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A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration

ABSTRACT: The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Hydra Vulgaris

TISSUE(S): Whole Body

SUBMITTER: Hendrik Petersen

LAB HEAD: Thomas Wilhelm Holstein

PROVIDER: PXD008039 | Pride | 2017-10-27

REPOSITORIES: Pride

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			Action	DRS
	130319_HP_SILAC_3_1_01.RAW	Raw
	130319_HP_SILAC_3_1_03.RAW	Raw
	130319_HP_SILAC_3_1_04.RAW	Raw
	130319_HP_SILAC_3_1_05.RAW	Raw
	130319_HP_SILAC_3_1_06.RAW	Raw

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Publications

A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration.

Petersen Hendrik O HO Höger Stefanie K SK Looso Mario M Lengfeld Tobias T Kuhn Anne A Warnken Uwe U Nishimiya-Fujisawa Chiemi C Schnölzer Martina M Krüger Marcus M Özbek Suat S Simakov Oleg O Holstein Thomas W TW

Molecular biology and evolution 20150403 8

The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps. As major contributors to head regeneration, we identified diverse signaling pathways adopted for the regeneration response as well as enriched novel genes. Our global analysis reveals two distinct mol ...[more]

PMID: 25841488

Similar Datasets

A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration

Project description:The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps.

2017-10-26 | PXD008048 | Pride

The Hydra magnipapillata head regeneration transcriptome

Project description:Hydra has long been studied for its remarkable ability to regenerate its head. Previous studies focusing on molecular mechanisms of axial patterning and head regeneration using a candidate gene approach have revealed a central role for the canonical Wnt pathway. We performed a global gene expression analysis during Hydra magnipapillata head regeneration using RNA-seq to identify additional genes that are transcriptionally regulated during the regeneration of the head organizer in hydra. Differential expression analysis revealed a set of 4,978 genes with significant changes during a 48-hour head regeneration time-course that includes many key genes in the Wnt, TGF-M-NM-2/BMP and MAP kinase pathways. We observed the differential regulation of several genes that are part of the epithelial-to-mesenchymal transition in bilaterians such as Snail. We assembled 806 novel putative lincRNAs with 176 of these are differentially expressed during the time course. We observed the coordinated transcriptional regulation of several factors that regulate the effective pool of free M-NM-2-catenin that together synergize to increase the amount of M-NM-2-catenin available for transcriptional regulation of downstream genes. The differential expression of Snail and some of its interacting regulators and downstream targets suggests that a partial-EMT-like response is involved in hydra head regeneration. This time-course is a valuable resource for the study of the transcriptional dynamics of head regeneration in hydra. mRNA profiling of regenerating head from 6 time points post bisection of Hydra head (H. magnipapillata), generated by deep sequencing, in duplicates, using Illumina HiSeq2500.

2014-12-13 | E-GEOD-64127 | biostudies-arrayexpress

Proteomic of Hydra vulgaris

Project description:This study aimed to identify the total proteome of Hydra vulgaris, a freshwater polyp, belongs to the cnidarians family with feature of not having a visual eye, while being sensitive to light. Proteins were identified using a combination of gel electrophoresis and data-independent nanoflow liquid chromatography mass spectrometry resulting in the identification of more than 5,200 proteins from all cellular components

2022-02-28 | PXD005828 | Pride

Analysis of gene expression in MyD88-Knockdown-Hydra vulgaris (AEP)

Project description:Analysis of MyD88 as a putative mediator in host-microbe-interactions MyD88-Hairpin was micro-injected in Hydra AEP embryos. The resulting Hatchling D3 showed a patchy distribution of the transgene observed by GFP. By asexual reproduction via budding and constant selection for the marker gene GFP the transgene could be driven into different cell ines. Therefore two different cultures were established. Polyps that showed no GFP-Signal anymore (control) and Polyps with both, endodermal and ectodermal transgenic cell-lines (knockdown).

2012-10-08 | E-GEOD-32383 | biostudies-arrayexpress

Invasive tumors in Hydra

Project description:The molecular nature of malignant tumors is well studied in vertebrates, while their evolutionary origin remains unknown. In particular, there is no evidence for naturally occurring malignant tumors in pre-bilaterian animals, such as sponges and cnidarians. This is somewhat surprising given that recent computational studies have predicted that all metazoans are prone to develop tumors. Here we provide first evidence for naturally occurring tumors in Hydra oligactis. Histological, cellular and molecular data reveal that these tumors are transplantable and caused by differentiation arrest of female gametes. Growth of tumor cells is independent from the cellular environment. Tumor bearing polyps have significantly reduced fitness. In addition, Hydra tumors show a greatly altered transcriptome that mimics expression shifts in vertebrate cancers. Therefore, this study shows, that invasive tumors have deep roots in animal phylogeny, and that early branching animals may be informative in revealing the fundamental mechanisms of tumorigenesis. We compared four samples of Hydra oligactis tumor-bearing animals to three samples of female polyps undergoing oogenesis and six samples of female asexual control polyps

