Front Plant Sci. 2025 Jan 28;16:1533442. doi: 10.3389/fpls.2025.1533442. eCollection 2025.

ABSTRACT

INTRODUCTION: The genetic wealth present in pigmented rice varieties offer abundant variation in different sources of antioxidants to meet nutritional security targets among rice-consuming communities. There is limited knowledge of the dynamic changes in the lipidome of rice during germination and the corresponding genes associated with the antioxidant and anti-cancerous properties of lipophilic fractions of pigmented rice sprouts (PRS).

METHODS: In this study, we profiled the lipidome of diverse pigmented rice collections of germinated sprouts. Further, we employed Genome-wide association studies (GWAS), gene-set analysis, and targeted association analysis to identify the candidate genes linked to these lipids.

RESULTS: The genetic analyses revealed 72 candidate genes involved in the regulation of these accumulating lipids in PRS. Marker trait associations (MTA) analysis shown that the combination GGTAAC/ACAAGCTGGGCCC was associated with increased levels of unsaturated lipids and carotenoids, which likely underlie these beneficial effects. This superior MTA combination exhibited potent inhibitory activity against HCT116 and A549 cell lines, with average 1/IC50 values of 0.03 and 0.02 (mL/μg), respectively, compared to the inferior MTAs.

DISCUSSION: Collectively, our findings demonstrate that MTAs linked to selected GDSL esterase/lipase (GELP) genes, OsACP1, and lecithin-cholesterol acyltransferase significantly enhance antioxidant and anti-cancer properties, potentially through the mobilization of unsaturated lipids and carotenoids during germination. This study offers valuable insights into the health-promoting potential of germinated rice sprouts as a rich dietary source of antioxidants beneficial to human health.

PMID:39935946 | PMC:PMC11810972 | DOI:10.3389/fpls.2025.1533442

Front Genet. 2025 Jan 28;16:1547943. doi: 10.3389/fgene.2025.1547943. eCollection 2025.

NO ABSTRACT

PMID:39935834 | PMC:PMC11810898 | DOI:10.3389/fgene.2025.1547943

Front Plant Sci. 2025 Jan 28;15:1520474. doi: 10.3389/fpls.2024.1520474. eCollection 2024.

ABSTRACT

Seagrasses are a paraphyletic group of marine angiosperms and retain certain adaptations from the ancestors of all embryophytes in the transition to terrestrial environments. Among these adaptations is the production of flavonoids, versatile phenylpropanoid secondary metabolites that participate in a variety of stress responses. Certain features, such as catalytic promiscuity and metabolon interactions, allow flavonoid metabolism to expand to produce novel compounds and respond to a variety of stimuli. As marine environments expose seagrasses to a unique set of stresses, these plants display interesting flavonoid profiles, the functions of which are often not completely clear. Flavonoids will likely prove to be effective and versatile agents in combating the new host of stress conditions introduced to marine environments by anthropogenic climate change, which affects marine environments differently from terrestrial ones. These new stresses include increased sulfate levels, changes in salt concentration, changes in herbivore distributions, and ocean acidification, which all involve flavonoids as stress response mechanisms, though the role of flavonoids in combatting these climate change stresses is seldom discussed directly in the literature. Flavonoids can also be used to assess the health of seagrass meadows through an interplay between flavonoid and simple phenolic levels, which may prove to be useful in monitoring the response of seagrasses to climate change. Studies focusing on the genetics of flavonoid metabolism are limited for this group, but the large chalcone synthase gene families in some species may provide an interesting topic of research. Anthocyanins are typically studied separately from other flavonoids. The phenomenon of reddening in certain seagrass species typically focuses on the importance of anthocyanins as a UV-screening mechanism, while the role of anthocyanins in cold stress is discussed less often. Both of these stress response functions would be useful for adaptation to climate change-induced deviations in tidal patterns and emersion. However, ocean warming will likely lead to a decrease in anthocyanin content, which may impact the performance of intertidal seagrasses. This review highlights the importance of flavonoids in angiosperm stress response and adaptation, examines research on flavonoids in seagrasses, and hypothesizes on the importance of flavonoids in these organisms under climate change.

