J Proteome Res. 2025 Mar 4. doi: 10.1021/acs.jproteome.4c00795. Online ahead of print.

ABSTRACT

A nanosheath-flow capillary electrophoresis mass spectrometry (CE-MS) system with electrospray ionization was used to profile cationic metabolite cargo in exosomes secreted by nontumorigenic MCF-10A and tumorigenic MDA-MB-231 breast epithelial cells. An in-house-produced sheath liquid interface was developed and machined from PEEK to enable nanoflow volumes. Normalization of CE-MS peak areas to the total UV signal was employed to enhance quantitative accuracy and reduce variability. CE-MS-based metabolomics revealed increased purine synthesis intermediates and increased carnitine synthesis metabolites in MDA-MB-231-derived exosomes, with pathway enrichment indicating the activation of de novo purine pathways and upregulation of carnitine metabolism. In addition, nano-LC-MS-based proteomics revealed differential expression of ecto-5'-nucleotidase (NT5E) and mitochondrial aldehyde dehydrogenase (ALDH9A1), demonstrating metabolic alterations in related enzymatic steps. This study demonstrates the application of nanosheath-flow CE-MS for comprehensive and quantitative exosome metabolomics, uncovering metabolic reprogramming in purine and carnitine pathways between normal and cancerous breast cell lines and providing insight into exosome-mediated signaling of breast cancer metabolism.

PMID:40036676 | DOI:10.1021/acs.jproteome.4c00795

J Proteome Res. 2025 Mar 4. doi: 10.1021/acs.jproteome.4c00968. Online ahead of print.

ABSTRACT

Liquid chromatography-tandem mass spectrometry employing data-dependent acquisition (DDA) is a mature, widely used proteomics technique routinely applied to proteome profiling, protein-protein interaction studies, biomarker discovery, and protein modification analysis. Numerous tools exist for searching DDA data and myriad file formats are output as results. While some search and post processing tools include data visualization features to aid biological interpretation, they are often limited or tied to specific software pipelines. This restricts the accessibility, sharing and interpretation of data, and hinders comparison of results between different software pipelines. We developed Limelight, an easy-to-use, open-source, freely available tool that provides data sharing, analysis and visualization and is not tied to any specific software pipeline. Limelight is a data visualization tool specifically designed to provide access to the whole "data stack", from raw and annotated scan data to peptide-spectrum matches, quality control, peptides, proteins, and modifications. Limelight is designed from the ground up for sharing and collaboration and to support data from any DDA workflow. We provide tools to import data from many widely used open-mass and closed-mass search software workflows. Limelight helps maximize the utility of data by providing an easy-to-use interface for finding and interpreting data, all using the native scores from respective workflows.

PMID:40036265 | DOI:10.1021/acs.jproteome.4c00968

Proc Natl Acad Sci U S A. 2025 Mar 11;122(10):e2420499122. doi: 10.1073/pnas.2420499122. Epub 2025 Mar 4.

ABSTRACT

Cardiomyocyte hypertrophy is a key clinical predictor of heart failure. High-throughput and AI-driven screens have the potential to identify drugs and downstream pathways that modulate cardiomyocyte hypertrophy. Here, we developed LogiRx, a logic-based mechanistic machine learning method that predicts drug-induced pathways. We applied LogiRx to discover how drugs discovered in a previous compound screen attenuate cardiomyocyte hypertrophy. We experimentally validated LogiRx predictions in neonatal cardiomyocytes, adult mice, and two patient databases. Using LogiRx, we predicted antihypertrophic pathways for seven drugs currently used to treat noncardiac disease. We experimentally validated that escitalopram (Lexapro) and mifepristone inhibit hypertrophy of cultured cardiomyocytes in two contexts. The LogiRx model predicted that escitalopram prevents hypertrophy through an "off-target" serotonin receptor/PI3Kγ pathway, mechanistically validated using additional investigational drugs. Further, escitalopram reduced cardiomyocyte hypertrophy in a mouse model of hypertrophy and fibrosis. Finally, mining of both FDA and University of Virginia databases showed that patients with depression on escitalopram have a lower incidence of cardiac hypertrophy than those prescribed other serotonin reuptake inhibitors that do not target the serotonin receptor. Mechanistic machine learning by LogiRx discovers drug pathways that perturb cell states, which may enable repurposing of escitalopram and other drugs to limit cardiac remodeling through off-target pathways.

