J Invest Dermatol. 2025 May 29:S0022-202X(25)00540-8. doi: 10.1016/j.jid.2025.04.041. Online ahead of print.

ABSTRACT

The sebaceous gland is essential for skin homeostasis by producing sebum to lubricate and protect the skin. Dysfunctions in sebaceous gland activity are associated with skin disorders such as acne, seborrheic dermatitis, and alopecia. However, its cellular and molecular mechanisms in humans remain poorly understood as most studies have been conducted in mouse models. This study provides a comprehensive molecular analysis of the human sebaceous gland, focusing on cellular interactions, sebocyte differentiation, and, to our knowledge, previously unreported gene markers. By integrating Stereo-seq spatial transcriptomics, single-cell RNA sequencing, and validation by MERFISH, we identified four distinct stages of sebocyte differentiation, each characterized by unique gene signatures. These results reveal that sebocyte differentiation is a dynamic and complex process. Our findings enhance the understanding of sebaceous gland biology and provide a valuable reference for future research and the development of therapies for sebaceous gland-related disorders, including acne.

PMID:40449655 | DOI:10.1016/j.jid.2025.04.041

J Physiol. 2025 May 31. doi: 10.1113/JP288757. Online ahead of print.

NO ABSTRACT

PMID:40448977 | DOI:10.1113/JP288757

Mamm Genome. 2025 May 31. doi: 10.1007/s00335-025-10136-w. Online ahead of print.

ABSTRACT

Innate immunity, the primary defence mechanism, encompasses a range of protective processes like anatomical barriers, cytokine secretion, and the action of various immune cells. Cattle breeds might differ in these processes because of their genetic differences such as copy number variations (CNVs). Therefore, the present investigation employed an array comparative genomic hybridisation (aCGH) approach on breed representative pooled DNA samples to evaluate CNVs across six cattle breeds: four indigenous Indian breeds, Kangayam (KNG), Tharparkar (TP), Sahiwal (SW), Gir (GIR), one crossbred Karan Fries (KF), and one exotic breed, Holstein Friesian (HF). In aCGH, HF DNA was used as control, while test DNA was from the other breeds. Each pooled test DNA sample was a representative of 18 animals belonging to three distinct geographical locations of India. The study using Aberration Detection Method 2 (ADM-2) of Agilent Genomic Workbench revealed the highest number of duplications in KNG (1189 genes), followed by TP (534 genes), and the greatest number of deletions in SW (774 genes). Among these genes, 183 and 76 innate immune genes with hub genes TGF-β1, CD79A, and IL4 showed duplications in KNG and TP, respectively. In SW, 113 innate immune genes with hub genes PSMC5, MAPK1, and AXIN1 showed deletions. In contrast, KF and HF showed no genes with deletions and fewer duplicated innate immunity genes, reflecting either lower genetic variability in their immune gene repertoire or a potential bias due to HF DNA as a control in aCGH. Functional enrichment of innate immune genes revealed duplications in KNG enriched in interleukin-1 receptor (IL1R) activity (p = 9.9 × 10-3) and nucleobase metabolism (p = 2.88 × 10⁻11), while duplications in TP were linked to DNA-binding transcription factor activity (p = 2.34 × 10⁻14). The KEGG pathway analysis highlighted Th17 cell differentiation (p = 1.3 × 10⁻4) in KNG and Hippo signalling (p = 3.7 × 10-2) in TP. Overall, these findings highlight the importance of genetic diversity in shaping innate immunity in indigenous Indian cattle breeds, favouring a balanced crossbreeding to sustain the Indian dairy sector.

PMID:40448838 | DOI:10.1007/s00335-025-10136-w

Mol Biol Rep. 2025 May 31;52(1):529. doi: 10.1007/s11033-025-10644-7.

ABSTRACT

BACKGROUND: Multidrug-resistant and biofilm-forming pathogens have become a global health challenge, contributing to persistent and hard-to-treat infections. The objective of this study was to characterize an active metabolite produced by a novel halo-thermophilic Streptomyces sp. CBN-1 that exhibits potent antibacterial and antibiofilm activities using a combined in-silico and experimental approach.