PMID:39935685 | PMC:PMC11810914 | DOI:10.3389/fpls.2024.1520474

Front Microbiol. 2025 Jan 28;16:1535114. doi: 10.3389/fmicb.2025.1535114. eCollection 2025.

ABSTRACT

Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) is a plant pathogenic bacterium that possesses complicated motility regulation pathways including a typical chemotaxis system. A significant portion of our understanding about the genes functioning in Pst DC3000 motility is based on comparison to other bacteria. This leaves uncertainty about whether gene functions are conserved, especially since specific regulatory modules can have opposite functions in sets of Pseudomonas. In this study, we used a competitive selection to enrich for mutants with altered swimming motility and used random barcode transposon-site sequencing (RB-TnSeq) to identify genes with significant roles in swimming motility. Besides many of the known or predicted chemotaxis and motility genes, our method identified PSPTO_0406 (dipA), PSPTO_1042 (chrR) and PSPTO_4229 (hypothetical protein) as novel motility regulators. PSPTO_0406 is a homolog of dipA, a known cyclic di-GMP degrading enzyme in P. aeruginosa. PSPTO_1042 is part of an extracytoplasmic sensing system that controls gene expression in response to reactive oxygen species, suggesting that PSPTO_1042 may function as part of a mechanism that enables Pst DC3000 to alter motility when encountering oxidative stressors. PSPTO_4229 encodes a protein containing an HD-related output domain (HDOD), but with no previously identified functions. We found that deletion and overexpression of PSPTO_4229 both reduce swimming motility, suggesting that its function is sensitive to expression level. We used the overexpression phenotype to screen for nonsense and missense mutants of PSPTO_4229 that no longer reduce swimming motility and found a pair of conserved arginine residues that are necessary for motility suppression. Together these results provide a global perspective on regulatory and structural genes controlling flagellar motility in Pst DC3000.

PMID:39935648 | PMC:PMC11813219 | DOI:10.3389/fmicb.2025.1535114

Front Microbiol. 2025 Jan 28;16:1534826. doi: 10.3389/fmicb.2025.1534826. eCollection 2025.

ABSTRACT

[This corrects the article DOI: 10.3389/fmicb.2024.1481702.].

PMID:39935631 | PMC:PMC11813217 | DOI:10.3389/fmicb.2025.1534826

Alzheimers Dement (N Y). 2025 Feb 11;11(1):e70051. doi: 10.1002/trc2.70051. eCollection 2025 Jan-Mar.

ABSTRACT

INTRODUCTION: Brain steady-state gamma oscillations evoked using a non-invasive medical device (Spectris) have shown potential clinical benefits in patients with mild-moderate Alzheimer's disease (AD), including reduced functional and cognitive decline, reduced brain volume and myelin loss, and increased brain functional connectivity. We analyzed changes in cerebrospinal fluid (CSF) proteins after Spectris treatment in mild cognitive impairment (MCI) and their relationship to established biological pathways implicated in AD.

METHODS: Unbiased proteomic analysis of CSF samples from participants with amyloid-positive MCI (n = 10) was conducted from the FLICKER (NCT03543878) clinical trial. Participants used the Cognito Therapeutics medical device (Spectris), confirmed to evoke steady-state gamma oscillations. Participants were instructed to use the device daily for 1 hour each day during the trial. CSF was collected prior to the start of stimulation and after 4 and 8 weeks of treatment. The proteome was analyzed using tandem mass tag mass spectrometry.