PMID:40035765 | DOI:10.1073/pnas.2420499122

FASEB J. 2025 Mar 15;39(5):e70443. doi: 10.1096/fj.202403156R.

ABSTRACT

AGGF1 encodes an angiogenic factor that causes vascular disease Klippel-Trenaunay syndrome when mutated. AGGF1 also acts at the top of the genetic regulatory hierarchy for mesodermal differentiation of hemangioblasts, multipotent stem cells for differentiation of blood cells and vascular cells. Alternative splicing (AS) is a post-transcriptional process that generates multiple mature mRNAs from a single primary transcript (pre-mRNA), producing protein diversity. Deregulation of AS leads to many human diseases. The physiological role and mechanism of AGGF1 in AS are not clear. Full-length transcriptome sequencing of human pulmonary artery endothelial cells (HPAECs) with AGGF1 silencing revealed 63 121 genes, including 1144 new unannotated genes, and showed that AGGF1 is a general splicing factor regulating AS of 436 genes, including SRSF6 regulating AS of many target genes. AGGF1 promoted the skipping of exon 3 that produces the full-length SRSF6 protein, an evolutionarily conserved AS event. Overexpression of full-length SRSF6 reversed the reduced cell proliferation, migration, and capillary tube formation of HPAECs with AGGF1 silencing. Knockdown of SRSF6 and overexpression of the shorter, alternatively spliced isoform of SRSF6 both inhibited HPAEC proliferation, migration, and capillary tube formation, whereas opposite results were obtained for overexpression of full-length SRSF6. Knockdown of srsf6 impaired development of ISVs in zebrafish, whereas overexpression of srsf6 enhanced vascular development and partially rescued impaired ISV development in zebrafish embryos with aggf1 knockdown. Overall, our findings reveal that AGGF1 is a general splicing factor, and that AGGF1-mediated exon 3 skipping of SRSF6 pre-mRNA is important for endothelial cell functions, angiogenesis, and vascular development.

PMID:40035560 | DOI:10.1096/fj.202403156R

Biotechnol Rep (Amst). 2025 Feb 9;45:e00882. doi: 10.1016/j.btre.2025.e00882. eCollection 2025 Mar.

ABSTRACT

Quality by design (QbD) is applied to the upstream process to maximize the RBD-Fc fusion protein production in CHO cells. The three factors (culture duration, temperature, and polyethyleneimine to plasmid DNA (PEI-Max/pDNA) ratio) were identified as critical process attributes based on risk analysis (FMEA) and further optimized by response surface to maximize the protein yields. Using a Box-Behnken design, the optimal conditions for RBD-Fc production were determined to be a culture duration of 5 days, a culture temperature of 34.4 °C, and a PEI-Max/pDNA ratio of 4.2:1 (w/w) with a predictive value of 48 mg/L (desirability of 92.8 %). The PEI-Max/pDNA ratio and its interaction with culture duration to express the highest yield (47.78 ± 2.30 mg/l). In addition, the purified CHO-produced RBD-Fc fusion protein was highly pure and strongly bound to its receptor, ACE2. Our finding demonstrated that the QBD tools can identify the critical parameters to facilitate scaling-up production.

PMID:40034964 | PMC:PMC11872631 | DOI:10.1016/j.btre.2025.e00882

J Pharm Anal. 2025 Feb;15(2):101047. doi: 10.1016/j.jpha.2024.101047. Epub 2024 Jul 25.

ABSTRACT

Image 1.

PMID:40034864 | PMC:PMC11874559 | DOI:10.1016/j.jpha.2024.101047

Front Immunol. 2025 Feb 17;16:1488851. doi: 10.3389/fimmu.2025.1488851. eCollection 2025.

