Mapping Mouse Prenatal Development with Single Cell Resolution

Excited to share our lab's latest preprint, led by @CXchengxiangQIU, @bethkarenmartin & Ian Welsh of @jacksonlab.

We set out to build a single cell roadmap for all of mouse prenatal development, from single cell zygote to free-living pup.

Preprint: https://t.co/GDS65Qf58X 1/n pic.twitter.com/LtNcaZ1l5p

— Jay Shendure (@JShendure) April 6, 2023

This was a collaboration with @jacksonlab, where Ian Welsh precisely staged 523 embryos spanning E8 to P0, identifying 74 that would give us 2 hour temporal resolution during somitogenesis (0-34 somite counts) and 6 hour resolution through to birth. 2/n pic.twitter.com/AYXflEiK9A

— Jay Shendure (@JShendure) April 6, 2023

The embryos were shipped to the remarkable @bethkarenmartin in Seattle, who applied her optimized sci-RNA-seq3 protocol (original by the brilliant @junyue_cao @RockefellerInst) to profile 12.4 million single nuclei (median 2545 UMIs per nucleus). 3/n pic.twitter.com/ovy66ExDV4

— Jay Shendure (@JShendure) April 6, 2023

After identifying & annotating cell types, @CXchengxiangQIU performed deeper dives into ontogenesis of the posterior gastrula, kidney, mesenchyme, retina, early neurons & other systems. I can't do these justice here; please see preprint for details (https://t.co/GDS65Qf58X) 5/n pic.twitter.com/cjkkB2BvNA

— Jay Shendure (@JShendure) April 6, 2023

How to summarize the complexity of development? @CXchengxiangQIU developed a simple heuristic for linking cell types based on excessive sharing of temporally coincident, mutual nearest neighbors in PCA space. 6/n pic.twitter.com/wmD9dqUK3I

— Jay Shendure (@JShendure) April 6, 2023

The complexity of mammalian development is such that this required some manual curation, but we broke down the problem by wrangling each of 12 subsystems separately, e.g. hematopoiesis. 7/n pic.twitter.com/aUeBJXVovi

— Jay Shendure (@JShendure) April 6, 2023

Building on what had worked for us before (https://t.co/bwcdN2KGfb), we also applied this approach to 4 other sc-RNA-seq datasets that collectively traversed development from zygote to gastrula, and put these all together. 8/n pic.twitter.com/sdyLJwdm5X

— Jay Shendure (@JShendure) April 6, 2023

The result is a cell type tree that traverses mouse development from single cell zygote to free-living pup. 9/n pic.twitter.com/nSxzChViVU

— Jay Shendure (@JShendure) April 6, 2023

What surprised us the most in these data? We oddly observed that in some cell types, there were MASSIVE differences between E18.75 and P0 mice. 10/n pic.twitter.com/nJ5Hqld3ay

— Jay Shendure (@JShendure) April 6, 2023

Technical or analytical artifact, perhaps? Validation experiments confirmed the finding, and narrowed its initiation to the hour immediately following birth. 11/n pic.twitter.com/ntSHZOSmH5

— Jay Shendure (@JShendure) April 6, 2023

What's going on here? On brief reflection, it's immediately apparent that one of these things is not like the other. (credit to R. Bejema for illustrations) 12/n pic.twitter.com/U1ToBXdd0w

— Jay Shendure (@JShendure) April 6, 2023

In particular, the transition from the uterus to the extrauterine world is a rather large change in circumstances for any mammal. 13/n pic.twitter.com/0UFgTgyfsH

— Jay Shendure (@JShendure) April 6, 2023

We speculate that these rapid, cell type-restricted changes are poised physiological adapations that are triggered by birth, e.g. gluoconeogenesis in the liver (cut off from mom), thermogenesis by fat (the real world is cold), etc. 14/n pic.twitter.com/04jyML7vhv

— Jay Shendure (@JShendure) April 6, 2023

Why did we do this, and where might we go next? Again please see the preprint but also a somewhat philosophical perspective that @sdomcke and I wrote that tries to capture the broader context for this line of work. 15/nhttps://t.co/NLAPdHcwFl

— Jay Shendure (@JShendure) April 6, 2023

Many people to thank, but in particular this work was largely executed by three people: @CXchengxiangQIU (all of the analysis!), @bethkarenmartin (vast majority of the data generation!) and Ian Welsh at JAX (all of the embryo staging!). 16/n

— Jay Shendure (@JShendure) April 6, 2023

Building on longstanding collaborations with @coletrapnell, experimental methods from @junyue_cao, the vision of @malte_spielmann, and a wonderful collaboration w/ Steve Murray's lab @jacksonlab. 17/n

— Jay Shendure (@JShendure) April 6, 2023

Copious guidance from @schierlab @Nobu_Hamazaki @CeciliaMoens @thabangh @SRsrivatsan @evaknichols (& others not on Twitter or whose handles I missed). And a huge thank you to @BrotmanBaty @AllenInstitute @HHMINEWS @jacksonlab @NIHFunding for funding the work. 18/n

— Jay Shendure (@JShendure) April 6, 2023