Chenopodium ficifolium is a close diploid relative of the tetraploid crop Chenopodium quinoa. Owing to its reproducible germination and seedling development, it becomes a promising model for studying floral induction, providing a basis for the comparison with C. quinoa. Two C. ficifolium genotypes differ in photoperiodic requirement: C. ficifolium 283 accelerates flowering under long days, whereas C. ficifolium 459 flowers earlier under short days. This study conducted a comprehensive transcriptomic and hormonomic analysis of floral induction in the long-day C. ficifolium 283 and compared the findings to previous experiments with the short-day C. ficifolium. Phytohormone concentrations and gene expression profiles during floral induction were largely similar between the two genotypes. However, a subset of genes exhibited contrasting expression patterns, aligning with the genotypes' differing photoperiodic requirements. These genes, predominantly homologs of flowering-related genes in Arabidopsis thaliana, were activated under long days in C. ficifolium 283 and under short days in C. ficifolium 459. Notably, the contrasting expression of the FLOWERING LOCUS T-LIKE 2-1 gene, which was previously shown to induce precocious flowering in A. thaliana, confirmed its role as a floral activator, despite its low expression levels.

• Klíčová slova
• Flowering, genes with contrasting expression trends, long-day Chenopodium ficifolium, phytohormones, transcriptome,
• MeSH
• Chenopodium * genetika   MeSH
• fotoperioda MeSH
• genotyp MeSH
• květy * genetika   růst a vývoj   MeSH
• regulace genové exprese u rostlin * MeSH
• regulátory růstu rostlin metabolismus   MeSH
• rostlinné geny MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• regulátory růstu rostlin MeSH
• rostlinné proteiny MeSH

Epithelial-mesenchymal transition (EMT) generates heterogeneity in circulating tumor cells (CTCs), affecting their biological properties and hampering their detection. This limits our understanding of the mechanisms underlying hematogenous dissemination, especially in early breast cancer (BC), where CTCs are rare. Here, we aimed to detect CTCs with different EMT statuses from BC patients. CTCs in blood samples from 107 BC patients were evaluated using immunomagnetic depletion and multi-marker immunofluorescence (EpCAM, E-cadherin, MCAM, cell surface vimentin, CD31, CD45), followed by single-cell transcriptomics. CTCs were detected in 51.9% of therapy-naïve early BC cases, with 3.8% showing only epithelial CTCs (eCTCs), 5.8% epithelial-mesenchymal (emCTCs), 26.0% mesenchymal (mCTCs), and 16.3% mixed phenotypes. CTC heterogeneity was more frequent in triple-negative (86%) than in luminal BC (17%, P = 0.008). Lymph node involvement strongly predicted dissemination of all CTC phenotypes, while tumor size correlated with mCTC abundance. Single-cell RNA sequencing revealed downregulation of ribosomal genes and translation inhibition in CTCs with mesenchymal features, linked to mTORC1 signaling. Findings were also validated in an independent dataset, highlighting vulnerabilities in CTCs during dissemination.

• Klíčová slova
• RNA‐Seq, breast cancer, circulating tumor cells, epithelial–mesenchymal transition, metastasis, single cell transcriptomics,
• Publikační typ
• časopisecké články MeSH

Donor kidney tissue based transcriptomics may represent new dimension for prediction of kidney transplant outcomes. In this prospective, single-center study, 276 kidneys from 174 deceased brain-death donors were assessed by microarrays to identify phenotypes of procurement biopsies. Molecular classifiers (extreme gradient boosting, logistic and Poisson regression) with 10-fold cross-validation were employed to categorize donors based on clinical variables (age, BMI, hypertension, ECD kidney) and histological scores (vascular fibrous intimal thickening, interstitial fibrosis, tubular atrophy, arteriolar hyaline thickening). Archetypal analysis and linear mixed model were applied to determine molecular phenotypes and their association with posttransplant 1-year eGFR in 234 donor kidneys. Three molecular archetypes were identified. The "ideal" archetype (median donor age 42 years, low KDRI, minimal chronic histological changes) was associated with the highest 1-year eGFR, while the "marginal" archetype (68 years, extensive chronic changes, high KDRI) with the lowest one. The "intermediate" archetype yielded better 1-year eGFR despite donor profiles similar to the marginal group. While KDRI predicted 1-year eGFR, adding molecular archetypes improved model performance (AIC 80.0 vs. 83.7;p<0.05). External validation in an independent dataset (n=174, GSE147451) confirmed predictive value of the model. Molecular profiling of procurement biopsies may help to identify donor kidneys with higher posttransplant eGFR.