ABSTRACT

We describe the establishment and current content of the ImmuneCODE™ database, which includes hundreds of millions of T-cell Receptor (TCR) sequences from over 1,400 subjects exposed to or infected with the SARS-CoV-2 virus, as well as over 160,000 high-confidence SARS-CoV-2-associated TCRs. This database is made freely available, and the data contained in it can be used to assist with global efforts to understand the immune response to the SARS-CoV-2 virus and develop new interventions.

PMID:40034696 | PMC:PMC11873104 | DOI:10.3389/fimmu.2025.1488851

Bioinform Biol Insights. 2025 Mar 2;19:11779322241271565. doi: 10.1177/11779322241271565. eCollection 2025.

ABSTRACT

Breast cancer is a highly heterogeneous disorder characterized by dysregulated expression of number of genes and their cascades. It is one of the most common types of cancer in women posing serious health concerns globally. Recent developments and discovery of specific prognostic biomarkers have enabled its application toward developing personalized therapies. The basic premise of this study was to investigate key signature genes and signaling pathways involved in triple-negative breast cancer using bioinformatics approach. Microarray data set GSE65194 from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus was used for identification of differentially expressed genes (DEGs) using R software. Gene ontology and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analyses were carried out using the ClueGO plugin in Cytoscape software. The up-regulated DEGs were primarily engaged in the regulation of cell cycle, overexpression of spindle assembly checkpoint, and so on, whereas down-regulated DEGs were employed in alteration to major signaling pathways and metabolic reprogramming. The hub genes were identified using cytoHubba from protein-protein interaction (PPI) network for top up-regulated and down-regulated DEG's plugin in Cytoscape software. The hub genes were validated as potential signature biomarkers by evaluating the overall survival percentage in breast cancer patients.

PMID:40034579 | PMC:PMC11873876 | DOI:10.1177/11779322241271565

Synth Syst Biotechnol. 2025 Feb 8;10(2):511-522. doi: 10.1016/j.synbio.2025.02.002. eCollection 2025 Jun.

ABSTRACT

Corynebacterium glutamicum is a versatile industrial microorganism for producing various amino acids. However, there have been no reports of well-defined C. glutamicum strains capable of hyperproducing l-tryptophan. This study presents a comprehensive metabolic engineering approach to establish robust C. glutamicum strains for l-tryptophan biosynthesis, including: (1) identification of potential targets by enzyme-constrained genome-scale modeling; (2) enhancement of the l-tryptophan biosynthetic pathway; (3) reconfiguration of central metabolic pathways; (4) identification of metabolic bottlenecks through comparative metabolome analysis; (5) engineering of the transport system, shikimate pathway, and precursor supply; and (6) repression of competing pathways and iterative optimization of key targets. The resulting C. glutamicum strain achieved a remarkable l-tryptophan titer of 50.5 g/L in 48h with a yield of 0.17 g/g glucose in fed-batch fermentation. This study highlights the efficacy of integrating computational modeling with systems metabolic engineering for significantly enhancing the production capabilities of industrial microorganisms.

PMID:40034180 | PMC:PMC11872490 | DOI:10.1016/j.synbio.2025.02.002

ArXiv [Preprint]. 2025 Feb 21:arXiv:2502.15597v1.

ABSTRACT

Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data and models are key to progress. For this reason, and recognizing that such models are a very special type of 'data', we argue that computational models, especially mechanistic models prevalent in medicine, physiology and systems biology, deserve a complementary set of guidelines. We propose the CURE principles, emphasizing that models should be Credible, Understandable, Reproducible, and Extensible. We delve into each principle, discussing verification, validation, and uncertainty quantification for model credibility; the clarity of model descriptions and annotations for understandability; adherence to standards and open science practices for reproducibility; and the use of open standards and modular code for extensibility and reuse. We outline recommended and baseline requirements for each aspect of CURE, aiming to enhance the impact and trustworthiness of computational models, particularly in biomedical applications where credibility is paramount. Our perspective underscores the need for a more disciplined approach to modeling, aligning with emerging trends such as Digital Twins and emphasizing the importance of data and modeling standards for interoperability and reuse. Finally, we emphasize that given the non-trivial effort required to implement the guidelines, the community moves to automate as many of the guidelines as possible.

