Evidence map›Paper›PMID 41427418›Full record

ArticlebioRxiv : the preprint server for biology2025

Optogenetic Rescue Reveals Spatiotemporal Rules of Germ-Layer Patterning.

Naomi Baxter, Robert Piscopio, Joseph Rufo, Dasol Han, Isobel Whitehead, Jasmine Dhillon, Siddharth S Dey, Maxwell Z Wilson

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Naomi BaxterDepartment of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA.ORCID 0000-0001-9249-9184
Robert PiscopioDepartment of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA.ORCID 0000-0002-4115-2874
Joseph RufoDepartment of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA.ORCID 0000-0001-7408-2393
Dasol HanDepartment of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA.ORCID 0000-0002-3181-7465
Isobel WhiteheadDepartment of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
Jasmine DhillonDepartment of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
Siddharth S DeyDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA.ORCID 0000-0002-1161-1654
Maxwell Z WilsonDepartment of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA.ORCID 0000-0003-0768-7004

Funding

A marker-free technology for mapping the epigenome of cell types in mammalian tissuesR01HG011013 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI DEY, SIDDHARTH SUBHAS · 2020 to 2024
$1.8M
Optical dissection of human embryonic germ layer patterning mechanisms using microengineered stem cell modelsR01HD108803 · NICHD · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI Maxwell Zane Wilson · 2022 to 2026
$1.6M
Understanding DNA methylation reprogramming dynamics during preimplantation development using single-cell sequencingR01HD099517 · NICHD · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI DEY, SIDDHARTH SUBHAS · 2019 to 2023
$1.4M
Shining light on the mechanisms of primate gastrulation: development of high-throughput, optogenetic tools for understanding embryonic developmentF32HD114539 · NICHD · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI Joseph Rufo · 2024 to 2026
$234k
Dissecting the role of Erk signaling dynamics in positioning and coordinating germ layer fatesF31HD108952 · NICHD · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI BAXTER, NAOMI JESSIE · 2022 to 2024
$121k
NHGRI NIH HHS R01 HG011013NICHD NIH HHS F31 HD108952NICHD NIH HHS F32 HD114539NICHD NIH HHS R01 HD099517NICHD NIH HHS R01 HD108803
6 · The paper itself

Abstract

Embryonic cells must interpret morphogen signals that vary in both time and space, but the rules by which they decode these dynamics remain unclear. Here we combine optogenetics with human 2D gastruloids to define minimal WNT signaling rules for germ-layer patterning. We block endogenous WNT secretion to create a "blank canvas" and reconstitute signaling using light-gated LRP6. Systematic temporal scans reveal a narrow competence window when the onset and duration of WNT signaling specify mesoderm; this window is shifted by cell density and amplified by BMP priming, whereas identical WNT inputs outside it invert germ-layer order or generate alternative mesodermal subtypes. Using micromirror-based illumination, we restricted WNT activation to a mid-ring during this temporal window; combined with BMP4, this fully restored germ layer domains with boundaries sharper than those generated by ligand stimulation. Thus, precise spatiotemporal control of a single pathway is sufficient to optically rebuild germ-layer architecture and reveals WNT as a temporal morphogen.

Identifiers

PMID41427418
PMCPMC12713756

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.