Planarian Regeneration — A Model of Whole-Body Repair
Planarians (Schmidtea mediterranea) are freshwater flatworms with extraordinary regenerative ability — they can regrow any missing body part, including the entire head and central nervous system, from a tiny fragment. This power stems from neoblasts, pluripotent adult stem cells comprising ~25–30% of somatic cells.
This viewer explores the 4D spatiotemporal transcriptomic atlas of planarian regeneration, combining spatial transcriptomics (10x Visium) with single-cell RNA-seq across the complete regeneration timeline (0h → 7 days post-amputation).
Study Design
Spatial transcriptomics: 89 whole-worm coronal cryosections at 6 timepoints (0, 6, 12, 24 hpa; 3, 7 dpa) profiled with 10x Visium.
scRNA-seq: Same batch samples at 8 timepoints (adding 2 and 5 dpa).
3D reconstruction: Serial sections integrated via Cell2location + STAGATE + Imaris to build volumetric cell-type maps.
Analysis pipeline: Hotspot spatial modules → spatially variable genes → functional screening → RNAi validation.
Key Discoveries
- Novel omnipotent neoblast subcluster with unique marker genes
- Spatial modules capturing wound-specific and pole-specific expression
- plk1 identified as critical early-response gene for blastema formation
- Dynamic reshaping of morphogenetic gradients during regeneration
- 3D cell-type distribution maps at each timepoint
- Online resource: STAPR visualization platform
Planarian Body Plan
Spatial Gene Expression Body Map
Select a gene or pathway to visualize its spatial expression pattern across the planarian body. Expression intensity is shown as a color gradient on the body silhouette.
Spatial Expression Heatmap
Anterior-posterior expression levels for selected morphogens (normalized, log-scale):
Dorsal-Ventral Axis Genes
BMP/Wnt crosstalk patterns orthogonal body axes:
Position Control Genes (PCGs)
These genes form concentration gradients along body axes, serving as spatial coordinates for regenerating tissue:
Morphogenetic Gradient Explorer
Morphogen gradients provide positional information during regeneration. Explore how the three major signaling pathways pattern the planarian body along two orthogonal axes.
Anterior-Posterior Axis: Wnt Gradient
Dorsal-Ventral Axis: BMP Gradient
BMP4 activity is highest dorsally; the BMP inhibitor noggin-1 (nog1) is expressed ventrally, creating the D-V axis.
Medial-Lateral: Hedgehog & Slit
Slit and Hedgehog signaling pattern the medial-lateral axis, with highest expression at the ventral midline.
Gradient Interaction Simulator
Adjust morphogen concentrations to see how the combinatorial code specifies regional identity:
Regeneration Timeline
Click a timepoint to explore the spatial transcriptomic snapshot at each stage of planarian regeneration.
Neoblast Proliferation Dynamics
Gene Module Activation
plk1: Critical Blastema Initiator
Cell Type Atlas
The planarian body contains ~40 distinct cell types, all derived from neoblast stem cells. Spatial transcriptomics reveals their precise distribution and dynamics during regeneration.
Cell Type Composition
Cell Type Database
| Cell Type | Proportion | Key Markers | Location | Regen Role |
|---|
Neoblast Subtypes
Spatial Distribution Score
Signaling Pathway Network
Planarian regeneration requires coordinated activation of multiple signaling pathways. These interact to establish polarity, drive proliferation, and specify cell fate.
Core Regeneration Pathways
Pathway Crosstalk Network
Pathway Activity Over Regeneration
Bibliography
- Cui, G. et al. "Spatiotemporal transcriptomic atlas reveals the dynamic characteristics and key regulators of planarian regeneration." Nature Communications 14, 3205 (2023). DOI
- "4D Single-Cell Spatial Transcriptomics Reveals Dynamic Morphogenetic Gradients and Regenerative Domains in Planarians." bioRxiv 2026.02.18.706529 (2026). DOI
- Kleshchevnikov, V. et al. "Cell2location maps fine-grained cell types in spatial transcriptomics." Nature Biotechnology 40, 661 (2022).
- DenBoer, M. L. et al. "Planarians employ diverse and dynamic stem cell microenvironments." bioRxiv (2023).
- Gurley, K. A., Rink, J. C. & Alvarado, A. S. "β-catenin defines head versus tail identity during planarian regeneration and homeostasis." Science 319, 323 (2008).
- Molina, M. D. et al. "Noggin and noggin-like genes control dorsoventral axis regeneration in planarians." Current Biology 21, 300 (2011).
- Rink, J. C. et al. "Planarian Hh signaling regulates regeneration polarity and links Hh pathway evolution to cilia." Science 326, 1406 (2009).
- Wagner, D. E. et al. "Clonogenic neoblasts are pluripotent adult stem cells that underlie planarian regeneration." Science 332, 811 (2011).
- Fincher, C. T. et al. "Cell type transcriptome atlas for the planarian Schmidtea mediterranea." Science 360, eaaq1736 (2018).
- Petersen, C. P. & Reddien, P. W. "Wnt signaling and the polarity of the primary body axis." Cell 139, 1056 (2009).
- Hill, E. M. & Petersen, C. P. "Wnt/Notum spatial feedback inhibition controls neoblast differentiation to regulate reversible growth of the planarian brain." Development 142, 4217 (2015).
- Stückemann, T. et al. "Antagonistic self-organizing patterning systems control maintenance and regeneration of the anteroposterior axis in planarians." Developmental Cell 40, 248 (2017).