JHEP Rep. 2023 Mar 23;5(6):100729. doi: 10.1016/j.jhepr.2023.100729. eCollection 2023 Jun.

ABSTRACT

BACKGROUND & AIMS: Primary sclerosing cholangitis (PSC) is a chronic, progressive cholestatic liver disease that can lead to end-stage liver disease and cholangiocarcinoma. High-dose ursodeoxycholic acid (hd-UDCA, 28-30 mg/kg/day) was evaluated in a previous multicentre, randomised placebo-controlled trial; however, the study was discontinued early because of increased liver-related serious adverse events (SAEs), despite improvement in serum liver biochemical tests. We investigated longitudinal changes in serum miRNA and cytokine profiles over time among patients treated with either hd-UDCA or placebo in this trial as potential biomarkers for PSC and response to hd-UDCA, as well as to understand the toxicity associated with hd-UDCA treatment.

METHODS: Thirty-eight patients with PSC were enrolled in a multicentred, randomised, double-blinded trial of hd-UDCA vs. placebo.

RESULTS: Significant alterations in serum miRNA profiles were found over time in both patients treated with hd-UDCA or placebo. Additionally, there were striking differences between miRNA profiles in patients treated with hd-UDCA compared with placebo. In patients treated with placebo, the changes in concentration of serum miRNAs miR-26a, miR-199b-5p, miR-373, and miR-663 suggest alterations of inflammatory and cell proliferative processes consistent with disease progression. However, patients treated with hd-UDCA exhibited a more pronounced differential expression of serum miRNAs, suggesting that hd-UDCA induces significant cellular miRNA changes and tissue injury. Pathway enrichment analysis for UDCA-associated miRNAs suggested unique dysregulation of cell cycle and inflammatory response pathways.

CONCLUSIONS: Patients with PSC have distinct miRNAs in the serum and bile, although the implications of these unique patterns have not been studied longitudinally or in relation to adverse events related to hd-UDCA. Our study demonstrates marked changes in miRNA serum profiles with hd-UDCA treatment and suggests mechanisms for the increased liver toxicity with therapy.

IMPACT AND IMPLICATIONS: Using serum samples from patients with PSC enrolled in a clinical trial comparing hd-UDCA with placebo, our study found distinct miRNA changes in patients with PSC who are treated with hd-UDCA over a period of time. Our study also noted distinct miRNA patterns in patients who developed SAEs during the study period.

PMID:37179785 | PMC:PMC10172698 | DOI:10.1016/j.jhepr.2023.100729

Cell. 2023 May 8:S0092-8674(23)00408-7. doi: 10.1016/j.cell.2023.04.012. Online ahead of print.

ABSTRACT

The generation of distinct messenger RNA isoforms through alternative RNA processing modulates the expression and function of genes, often in a cell-type-specific manner. Here, we assess the regulatory relationships between transcription initiation, alternative splicing, and 3' end site selection. Applying long-read sequencing to accurately represent even the longest transcripts from end to end, we quantify mRNA isoforms in Drosophila tissues, including the transcriptionally complex nervous system. We find that in Drosophila heads, as well as in human cerebral organoids, 3' end site choice is globally influenced by the site of transcription initiation (TSS). "Dominant promoters," characterized by specific epigenetic signatures including p300/CBP binding, impose a transcriptional constraint to define splice and polyadenylation variants. In vivo deletion or overexpression of dominant promoters as well as p300/CBP loss disrupted the 3' end expression landscape. Our study demonstrates the crucial impact of TSS choice on the regulation of transcript diversity and tissue identity.

PMID:37178687 | DOI:10.1016/j.cell.2023.04.012

Biochem Biophys Res Commun. 2023 May 6;666:92-100. doi: 10.1016/j.bbrc.2023.04.089. Online ahead of print.

ABSTRACT

AMP-activated protein kinase (AMPK) is a heterotrimeric serine/threonine kinase comprising α, β, and γ subunits. AMPK is involved in intracellular energy metabolism and functions as a switch that turns various biological pathways in eukaryotes on and off. Several post-translational modifications regulating AMPK function have been demonstrated, including phosphorylation, acetylation, and ubiquitination; however, arginine methylation has not been reported in AMPKα1. We investigated whether arginine methylation occurs in AMPKα1. Screening experiments revealed arginine methylation of AMPKα1 mediated by protein arginine methyltransferase 6 (PRMT6). In vitro methylation and co-immunoprecipitation assays indicated that PRMT6 can directly interact with and methylate AMPKα1 without involvement of other intracellular components. In vitro methylation assays with truncated and point mutants of AMPKα1 revealed that Arg403 is the residue methylated by PRMT6. Immunocytochemical studies showed that the number of AMPKα1 puncta was enhanced in saponin-permeabilized cells when AMPKα1 was co-expressed with PRMT6, suggesting that PRMT6-mediated methylation of AMPKα1 at Arg403 alters the physiological characteristics of AMPKα1 and may lead to liquid-liquid phase separation.

