bioRxiv [Preprint]. 2025 Feb 16:2025.02.13.637616. doi: 10.1101/2025.02.13.637616.

ABSTRACT

The human microbiome plays a crucial role in metabolism and thereby influences health and disease. Constraint-based reconstruction and analysis (COBRA) has proven an attractive framework to generate mechanism-derived hypotheses along the nutrition-host-microbiome-disease axis within the computational systems biology community. Unlike for human, no large-scale visualisation resource for microbiome metabolism has been available to date. To address this gap, we created the MicroMap, a manually curated microbiome metabolic network visualisation, which captures the metabolic content of over a quarter million microbial genome-scale metabolic reconstructions. The MicroMap contains 5,064 unique reactions and 3,499 unique metabolites, including for 98 drugs. The MicroMap allows users to intuitively explore microbiome metabolism, inspect microbial metabolic capabilities, and visualise computational modelling results. Further, the MicroMap shall serve as an educational tool to make microbiome metabolism accessible to broader audiences beyond computational modellers. For example, we utilised the MicroMap to generate a comprehensive collection of 257,429 visualisations, corresponding to the entire scope of our current microbiome reconstruction resources, to enable users to visually compare and contrast the metabolic capabilities for different microbes. The MicroMap seamlessly integrates with the Virtual Metabolic Human (VMH, www.vmh.life) and the COBRA Toolbox (opencobra.github.io), and is freely accessible at the MicroMap dataverse (https://dataverse.harvard.edu/dataverse/micromap), in addition to all the generated reconstruction visualisations.

PMID:39990405 | PMC:PMC11844556 | DOI:10.1101/2025.02.13.637616

Front Cell Dev Biol. 2025 Feb 7;13:1528281. doi: 10.3389/fcell.2025.1528281. eCollection 2025.

NO ABSTRACT

PMID:39989984 | PMC:PMC11842372 | DOI:10.3389/fcell.2025.1528281

Genetics. 2025 Feb 24:iyaf026. doi: 10.1093/genetics/iyaf026. Online ahead of print.

ABSTRACT

The contributions of genetic interactions to natural trait variation are challenging to estimate experimentally, as current approaches for detecting epistasis are often underpowered. Powerful mapping approaches such as bulk segregant analysis, wherein individuals with extreme phenotypes are pooled for genotyping, obscure epistasis by averaging over genotype combinations. To accurately characterize and quantify epistasis underlying natural trait variation, we have engineered strains of the budding yeast Saccharomyces cerevisiae to enable crosses where one parent's chromosome is fixed while the rest of the chromosomes segregate. These crosses allow us to use bulk segregant analysis to identify quantitative trait loci (QTL) whose effects depend on alleles on the fixed parental chromosome, indicating a genetic interaction with that chromosome. Our method, which we term epic-QTL (for epistatic-with-chromosome QTL) analysis, can thus identify interaction loci with high statistical power. Here we perform epic-QTL analysis of copper resistance with chromosome I or VIII fixed in a cross between divergent naturally derived strains. We find seven loci that interact significantly with chromosome VIII and none that interact with chromosome I, the smallest of the 16 budding yeast chromosomes. Each of the seven interactions alters the magnitude, rather than the direction, of an additive QTL effect. We also show that fixation of one source of variation-in this case chromosome VIII, which contains the large-effect QTL mapping to CUP1-increases power to detect the contributions of other loci to trait differences.

PMID:39989051 | DOI:10.1093/genetics/iyaf026

Mucosal Immunol. 2025 Feb 21:S1933-0219(25)00023-6. doi: 10.1016/j.mucimm.2025.02.005. Online ahead of print.