METHODS & RESULTS: In this study, a halo-thermophilic Streptomyces sp. CBN-1 strain was selected for its ability to grow in 10% NaCl at 40 °C. This strain was identified using phenotypic characterizations and 16S rRNA gene sequence analysis as Streptomyces rochei NRRL B-2410 with 99.15% similarity. An active metabolite, CBNa-1, was extracted using n-butanol solvent from ISP2 broth medium and purified by HPLC. Structural characterization using electrospray ionization mass spectrometry and NMR spectroscopy identified CBNa-1 as an aromatic heterocyclic compound regulated by non-ribosomal peptide synthetase (NRPS) and type II polyketide synthase (PKS) genes. It exhibited potent activity with minimum inhibitory concentrations (MIC) ranging from 4 to 5 µg/mL and minimum biofilm inhibitory concentrations (MBIC50%) at ½ MIC. Additionally, in-silico docking analyses showed that CBNa-1 had stronger binding affinities from - 8.7 to -8.1 kcal/mol with isoleucyl-tRNA synthetase, glucosamine-6-phosphate synthase, penicillin-binding protein 1a, type II DNA topoisomerases, and quorum sensing compared to antibiotics (-5.7 to -7.9 kcal/mol). Furthermore, molecular dynamic (MD) simulation showed the stability of the protein-ligand complex under physiological conditions.

CONCLUSION: This study reports the first identification of CBNa-1, a metabolite from prokaryotic cells, with potent antibacterial and anti-biofilm properties to combat nosocomial infections caused by MDR pathogens, including bacteria resistant to third-generation cephalosporins.

PMID:40448741 | DOI:10.1007/s11033-025-10644-7

ISME J. 2025 May 31:wraf109. doi: 10.1093/ismejo/wraf109. Online ahead of print.

ABSTRACT

Microbial consortia play pivotal roles in nutrient cycling across diverse ecosystems, where the functionality and composition of microbial communities are shaped by metabolic interactions. Despite the critical importance of understanding these interactions, accurately mapping and manipulating microbial interaction networks to achieve specific outcomes remains challenging. Genome-scale metabolic models (GEMs) offer significant promise for predicting microbial metabolic functions from genomic data; however, traditional community GEMs typically rely on species abundance information, which may limit their predictive accuracy due to the absence of condition-specific gene expression or protein abundance data. Here, we introduce the Integration of Metatranscriptomes Into Community GEMs (IMIC) approach, which utilizes metatranscriptomic data to construct context-specific community models for predicting individual growth rates and metabolic interactions. By incorporating metatranscriptomic profiles, which reflect both gene expression activity and partially encode abundance information, IMIC could predict condition-specific flux distributions that enable the investigation of metabolite interactions among community members. Our results show that growth rates predicted by IMIC correlate strongly with relative as well as absolute abundance of species and offer a streamlined, automated procedure for estimating the single intrinsic parameter. Specifically, IMIC results in improved predictions of measured metabolite concentration changes compared with other approaches in our case study. We further demonstrate that this improvement is driven by the network-wide adjustment of flux bounds based on gene expression profiles. In conclusion, IMIC approach enables the accurate prediction of individual growth rates and improves the model performance of predicting metabolite interactions, facilitating a deeper understanding of metabolic interdependencies within microbial communities.

PMID:40448581 | DOI:10.1093/ismejo/wraf109

Vet Rec. 2025 May 30:e5325. doi: 10.1002/vetr.5325. Online ahead of print.

ABSTRACT

BACKGROUND: Bovine viral diarrhoea (BVD) is an endemic disease in the UK. In England, a voluntary control and eradication scheme, BVDFree England, has been running since 2016.

METHODS: We analysed test results from 7005 herds that were submitted to BVDFree England between 2016 and 2023 to investigate changes in the prevalence of BVD in participating herds and engagement by farmers since the previously published analysis covering the period up to 2020.

RESULTS: Herds that tested for multiple consecutive years were more likely to be BVD negative in later testing years than when starting. Few herds were still positive after 5 years of testing. Overall, the prevalence of BVD-positive herds in the dataset declined between 2020 and 2023; however, fewer farmers joined the scheme for the first time each year since 2019 (214 in 2023 compared with 2614 in 2019).

LIMITATIONS: This dataset represents the herds that submit tests to BVDFree England and is not representative of all cattle herds in England.

CONCLUSION: Herds that tested for multiple consecutive years in the scheme were less likely to be BVD positive in later years of testing, and the prevalence of BVD in participating herds has continued to fall since 2020.

PMID:40448356 | DOI:10.1002/vetr.5325

BMC Genomics. 2025 May 30;26(1):550. doi: 10.1186/s12864-025-11734-3.

