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Reposted by Sudarshan Pinglay

Nobu Hamazaki @nobuhamazaki.bsky.social · 12d

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...

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Sudarshan Pinglay @sudpinglay.bsky.social · Aug 13

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!

Jobs

We are working to solve the biggest mysteries in bioscience.

alleninstitute.org

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Reposted by Sudarshan Pinglay

Abby Buchwalter @abbybuch.bsky.social · Jul 21

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/...

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. ...

www.molbiolcell.org

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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!

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...

www.biorxiv.org

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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

Pinglay Lab

www.pinglay-lab.com

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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.

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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!

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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

any feedback would be highly appreciated!

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...

doi.org

Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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

Pinglay Lab

www.pinglay-lab.com

1

Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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.

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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!

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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.

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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...

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.

doi.org

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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.

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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.

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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.

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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.

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Sudarshan Pinglay @sudpinglay.bsky.social · Jul 14

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...

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...

doi.org

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Reposted by Sudarshan Pinglay

Evgeny Kvon @evgenykvon.bsky.social · Jul 2

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/

Range extender mediates long-distance enhancer activity - Nature

The REX element is associated with long-range enhancer–promoter interactions.

www.nature.com

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Reposted by Sudarshan Pinglay

Nozomu Yachie @nzmyachie.bsky.social · Jun 20

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☺️

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Reposted by Sudarshan Pinglay

Nozomu Yachie @nzmyachie.bsky.social · May 21

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...

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.

www.nature.com

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Sudarshan Pinglay @sudpinglay.bsky.social · Apr 25

Such a cool story Maximus! Congrats

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Sudarshan Pinglay @sudpinglay.bsky.social · Apr 11

Let’s gooo! Congrats Dave and team - glad to see this out.

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Reposted by Sudarshan Pinglay

Dave Truong @davidmtruong.bsky.social · Apr 11

Need a site-specific, dox-inducible system for human cells?
Low leakage, silencing-resistant, and modular?
It’s here in the first paper from my lab, led by Tomoki Yanagi MD, PhD.
Bonus: forward programming of TEC-like cells from hiPSCs.

tinyurl.com/trunod01

Termination sequence between an inducible promoter and ubiquitous chromatin opening element (UCOE) reduces gene expression leakage and silencing - Journal of Biological Engineering

Background Inducible gene expression circuits enable precise control over target gene activation and are widely used in direct reprogramming. However, their usability is often compromised by DNA methy...

tinyurl.com

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Sudarshan Pinglay @sudpinglay.bsky.social · Mar 28

We are hiring a person to join our team at the Seattle Hub for Synthetic Biology. Please share the word!

Link to apply:
alleninstitute.org/careers/jobs...

Jobs

We are working to solve the biggest mysteries in bioscience.

alleninstitute.org