RESULTS: Differential expression analysis of proteins at baseline and after 8 weeks of treatment (N = 5) revealed that 110 out of 2951 proteins met the significance threshold (analysis of variance, P < 0.05, no false discovery rate). Sixty proteins were upregulated, and 50 proteins were downregulated after treatment. Changes in protein expression were mapped to the consensus human AD protein network, representing co-expressed and functionally linked modules linked to cell type and biochemical pathways. Treatment altered CSF proteins linked to AD-related brain proteome modules, including those involved in myelination (proteolipid protein 1, ecotropic viral integration site 2A), synaptic and neuroimmune functions, and regulation of cellular lipid transportation. Biological pathway analysis revealed that most impacted pathways were associated with lipoproteins, cholesterol, phospholipids processing, and phosphatidylcholine biosynthesis.

DISCUSSION: The CSF proteomic changes observed in this study suggest pleiotropic effects on multiple pathways involved in AD, including myelination, synaptic and neuroimmune function, and lipid transport. These findings are also consistent with observations of white matter and myelin preservation after Spectris treatment of AD.

HIGHLIGHTS: We analyzed changes in cerebrospinal fluid (CSF) proteins in response to sensory-evoked gamma oscillations in individuals with mild cognitive impairment.Sensory evoked steady-state gamma oscillations were evoked by Spectris medical device.Changes in CSF proteins were observed after 8 weeks of daily 1 hour treatment.Affected proteins were related to myelination, synaptic and neuroimmune functions, and regulation of cellular lipid transportation.Proteomic changes support clinical outcomes and myelin preservation of Spectris treatment.

PMID:39935616 | PMC:PMC11812123 | DOI:10.1002/trc2.70051

F1000Res. 2024 Jul 9;13:1. doi: 10.12688/f1000research.145146.2. eCollection 2024.

ABSTRACT

Protein phosphatase 2A is a serine/threonine phosphatase with activity dependent on an associated regulatory subunit, serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta (δ) isoform (PPP2R5D). PPP2R5D is the δ isoform in the B56 family of regulatory subunits. Abundantly expressed in the brain and involved in a broad range of cellular processes, PPP2R5D plays an essential role in modulating key neuronal pathways and signalling. Pathogenic mutations in the PPP2R5D gene are linked to clinical symptoms characterized by neurodevelopmental delay, intellectual disability, and autism spectrum disorders. The etiology of these genetic disorders remains unknown, which can partly be due to the lack of independently characterized antibodies. Here we have characterized six PPP2R5D commercial antibodies for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a larger, collaborative initiative seeking to address antibody reproducibility by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.

PMID:39935523 | PMC:PMC11811605 | DOI:10.12688/f1000research.145146.2

Microbiome. 2025 Feb 11;13(1):50. doi: 10.1186/s40168-024-02015-4.

ABSTRACT

BACKGROUND: Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities.

RESULTS: Here, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof of concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFunc's performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pypi.org/project/phylofunc/ ), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset.

CONCLUSIONS: Unlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study. Video Abstract.

PMID:39934908 | DOI:10.1186/s40168-024-02015-4

BMC Bioinformatics. 2025 Feb 11;26(1):48. doi: 10.1186/s12859-025-06051-1.

ABSTRACT

BACKGROUND: Alterations of metabolism, including changes in mitochondrial metabolism as well as glutathione (GSH) metabolism are a well appreciated hallmark of many cancers. Mitochondrial GSH (mGSH) transport is a poorly characterized aspect of GSH metabolism, which we investigate in the context of cancer. Existing functional annotation approaches from machine (ML) or deep learning (DL) models based only on protein sequences, were unable to annotate functions in biological contexts.

RESULTS: We develop a flexible ML framework for functional annotation from diverse feature data. This hybrid ML framework leverages cancer cell line multi-omics data and other biological knowledge data as features, to uncover potential genes involved in mGSH metabolism and membrane transport in cancers. This framework achieves strong performance across functional annotation tasks and several cell line and primary tumor cancer samples. For our application, classification models predict the known mGSH transporter SLC25A39 but not SLC25A40 as being highly probably related to mGSH metabolism in cancers. SLC25A10, SLC25A50, and orphan SLC25A24, SLC25A43 are predicted to be associated with mGSH metabolism in multiple biological contexts and structural analysis of these proteins reveal similarities in potential substrate binding regions to the binding residues of SLC25A39.