PMID:37178510 | DOI:10.1016/j.bbrc.2023.04.089

Cell Rep. 2023 May 12;42(5):112499. doi: 10.1016/j.celrep.2023.112499. Online ahead of print.

ABSTRACT

Physical activity is associated with beneficial adaptations in human and rodent metabolism. We studied over 50 complex traits before and after exercise intervention in middle-aged men and a panel of 100 diverse strains of female mice. Candidate gene analyses in three brain regions, muscle, liver, heart, and adipose tissue of mice indicate genetic drivers of clinically relevant traits, including volitional exercise volume, muscle metabolism, adiposity, and hepatic lipids. Although ∼33% of genes differentially expressed in skeletal muscle following the exercise intervention are similar in mice and humans independent of BMI, responsiveness of adipose tissue to exercise-stimulated weight loss appears controlled by species and underlying genotype. We leveraged genetic diversity to generate prediction models of metabolic trait responsiveness to volitional activity offering a framework for advancing personalized exercise prescription. The human and mouse data are publicly available via a user-friendly Web-based application to enhance data mining and hypothesis development.

PMID:37178122 | DOI:10.1016/j.celrep.2023.112499

STAR Protoc. 2023 May 12;4(2):102306. doi: 10.1016/j.xpro.2023.102306. Online ahead of print.

ABSTRACT

Precise signal synchronization is vital for accurate analysis in systems neuroscience. Here, we present a protocol for synchronizing electrophysiology, videography, and audio recordings using a custom-made pulse generator. We describe steps for building the pulse generator, installing software, connecting devices, and running experimental sessions. We then detail signal analysis, temporal alignment, and duration normalization. This protocol offers flexibility and cost-effectiveness, addressing limited shared knowledge and providing a solution for signal synchronization in various experimental setups.

PMID:37178112 | DOI:10.1016/j.xpro.2023.102306

Nucleic Acids Res. 2023 May 13:gkad405. doi: 10.1093/nar/gkad405. Online ahead of print.

ABSTRACT

MBROLE (Metabolites Biological Role) facilitates the biological interpretation of metabolomics experiments. It performs enrichment analysis of a set of chemical compounds through statistical analysis of annotations from several databases. The original MBROLE server was released in 2011 and, since then, different groups worldwide have used it to analyze metabolomics experiments from a variety of organisms. Here we present the latest version of the system, MBROLE3, accessible at http://csbg.cnb.csic.es/mbrole3. This new version contains updated annotations from previously included databases as well as a wide variety of new functional annotations, such as additional pathway databases and Gene Ontology terms. Of special relevance is the inclusion of a new category of annotations, 'indirect annotations', extracted from the scientific literature and from curated chemical-protein associations. The latter allows to analyze enriched annotations of the proteins known to interact with the set of chemical compounds of interest. Results are provided in the form of interactive tables, formatted data to download, and graphical plots.

PMID:37178003 | DOI:10.1093/nar/gkad405

Nucleic Acids Res. 2023 May 13:gkad378. doi: 10.1093/nar/gkad378. Online ahead of print.

ABSTRACT

The spatial folding of eukaryotic genome plays a key role in genome function. We report here that our recently developed method, Hi-TrAC, which specializes in detecting chromatin loops among accessible genomic regions, can detect active sub-TADs with a median size of 100 kb, most of which harbor one or two cell specifically expressed genes and regulatory elements such as super-enhancers organized into nested interaction domains. These active sub-TADs are characterized by highly enriched histone mark H3K4me1 and chromatin-binding proteins, including Cohesin complex. Deletion of selected sub-TAD boundaries have different impacts, such as decreased chromatin interaction and gene expression within the sub-TADs or compromised insulation between the sub-TADs, depending on the specific chromatin environment. We show that knocking down core subunit of the Cohesin complex using shRNAs in human cells or decreasing the H3K4me1 modification by deleting the H3K4 methyltransferase Mll4 gene in mouse Th17 cells disrupted the sub-TADs structure. Our data also suggest that super-enhancers exist as an equilibrium globule structure, while inaccessible chromatin regions exist as a fractal globule structure. In summary, Hi-TrAC serves as a highly sensitive and inexpensive approach to study dynamic changes of active sub-TADs, providing more explicit insights into delicate genome structures and functions.