• Klíčová slova
• donor kidney quality, gene expression, kidney transplantation, microarray,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Despite advances in therapeutic development, an anthracycline-cytarabine induction regimen remains the gold standard for acute myeloid leukaemia (AML) treatment. However, reliable predictive markers for assessing treatment sensitivity, adjusting therapy intensity, and guiding the use of experimental therapies are still lacking. This study aimed to develop a predictive model of AML chemoresistance. METHODS: Transcriptome sequencing and DNA methylation analysis of leukaemic blasts were performed to identify differentially expressed and methylated genes between responding (RES) and non-responding (non-RES) patients. A logistic regression nomogram model was developed using obtained data to predict complete remission (CR) and was further validated. RESULTS: Compared to RES patients, non-RES patients exhibited a significant overexpression of interferon-related DNA damage resistance signature (IRDS) genes at diagnosis. Based on the expression of three IRDS genes (IFIT5, IFI44L, IFI44), we developed the IRDS score, which demonstrated high predictive accuracy, with calculated probabilities of CR of 0.71 for RES patients and 0.31 for non-RES patients. Downregulation of histone and chromatin remodelling genes following therapy administration was a hallmark of a successful treatment response. Integrative analysis revealed 1108 genes with concordant changes in both gene expression and DNA methylation between RES and non-RES patients, including IRDS genes IFIT5 and IFI44L. CONCLUSIONS: The IRDS score-based model predicts AML chemoresistance with high accuracy and feasibility. It is quick, cost effective, and requires readily available biological material. This tool shows promise for guiding treatment decisions and identifying candidates for intensified or experimental therapies.

• Klíčová slova
• Acute myeloid leukaemia, Chemoresistance, Gene expression signature, Interferon-stimulated genes, Predictive biomarker,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Biopsy-based transcriptomics (BBT) was implemented in Central Europe in 2022 to improve kidney transplant diagnostics. Differences in diagnostic practices across transplant centers remain underexplored. METHODS: This retrospective multicenter study analyzed 474 kidney graft biopsies from 10 transplant centers between August 2022 and May 2024, where, besides routine histology, BBT using the Molecular Microscope Diagnostic System (MMDx) was performed. Differences in BBT indications and discrepancies between histology assessment by Banff 2022 and MMDx sign-outs among transplant centers were evaluated. RESULTS: Most centers used BBT in only 12%-31% of all performed biopsies, relying on histology alone for most diagnostic decisions. BBT indications varied across centers: 3 focused on histological no-rejection with clinical discrepancy (44%, 45%, and 70%), 2 on chronic or chronic-active antibody-mediated rejection (AMR; clinical discrepancy 44% and 48%), and 2 on borderline changes (clinical discrepancy 30% and 33%). BBT showed moderate agreement with histology (κ = 0.49), with similar discrepancy rates between high- and low-volume centers. Molecular AMR was found in 44% of probable AMR, 63% of active AMR, 63% of microvascular inflammation, C4d- and donor-specific antibody (DSA)-, 77% of chronic-active AMR, and 21% chronic AMR. Molecular T cell-mediated rejection (TCMR) was confirmed in 26% of histologically active TCMR, in 9% of chronic TCMR, and in 16% of borderline changes. In histologic no-rejection cases, molecular AMR was present in 10% of DSA- and 34% of DSA+ biopsies. CONCLUSIONS: A moderate discrepancy between histology and MMDx sign-outs was found regardless of the center volume. BBT indications notably varied among centers. Standardized indications should be defined to improve the integration of molecular diagnostics into routine care.