CONCLUSION: These findings have implications for a better understanding of cancer cell metabolism and novel therapeutic targets with respect to GSH metabolism through potential novel functional annotations of genes. The hybrid ML framework proposed here can be applied to other biological function classifications or multi-omics datasets to generate hypotheses in various biological contexts. Code and a tutorial for generating models and predictions in this framework are available at: https://github.com/lkenn012/mGSH_cancerClassifiers .

PMID:39934670 | DOI:10.1186/s12859-025-06051-1

Transl Stroke Res. 2025 Feb 11. doi: 10.1007/s12975-025-01332-6. Online ahead of print.

ABSTRACT

Cerebral small vessel disease (CSVD) is a global brain disorder that is characterized by a series of clinical, neuroimaging, and neuropathological manifestations. However, the molecular pathophysiological mechanisms of CSVD have not been thoroughly investigated. Liquid chromatography-tandem mass spectrometry-based proteomics has broad application prospects in biomedicine. It is used to elucidate disease-related molecular processes and pathophysiological pathways, thus providing an important opportunity to explore the pathophysiological mechanisms of CSVD. Serum samples were obtained from 96 participants (58 with CSVD and 38 controls) consecutively recruited from The First Affiliated Hospital of Zhengzhou University. After removing high-abundance proteins, the serum samples were analyzed using high-resolution mass spectrometry. Bioinformatics methods were used for in-depth analysis of the obtained proteomic data, and the results were verified experimentally. Compared with the control group, 52 proteins were differentially expressed in the sera of the CSVD group. Furthermore, analyses indicated the involvement of these differentially expressed proteins in CSVD through participation in the overactivation of complement and coagulation cascades and dysregulation of insulin-like growth factor-binding proteins. The proteomic biomarker panel identified by the machine learning model combined with clinical features is expected to facilitate the diagnosis of CSVD (AUC = 0.947, 95% CI = 0.895-0.978). The study is the most in-depth study on CSVD proteomics to date and suggests that the overactivation of the complement cascade and the dysregulation of IGFBP on- IGF may be closely correlated with the occurrence and progression of CSVD, offering the potential to develop peripheral blood biomarkers and providing new insights into the biological basis of CSVD.

PMID:39934548 | DOI:10.1007/s12975-025-01332-6

Nat Microbiol. 2025 Feb 11. doi: 10.1038/s41564-025-01951-7. Online ahead of print.

NO ABSTRACT

PMID:39934405 | DOI:10.1038/s41564-025-01951-7

Nat Chem Biol. 2025 Feb 11. doi: 10.1038/s41589-025-01846-y. Online ahead of print.

ABSTRACT

Measuring pharmacodynamics (PD)-the biochemical effects of drug dosing-and correlating them with therapeutic efficacy in animal models is crucial for the development of effective drugs but traditional PD studies are labor and resource intensive. Here we developed a kinase-modulated bioluminescent indicator (KiMBI) for rapid, noninvasive PD assessment of Akt-targeted drugs, minimizing drug and animal use. Using KiMBI, we performed a structure-PD relationship analysis on the brain-active Akt inhibitor ipatasertib by generating and characterizing two novel analogs. One analog, ML-B01, successfully inhibited Akt in both the brain and the body. Interestingly, capivasertib, ipatasertib and ML-B01 all exhibited PD durations beyond their pharmacokinetic profiles. Furthermore, KiMBI revealed that the PD effects of an Akt-targeted proteolysis-targeting chimera degrader endured for over 3 days. Thus, bioluminescence imaging with Akt KiMBI provides a noninvasive and efficient method for in vivo visualization of the PD of Akt inhibitors and degraders.