ABSTRACT

Interleukin-10 (IL-10) is an immunomodulatory cytokine critical for intestinal immune homeostasis. IL-10 is produced by various immune cells but IL-10 receptor signaling in intestinal CX3CR1+ mononuclear phagocytes is necessary to prevent spontaneous colitis in mice. Here, we utilized fluorescent protein reporters and cell-specific targeting and found that Rorc-expressing innate lymphoid cells (ILCs) produce IL-10 in response to anti-CD40-mediated intestinal inflammation. Deletion of Il10 specifically in Rorc-expressing ILCs led to phenotypic changes in intestinal macrophages and exacerbated both innate and adaptive immune-mediated models of experimental colitis. The population of IL-10+ producing ILCs shared markers with both ILC2 and ILC3 with nearly all ILC3s being of NCR+ subtype. Interestingly, Ccl26 was enriched in IL-10+ ILCs and markedly reduced in IL-10-deficient ILC3s. Since CCL26 is a ligand for CX3CR1, we employed RNA in situ hybridization and observed increased numbers of ILCs in close proximity to Cx3cr1-expressing cells under inflammatory conditions. Finally, we generated a transgenic RorctdTomato reporter mouse that faithfully marked RORγt+ cells that could rescue disease pathology and aberrant macrophage phenotype following adoptive transfer into mice with selective Il10 deficiency in ILC3s. These results demonstrate that IL-10 production by a population of ILCs functions to promote immune homeostasis in the intestine possibly via direct effects on intestinal macrophages.

PMID:39988202 | DOI:10.1016/j.mucimm.2025.02.005

Metab Eng. 2025 Feb 21:S1096-7176(25)00024-2. doi: 10.1016/j.ymben.2025.02.009. Online ahead of print.

ABSTRACT

Polyhydroxyalkanoates (PHA) with high 3-hydroxyvalerate (3HV) monomer ratios lead to their accelerated biodegradation and improved thermal and mechanical properties. In this study, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) with a broad range of 3HV ratios were produced and characterized using the next generation industrial biotechnology (NGIB) chassis Halomonas bluephagenesis (H. bluephagenesis). Wild type H. bluephagenesis was found to produce P(3HB-co-66.31mol% 3HV) when cultured in the presence of valerate. Deletion on the functional enoyl-CoA hydratase (fadB1) increased to 93.11 mol% 3HV in the PHBV copolymers. Through tuning the glucose and valerate co-feeding, PHBV with controllable 3HV ratios were adjusted to range from 0-to-93.6 mol% in shake-flask studies. Metabolic weakening of the β-oxidation pathway paired with flux limitation to the native 3HB synthesis pathway were used to reach the highest reported 98.3 mol% 3HV by H. bluephagenesis strain G34B grown in shake flasks. H. bluephagenesis strain G34B was grown to 71.42 g/L cell dry weight (CDW) containing 74.12 wt% P(3HB-co-17.97 mol% 3HV) in 7 L fermentors. Mechanical properties of PHBV with 0, 22.81, 42.76, 73.49 and 92.17 mol% 3HV were characterized to find not linearly related to increased 3HV ratios. Engineered H. bluephagenesis has demonstrated as a platform for producing PHBV of various properties.

PMID:39988026 | DOI:10.1016/j.ymben.2025.02.009

ISME J. 2025 Feb 23:wraf034. doi: 10.1093/ismejo/wraf034. Online ahead of print.

ABSTRACT

Numerous studies and clinical applications have underscored the therapeutic potential of the indigenous gut bacterium Akkermansia muciniphila in various diseases. However, our understanding of how A. muciniphila senses and responds to host gastrointestinal signals remains limited. Here, we demonstrate that A. muciniphila exhibits rapid growth, facilitated by its self-produced carbon dioxide, with key enzymes such as glutamate decarboxylase, carbonic anhydrase, and pyruvate ferredoxin oxidoreductase playing pivotal roles. Additionally, we design a novel delivery system, comprising calcium carbonate, inulin, A. muciniphila, and sodium alginate, which enhances A. muciniphila growth and facilitates the expression of part probiotic genes in mice intestinal milieu. Notably, the administration of this delivery system induces weight loss in mice fed high-fat diets. Furthermore, we elucidate the significant impact of carbon dioxide on the composition and functional genes of the human gut microbiota, with genes encoding carbonic anhydrase and amino acid metabolism enzymes exhibiting heightened responsiveness. These findings reveal a novel mechanism by which gut commensal bacteria sense and respond to gaseous molecules, thereby promoting growth. Moreover, they suggest the potential for designing rational therapeutic strategies utilizing live bacterial delivery systems to enhance probiotic growth and ameliorate gut microbiota-related diseases.