PMID:37177993 | DOI:10.1093/nar/gkad378

J Exp Bot. 2023 May 13:erad162. doi: 10.1093/jxb/erad162. Online ahead of print.

ABSTRACT

Running crop growth models (CGM) coupled with whole genome prediction (WGP), as a CGM-WGP model, introduces environmental information to WGP and genomic relatedness information to the genotype-specific parameters (GSPs) modelled through CGMs. Previous studies have primarily used CGM-WGP to infer prediction accuracy without exploring its potential to enhance CGM and WGP. Here, we implemented a heading date and a heading and maturity date wheat phenology model within a CGM-WGP framework and compared it to CGM and WGP. The CGM-WGP resulted in more heritable GSPs with more biologically realistic correlation structures between GSPs and phenology traits compared to CGM-modelled GSPs that reflected the correlation of measured phenotypes. Another advantage of CGM-WGP is the ability to infer accurate prediction with much smaller and less diverse reference data compared to that required for CGM. A genome-wide association analysis linked the GSPs from the CGM-WGP model to nine significant phenology loci including Vrn-A1 and the three PPD1 genes, which were not detected for CGM-modelled GSPs. Selection on GSPs could be simpler than on observed phenotypes. For example, thermal time traits are theoretically more independent candidates, compared to the highly correlated heading and maturity dates, which could be used to achieve an environment-specific optimal flowering period. CGM-WGP combines the advantages of CGM and WGP to predict more accurate phenotypes for new genotypes under alternative or future environmental conditions.

PMID:37177829 | DOI:10.1093/jxb/erad162

Plants (Basel). 2023 Apr 26;12(9):1771. doi: 10.3390/plants12091771.

ABSTRACT

The genus Nuphar (Nymphaeaceae) comprises aquatic plant species inhabiting freshwater bodies of the Northern hemisphere temperate regions known as yellow water-lilies. Nuphar lutea and N. pumila are the only representatives in the European continent and present different ecologies: the former is a widespread generalist, while the latter is restricted to northern latitudes or high-altitudes due to its requirements for colder and oligotrophic waters. The Central Europe mountainous areas, the Massif Central (France) and the Cantabrian Mountains (north Iberian Peninsula) harbor relict isolated N. pumila populations endangered by eutrophication and hybridization with N. lutea. We aim to detect hybridization processes in the Massif Central and Cantabrian Mountains populations and compare the genetic diversity of N. pumila in the relict populations of Central Europe by using microsatellite (SSR) markers. No evidence of hybridization was found in the Iberian population, whereas the admixture between N. pumila and N. lutea in the Massif Central populations could be due to hybridization or ancient introgression. Our current knowledge would benefit from genetic diversity studies focusing on both species throughout their distributional range. The Iberian and Massif Central N. pumila populations were genetically distinct, representing two different clusters from other relict populations, with low genetic diversity and a genetic boundary within Central Europe.

PMID:37176829 | DOI:10.3390/plants12091771

Int J Mol Sci. 2023 May 8;24(9):8422. doi: 10.3390/ijms24098422.

ABSTRACT

The complexity of the cellular and non-cellular milieu surrounding human tumors plays a decisive role in the course and outcome of disease. The high variability in the distribution of the immune and non-immune compartments within the tumor microenvironments (TME) among different patients governs the mode of their response or resistance to current immunotherapeutic approaches. Through deciphering this diversity, one can tailor patients' management to meet an individual's needs. Single-cell (sc) omics technologies have given a great boost towards this direction. This review gathers recent data about how multi-omics profiling, including the utilization of single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin with sequencing (scATAC-seq), T-cell receptor sequencing (scTCR-seq), mass, tissue-based, or microfluidics cytometry, and related bioinformatics tools, contributes to the high-throughput assessment of a large number of analytes at single-cell resolution. Unravelling the exact TCR clonotype of the infiltrating T cells or pinpointing the classical or novel immune checkpoints across various cell subsets of the TME provide a boost to our comprehension of adaptive immune responses, their antigen specificity and dynamics, and grant suggestions for possible therapeutic targets. Future steps are expected to merge high-dimensional data with tissue localization data, which can serve the investigation of novel multi-modal biomarkers for the selection and/or monitoring of the optimal treatment from the current anti-cancer immunotherapeutic armamentarium.

