Spatial transcriptomics of the nematode Caenorhabditis elegans using RNA tomography

Schild,; Mars, Jonas; Ebbing, Annabel; Vivié, Judith; Betist, Marco C.; Korswagen, Hendrik C.

doi:10.1016/j.xpro.2021.100411

Cited by 4 publications

(2 citation statements)

References 8 publications

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“…The uncovering of cell protrusions mediating the communication within the stem cell niche adds to the structural similarities between C. elegans and Drosophila gonadal niches [64,65]; similar structures were recorded in the gonads of a milkweed bug [66]. As in Drosophila, new technologies that allow the construction of expression maps with singlecell resolution (e.g., transcriptome profiling [67] or RNA tomography [68]) have been extremely useful in dissecting the multiple components that regulate the cellular interactions within the GSC niche.…”

Section: Germ Stem Cell Nichesmentioning

confidence: 95%

Articulating the “stem cell niche” paradigm through the lens of non-model aquatic invertebrates

et al. 2022

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Stem cells (SCs) in vertebrates typically reside in “stem cell niches” (SCNs), morphologically restricted tissue microenvironments that are important for SC survival and proliferation. SCNs are broadly defined by properties including physical location, but in contrast to vertebrates and other “model” organisms, aquatic invertebrate SCs do not have clearly documented niche outlines or properties. Life strategies such as regeneration or asexual reproduction may have conditioned the niche architectural variability in aquatic or marine animal groups. By both establishing the invertebrates SCNs as independent types, yet allowing inclusiveness among them, the comparative analysis will allow the future functional characterization of SCNs.

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Section: Germ Stem Cell Nichesmentioning

confidence: 95%

Articulating the “stem cell niche” paradigm through the lens of non-model aquatic invertebrates

et al. 2022

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“…S1a). Briefly, this technique combines tissue cryo-sectioning with RNA sequencing on individual sections to generate an expression atlas with uni-dimensional spatial information (22)(23)(24). We processed six polyps at a resolution of 20 µm slices, yielding a total of 331 slices (Fig.…”

Section: Spatial Transcriptomics Of Intact Polypsmentioning

confidence: 99%

Systemic coordination of whole-body tissue remodeling in sea anemone local regeneration

Cheung,

Bredikhin,

Gerber

et al. 2024

Preprint

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The complexity of regeneration extends beyond local wound responses, eliciting systemic processes that engage the entire organism. However, their functional relevance, and the spatial and temporal orchestration of the underlying molecular processes distant from the injury site remain unknown. Here, we demonstrate that local regeneration in the cnidarian Nematostella vectensis involves a systemic homeostatic response, leading to coordinated whole-body remodeling. Leveraging spatial transcriptomics, endogenous protein tagging, and live imaging, we comprehensively dissect this systemic response at the organismal scale. We identify proteolysis as a critical process driven by both local and systemic upregulation of metalloproteases. We show that metalloproteinase expression levels and activity scale with the extent of tissue loss, leading to proportional long-range movement of tissue and its associated extracellular matrix. Our findings illuminate the adaptive nature of the systematic response in regeneration. We propose that this integrated regenerative mechanism, shifting the system from a steady to a dynamic homeostatic state, allows the organism to cope with a wide range of injuries.

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Combined matrix‐assisted laser desorption/ionisation‐mass spectrometry imaging with liquid chromatography‐tandem mass spectrometry for observing spatial distribution of lipids in whole Caenorhabditis elegans

Vandenbosch,

van Hove,

Mohren

et al. 2024

Rapid Comm Mass Spectrometry

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RationaleMatrix‐assisted laser desorption/ionisation‐mass spectrometry imaging (MALDI‐MSI) is a powerful label‐free technique for biomolecule detection (e.g., lipids), within tissue sections across various biological species. However, despite its utility in many applications, the nematode Caenorhabditis elegans is not routinely used in combination with MALDI‐MSI. The lack of studies exploring spatial distribution of biomolecules in nematodes is likely due to challenges with sample preparation.MethodsThis study developed a sample preparation method for whole intact nematodes, evaluated using cryosectioning of nematodes embedded in a 10% gelatine solution to obtain longitudinal cross sections. The slices were then subjected to MALDI‐MSI, using a RapifleX Tissuetyper in positive and negative polarities. Samples were also prepared for liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) analysis using an Exploris 480 coupled to a HPLC Vanquish system to confirm the MALDI‐MSI results.ResultsAn optimised embedding method was developed for longitudinal cross‐sectioning of individual worms. To obtain longitudinal cross sections, nematodes were frozen at −80°C so that all worms were rod shaped. Then, the samples were defrosted and transferred to a 10% gelatine matrix in a cryomold; the worms aligned, and the whole cryomold submerged in liquid nitrogen. Using MALDI‐MSI, we were able to observe the distribution of lipids within C. elegans, with clear differences in their spatial distribution at a resolution of 5 μm. To confirm the lipids from MALDI‐MSI, age‐matched nematodes were subjected to LC‐MS/MS. Here, 520 lipids were identified using LC‐MS/MS, indicating overlap with MALDI‐MSI data.ConclusionsThis optimised sample preparation technique enabled (un)targeted analysis of spatially distributed lipids within individual nematodes. The possibility to detect other biomolecules using this method thus laid the basis for prospective preclinical and toxicological studies on C. elegans.

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Spatial transcriptomics of the nematode Caenorhabditis elegans using RNA tomography

Cited by 4 publications

References 8 publications

Articulating the “stem cell niche” paradigm through the lens of non-model aquatic invertebrates

Articulating the “stem cell niche” paradigm through the lens of non-model aquatic invertebrates

Systemic coordination of whole-body tissue remodeling in sea anemone local regeneration

Combined matrix‐assisted laser desorption/ionisation‐mass spectrometry imaging with liquid chromatography‐tandem mass spectrometry for observing spatial distribution of lipids in whole Caenorhabditis elegans

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