PMID:40034129 | PMC:PMC11875277

New Phytol. 2025 Mar 3. doi: 10.1111/nph.20446. Online ahead of print.

ABSTRACT

Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is a crucial first step toward engineering improved drought resilience. However, the molecular responses to drought are complex as they depend on multiple factors, including the severity of drought, the profiled organ, its developmental stage or even the cell types therein. Thus, deciphering the transcriptional responses to drought is especially challenging. In this study, we investigated tissue-specific responses to mild drought (MD) in young Arabidopsis thaliana (Arabidopsis) leaves using single-cell RNA sequencing (scRNA-seq). To preserve transcriptional integrity during cell isolation, we inhibited RNA synthesis using the transcription inhibitor actinomycin D, and demonstrated the benefits of transcriptome fixation for studying mild stress responses at a single-cell level. We present a curated and validated single-cell atlas, comprising 50 797 high-quality cells from almost all known cell types present in the leaf. All cell type annotations were validated with a new library of reporter lines. The curated data are available to the broad community in an intuitive tool and a browsable single-cell atlas (http://www.single-cell.be/plant/leaf-drought). We show that the mesophyll contains two spatially separated cell populations with distinct responses to drought: one enriched in canonical abscisic acid-related drought-responsive genes, and another one enriched in genes involved in iron starvation responses. Our study thus reveals a dual adaptive mechanism of the leaf mesophyll in response to MD and provides a valuable resource for future research on stress responses.

PMID:40033544 | DOI:10.1111/nph.20446

Nat Struct Mol Biol. 2025 Mar 3. doi: 10.1038/s41594-025-01482-z. Online ahead of print.

ABSTRACT

Spermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution three-dimensional (3D) chromatin architecture of mouse male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin dictates the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin interactions between meiosis-specific super-enhancers (SEs) and their target genes precede activation of these SEs on autosomes. These meiotic SEs recruit the master transcription factor A-MYB (MYBL1) in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 facilitates the resolution of chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB help shape the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization regulates epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.

PMID:40033153 | DOI:10.1038/s41594-025-01482-z

Nat Microbiol. 2025 Mar 3. doi: 10.1038/s41564-025-01938-4. Online ahead of print.

ABSTRACT

Diet, microbiome, inflammation and host genetics have been linked to colorectal cancer development; however, it is not clear whether and how these factors interact to promote carcinogenesis. Here we used Il10-/- mice colonized with bacteria previously associated with colorectal cancer: enterotoxigenic Bacteroides fragilis, Helicobacter hepaticus or colibactin-producing (polyketide synthase-positive (pks+)) Escherichia coli and fed either a low-carbohydrate (LC) diet deficient in soluble fibre, a high-fat and high-sugar diet, or a normal chow diet. Colonic polyposis was increased in mice colonized with pks+ E. coli and fed the LC diet. Mechanistically, mucosal inflammation was increased in the LC-diet-fed mice, leading to diminished colonic PPAR-γ signalling and increased luminal nitrate levels. This promoted both pks+ E. coli growth and colibactin-induced DNA damage. PPAR-γ agonists or supplementation with dietary soluble fibre in the form of inulin reverted inflammatory and polyposis phenotypes. The pks+ E. coli also induced more polyps in mismatch-repair-deficient mice by inducing a senescence-associated secretory phenotype. Moreover, oncogenic effects were further potentiated by inflammatory triggers in the mismatch-repair-deficient model. These data reveal that diet and host genetics influence the oncogenic potential of a common bacterium.

PMID:40033140 | DOI:10.1038/s41564-025-01938-4

Commun Biol. 2025 Mar 3;8(1):355. doi: 10.1038/s42003-025-07768-8.

