reconstructing the mammalian cell fate decision. searlescholars.org/2025/04/14/s...

SEARLE SCHOLARS PROGRAM NAMES 15 SCIENTISTS AS SEARLE SCHOLARS FOR 2025

Members of the new class of Searle Scholars pursue ground-breaking research in chemistry and the biomedical sciences. Each receives an award of $300,000 in flexible funding to support his, her, or …

searlescholars.org

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Junhong Choi @choijunhong.bsky.social · May 6

We are very thankful to Jay Shendure @jshendure.bsky.social and the lab for fostering our views that led to this review, @cp-trendsgenetics.bsky.social for all their help, and the funding agencies (NHGRI, NCI, and @damonrunyon.org) that made this work (and our previous works) possible! (2/2)

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Junhong Choi @choijunhong.bsky.social · May 6

Happy to share our new review on molecular circuits for genomic recording with @chenomics.bsky.social! Here, we present our views on the remaining challenges in the field of genomic recording for reconstructing cell-fate decisions. (1/2)

Trends in Genetics @cp-trendsgenetics.bsky.social · May 6

Online now -- a new Review:

"Molecular circuits for genomic recording of cellular events"
by Wei Chen & Junhong Choi (@choijunhong.bsky.social)

FREE to read till June 25th using this link:
authors.elsevier.com/a/1l2gMcQbJF...

Figure 1. Reconstructing cell signaling history with genomic recording circuits.

(A) Concept overview: cellular signals (e.g., environmental changes, signaling molecules, or cell–cell interactions) are converted into genomic recordings via event sensors in each cell. Recorded information is retrieved through sequencing assays to reconstruct each cell’s signaling history and its role in cell fate decisions. (B) Key advancements enabling genomic recording: the discovery of CRISPR-Cas9 provided precise, programmable genome editing. Single-cell profiling methods facilitated the accurate retrieval of genomic recordings. Advances in protein design and synthetic biology are transforming the development of cellular event sensors for genomic recording.

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Reposted by Junhong Choi

Caleb Lareau @caleblareau.bsky.social · Mar 14

Trying a slightly new model (for us at least) of #openscience. With @ronanchaligne.bsky.social and @karolisk.bsky.social, we pitted 10x Genomics Chromium GEM-X against Illumina PIPseq V head-to-head to understand these two platforms for single-cell genomics. Some thoughts off the bleeding edge: /1

a baby is eating a piece of food while sitting on the ground .

ALT: a baby is eating a piece of food while sitting on the ground .

media.tenor.com

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Reposted by Junhong Choi

Naama Aviram @naamaaviram.bsky.social · Jan 2

New year, new beginnings! 🎉

The Aviram Lab will officially open its doors on March 1st @mskcancercenter.bsky.social!

We’ll study microbial immune systems and their connection to fundamental cellular processes like #RNA transcription and #DNA integrity.

#NewPI #AcademicSky #WomenInSTEM
(1/2)

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Reposted by Junhong Choi

James Briscoe @jamesbriscoe.bsky.social · Dec 19

Our latest: how to generate the notochord
"Timely TGFβ signalling inhibition induces notochord"

A thread:

www.nature.com/articles/s41...

Timely TGFβ signalling inhibition induces notochord - Nature

Through analysis of developing chick embryos and in vitro differentiation of embryonic stem cells, a study develops a method to generate a model of the human trunk with a notochord.

www.nature.com

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