PMID:37176128 | DOI:10.3390/ijms24098422

Int J Mol Sci. 2023 May 8;24(9):8416. doi: 10.3390/ijms24098416.

ABSTRACT

The Health Effects of Cardiac Fluoroscopy and Modern Radiotherapy (photon and proton) in Pediatrics (HARMONIC) is a five-year project funded by the European Commission that aimed to improve the understanding of the long-term ionizing radiation (IR) risks for pediatric patients. In this paper, we provide a detailed overview of the rationale, design, and methods for the biological aspect of the project with objectives to provide a mechanistic understanding of the molecular pathways involved in the IR response and to identify potential predictive biomarkers of individual response involved in long-term health risks. Biological samples will be collected at three time points: before the first exposure, at the end of the exposure, and one year after the exposure. The average whole-body dose, the dose to the target organ, and the dose to some important out-of-field organs will be estimated. State-of-the-art analytical methods will be used to assess the levels of a set of known biomarkers and also explore high-resolution approaches of proteomics and miRNA transcriptomes to provide an integrated assessment. By using bioinformatics and systems biology, biological pathways and novel pathways involved in the response to IR exposure will be deciphered.

PMID:37176123 | DOI:10.3390/ijms24098416

Int J Mol Sci. 2023 May 4;24(9):8248. doi: 10.3390/ijms24098248.

ABSTRACT

1,5-Anhydro-D-fructose (1,5-AF) is a bioactive monosaccharide that is produced by the glycogenolysis in mammalians and is metabolized to 1,5-anhydro-D-glucitol (1,5-AG). 1,5-AG is used as a marker of glycemic control in diabetes patients. 1,5-AF has a variety of physiological activities, but its effects on energy metabolism, including feeding behavior, are unclarified. The present study examined whether 1,5-AF possesses the effect of satiety. Peroral administration of 1,5-AF, and not of 1,5-AG, suppressed daily food intake. Intracerebroventricular (ICV) administration of 1,5-AF also suppressed feeding. To investigate the neurons targeted by 1,5-AF, we investigated c-Fos expression in the hypothalamus and brain stem. ICV injection of 1,5-AF significantly increased c-Fos positive oxytocin neurons and mRNA expression of oxytocin in the paraventricular nucleus (PVN). Moreover, 1,5-AF increased cytosolic Ca2+ concentration of oxytocin neurons in the PVN. Furthermore, the satiety effect of 1,5-AF was abolished in oxytocin knockout mice. These findings reveal that 1,5-AF activates PVN oxytocin neurons to suppress feeding, indicating its potential as the energy storage monitoring messenger to the hypothalamus for integrative regulation of energy metabolism.

PMID:37175953 | DOI:10.3390/ijms24098248

Int J Mol Sci. 2023 Apr 28;24(9):8018. doi: 10.3390/ijms24098018.

ABSTRACT

Psoriasis and atopic dermatitis (AD) are multifactorial and heterogeneous inflammatory skin diseases, while years of research have yielded no cure, and the costs associated with caring for people suffering from psoriasis and AD are a huge burden on society. Integrating several omics datasets will enable coordinate-based simultaneous analysis of hundreds of genes, RNAs, chromatins, proteins, and metabolites in particular cells, revealing networks of links between various molecular levels. In this review, we discuss the latest developments in the fields of genomes, transcriptomics, proteomics, and metabolomics and discuss how they were used to identify biomarkers and understand the main pathogenic mechanisms underlying these diseases. Finally, we outline strategies for achieving multi-omics integration and how integrative omics and systems biology can advance our knowledge of, and ability to treat, psoriasis and AD.

PMID:37175722 | DOI:10.3390/ijms24098018

Int J Mol Sci. 2023 Apr 27;24(9):7942. doi: 10.3390/ijms24097942.

ABSTRACT

Potassium channels emerge as one of the crucial groups of proteins that shape the biology of cancer cells. Their involvement in processes like cell growth, migration, or electric signaling, seems obvious. However, the relationship between the function of K+ channels, glucose metabolism, and cancer glycome appears much more intriguing. Among the typical hallmarks of cancer, one can mention the switch to aerobic glycolysis as the most favorable mechanism for glucose metabolism and glycome alterations. This review outlines the interconnections between the expression and activity of potassium channels, carbohydrate metabolism, and altered glycosylation in cancer cells, which have not been broadly discussed in the literature hitherto. Moreover, we propose the potential mediators for the described relations (e.g., enzymes, microRNAs) and the novel promising directions (e.g., glycans-orinented drugs) for further research.