ABSTRACT

Plants cope with the environment by displaying large phenotypic variation. Two spectra of global plant form and function have been identified: a size spectrum from small to tall species with increasing stem tissue density, leaf size, and seed mass; a leaf economics spectrum reflecting slow to fast returns on investments in leaf nutrients and carbon. When species assemble to communities it is assumed that these spectra are filtered by the environment to produce community level functional composition. It is unknown what are the main drivers for community functional composition in a large area such as Amazonia. We use 13 functional traits, including wood density, seed mass, leaf characteristics, breeding system, nectar production, fruit type, and root characteristics of 812 tree genera (5211 species), and find that they describe two main axes found at the global scale. At community level, the first axis captures not only the 'fast-slow spectrum', but also most size-related traits. Climate and disturbance explain a minor part of this variance compared to soil fertility. Forests on poor soils differ largely in terms of trait values from those on rich soils. Trait composition and soil fertility exert a strong influence on forest functioning: biomass and relative biomass production.

PMID:40033015 | DOI:10.1038/s42003-025-07768-8

Nat Rev Rheumatol. 2025 Mar 3. doi: 10.1038/s41584-025-01231-y. Online ahead of print.

NO ABSTRACT

PMID:40032952 | DOI:10.1038/s41584-025-01231-y

Genome Res. 2025 Mar 3:gr.280021.124. doi: 10.1101/gr.280021.124. Online ahead of print.

ABSTRACT

SQANTI-reads leverages SQANTI3, a tool for the analysis of the quality of transcript models, to develop a read-level quality control framework for replicated long-read RNA-seq experiments. The number and distribution of reads, as well as the number and distribution of unique junction chains (transcript splicing patterns), in SQANTI3 structural categories are informative of raw data quality. Multisample visualizations of QC metrics are presented by experimental design factors to identify outliers. We introduce new metrics for 1) the identification of potentially under-annotated genes and putative novel transcripts and for 2) quantifying variation in junction donors and acceptors. We applied SQANTI-reads to two different datasets, a Drosophila developmental experiment and a multiplatform dataset from the LRGASP project and demonstrate that the tool effectively reveals the impact of read coverage on data quality, and readily identifies strong and weak splicing sites.

PMID:40032587 | DOI:10.1101/gr.280021.124

Genome Res. 2025 Mar 3:gr.279865.124. doi: 10.1101/gr.279865.124. Online ahead of print.

ABSTRACT

Long-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full-length transcripts. Using these technologies, researchers have reported tens of thousands of novel transcripts, even in well-annotated genomes, while developing new algorithms and experimental approaches to handle the noisy data. The LRGASP community effort benchmarked LRS methods in transcriptomics and validated many novel, lowly-expressed, sample-specific transcripts identified by long reads. These molecules represent deviations of the major transcriptional program, that were easily overlooked by short-read sequencing methods but are now captured by the full-length, single-molecule approach. This Perspective discusses the challenges and opportunities associated with LRS' capacity to unravel this fraction of the transcriptome, both in terms of transcriptome biology and genome annotation. For transcriptome biology, we need to develop novel experimental and computational methods to effectively differentiate technology errors from rare but real molecules. For genome annotation, we must agree on the strategy to capture molecular variability while still defining reference annotations that are useful for genome research.

PMID:40032585 | DOI:10.1101/gr.279865.124

Environ Pollut. 2025 Mar 1:125914. doi: 10.1016/j.envpol.2025.125914. Online ahead of print.