ABSTRACT

BACKGROUND: Crossover and recombination create genetic diversity that reflects differences in the DNA sequences of different organisms. We previously reported that trinucleotide 2-repeat units (T2Us) are sites of crossover and consequent colonization, which are massively spread and shared across the genomes of human and several other primates. These sites underscore the preference for AT- over CG-rich sequences as recombination sites.

METHODS: We extended our study to simpler repeat cores, consisting of AT/TA and CG/GC dinucleotides. An algorithm was designed to extract the genomic regions with a higher probability of recombination. To this end, we hypothesized that dinucleotide 3-repeat units (D3Us) are, at least in part, the basic overlapping units resulting from unequal crossover between dinucleotide 2-repeat units (D2Us). We mapped TATATA, ATATAT, CGCGCG, and GCGCGC across the human genome and analyzed their colonization (the distance between consecutive D3Us < 500 bp). We also studied several randomly selected colonies of diverse sizes in up to 100 vertebrate species using the UCSC and Ensembl Genome Browsers.

RESULTS: We found approximately four million AT/TA D3Us and one hundred thousand CG/GC D3Us across the human genome. The majority of these D3Us resided in colonies and spread ubiquitously along all chromosomes. AT/TA colonies were significantly larger and more intricate than CG/GC colonies. D2Us and D3Us were the primary sites of unequal crossover in these colonies, resulting in the emergence of primary recombinants (overlapping recombinants of D2Us/D3Us) and a vast repertoire of secondary recombinants (non-overlapping recombinants of D2Us/D3Us) and eventually, colonies of enormous intricacy and significance based on Poisson distribution. Intricacy was consistently detected across diverse colony sizes, from the smallest to the largest. The randomly selected colonies that were studied in other species were specific to or of their largest size in human.

CONCLUSION: We report ubiquitous and intricate colonies, in which D2Us and D3Us were the primary sites of crossover and recombination. It is plausible that minimal repeats such as D2Us, D3Us, and T2Us mark recombination as a ubiquitous rule across the human genome. This phenomenon is likely to transform our understanding of the magnitude, biological, and evolutionary outcomes of crossover and recombination.

PMID:40447998 | DOI:10.1186/s12864-025-11734-3

Geroscience. 2025 May 31. doi: 10.1007/s11357-025-01716-4. Online ahead of print.

ABSTRACT

Certain epigenetic modifications, such as the methylation of CpG sites, can serve as biomarkers for chronological age. Previously, we introduced the BayesAge frameworks for accurate age prediction through the use of locally weighted scatterplot smoothing (LOWESS) to capture the nonlinear relationship between methylation or gene expression and age, and maximum likelihood estimation (MLE) for bulk bisulfite and RNA sequencing data. Here, we introduce MicroBayesAge, a maximum likelihood framework for age prediction using DNA microarray data that provides less biased age predictions compared to commonly used linear methods. Furthermore, MicroBayesAge enhances prediction accuracy relative to previous versions of BayesAge by subdividing input data into age-specific cohorts and employing a new two-stage process for training and testing. Additionally, we explored the performance of our model for sex-specific age prediction which revealed slight improvements in accuracy for male patients, while no changes were observed for female patients.

PMID:40447915 | DOI:10.1007/s11357-025-01716-4

Nat Commun. 2025 May 30;16(1):5041. doi: 10.1038/s41467-025-59435-5.

ABSTRACT

Transfer RNA (tRNA) is the most abundant cellular RNA family in terms of copy numbers. It not only folds into defined structures but also has complex cellular interaction networks involving aminoacyl-tRNA synthetases, translation factors, and ribosomes. The human tRNAome is comprised of chromosomal-encoded tRNAs with a large sequence diversity and mitochondrial-encoded tRNAs with A/U-rich sequences and noncanonical tertiary interactions. How tRNA folding and interactions in a eukaryotic cell respond to stress is poorly understood. Here, we develop DM-DMS-MaPseq, which utilizes in vivo dimethyl-sulfate (DMS) chemical probing and mutational profiling (MaP) coupled with demethylase (DM) treatment in transcriptome-wide tRNA sequencing to profile structures and the cellular interactions of human chromosomal and mitochondrial-encoded tRNAs. We found that tRNAs maintain stable structures in vivo, but the in vivo DMS profiles are vastly different from those in vitro, which can be explained by their interactions with cellular proteins and the ribosome. We also identify cytosolic and mitochondrial tRNA structure and interaction changes upon arsenite treatment, a type of oxidative stress that induces translational reprogramming, which is consistent with global translation repression in both compartments. Our results reveal variations of tRNA structurome and dynamic interactome that have functional consequences in translational regulation.

