Junhong Choi

🎉 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

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

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...

Thank you, Emma!!

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)

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...

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)

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

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)

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.

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)

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...

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)

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

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 the lineage tree of monoclonal gastruloid.

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)

(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)

Image describing the monoclonal gastruloid induction protocol.

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

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

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)

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.

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)

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...

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)

Thank you for kind words!!

Thanks, Eric!

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 …

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...

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)

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)

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 .

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

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)

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.

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

A thread:

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

Engineered extrachromosomal oncogene amplifications promote tumorigenesis - Nature Large extrachromosomal DNAs are engineered using a CRISPR- and Cre–loxP-based approach and shown to drive cancer in mouse models, with potential applications in determining the role of oncogene a...

🧪1/ 🚨New paper on ecDNAs from our lab!
We reveal a strategy to engineer extrachromosomal DNA (ecDNA) amplifications in cells & mice. Let's dive in! Let’s dive in! 🧵👇
www.nature.com/articles/s41...

‘DNA Typewriters’ Can Record a Cell’s History Labs around the world are trying to turn cells into autobiographers, tracking their own development from embryos to adults.

Imagine a mouse in which all 10 billion cells keep a diary from fertilization. Imagine sentinel cells recording your experiences and sending out dispatches in the form of DNA. Here's a story I wrote about cell recorders 🧪 Gift link: nyti.ms/3Z3Mqza

‘DNA Typewriters’ Can Record a Cell’s History Labs around the world are trying to turn cells into autobiographers, tracking their own development from embryos to adults.

Pretty excited to see our review & DNA Typewriter covered by NY Times! Perhaps too much excitement for one Monday 🥲 www.nytimes.com/2024/11/25/s...

The lives of cells, recorded - Nature Reviews Genetics Recent advances in genome engineering are enabling the recording of cellular histories into genomes, with single-cell and spatial omics technologies enabling their reconstruction into cellular lineage...

"The lives of cells, recorded"--our new review on genomic recording systems and how they can reveal the dynamics of multicellular development. A pleasure to work on this with amazing colleagues from the Allen Discovery Center for Cell Lineage Tracing.
www.nature.com/articles/s41...

The single-molecule accessibility landscape of newly replicated mammalian chromatin By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...

The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics