Biology subjects

Kappes, V.

Publications and source records attributed to Kappes, V..

4 recordsLinked to original sources

bioRxiv2026

An optimized workflow for spatial transcriptomics across early development in Xenopus

How gene expression patterns change spatially as the embryo transitions from simple to complex structures remains a major developmental biology question. Recently developed imaging-based spatial transcriptomics (ST) enable mapping expression of multiple gene at a single-cell resolution. Although Xenopus is a key model in embryology there is no established ST pipeline, and commercially available techniques face many challenges (sample preparation, probe design, cell segmentation). Furthermore, the highly diverse cell shapes and sizes across developmental stages and between different tissues represent major hurdles to accurately defining cells. Here, we describe an optimized workflow for ST in blastula-to-tailbud-stage frog embryos using Merscope, commercial MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization) originally designed for standard mammalian tissues. With stringent quality control and tailored computational pipelines, we optimize this technology for robust, semi-quantitative profiling of spatial transcriptomic landscapes in non-mammalian embryos. Reliable tissue preservation and cell-segmentation enable high-resolution mapping of gene expression during the development of a complex multi-tissue organization. This versatile strategy applies broadly to various dynamic systems, from embryos of various model organisms to complex and heterogeneous organs in mammals. Summary statementThis Single-cell Spatial Transcriptomics pipeline and reference atlas in Xenopus - a model organism in embryology - overcome technical challenges and resolve dynamic changes in patterning during development.

developmental biology↗

bioRxiv2025

Zebrafish Xenografts Reveal a Context-dependent Roleof PFKFB4 in Melanoma Cell.

Cutaneous melanoma is a highly metastatic cancer in which tumor cell plasticity drives transitions between proliferative and invasive states. The glycolytic regulator PFKFB4 has been implicated in cancer cell motility, but its role in melanoma progression in vivo remains unclear. Using zebrafish larval xenografts, we found that PFKFB4 depletion reduced invasion in MeWo cells without affecting tumor growth, whereas in A375P cells it decreased tumor growth but had no effect on invasion or metastasis. In MeWo, PFKFB4 loss was associated with reduced SNAIL2 expression, while no effect on EMT transcription factors was observed in A375P cells. Rescue experiments indicated that PFKFB4 and SNAIL2 acted independently in regulating Mewo migration in vitro. These findings identify PFKFB4 as a context-dependent regulator of melanoma progression.

cancer biology↗

bioRxiv2022

From neural border to migratory stage: A comprehensive single cell roadmap of the timing and regulatory logic driving cranial and vagal neural crest emergence

Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of molecular choices orchestrating the emergence of neural crest heterogeneity from the embryonic ectoderm remains elusive. Gene-regulatory-networks (GRN) govern early development and cell specification towards definitive neural crest. Here, we combine ultra-dense single cell transcriptomes with machine-learning and large-scale experimental validation to provide a comprehensive GRN underlying neural crest fate diversification from induction to early migration stages in the frog Xenopus tropicalis. During gastrulation, a transient neural border zone state precedes the choice between neural crest and placodes which includes multiple and converging gene programs. Transcription factor connectome and bifurcation analyses demonstrate the early emergence of neural crest fates at the neural plate stage, alongside an unbiased multipotent lineage persisting until after epithelial-mesenchymal transition. We decipher the circuits driving cranial and vagal neural crest formation and provide a broadly applicable strategy for investigating SC transcriptomes in vertebrate GRNs in development, evolution, and disease.

developmental biology↗

bioRxiv2021

Cell type- and region-specific modulation of cocaine seeking by micro-RNA-1 in striatal projection neurons

The persistent and experience-dependent nature of drug addiction may result in part from epigenetic alterations, including non-coding micro-RNAs (miRNAs), which are both critical for neuronal function and modulated by cocaine in the striatum. Two major striatal cell populations, the striato-nigral and striato-pallidal projection neurons, express respectively the D1 (D1-SPNs) and D2 (D2-SPNs) dopamine receptor, and display distinct but complementary functions in drug-evoked responses. However, a cell-type-specific role for miRNAs action has yet to be clarified. Here, we evaluated the expression of a subset of miRNAs proposed to modulate cocaine effects in the nucleus accumbens (NAc) and dorsal striatum (DS) upon sustained cocaine exposure in mice and showed that these selected miRNAs were preferentially up-regulated in the NAc. We then focused on miR-1 considering the important role of some of its predicted mRNA targets, such as fosb and npas4, in the effects of cocaine. We validated these targets in vitro and in vivo and further showed that overexpression of miR-1 in D1-SPNs of the DS reduced cocaine-induced CPP reinstatement, whereas it increased cue-induced reinstatement of cocaine-SA, without affecting other cocaine-mediated adaptive behavior. In addition, miR-1 overexpression in D2-SPNs of the DS reduced the motivation to self-administer cocaine but did not modify other measured behaviors. Together, our results highlight a precise cell-type- and region-specific control of relapse to cocaine-seeking behaviors by miR-1, and illustrate the importance of cell-specific investigations.

neuroscience↗