PMID:40447571 | DOI:10.1038/s41467-025-59435-5

Stem Cell Reports. 2025 May 20:102511. doi: 10.1016/j.stemcr.2025.102511. Online ahead of print.

ABSTRACT

Human embryonic stem cells (hESCs) are notable for their ability to self-renew and to differentiate into all tissue types in the body. NANOG is a core regulator of hESC identity, and dynamic control of its expression is crucial to maintain the balance between self-renewal and differentiation. Transcriptional regulation depends on enhancers, but NANOG enhancers in hESCs are not well characterized. Here, we report two NANOG enhancers discovered from a CRISPR interference screen in hESCs. Deletion of a single copy of either enhancer significantly reduced NANOG expression, compromising self-renewal and increasing differentiation propensity. Interestingly, these two NANOG enhancers are involved in a tandem duplication event found in certain primates including humans but not in mice. However, the duplicated counterparts do not regulate NANOG expression. This work expands our knowledge of functional enhancers in hESCs and highlights the sensitivity of the hESC state to the dosage of core regulators and their enhancers.

PMID:40446796 | DOI:10.1016/j.stemcr.2025.102511

Thorax. 2025 May 30:thorax-2024-222242. doi: 10.1136/thorax-2024-222242. Online ahead of print.

ABSTRACT

BACKGROUND: Despite significant clinical improvements, there is evidence of persisting airway inflammation in people with cystic fibrosis (CF) established on elexacaftor/tezacaftor/ivacaftor (ETI) therapy. As CF is a multi-system disease, systemic immune profiles can reflect local inflammation within the lungs and other organs. Understanding systemic inflammation after ETI therapy may reveal important translational insights. This study aims to profile systemic inflammatory changes and relate these to the well-documented improvements observed with ETI therapy.

METHODS: We conducted a single-centre longitudinal study with 57 CF subjects initiating ETI therapy. All participants were Phe508del homozygous or Phe508del/minimal function. Blood samples were collected pre-ETI and 3-12 months post-therapy initiation. Analyses included mass spectrometry-based proteomics, a multiplex immunoassay, and flow cytometry for peripheral immune cell counts and phenotype. Controls samples were provided by 29 age-matched healthy controls.

RESULTS: Systemic inflammation reduced with ETI therapy; however, the immune profile remained distinct from healthy controls. ETI reduced neutrophil counts and was associated with a more mature, less inflammatory phenotype, as well as a shift towards an immune resolving state associated with increased CD206 expression. Cytokines known to influence neutrophil levels reduced with therapy. Despite ETI therapy, neutrophil and monocyte counts remained elevated compared with healthy controls. There was no obvious association between the ETI-related improvements in systemic inflammation and lung function.

CONCLUSIONS: Patients with CF showed evidence of persisting systemic inflammation despite ETI therapy, which may have long-term potentially adverse effects on respiratory and other organ systems.

PMID:40447326 | DOI:10.1136/thorax-2024-222242

Cancer Cell. 2025 May 28:S1535-6108(25)00211-9. doi: 10.1016/j.ccell.2025.05.002. Online ahead of print.

ABSTRACT

Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is the vaccine against tuberculosis and an immunotherapy for bladder cancer. When administered intravenously, BCG reprograms bone marrow hematopoietic stem and progenitor cells (HSPCs), leading to heterologous protection against infections. Whether HSPC reprogramming contributes to the anti-tumor effects of BCG administered into the bladder is unknown. We demonstrate that BCG administered in the bladder colonizes the bone marrow and, in both mice and humans, reprograms HSPCs to alter and amplify myelopoiesis. BCG-reprogrammed HSPCs are sufficient to confer augmented anti-tumor immunity through production of neutrophils, monocytes, and dendritic cells that broadly remodel the tumor microenvironment, drive T cell-dependent anti-tumor responses, and synergize with checkpoint blockade. We conclude that bladder BCG acts systemically through hematopoiesis, highlighting the broad potential of HSPC reprogramming to enhance the innate drivers of T cell-dependent tumor immunity.

