2025, Sybilska, Ewa, Haddadi, Bahareh Sadat, Mur, Luis A. J., Beckmann, Manfred, Hryhorowicz, Szymon, Suszyńska-Zajczyk, Joanna, Knaur, Monika, Pławski, Andrzej, Daszkowska-Golec, Agata

Abstract Background Abscisic acid (ABA) regulates key plant processes, including seed germination, dormancy, and abiotic stress responses. While its physiological role in germination is well-documented, the molecular mechanisms are still poorly understood. To address this, we analyzed transcriptomic and metabolomic changes in ABA-treated germinating barley (Hordeum vulgare) embryos. To map ABA-responsive gene expression across embryonic tissues, we employed the Visium Spatial Transcriptomics (10× Genomics). This approach, which remains technically challenging to be applied in plant tissues, enabled the precise localization of gene expression across six embryo regions, offering insights into tissue-specific expression patterns that cannot be resolved by traditional RNA-seq. Results Transcriptomic analysis indicated that ABA acts primarily as a germination repressor. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses linked ABA-inhibited genes to energy metabolism, lignin biosynthesis, cell wall organization, and photosynthesis, while induced genes were associated with environmental adaptation and phytohormone signaling. Differentially expressed genes (DEGs) correlated with metabolites involved in phytohormone pathways, including gibberellins, jasmonates, brassinosteroids, salicylic acid, auxins, and ABA metabolism. Comparisons with developing seed transcriptomes suggested an ABA-associated gene expression signature in embryos. Spatial transcriptomics technique made possible the precise identification of ABA-induced transcriptional changes within distinct embryonic tissues. Conclusions Integrating transcriptomics, metabolomics and spatial transcriptomics defined the molecular signature of ABA-induced modulation of phytohormonal crosstalk, energy metabolism, and tissue-specific gene activity in germinating seeds. The successful use of spatial transcriptomics adds a novel layer of resolution for understanding tissue-specific ABA responses during barley seed germination. These findings offer new insights into the ABA role in seed germination and potential strategies for enhancing crop resilience.

2026, Blatkiewicz, Małgorzata, Szyszka, Marta, Hryhorowicz, Szymon, Suszyńska-Zajczyk, Joanna, Porzionato, Andrea, Plewiński, Adam, Malendowicz, Ludwik K., Rucinski, Marcin

Abstract The adrenal glands are essential endocrine organs whose cortex and medulla maintain systemic homeostasis and mediate stress responses via steroid hormone and catecholamine secretion. Despite anatomical and functional similarities between human and mouse adrenal glands, notable species-specific differences exist. Here, we leveraged spatial transcriptomics (10× Genomics Visium) to comprehensively map gene expression in adult human and mouse adrenal glands, aiming to identify canonical marker genes conserved across species. The analysis was based on a 31-year-old female human sample (GEO dataset) and four 10-week-old male CD-1 mice. Human adrenal sections were processed using optimal cutting temperature (OCT) embedding, whereas mouse adrenal sections were processed as formalin-fixed paraffin-embedded (FFPE) samples, highlighting differences in sample preparation. Using unsupervised clustering of spatial gene expression data, we delineated distinct adrenal cortex and medulla zones in both species, confirming known zonation patterns. Our cross-species analysis revealed highly conserved spatial expression of key known marker genes characteristic of the adrenal cortex (e.g., CYP11B2 for ZG, CYP11B1 for ZF) and medullary chromaffin cells (e.g., TH ), as well as a core set of additional marker genes previously less characterized in adrenal biology. By integrating transcriptional profiles, we generated a catalogue of conserved canonical marker genes that define adrenal zonation and function in both humans and mice. These results highlight the fundamental molecular conservation of adrenal gland organization and support the translational value of mouse models in adrenal research. Our findings provide new insights into the evolutionary preservation of adrenal function and a valuable resource for studies on adrenal physiology and disease.