• Publikační typ
• časopisecké články MeSH

BACKGROUND: Synonymous mutations (SMs) change the mRNA nucleotide sequences without altering the corresponding amino acid sequence and are usually overlooked due to their perceived lack of influence on protein function. However, emerging reports suggest that SMs play a significant role in disease development and progression. METHODS: Whole exome sequencing, RNA-sequencing, and droplet digital PCR were performed to identify the SMs from the malignant glioma patients. MutaRNA was used to predict the effect of SMs on RNA structure in silico. SHAPE-MaP was performed to probe and assess the effect of SMs on RNA structure in-cellulo. RESULTS: Here, we report that a Cancer-Associated SM in TP53 codon valine 203 (CASM203) results in the induction of the alternative translation initiated p53 protein isoform, p47. In-cell high-throughput RNA structural mapping showed that CASM203 mimics the Protein Kinase RNA-Like ER Kinase (PERK)-mediated p53 mRNA secondary structure that induces p47 expression of during the unfolded protein response (UPR). CONCLUSIONS: Overall, the single gain-of-function SM mimics the UPR-mediated p53 stress response, by generating RNA secondary structures akin to the PERK-mediated p53 mRNA structural switch. This illustrates the link between RNA structures and cellular biology and underscores the importance of SMs in cancer biology and their potential to further refine genetic diagnostics.

• MeSH
• gliom * genetika   patologie   metabolismus   MeSH
• lidé MeSH
• messenger RNA genetika   chemie   MeSH
• nádorové buněčné linie MeSH
• nádorový supresorový protein p53 * genetika   biosyntéza   MeSH
• nádory mozku * genetika   MeSH
• protein - isoformy genetika   biosyntéza   MeSH
• sekvenování exomu MeSH
• signální dráha UPR genetika   MeSH
• tichá mutace * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• messenger RNA MeSH
• nádorový supresorový protein p53 * MeSH
• protein - isoformy MeSH
• TP53 protein, human MeSH Prohlížeč

While cytokinin (CK) can delay natural leaf senescence, its effects on abiotic stress accelerated leaf senescence are less studied. Here we show N-conjugated trans-zeatin CK forms (tZ7G and tZ9G, or tZNGs) have the ability to delay salt stress senescence. Using a modified dark-induced senescence bioassay with Arabidopsis leaves, exogenous salt treatment accelerated leaf senescence as measured by lower photosystem II efficiency (Fv/Fm) and chlorophyll content. tZNGs were able to delay these parameters at concentrations as low as 10 nM similar to tZ, indicating that tZ7G and tZ9G can function in delaying salt accelerated senescence (SAS). To better understand physiological effects regulating tZNG delay of senescence, transcriptomics, proteomics, as well as CK measurements were examined. Salt treatment has strong transcriptome and proteome effects in accelerating senescence and reducing overall CK levels. Exogenous CK treatments could be quickly detected from changes seen in endogenous CK measurements, where each CK has a distinct profile contributing to transcript/protein alterations. Interestingly, transcriptomics show tZNGs are primarily responsive at later stages of salt senescence, in contrast to an immediate and continual response of tZ treatment. Known CK-regulated genes are induced by tZNGs and tZ, as corroborated by ARR:GUS reporter lines. Differences between tZNGs and tZ DEGs were revealed by WGCNA that included salt and CK specifically gene modules. In contrast, proteomic analysis revealed unique, but similar numbers of tZNG compared to tZ DAPs across senescence. GO term analysis of tZNG DEGs and DAPs showed enrichment of senescence, chloroplast, and CK signaling. Together this indicates tZNGs function as active CK forms in delaying salt accelerated leaf senescence.

• Klíčová slova
• Cytokinin level, Cytokinin-N-Glucosides, Leaf senescence, Proteome, Salt-stress, Transcriptome, WGCNA, trans-Zeatin,
• MeSH
• Arabidopsis * účinky léků   metabolismus   fyziologie   genetika   MeSH
• chlorid sodný * farmakologie   MeSH
• chlorofyl metabolismus   MeSH
• cytokininy metabolismus   MeSH
• glukosidy * farmakologie   metabolismus   MeSH
• listy rostlin * účinky léků   metabolismus   fyziologie   MeSH
• regulace genové exprese u rostlin účinky léků   MeSH
• senescence rostlin * účinky léků   MeSH
• zeatin * farmakologie   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• chlorid sodný * MeSH
• chlorofyl MeSH
• cytokininy MeSH
• glukosidy * MeSH
• zeatin * MeSH