PMID:37175655 | DOI:10.3390/ijms24097942

Int J Mol Sci. 2023 Apr 27;24(9):7948. doi: 10.3390/ijms24097948.

ABSTRACT

The pathogenesis of medication-related osteonecrosis of the jaw (MRONJ) is multifactorial and there is a substantial consensus on the role of antiresorptive drugs (ARDs), including bisphosphonates (BPs) and denosumab (Dmab), as one of the main determinants. The time exposure, cumulative dose and administration intensity of these drugs are critical parameters to be considered in the treatment of patients, as cancer patients show the highest incidence of MRONJ. BPs and Dmab have distinct mechanisms of action on bone, but they also exert different effects on immune subsets which interact with bone cells, thus contributing to the onset of MRONJ. Here, we summarized the main effects of ARDs on the different immune cell subsets, which consequently affect bone cells, particularly osteoclasts and osteoblasts. Data from animal models and MRONJ patients showed a deep interference of ARDs in modulating immune cells, even though a large part of the literature concerns the effects of BPs and there is a lack of data on Dmab, demonstrating the need to further studies.

PMID:37175652 | DOI:10.3390/ijms24097948

Int J Mol Sci. 2023 Apr 25;24(9):7818. doi: 10.3390/ijms24097818.

ABSTRACT

Patients with metabolic syndrome are often prescribed statins to prevent the development of cardiovascular disease. Conversely, data on their effects on non-alcoholic steatohepatitis (NASH) are lacking. We evaluated these effects by feeding APOE*3-Leiden mice a Western-type diet (WTD) with or without atorvastatin to induce NASH and hepatic fibrosis. Besides the well-known plasma cholesterol lowering (-30%) and anti-atherogenic effects (severe lesion size -48%), atorvastatin significantly reduced hepatic steatosis (-22%), the number of aggregated inflammatory cells in the liver (-80%) and hepatic fibrosis (-92%) compared to WTD-fed mice. Furthermore, atorvastatin-treated mice showed less immunohistochemically stained areas of inflammation markers. Atorvastatin prevented accumulation of free cholesterol in the form of cholesterol crystals (-78%). Cholesterol crystals are potent inducers of the NLRP3 inflammasome pathway and atorvastatin prevented its activation, which resulted in reduced expression of the pro-inflammatory cytokines interleukin (IL)-1β (-61%) and IL-18 (-26%). Transcriptome analysis confirmed strong reducing effects of atorvastatin on inflammatory mediators, including NLRP3, NFκB and TLR4. The present study demonstrates that atorvastatin reduces hepatic steatosis, inflammation and fibrosis and prevents cholesterol crystal formation, thereby precluding NLRP3 inflammasome activation. This may render atorvastatin treatment as an attractive approach to reduce NAFLD and prevent progression into NASH in dyslipidemic patients.

PMID:37175538 | DOI:10.3390/ijms24097818

Diagnostics (Basel). 2023 Apr 29;13(9):1596. doi: 10.3390/diagnostics13091596.

ABSTRACT

Colposcopy is an essential examination tool to identify cervical intraepithelial neoplasia (CIN), a precancerous lesion of the uterine cervix, and to sample its tissues for histological examination. In colposcopy, gynecologists visually identify the lesion highlighted by applying an acetic acid solution to the cervix using a magnifying glass. This paper proposes a deep learning method to aid the colposcopic diagnosis of CIN by segmenting lesions. In this method, to segment the lesion effectively, the colposcopic images taken before acetic acid solution application were input to the deep learning network, U-Net, for lesion segmentation with the images taken following acetic acid solution application. We conducted experiments using 30 actual colposcopic images of acetowhite epithelium, one of the representative types of CIN. As a result, it was confirmed that accuracy, precision, and F1 scores, which were 0.894, 0.837, and 0.834, respectively, were significantly better when images taken before and after acetic acid solution application were used than when only images taken after acetic acid solution application were used (0.882, 0.823, and 0.823, respectively). This result indicates that the image taken before acetic acid solution application is helpful for accurately segmenting the CIN in deep learning.

PMID:37174987 | DOI:10.3390/diagnostics13091596

Cells. 2023 May 5;12(9):1325. doi: 10.3390/cells12091325.