PMID:39987558 | DOI:10.1093/ismejo/wraf034

Br J Cancer. 2025 Feb 22. doi: 10.1038/s41416-025-02958-x. Online ahead of print.

ABSTRACT

Acute lymphoblastic leukaemia (ALL) is a rare and heterogeneous disease. The ALLTogether consortium has implemented a treatment protocol to improve outcome and reduce treatment-related toxicity across much of Europe. The consortium provides the opportunity to design translational research on patient material stored in national biobanks. However, there are currently no standardized guidelines for the types of material, processing, and storage for leukaemia biobanking. To address this gap, we conducted a modified Delphi survey among 53 experts in different roles related to leukaemia. The first round consisted of 63 statements asking for level of agreement. The second round refined some to reach consensus, using yes-no and multiple-option answers. Key recommendations include cryopreservation of cells from diagnosis, post-induction, post-consolidation, and relapse, with at least two aliquots of plasma and serum, and cerebrospinal fluid from diagnosis, day15, and post-induction. It was advised to distribute cells across multiple vials for various research projects, and to collect data on sample processing, cell viability, and blast percentage. Quality monitoring and user feedback were strongly recommended. The Delphi survey resulted in strong recommendations that can be used by national biobanks to harmonize storage of samples from patients with ALL and ensure high-quality cryopreserved cells for research studies.

PMID:39987377 | DOI:10.1038/s41416-025-02958-x

Commun Biol. 2025 Feb 22;8(1):279. doi: 10.1038/s42003-025-07594-y.

ABSTRACT

The identification of microglia subtypes is important for understanding the role of innate immunity in neurodegenerative diseases. Current methods of unsupervised cell type identification assume a small noise-to-signal ratio of transcriptome measurements to produce well-separated cell clusters. However, identification of subtypes can be obscured by gene expression noise, which diminishes the distances in transcriptome space between distinct cell types, blurs boundaries, and reduces reproducibility. Here we use Fokker-Planck (FP) diffusion maps to model cellular differentiation as a stochastic process whereby cells settle into local minima that correspond to cell subtypes, in a potential landscape constructed from transcriptome data using a nearest neighbor graph approach. By applying critical transition fields, we identify individual cells on the verge of transitioning between subtypes, revealing microglial cells in an inactivated, homeostatic state before radially transitioning into various specialized subtypes. Specifically, we show that cells from Alzheimer's disease patients are enriched in a microglia subtype associated to antigen presentation and T-cell recruitment, and are depleted in an anti-inflammatory subtype.

PMID:39987247 | DOI:10.1038/s42003-025-07594-y

Cell Genom. 2025 Feb 16:100775. doi: 10.1016/j.xgen.2025.100775. Online ahead of print.

ABSTRACT

Most GWAS loci are presumed to affect gene regulation; however, only ∼43% colocalize with expression quantitative trait loci (eQTLs). To address this colocalization gap, we map eQTLs, chromatin accessibility QTLs (caQTLs), and histone acetylation QTLs (haQTLs) using molecular samples from three early developmental-like tissues. Through colocalization, we annotate 10.4% (n = 540) of GWAS loci in 15 traits by QTL phenotype, temporal specificity, and complexity. We show that integration of chromatin QTLs results in a 2.3-fold higher annotation rate of GWAS loci because they capture distal GWAS loci missed by eQTLs, and that 5.4% (n = 13) of GWAS colocalizing eQTLs are early developmental specific. Finally, we utilize the iPSCORE multiomic QTLs to prioritize putative causal variants overlapping transcription factor motifs to elucidate the potential genetic underpinnings of 296 GWAS-QTL colocalizations.

