PXD066565-1

PXD066565 is an original dataset announced via ProteomeXchange.

Title	Multiomics profiling of zebrafish embryonic cell line PAC2 across growth phases to assess its relevance for toxicological studies
Description	Permanent fish cell lines offer promising alternatives to traditional animal models for environmental risk assessment of chemicals. However, to facilitate broader uptake into toxicity testing practice, a better understanding of functional capacities and expression of toxicologically relevant molecular targets is needed. Here, we present an extensive molecular profiling of the zebrafish embryonic cell line PAC2, combining global proteomics across cell population growth phases (over 7300 protein groups) with matched transcriptomics at exponential and stationary phases (over 14500 transcripts). Proteome coverage was sufficiently deep to reveal functional insights consistent with those derived from transcriptomics data, despite differences in the total number of measured genes. Major gene expression shifts detected upon transition from exponential to stationary cell population growth phase indicated reduction in DNA replication, translation, metabolism, and cell cycle regulation, along with increased stress and immune system responses, and extracellular matrix remodeling. Functional annotation revealed expression of core cellular processes along with a number of toxicologically relevant pathways, including xenobiotic metabolism, stress signaling, and nuclear receptors responsive to important chemical classes, such as steroids (e.g., estrogens, glucocorticoids) and chemicals known to disrupt lipid metabolism, such as through interaction with peroxisome proliferation activating receptors. These findings reinforce the potential of PAC2 cells to offer a versatile in vitro model for studying fish cell biology and omics-enhanced exploration of chemical toxicity mechanisms, aided by the well-developed molecular annotation in zebrafish. Moreover, the analysis approaches developed in this work offer a blueprint for molecular baseline characterization of other fish cell lines. This work thus strengthens the mechanistic foundation supporting the use of fish cell lines as alternative models in aquatic toxicity testing and risk assessment.
HostingRepository	PRIDE
AnnounceDate	2025-12-06
AnnouncementXML	Submission_2025-12-05_18:51:24.108.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ksenia Groh
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: NEWT:7955;
ModificationList	methionine oxidation with neutral loss of 80 Da; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-24 13:18:48	ID requested
⏵ 1	2025-12-05 18:51:24	announced

Dataset with its publication pending

submitter keyword: None

Ksenia Groh
contact affiliation	Head of Bioanalytics Group, Department of Environmental Toxicology (Utox), Eawag – Swiss Federal Institute of Aquatic Science and Technology, 8600 Duebendorf, Switzerland
contact email	Ksenia.Groh@eawag.ch
lab head
Ksenia Groh
contact affiliation	Eawag - Swiss Federal Institute of Aquatic Science and Technology
contact email	ksenia.groh@eawag.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD066565
     1. Label: PRIDE project
     2. Name: Multiomics profiling of zebrafish embryonic cell line PAC2 across growth phases to assess its relevance for toxicological studies