ABSTRACT

The metabotropic glutamate receptor 1 (mGlu1) plays a pivotal role in synaptic transmission and neuronal plasticity. Despite the fact that several interacting proteins involved in the mGlu1 subcellular trafficking and intracellular transduction mechanisms have been identified, the protein network associated with this receptor in specific brain areas remains largely unknown. To identify novel mGlu1-associated protein complexes in the mouse cerebellum, we used an unbiased tissue-specific proteomic approach, namely co-immunoprecipitation followed by liquid chromatography/tandem mass spectrometry analysis. Many well-known protein complexes as well as novel interactors were identified, including G-proteins, Homer, δ2 glutamate receptor, 14-3-3 proteins, and Na/K-ATPases. A novel putative interactor, KCTD12, was further investigated. Reverse co-immunoprecipitation with anti-KCTD12 antibodies revealed mGlu1 in wild-type but not in KCTD12-knock-out homogenates. Freeze-fracture replica immunogold labeling co-localization experiments showed that KCTD12 and mGlu1 are present in the same nanodomain in Purkinje cell spines, although at a distance that suggests that this interaction is mediated through interposed proteins. Consistently, mGlu1 could not be co-immunoprecipitated with KCTD12 from a recombinant mammalian cell line co-expressing the two proteins. The possibility that this interaction was mediated via GABAB receptors was excluded by showing that mGlu1 and KCTD12 still co-immunoprecipitated from GABAB receptor knock-out tissue. In conclusion, this study identifies tissue-specific mGlu1-associated protein clusters including KCTD12 at Purkinje cell synapses.

PMID:37174725 | DOI:10.3390/cells12091325

Cells. 2023 May 2;12(9):1299. doi: 10.3390/cells12091299.

ABSTRACT

The evolution of protein-coding genes has both structural and regulatory components. The first can be assessed by measuring the ratio of non-synonymous to synonymous nucleotide substitutions. The second component can be measured as the normalized proportion of transposable elements that are used as regulatory elements. For the first time, we characterized in parallel the regulatory and structural evolutionary profiles for 10,890 human genes and 2972 molecular pathways. We observed a ~0.1 correlation between the structural and regulatory metrics at the gene level, which appeared much higher (~0.4) at the pathway level. We deposited the data in the publicly available database RetroSpect. We also analyzed the evolutionary dynamics of six cancer pathways of two major axes: Notch/WNT/Hedgehog and AKT/mTOR/EGFR. The Hedgehog pathway had both components slower, whereas the Akt pathway had clearly accelerated structural evolution. In particular, the major hub nodes Akt and beta-catenin showed both components strongly decreased, whereas two major regulators of Akt TCL1 and CTMP had outstandingly high evolutionary rates. We also noticed structural conservation of serine/threonine kinases and the genes related to guanosine metabolism in cancer signaling: GPCRs, G proteins, and small regulatory GTPases (Src, Rac, Ras); however, this was compensated by the accelerated regulatory evolution.

PMID:37174700 | DOI:10.3390/cells12091299

Cancers (Basel). 2023 Apr 30;15(9):2572. doi: 10.3390/cancers15092572.

ABSTRACT

Pancreatic Ductal Adenocarcinoma (PDAC) is characterized by an acidic microenvironment, which contributes to therapeutic failure. So far there is a lack of knowledge with respect to the role of the acidic microenvironment in the invasive process. This work aimed to study the phenotypic and genetic response of PDAC cells to acidic stress along the different stages of selection. To this end, we subjected the cells to short- and long-term acidic pressure and recovery to pHe 7.4. This treatment aimed at mimicking PDAC edges and consequent cancer cell escape from the tumor. The impact of acidosis was assessed for cell morphology, proliferation, adhesion, migration, invasion, and epithelial-mesenchymal transition (EMT) via functional in vitro assays and RNA sequencing. Our results indicate that short acidic treatment limits growth, adhesion, invasion, and viability of PDAC cells. As the acid treatment progresses, it selects cancer cells with enhanced migration and invasion abilities induced by EMT, potentiating their metastatic potential when re-exposed to pHe 7.4. The RNA-seq analysis of PANC-1 cells exposed to short-term acidosis and pHe-selected recovered to pHe 7.4 revealed distinct transcriptome rewiring. We describe an enrichment of genes relevant to proliferation, migration, EMT, and invasion in acid-selected cells. Our work clearly demonstrates that upon acidosis stress, PDAC cells acquire more invasive cell phenotypes by promoting EMT and thus paving the way for more aggressive cell phenotypes.

PMID:37174038 | DOI:10.3390/cancers15092572