PMID:40446799 | DOI:10.1016/j.ccell.2025.05.002

PLoS Genet. 2025 May 30;21(5):e1011492. doi: 10.1371/journal.pgen.1011492. Online ahead of print.

ABSTRACT

Genome-wide association studies (GWAS) have identified many quantitative trait loci (QTL) associated with complex traits, predominantly in non-coding regions, posing challenges in pinpointing the causal variants and their target genes. Three types of evidence can help identify the gene through which QTL acts: (1) proximity to the most significant GWAS variant, (2) correlation of gene expression with the trait, and (3) the gene's physiological role in the trait. However, there is still uncertainty about the success of these methods in identifying the correct genes. Here, we test the ability of these methods in a comparatively simple series of traits associated with the concentration of polar lipids in milk. We conducted single-trait GWAS for ~14 million imputed variants and 56 individual milk polar lipid (PL) phenotypes in 336 cows. A multi-trait meta-analysis of GWAS identified 10,063 significant SNPs at FDR ≤ 10% (P ≤ 7.15E-5). Transcriptome data from blood (~12.5K genes, 143 cows) and mammary tissue (~12.2K genes, 169 cows) were analyzed using the genetic score omics regression (GSOR) method. This method links observed gene expression to genetically predicted phenotypes and was used to find associations between gene expression and 56 PL phenotypes. GSOR identified 2,186 genes in blood and 1,404 in mammary tissue associated with at least one PL phenotype (FDR ≤ 1%). We partitioned the genome into non-overlapping windows of 100 Kb to test for overlap between GSOR-identified genes and GWAS signals. We found a significant overlap between these two datasets, indicating that GSOR-significant genes were more likely to be located within 100 Kb windows that include GWAS signals than those that do not (P = 0.01; odds ratio = 1.47). These windows included 70 significant genes expressed in mammary tissue and 95 in blood. Compared to all expressed genes in each tissue, these genes were enriched for lipid metabolism gene ontology (GO). That is, seven of the 70 significant mammary transcriptome genes (P < 0.01; odds ratio = 3.98) and five of the 95 significant blood genes (P < 0.10; odds ratio = 2.24) were involved in lipid metabolism GO. The candidate causal genes include DGAT1, ACSM5, SERINC5, ABHD3, CYP2U1, PIGL, ARV1, SMPD5, and NPC2, with some overlap between the two tissues. The overlap between GWAS, GSOR, and GO analyses suggests that together, these methods are more likely to identify genes mediating QTL, though their power remains limited, as reflected by modest odds ratios. Larger sample sizes would enhance the power of these analyses, but issues like linkage disequilibrium would remain.

PMID:40446200 | DOI:10.1371/journal.pgen.1011492

Development. 2025 May 30:dev.204606. doi: 10.1242/dev.204606. Online ahead of print.

ABSTRACT

Self-organization, such as the emergence of a pattern from a homogenous state, is a fascinating property of biological systems. Early limb bud outgrowth and patterning in mice are controlled by a robust and self-regulatory signaling system, and initiation of the periodic digit-interdigit pattern appears under control of a self-regulatory Turing system. Previous studies established the requirement of WNT and BMP signaling for both early limb bud and digit-interdigit morphogenesis, but the molecular changes underlying the transition from early limb bud signaling to the digit-interdigit patterning system remained unknown. Here, we use small molecule inhibitors to rapidly but transiently block WNT signaling to identify the early transcriptional targets that are altered during disruption and recovery of limb bud and digit development. Together, this study highlights the overarching role of WNT signaling in controlling early limb bud outgrowth and patterning, and establishment of the periodic digit-interdigit pattern. Finally, the transient WNT signaling disruption approach reveals the plasticity and robustness of these self-organizing limb bud and digit patterning systems.

PMID:40446196 | DOI:10.1242/dev.204606

Sci Adv. 2025 May 30;11(22):eadu1864. doi: 10.1126/sciadv.adu1864. Epub 2025 May 30.