2014-06-24 | E-GEOD-56287 | biostudies-arrayexpress

RNA-seq of Hydra body segments and regenerated Hydra animals

Project description:Positional RNA-sequencing of isolated Hydra body pieces and RNA-sequencing of fully regenerated Hydra animal was combined with RNA-sequencing of actively regenerating spheroids (see submission E-MTAB-9672) in order to elucidate the role of tissue stretching on regeneration and body pattern formation.

2022-10-13 | E-MTAB-9676 | biostudies-arrayexpress

Hydra vulgaris extracellular vesicles

Project description:Recent body of evidence demonstrates that extracellular vesicles (EVs) represent the first language of cell-cell communication emerged during evolution. In aquatic environments, transferring signals between cells by EVs offer protection against degradation, allowing delivering of chemical information in high local concentrations to the target cells. The packaging of multiple signals, including those of hydrophobic nature, ensures target cells to receive the same EV-conveyed messages, and the coordination of a variety of physiological processes across cells of a single organisms, or at the population level, i.e. mediating the population´s response to changing environmental conditions. Here, we purified EVs from the medium of the freshwater invertebrate Hydra vulgaris, and the molecular profiling by proteomic and transcriptomic analyses revealed multiple markers of the exosome EV subtype. Moreover, positive and negative regulators of the Wnt/β-catenin signaling pathway, the major developmental pathway acting in body axial patterning, were identified. Functional analysis on amputated polyps revealed EV ability to interfere with both head and foot regeneration, suggesting an active role in setting up tissue gradients and oro-aboral polarity through delivery of short and long-distance signals. Our results open the path to unravel EV biogenesis and function in all cnidarian species, tracing back the origin of the cell-cell, cross-species or cross-kingdom communication in aquatic ecosystems

2022-02-17 | PXD027774 | Pride

Stem cell differentiation trajectories in Hydra resolved at single cell resolution

Project description:The adult Hydra polyp continuously renews all of its cells using three separate stem cell populations but the genetic pathways enabling these dynamic tissue properties are not well understood. We used Drop-seq to sequence 24,985 Hydra cells and identified the molecular signatures of a broad spectrum of cell states, from stem cells to terminally differentiated cells. We constructed differentiation trajectories for each cell lineage and identified the transcription factors expressed along these trajectories, thus creating a comprehensive map of all developmental lineages in the adult animal. We unexpectedly found that neuron and gland cell differentiation transits through a common progenitor state, suggesting a shared evolutionary history for these secretory cell types. Finally, we have built the first gene expression map of the Hydra nervous system. By producing a comprehensive molecular description of the adult Hydra polyp, we have generated a resource for addressing fundamental questions regarding the evolution of developmental processes and nervous system function.

2018-11-02 | GSE121617 | GEO

Comparative Wnt dependent Hydra ECM proteome

Project description:Comparative proteome of extracted Hydra vulgaris AEP extracellular matrix form Wnt9/10 knock out and Azakenpaullone treated animals. Used to analyse the changes in molecular composition of the mesoglea (ECM) of normal and Wnt depleted animals

2023-05-10 | PXD039846 | Pride

The Hydra magnipapillata head regeneration transcriptome

Project description:Hydra has long been studied for its remarkable ability to regenerate its head. Previous studies focusing on molecular mechanisms of axial patterning and head regeneration using a candidate gene approach have revealed a central role for the canonical Wnt pathway. We performed a global gene expression analysis during Hydra magnipapillata head regeneration using RNA-seq to identify additional genes that are transcriptionally regulated during the regeneration of the head organizer in hydra. Differential expression analysis revealed a set of 4,978 genes with significant changes during a 48-hour head regeneration time-course that includes many key genes in the Wnt, TGF-β/BMP and MAP kinase pathways. We observed the differential regulation of several genes that are part of the epithelial-to-mesenchymal transition in bilaterians such as Snail. We assembled 806 novel putative lincRNAs with 176 of these are differentially expressed during the time course. We observed the coordinated transcriptional regulation of several factors that regulate the effective pool of free β-catenin that together synergize to increase the amount of β-catenin available for transcriptional regulation of downstream genes. The differential expression of Snail and some of its interacting regulators and downstream targets suggests that a partial-EMT-like response is involved in hydra head regeneration. This time-course is a valuable resource for the study of the transcriptional dynamics of head regeneration in hydra.

2014-12-13 | GSE64127 | GEO

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