Linking meta-omics and biogeochemistry approaches in soils has remained challenging. This study evaluates the use of an internal RNA extraction standard and its potential for making quantitative estimates of a given microbial community size (biomass) in soil metatranscriptomics. We evaluate commonly used laboratory protocols for RNA processing, metatranscriptomic sequencing and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Metatranscriptomic profiles from soil samples were generated using two library preparation protocols and prepared in triplicates. RNA extracted from pure cultures of Saccharolobus solfataricus was added to the samples as an internal nucleic acid extraction standard (NAEstd). RNA reads originating from NAEstd were identified with a 99.9% accuracy. A remarkable replication consistency between triplicates was seen (average Bray-Curtis dissimilarity 0.03 ± 0.02), in addition to a clear library preparation bias. Nevertheless, the between-sample pattern was not affected by library type. Estimates of 16S rRNA transcript abundance derived from qRT-PCR experiments, NAEstd and a previously published quantification method of metatranscriptomics (hereafter qMeTra) were compared with microbial biomass carbon (MBC) and nitrogen (MBN) extracts. The derived biomass estimates differed by orders of magnitude. While most estimates were significantly correlated with each other, no correlation was observed between NAEstd and MBC extracts. We discuss how simultaneous changes in community size and the soils nucleic acid retention strength might hamper accurate biomass estimation. Adding NAEstd has the potential to shed important light on nucleic acid retention in the substance matrix (e.g., soil) during extraction.

• Klíčová slova
• RNA, biomass estimates, extraction standard, metatranscriptomics, quantitative transcriptomics,
• MeSH
• Bacteria * genetika   klasifikace   MeSH
• metagenomika * metody   MeSH
• mikrobiota * MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• RNA ribozomální 16S genetika   MeSH
• stanovení celkové genové exprese * metody   MeSH
• transkriptom MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• půda MeSH
• RNA ribozomální 16S MeSH

Critical care syndromes such as sepsis, acute respiratory distress syndrome (ARDS) and trauma continue to have unacceptably high morbidity and mortality, with progress limited by the inherent heterogeneity within syndromic illnesses. Although numerous immune endotypes have been proposed for sepsis and critical care, the similarities and differences between these endotypes remain unclear, hindering clinical translation. The SUBSPACE consortium is an international consortium that aims to advance precision medicine in critical care through the sharing of transcriptomic data. Here, evaluating the overlap of existing immune endotypes in sepsis across >7,074 samples from 37 independent cohorts, we developed cell-type-specific gene expression signatures to quantify dysregulation within immune compartments. Myeloid and lymphoid dysregulation were associated with disease severity and mortality across all cohorts. Importantly, this dysregulation was also observed in patients with ARDS, trauma and burns, suggesting a conserved mechanism across various critical illness syndromes. Moreover, analysis of randomized controlled trial data revealed that myeloid and lymphoid dysregulation are associated with differential mortality in patients treated with anakinra in the SAVE-MORE trial (n = 452) and corticosteroids in the VICTAS (n = 89) and VANISH (n = 117) trials, underscoring their prognostic and therapeutic implications. In conclusion, our proposed immunology-based framework for quantifying cellular compartment dysregulation offers a potentially valuable tool for understanding immune dysregulation in critical illness with prognostic and therapeutic significance.

• Publikační typ
• časopisecké články MeSH

Fibroblasts are stromal cells found in connective tissue that are critical for organ development, tissue homeostasis and pathology. Single-cell transcriptomic analyses have revealed a high level of inter- and intra-organ heterogeneity of fibroblasts. However, the functional implications and lineage relations of different fibroblast subtypes remained unexplored, especially in the mammary gland. Here, we provide a comprehensive characterization of pubertal mouse mammary fibroblasts, through single-cell RNA sequencing, spatial mapping, functional assays, and in vivo lineage tracing. We unravel a transient niche-forming population of specialized contractile fibroblasts that exclusively localize around the tips of the growing mammary epithelium and are recruited from preadipocytes in the surrounding fat pad stroma. Using organoid-fibroblast co-cultures we reveal that different fibroblast populations can acquire contractile features when in direct contact with the epithelium, promoting organoid branching. The detailed in vivo characterization of these specialized cells and their lineage history provides insights into fibroblast heterogeneity and implicates their importance for creating a signalling niche during mouse mammary gland development.

• MeSH
• analýza jednotlivých buněk MeSH
• buněčný rodokmen MeSH
• epitel metabolismus   růst a vývoj   MeSH
• epitelové buňky cytologie   MeSH
• fibroblasty * cytologie   metabolismus   fyziologie   MeSH
• kokultivační techniky MeSH
• mléčné žlázy zvířat * cytologie   růst a vývoj   metabolismus   MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• organoidy cytologie   metabolismus   MeSH
• tukové buňky cytologie   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH