Sudarshan Pinglay

We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here:

journals.biologists.com/dev/article/...

We are hiring a staff member to support various projects in our lab. Please reach out with questions!

wd5.myworkdaysite.com/recruiting/u...

if you are excited about these areas, come join our lab
@uwgenome.bsky.social and the Seattle Hub for Synthetic Biology! We are hiring at all levels.

t.co/wAehoBsJ5F

We also discuss current bottlenecks for mammalian genome writing (mainly throughput and size), mechanisms to address them, and future directions for the technology. We think it is particularly poised to revolutionize generating training data for genomic AI models.

Engineering mammalian cells with large synthetic DNA payloads promises to be highly enabling for understanding mammalian gene regulation, dissecting GWAS haplotypes, engineering better animal models for human disease, and encoding multi-gene functions for cell therapy and biotech

Mammalian genome writing: Unlocking new length scales for genome engineering The ability to design and engineer mammalian genomes across arbitrary length scales would transform biology and medicine. Such capabilities would enab…

Happy to share that our review on mammalian genome writing with Jack Atwater, Ran Brosh, Jef Boeke, @jshendure.bsky.social and Matt Maurano is now out in @cellpress.bsky.social!

www.sciencedirect.com/science/arti...

Please 🔁! #MASSIV will be held in Vancouver from January 19-22, 2026. 4-day meeting on #synbio x #tissueengineering.

Some trainee-focused events. >50 talks (10 from abstracts), posters, panel & publishing insights sessions.

www.massivconference.com

Abstract deadline: Nov 14

Please RP! A 4-day synbio and tissue engineering conference #MASSIV to transform biology and medicine together.

Couldn't list all amazing speakers, so please check out this 👉https://www.massivconference.com/

Poster due is Nov 7, but will be extended.

With @stemcellnetwork.ca and JST.

New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...

Jobs We are working to solve the biggest mysteries in bioscience.

We are hiring a scientist to lead our 'Build' team at the Seattle Hub for Synthetic Biology. @alleninstitute.org

Job posting below:
alleninstitute.org/careers/jobs...

Please reach out if you have any questions!

Lamin B1 and LAP2β resist cytoskeletal force to maintain lamin A/C meshwork organization and preserve nuclear integrity | Molecular Biology of the Cell The nuclear lamins are extremely long-lived proteins in most cell types. As a consequence, lamin function cannot be effectively dissected with temporal precision using standard knock-down approaches. ...

The nuclear lamina strengthens the nucleus and organizes the genome. So what happens when you acutely degrade it in living cells? Not what we thought! (1/n)
www.molbiolcell.org/doi/10.1091/...

A shotgun approach for highly multiplexed mammalian metabolic engineering Mammalian metabolic engineering is critical to advancing basic biology, bioproduction, and cell therapy. However, as pathway complexity increases, so does the size of both the combinatorial design spa...

Here's a link to the preprint if you made it this far:
www.biorxiv.org/content/10.1...

any feedback would be highly appreciated!

Pinglay Lab

A big thank you to all co-authors - looking forward to seeing where we can take this approach.

If you are interested in joining us on this effort, check out our website: www.pinglay-lab.com

Finally, we demonstrate that data resulting from SGE is compatible with training predictive machine learning models.

We are very excited about using SGE to generate the synthetic data needed to train the next generation of models for biological design.

SGE is generalizable across cell types. We engineer T-cells (Jurkat) to grow without valine.

We believe a similar strategy could help create more resilient T-cells for therapy, capable of surviving and functioning in the metabolically depleted environments of tumors. Hopefully more here soon!

A shotgun approach for highly multiplexed mammalian metabolic engineering Mammalian metabolic engineering is critical to advancing basic biology, bioproduction, and cell therapy. However, as pathway complexity increases, so does the size of both the combinatorial design spa...

Here's a link to the preprint if you made it this far:
doi.org/10.1101/2025...

any feedback would be highly appreciated!

Pinglay Lab

A big thank you to all co-authors - looking forward to seeing where we can take this approach.

If you are interested in joining us on this effort, check out our website: www.pinglay-lab.com

Finally, we demonstrate that data resulting from SGE is compatible with training predictive machine learning models.

We are very excited about using SGE to generate the synthetic data needed to train the next generation of models for biological design.

We then used SGE to engineer CHO cells to grow without isoleucine, a feat we could not achieve via rational design and delivery of entire synthetic pathways.

Again, mitochondrial localization was favored, with individual clones reflecting ~40-50kb of integrated DNA!

Using SGE, we screened millions of pathway combinations in a single experiment to engineer CHO cells that grew at WT rate (~1.1 day/doubling) in valine-free medium.

Intriguingly, the best clones all employed mitochondrial localization of pathway components, not cytoplasm as in our prev. design.

Resurrecting essential amino acid biosynthesis in mammalian cells Mammalian cells were engineered to synthesize valine, a metabolic capacity that had been lost from the lineage of higher eukaryotes for >500 million years.

In collaboration with Harris Wang’s lab, we previously engineered cells to grow without valine by importing 4 genes from E.coli.

However, the cells grew 4x slower than normal - and we could not extend this strategy to enable any other amino acid prototrophies.

doi.org/10.7554/eLif...

As a test case, we used SGE to engineer essential amino acid prototrophy in mammalian cells, a behavior last seen over 500 million years ago.

Unlike E. coli, which can make all 20 proetinogenic amino acids, mammals lack the pathways for 9 “essential” ones and must obtain them through the diet.

In SGE, we clone and deliver a TU library at high MOI so that each cell gets a random mix, assembling a unique synthetic metabolic pathway per cell. Cells with the desired phenotype (e.g., survival or fluorescence) are selected, and TU barcodes are sequenced to identify functional combinations.

To address this, we developed Shotgun Genetic Engineering (SGE), which leverages the fact that building and delivering many small, barcoded transcription units - each with a gene, promoter and localization signal - is exponentially easier than delivering a single large construct to a mammalian cell.

Mammalian metabolic engineering is key to advancing bioproduction, cell therapy, and rejuvenation.

But as pathway complexity grows, so does the combinatorial design space! However, delivering large DNA constructs to mammalian cells is inefficient, making large unbiased screens intractable.

A shotgun approach for highly multiplexed mammalian metabolic engineering Mammalian metabolic engineering is critical to advancing basic biology, bioproduction, and cell therapy. However, as pathway complexity increases, so does the size of both the combinatorial design spa...

Excited to share our work with @julietrolle.bsky.social & Jef Boeke.

We developed a 'shotgun' method to screen millions of synthetic metabolic pathways to enable mammalian cells to grow without two essential nutrients for the first time in >500 million years!

doi.org/10.1101/2025...

Thread...

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

CAGT was fun! Thanks @carldeboer.bsky.social @sudpinglay.bsky.social and the de Boer lab for organizing! Folks from Seattle, Oregon, and other places. Great community. Arman gave a usual super talk, and Sanchit and Dayag won poster prizes☺️

A multi-kingdom genetic barcoding system for precise clone isolation - Nature Biotechnology A barcoded CRISPR base editing system isolates target clones from complex mammalian, yeast and bacterial populations.

CloneSelect published in Nature Biotechnology
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...

Such a cool story Maximus! Congrats