PMID:39934397 | DOI:10.1038/s41589-025-01846-y

Nat Commun. 2025 Feb 11;16(1):1549. doi: 10.1038/s41467-025-56797-8.

ABSTRACT

The TRAFAC (translation factors) GTPase OLA1 plays a critical role in various stress responses and is implicated in the regulation of tumor progression. It is conserved from bacteria to eukaryotes and regulates the translation through binding to the ribosome. Here, we report the cryo-electron microscopy structure of its Escherichia coli homolog, YchF, with the 50S subunit. In this structure, YchF is positioned at the side of the 50S subunit by engaging with uL14, bL19, and rRNA helix H62 through its helical and ATPase domains. We further demonstrate that the helical domain is essential for OLA1/YchF to function. A comprehensive analysis of the structure and Ribo-seq data points out that OLA1/YchF promotes the splitting of ribosomes into subunits on D/E-rich mRNA. Our findings provide crucial structural insights into the molecular mechanism of OLA1/YchF-associated translation-stalling regulation, which maintains the translation of genes involved in stress response and tumor progression.

PMID:39934121 | DOI:10.1038/s41467-025-56797-8

Curr Opin Biotechnol. 2025 Feb 10;92:103260. doi: 10.1016/j.copbio.2025.103260. Online ahead of print.

ABSTRACT

Development of microorganisms into mature bioproduction host strains has typically been a slow and circuitous process, wherein multiple groups apply disparate approaches with minimal coordination over decades. To help organize and streamline host development efforts, we introduce the Tier System for Host Development, a conceptual model and guide for developing microbial hosts that can ultimately lead to a systematic, standardized, less expensive, and more rapid workflow. The Tier System is made up of three Tiers, each consisting of a unique set of strain development Targets, including experimental tools, strain properties, experimental information, and process models. By introducing the Tier System, we hope to improve host development activities through standardization and systematization pertaining to nontraditional chassis organisms.

PMID:39933241 | DOI:10.1016/j.copbio.2025.103260

Proc Natl Acad Sci U S A. 2025 Feb 18;122(7):e2421623122. doi: 10.1073/pnas.2421623122. Epub 2025 Feb 11.

ABSTRACT

Acidic glycans are essential for the biology of multicellular eukaryotes. To utilize them, microbial life including symbionts and pathogens has evolved polysaccharide lyases (PL) that cleave their 1,4 glycosidic linkages via a β-elimination mechanism. PL family 33 (PL33) enzymes have the unusual ability to target a diverse range of glycosaminoglycans (GAGs), as well as the bacterial polymer, gellan gum. In order to gain more detailed insight into PL33 activities we recombinantly expressed 10 PL33 members derived from all major environments and further elucidated the detailed biochemical and biophysical properties of five, showing that their substrate specificity is conferred by variations in tunnel length and topography. The key amino acids involved in catalysis and substrate interactions were identified, and employing a combination of complementary biochemical, structural, and modeling approaches, we show that the tunnel topography is induced by substrate binding to the glycan. Structural and bioinformatic analyses revealed that these features are conserved across several lyase families as well as in mammalian GAG epimerases.

PMID:39932998 | DOI:10.1073/pnas.2421623122

PLoS Biol. 2025 Feb 11;23(2):e3003033. doi: 10.1371/journal.pbio.3003033. Online ahead of print.