ABSTRACT

H3K9 methylation, a conserved heterochromatin marker, is crucial for chromosome segregation and gene regulation. Clr4 is the sole known methyltransferase catalyzing H3K9 methylation in Schizosaccharomyces pombe. Clr4 K455/K472 automethylation and H3K14 ubiquitination (H3K14Ub) are vital activators of Clr4, ensuring appropriate heterochromatin deposition and preventing deleterious silencing. While automethylation's activation mechanism is uncovered, the mechanism of H3K14Ub's significantly stronger stimulation on Clr4 remains unclear. Here, we determined the crystal structures of Clr4 bound to ubiquitinated and unmodified H3 peptides at 2.60 and 2.39 angstrom, which revealed a synergistic mechanism underlying the pronounced stimulatory effect: H3K14Ub increases substrate affinity through multivalent interactions and facilitates the allosteric transition of Clr4 from an inactive apo conformation to a hyperactive "catalyzing state," including conformational changes in the αC-SET-insertion region, autoregulatory loop, and the β9/10 loop. We finally propose a multilevel structural model for the Clr4 catalytic-regulatory cycle. This work provides structural insights into the interplay between histone modifications and their collective impact on epigenetic regulation.

PMID:40446033 | DOI:10.1126/sciadv.adu1864

Adv Sci (Weinh). 2025 May 30:e01956. doi: 10.1002/advs.202501956. Online ahead of print.

ABSTRACT

Idiopathic pulmonary fibrosis (IPF) is a prototype of chronic, progressive, and fibrotic lung disease. While advancing age is recognized as the most significant risk factor for both the development and mortality associated with pulmonary fibrosis, precise mechanisms underlying this association remain elusive. Here, Nephronectin (NPNT) is identified as an antiaging molecule, a potential major regulator of the progression of pulmonary fibrosis. In IPF patients, a marked reduction in NPNT expression is detected in lung tissues, which correlated with a decline in lung function. The study reveals that NPNT deficiency exacerbates bleomycin-induced senescence in alveolar epithelial cells, potentially intensifying fibrosis severity due to diminishes extracellular matrix turnover. Conversely, NPNT overexpression in the alveolar epithelium improves lung respiratory function and enhances resistance to aging and fibrosis. Mechanistically, NPNT inhibits the hyperactivation of LATS1 and MOB1, facilitates YAP1 nuclear translocation, and suppresses YAP1 ubiquitination and degradation, contingent upon the interaction between NPNT and ITGA3. Notably, pharmacological elevation of NPNT protein levels using Escin has been shown to alleviate pulmonary fibrosis and improve lung function in mice. The findings shed light on the key mechanism underlying stress-induced senescence and fibrosis, and offer a promising framework for interventions targeting aging-related diseases.

PMID:40444575 | DOI:10.1002/advs.202501956

J Sci Food Agric. 2025 May 30. doi: 10.1002/jsfa.14400. Online ahead of print.

ABSTRACT

BACKGROUND: The present study aimed to measure bioavailability (BA) indicators, including epithelial barrier function, apparent permeability (Papp) and efflux ratio, of 84 types of phytochemicals using Caco-2 cell and to develop predictive model systems using machine learning with a quantitative structure-property relationship (QSPR) model based on BA indicators and an Isomeric Simplified Molecular Input Line Entry System (SMILES). Analysis of phytochemicals was carried out with a validated HPLC analytical method.

RESULTS: With these BA indicators, Isomeric SMILES including information such as the stereochemistry, chemical structure and properties of phytochemicals was encoded to molecular descriptors using PaDEL-Descriptor and alvaDesc. The validity of the dataset was verified using principal component analysis, leverage plot and Williams plot. In the case of transepithelial electrical resistance (TEER), R2 Train is 0.86, root mean square error (RMSE)Train is 55.25, R2 Test is 0.63 and RMSETest is 74.77, respectively. Regarding the Papp, the model demonstrated strong performance on the training set with RMSETrain of 4.54 × 10-6 and R2 Train of 0.95 with the test set results (RMSETest = 6.23 × 10-6 and R2 Test = 0.91). For the efflux ratio, the modle explains 92% of the variance with RMSETrain of 0.39, R2 Train of 0.92, R2 Test of 0.85 and RMSETest of 0.71.

CONCLUSION: The present study suggests that a prediction system for bioavailability, including TEER, Papp and efflux ratio, can be developed using a QSPR model, which could contribute to advancements in discover of functional ingredients and drugs. © 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

PMID:40444409 | DOI:10.1002/jsfa.14400

J Cell Sci. 2025 May 30:jcs.263830. doi: 10.1242/jcs.263830. Online ahead of print.