ABSTRACT

Microplastics are an increasingly prevalent form of pollution in coastal ecosystems. Current research focuses on understanding the impacts of such synthetic particles on the health and functioning of aquatic organisms. Recent studies have shown that invertebrates can accumulate microplastics in their tissue, impacting key functions such as growth, reproduction, feeding activity, and metabolism. Owing to their chemical composition, microplastics accumulating in the digestive tract of animals may alter the diversity and abundance of microbiota. Despite the important implications of such microbiota shifts on digestive ability and fitness, investigations on microplastics as causative agents are so far limited. In this study, we tested the effect of microfibers, on the digestive gland microbiota of the blue mussel Mytilus edulis after a 52-day exposure. Our findings show that exposure to microplastics can alter the composition of the digestive gland microbiota, with significant decreases in the classes of Actinobacteria, Bacteroidia, and significant increases for Alphaproteobacteria and Gammaproteobacteria. Furthermore, an increase in the number of genera containing potential pathogenic species for bivalves, such as Francisella and Vibrio, was detected. This suggests that accumulated microplastics pose a dual threat to filter-feeding organisms and the ecosystem services they provide. Further comparative studies are necessary to establish whether the microbiota shift is linked to the specific chemical composition of microplastics or whether there is an indirect link such as physiological stress resulting from ingestion.

PMID:40032227 | DOI:10.1016/j.envpol.2025.125914

Bone. 2025 Mar 1:117444. doi: 10.1016/j.bone.2025.117444. Online ahead of print.

ABSTRACT

Fracture healing is a complex biological process involving orchestrated interactions among cells, growth factors, and transcriptional pathways. Despite significant advancements in understanding bone repair, non-union and delayed healing remain prevalent, especially in patients with comorbidities such as aging, diabetes, or substance use. Murine models serve as a cornerstone in fracture healing research, offering genetic manipulability, cost-effectiveness, and biological relevance to humans. This scoping review consolidates findings from studies conducted between 2010 and 2024, focusing on mechanistic pathways derived from transcriptional analysis in secondary bone healing as identified through bulk RNA sequencing of murine models. Key mechanistic pathways were categorized and analyzed across the distinct phases of fracture healing-reactive, reparative, and remodeling-highlighting their unique roles in inflammation, ECM remodeling, cell proliferation, and tissue mineralization. The most recurrent mechanistic pathways included ECM-receptor interaction, focal adhesion, and signaling mechanisms such as MAPK and TGF-beta. Variability in methodologies and limited overlap among studies underscore the need for standardized protocols in RNA sequencing analysis. Additionally, comparisons across long bone fractures, hole defects, and craniofacial bone healing revealed shared molecular mechanisms alongside unique challenges, particularly in craniofacial models. This scoping review underscores the promise of integrating systems biology approaches with transcriptomic data to elucidate the intricate regulatory networks governing fracture repair. Addressing the identified gaps in early-phase healing and harmonizing research methodologies will advance therapeutic strategies to reduce non-union rates and improve clinical outcomes.

PMID:40032014 | DOI:10.1016/j.bone.2025.117444

Proc Natl Acad Sci U S A. 2025 Mar 11;122(10):e2417943122. doi: 10.1073/pnas.2417943122. Epub 2025 Mar 3.

ABSTRACT

Sperm morphogenesis is a tightly regulated differentiation process, disruption of which leads to sperm malfunction and male infertility. Here, we show that Tex38 knockout (KO) male mice are infertile. Tex38 KO spermatids exhibit excess retention of residual cytoplasm around the head, resulting in abnormal sperm morphology with backward head bending. TEX38 interacts and colocalizes with ZDHHC19, a testis-enriched acyltransferase catalyzing protein S-palmitoylation, at the plasma membrane of spermatids. ZDHHC19 and TEX38 are each downregulated in mouse testes lacking the other protein. TEX38 stabilizes and localizes ZDHHC19 to the plasma membrane of cultured cells and vice versa, consolidating their interdependence. Mice deficient in ZDHHC19 or harboring a C142S mutation that disables the palmitoyltransferase activity of ZDHHC19 display phenotypes resembling those of Tex38 KO mice. Strikingly, ZDHHC19 palmitoylates ARRDC5, an arrestin family protein regulating sperm differentiation. Overall, our findings indicate that TEX38 forms a stable complex with ZDHHC19 at the plasma membrane of spermatids, which governs downstream S-palmitoylation of proteins essential for morphological transformation of spermatids.

PMID:40030029 | DOI:10.1073/pnas.2417943122