ABSTRACT

Rodent and human data implicate the hippocampus in the arbitration of approach-avoidance conflict (AAC), which arises when an organism is confronted with a stimulus associated simultaneously with reward and punishment. Yet, the precise contributions of this structure are underexplored, particularly with respect to the decision-making processes involved. We assessed humans with hippocampal damage and matched neurologically healthy controls on a computerized AAC paradigm in which participants first learned whether individual visual images were associated with the reward or loss of game points and were then asked to approach or avoid pairs of stimuli with non-conflicting or conflicting valences. To assess hippocampal involvement more broadly in response conflict, we also administered a Stroop and a Go/No-go task. On the AAC paradigm, following similar learning outcomes in individuals with hippocampal damage and matched controls, both participant groups approached positive and negative image pairs at the same rate but critically, those with hippocampal damage approached conflict pairs more often than controls. Choice and response AAC data were interrogated using the hierarchical drift diffusion model, which revealed that, compared to controls, individuals with hippocampal damage were more biased towards approach, required less evidence to make a decision during conflict trials, and were slower to accumulate evidence towards avoidance when confronted with conflicting image pairs. No significant differences were found between groups in performance accuracy or response time on the response conflict tasks. Taken together, these findings demonstrate the importance of the hippocampus to the evidence accumulation processes supporting value-based decision-making under motivational conflict.

PMID:39932954 | DOI:10.1371/journal.pbio.3003033

Discov Nano. 2025 Feb 11;20(1):26. doi: 10.1186/s11671-025-04208-8.

ABSTRACT

BACKGROUND: Infected wounds are a major health problem as infection can delay wound healing. Wound dressings play an important part in wound care by maintaining a suitable environment that promotes healing. Silver sulfadiazine dressings have been used to prevent infection in burn wounds. Presently, many commercial silver dressings have obtained FDA clearance.

RESULTS: In this study, we report on a novel silver dressing using microporous aluminosilicate zeolites, termed ABF-XenoMEM. Silver and zinc ions are encapsulated in the zeolite supercages. We show that the silver-zinc zeolite (AM30) alone is effective at inhibiting biofilm formation. The encapsulation protects the silver from rapidly precipitating in biological fluids. We exploit the negatively charged zeolite surface to associate positively charged quaternary ammonium ions (quat) with the zeolite. The combination of the AM30 with the quat enhances the antimicrobial activity. The colloidal nature of the zeolite materials makes it possible to make uniform deposits on a commercial extracellular matrix membrane to develop the final dressing (ABF-XenoMEM). The optimum loading of silver, zinc, and quat on the dressing was found to be 30, 3.7, and 221 µg/cm2. Using a colony biofilm model, the activity of ABF-XenoMEM is compared with four well-studied silver-based commercial dressings towards mature biofilms of Pseudomonas aeruginosa PAO1 (ATCC 4708) and methicillin-resistant Staphylococcus aureus (ATCC 33592). Cytotoxicity of the dressings was examined in HepG2 cells using the MTT assay.

CONCLUSION: This study shows that the ABF-XenoMEM is competitive with extensively used commercial wound dressings in a colony biofilm model. Nanozeolite-entrapped silver/zinc antimicrobials in association with quat have the potential for application in biofilm-infected wounds and require animal and clinical studies for definitive proof.

PMID:39932517 | DOI:10.1186/s11671-025-04208-8

J Gerontol A Biol Sci Med Sci. 2025 Feb 11:glaf026. doi: 10.1093/gerona/glaf026. Online ahead of print.

ABSTRACT

The aging process is universal, and it is characterized by a progressive deterioration and decrease in physiological function leading to decline on the organismal level. Nevertheless, a number of genetic and non-genetic interventions have been described, which successfully extend healthspan and lifespan in different species. Furthermore, a number of clinical trials have been evaluating the feasibility of different interventions to promote human health. The goal of the annual Biological Sciences Section of the Gerontological Society of America meeting was to share current knowledge of different topics in aging research and provide a vision of the future of aging research. The meeting gathered international experts in diverse areas of aging research including basic biology, demography, and clinical and translational studies. Specific topics included metabolism, inflammaging, epigenetic clocks, frailty, senescence, neuroscience, stem cells, reproductive aging, inter-organelle crosstalk, comparative transcriptomics of longevity, circadian clock, metabolomics, and biodemography.

