RT @WhiteheadInst: PEtracer combines lineage tracing and spatial data, providing a detailed view of how cancer growth is influenced by both….

I'll be out at Stanford this coming Thursday hosted by my friend and collaborator @weallen1 where I'll be presenting a seminar on our recent PEtracer work ( Feel free to swing by-- info attached!

Excited to announce that this work is now live as a first release article @ScienceMagazine So grateful for this fantatic team and to see this work in wild!

There are of course tons of other cool findings in the paper and we hope you give it a read! This has been an incredible collaboration with @KatieEYost, @sclerei, @WilliamNColgan, as well as our co-authors (@MattG_Jones, @dianyang1117, @alexa_schnell, @sundakao, @_canergen) and.

13/14.Looking to the future, we see many impactful applications of PEtracer for understanding the drivers of cell fate in development and disease and to provide training datasets to create virtual embryos or tumors.

12/14.We looked at cancer cell fitness and heritability and were able to identify fitness programs driven more by where you came from (e.g. Cldn4) or more by where you ended up in the tumor (e.g. Fgf1).

11/14.To delve more deeply into drivers of tumor dynamics, we identified four spatially- and transcriptionally-coherent cancer cell modules. We could use our phylogeny to figure out that Module 4 (lung adjacent malignant cells) stuck out as highly heritable and highly fit.

10/14.Providing a really cool 3-D lineage map of tumor outgrowth (with paired cell state information!)

9/14.We can then take these same MERFISH-profiled samples and generate lineage profiles at tissue scale.

8/14.With confidence in our imaging readouts and the quality of our lineage tracing system, we used PEtracer to study a syngeneic model of murine lung metastasis. We transplant PEtracer 4T1 cells into mice, allow clonal lung tumors to form, and then perform MERFISH-based spatial

7/14.We then performed our first lineage tracing experiment, where we used static barcoding to validate the accuracy of PEtracer lineage trees. At two distinct time points our phylogenies exhibited almost perfect agreement with these orthogonal marks of shared ancestry.

6/14.Building off of elegant work from the @ElowitzLab @AskaryLab for in situ barcode readouts (see PMID: 31740838) , we perform extensive tissue digestion and clearing before amplifying lineage tracing cassettes using T7 polymerase. We then decode integration barcodes and edits

5/14.We exhaustively screened candidate LMs to identify those with high editing efficiency (enabling rapid labeling), balanced installation frequencies, and robust discrimination with FISH probes. We tuned editing rates using pegRNA protospacer mismatches to support tracing from

4/14.Guided by in silico modeling, we engineered PEtracer to install predefined 5 nucleotide lineage marks (LMs) using prime editing. At each site, one of eight pegRNA-encoded LMs is stochastically installed. The identity of the LM can then be read out with high-resolution,

3/14.To map cell fates in mammalian systems at organism or tissue-scales, we set out to build a system that continuously marks cell divisions throughout biological processes, jointly assays cell state and lineage while preserving relevant cellular tissue context, and captures

2/14.Since Virchow’s dictum “omnis cellula e cellula” (“all cells come from cells”), a key objective in biology has been to track the histories of individual cells as they grow and divide during development and disease. Modern approaches aim to map both cell state and lineage,

1/14.On behalf of the amazing team in @JswLab, we’re excited to share PEtracer ( a prime editing-based evolving lineage recorder compatible with both scRNA-seq and high-resolution imaging readouts in intact tissue. By applying PEtracer in a syngeneic mouse.

Special thanks to @JswLab @davidrliu @liugroup for your fantastic mentorship!.

Just received the word that my K99/R00 is officially funded! Huge thanks to my mentors, colleagues, and friends in science who’ve helped me get here. Excited for the science ahead– stay tuned! Nice to share good personal news and hope for those waiting on word from the NIH ◡̈.