ABSTRACT

Mitochondrial homeostasis is ensured through communication between diverse cellular organelles, including mitochondria, the endoplasmic reticulum (ER), lysosomes, and endosomes. While mitofusins regulate mitochondrial networks and ER contacts, their role in endosomal-mitochondrial interactions remains unclear. Previously, we reported that endosomal ubiquitin ligase, RFFL-positive vesicles are associated with damaged mitochondria and prime the organelle for PRKN recruitment. Now, we establish that RFFL is a ubiquitin ligase for MFN2. Using electron microscopy and confocal imaging analyses, we demonstrate that RFFL knockout cells exhibit enlarged mitochondrial morphology. RFFL interacts at an endogenous level with MFN2 and contributes to its ubiquitination upon mitochondrial damage. Recombinant RFFL interacts and ubiquitinates MFN2 protein in vitro. Furthermore, exogenous RFFL in a ligase-dependent manner specifically reduces the exogenous protein levels of both MFN1 and MFN2, but not that of DRP1, and also perturbs lipid homeostasis. Importantly, we show that hyperfused mitochondria morphology reported with expression of pathogenic disease mutants of MFN2 (T206I and R364W) of Charcot-Marie-Tooth disease type 2A can be rescued by RFFL co-expression. The study unravels novel mechanisms involving endosomal ubiquitin ligases in mitochondrial networks.

PMID:40444323 | DOI:10.1242/jcs.263830

Chem Sci. 2025 May 28. doi: 10.1039/d5sc01371b. Online ahead of print.

ABSTRACT

Thalidomide, lenalidomide, and their derivatives mimic glutarimide and aspartimide protein modifications that give rise to a motif recognized by the E3 ligase substrate adapter cereblon (CRBN). These cyclic imides have a chiral center that, given the biological significance of chirality, may influence CRBN's function and therapeutic applications. Here, we systematically examine cyclic imides in small molecules, peptides, and proteins to assess their racemization, CRBN engagement, ternary complex formation in vitro, and resulting degradation outcomes in cells. While the thalidomide-binding domain of CRBN consistently favors the (S)-stereoisomer across all cyclic imide small molecule ligands and engineered proteins, we find that, in some cases, the (R)-stereoisomer can bind to CRBN, either enhancing or hindering the eventual target engagement and degradation. Lenalidomide and its derivatives racemize more rapidly (t 50%ee = 4-5 h) than the C-terminal cyclic imide under non-enzymatic conditions. These findings highlight that although the (S)-stereoisomer of the cyclic imide is the primary ligand for the thalidomide-binding domain of CRBN, the (R)-stereoisomer, if present, has the potential to contribute to CRBN-dependent cellular activity.

PMID:40443985 | PMC:PMC12117711 | DOI:10.1039/d5sc01371b

Plant Commun. 2025 May 28:101389. doi: 10.1016/j.xplc.2025.101389. Online ahead of print.

ABSTRACT

Sugar regulation of hormonal signaling is crucial for optimizing growth under normal conditions and survival under environmental stresses. Previous studies indicate that sugar starvation causes the degradation of BRASSINAZOLE RESISTANT 1 (BZR1), the master transcription factor of the brassinosteroid (BR) signaling pathway, to inhibit growth. The molecular connection between sugar signaling and BZR1 degradation remains unknown. To identify the proteins that mediate starvation-induced BZR1 degradation, here, we performed a quantitative proteomic analysis of BZR1 interactome under starvation and identified UBIQUITIN PROTEIN LIGASE 3 (UPL3) as a sugar-regulated protein that mediates BZR1 degradation and regulates growth and survival according to sugar availability. The upl3 mutants show increased BZR1 accumulation and seedling size compared to the wild type when grown under sugar-limiting conditions but not when grown on sugar-containing media, indicating UPL3 mediates BZR1 degradation and growth inhibition under sugar-limiting conditions. While increasing growth under short-term starvation, the upl3 mutations substantially reduced survival after long-term starvation treatment. The increased-growth phenotype of upl3 is also observed when Target Of Rapamycin (TOR) is inactivated but not when BR synthesis is blocked, consistent with UPL3 regulating BZR1 degradation downstream of sugar-TOR signaling. Further, the UPL3 protein level is increased post-transcriptionally by starvation and TOR inhibition but decreased by sugar treatment. Our study identifies UPL3 as a key molecular link for sugar regulation of BR signaling. Sugar-TOR signaling inhibits UPL3 to promote BZR1 accumulation and growth, thereby optimizing growth and survival according to sugar availability.

PMID:40443036 | DOI:10.1016/j.xplc.2025.101389