PMID:39932386 | DOI:10.1093/gerona/glaf026

Elife. 2025 Feb 11;13:RP98427. doi: 10.7554/eLife.98427.

ABSTRACT

Excessive consumption of sucrose, in the form of sugar-sweetened beverages, has been implicated in the pathogenesis of metabolic dysfunction-associated fatty liver disease (MAFLD) and other related metabolic syndromes. The c-Jun N-terminal kinase (JNK) pathway plays a crucial role in response to dietary stressors, and it was demonstrated that the inhibition of the JNK pathway could potentially be used in the treatment of MAFLD. However, the intricate mechanisms underlying these interventions remain incompletely understood given their multifaceted effects across multiple tissues. In this study, we challenged rats with sucrose-sweetened water and investigated the potential effects of JNK inhibition by employing network analysis based on the transcriptome profiling obtained from hepatic and extrahepatic tissues, including visceral white adipose tissue, skeletal muscle, and brain. Our data demonstrate that JNK inhibition by JNK-IN-5A effectively reduces the circulating triglyceride accumulation and inflammation in rats subjected to sucrose consumption. Coexpression analysis and genome-scale metabolic modeling reveal that sucrose overconsumption primarily induces transcriptional dysfunction related to fatty acid and oxidative metabolism in the liver and adipose tissues, which are largely rectified after JNK inhibition at a clinically relevant dose. Skeletal muscle exhibited minimal transcriptional changes to sucrose overconsumption but underwent substantial metabolic adaptation following the JNK inhibition. Overall, our data provides novel insights into the molecular basis by which JNK inhibition exerts its metabolic effect in the metabolically active tissues. Furthermore, our findings underpin the critical role of extrahepatic metabolism in the development of diet-induced steatosis, offering valuable guidance for future studies focused on JNK-targeting for effective treatment of MAFLD.

PMID:39932177 | DOI:10.7554/eLife.98427

Acta Physiol (Oxf). 2025 Mar;241(3):e70018. doi: 10.1111/apha.70018.

ABSTRACT

BACKGROUND: The distal convoluted tubule (DCT) plays an indispensable role in magnesium (Mg2+) reabsorption in the kidney. Yet, the extrusion mechanism of Mg2+ has not been identified. The solute carrier 41A3 (SLC41A3) has been suggested to be involved in Mg2+ extrusion, but this has never been conclusively demonstrated.

METHODS: Using available RNA-sequencing data and real-time quantitative PCR, expression of two alternative Slc41a3 transcripts, encoding isoform (Iso) 1 or 2, were assessed in kidney and isolated DCT tubules. HEK293 or HAP1 cells were transfected with plasmids expressing either of the isoforms, followed by 25Mg2+ transport studies. Identification of cis-regulatory elements (CRE) was achieved by combining data from publicly available ATAC sequencing data and luciferase assays.

RESULTS: Gene expression studies revealed a distinct transcript of Slc41a3 in the DCT with an alternative promoter, leading to a protein with a unique N-terminus; SLC41A3-Iso 2. HEK293 cells overexpressing SLC41A3-Iso 2, but not -Iso 1, exhibited 2.7-fold and 1.6-fold higher 25Mg2+ uptake and extrusion, compared to mock, respectively. The transport was independent of Na+, of the Mg2+ channel TRPM7 or of transporters CNNM3 and -4. We identified a CRE accessible in the DCT, ±2.8kb upstream of the transcript. The presence of the CRE increased the Slc41a3-Iso 2 promoter activity 3.8-fold following luciferase assays, indicating the CRE contains an enhancer function.

CONCLUSION: In conclusion, we identified two alternative transcripts of Slc41a3 in mouse. Slc41a3-Iso 2 is enriched within the DCT using specific gene regulatory elements. We speculate that specifically in the DCT, SLC41A3-Iso 2 orchestrates Mg2+ extrusion.

PMID:39931759 | DOI:10.1111/apha.70018