PMID:39986281 | DOI:10.1016/j.xgen.2025.100775

Plant J. 2025 Feb;121(4):e70019. doi: 10.1111/tpj.70019.

ABSTRACT

Sugarcane is a crop that accumulates sucrose with high photosynthesis efficiency. Therefore, the feedback regulation of sucrose on photosynthesis is crucial for improving sugarcane yield. Saccharum spontaneum and Saccharum officinarum are the two founding Saccharum species for modern sugarcane hybrids. S. spontaneum exhibits a higher net photosynthetic rate but lower sucrose content than S. officinarum. However, the mechanism underlying the negative feedback regulation of photosynthesis by sucrose remains poorly understood. This study investigates the effects of exogenous sucrose treatment on S. spontaneum and S. officinarum. Exogenous sucrose treatment increases sucrose content in the leaf base but inhibits photosynthetic efficiency and the expression of photosynthesis-related pathway genes (including RBCS and PEPC) in both species. However, gene expression patterns differed significantly, with few differentially expressed genes (DEGs) shared between the two species, indicating a differential response to exogenous sucrose. The expression networks of key genes involved in sugar metabolism, sugar transport, and PEPC and RBCS showed divergence between two species. Additionally, DEGs involved in the pentose phosphate pathway and the metabolism of alanine, aspartate, and glutamate metabolism were uniquely enriched in S. spontaneum, potentially contributing to the differential changes in sucrose content in the tip between the two species. We propose a model of the mechanisms underlying the negative feedback regulation of photosynthesis by sucrose in the leaves of S. spontaneum and S. officinarum. Our findings enhance the understanding of sucrose feedback regulation on photosynthesis and provide insights into the divergent molecular mechanisms of sugar accumulation in Saccharum.

PMID:39985806 | DOI:10.1111/tpj.70019

Proteins. 2025 Feb 22. doi: 10.1002/prot.26810. Online ahead of print.

ABSTRACT

Protein sequence design is a highly challenging task, aimed at discovering new proteins that are more functional and producible under laboratory conditions than their natural counterparts. Deep learning-based approaches developed to address this problem have achieved significant success. However, these approaches often do not adequately emphasize the functional properties of proteins. In this study, we developed a heuristic optimization method to enhance key functionalities such as solubility, flexibility, and stability, while preserving the structural integrity of proteins. This method aims to reduce laboratory demands by enabling a design that is both functional and structurally sound. This approach is particularly valuable for the synthetic production of proteins with anti-inflammatory properties and those used in gene therapy. The designed proteins were initially evaluated for their ability to preserve natural structures using recovery and confidence metrics, followed by assessments with the AlphaFold tool. Additionally, natural protein sequences were mutated using a genetic algorithm and compared with those designed by our method. The results demonstrate that the protein sequences generated by our method exhibit much greater similarity to native protein sequences and structures. The code and sequences for the designed proteins are available at https://github.com/aysenursoyturk/HMHO.

PMID:39985803 | DOI:10.1002/prot.26810

STAR Protoc. 2025 Feb 21;6(1):103649. doi: 10.1016/j.xpro.2025.103649. Online ahead of print.

ABSTRACT

The tri-methylation of histone H3 on K4 (H3K4me3) is a key epigenetic modification that is predominantly found at active gene promoters and is deposited by the complex of proteins associated with SET1 (COMPASS). CXXC zinc finger protein 1 (Cfp1) regulates this process by recruiting SET1 to chromatin and recognizing H3K4me3 via its plant homeodomain (Cfp1PHD). Here, we present a protocol for the purification and crystallization of the Drosophila melanogaster Cfp1PHD domain in complex with an H3K4me3 peptide (PDB: 9C0O). We describe steps for obtaining highly pure Cfp1PHD and diffraction-quality crystals. We then detail procedures for rapidly identifying crystals containing the H3K4me3-bound form of the Cfp1PHD domain. For complete details on the use and execution of this protocol, please refer to Grégoire et al.1.

PMID:39985772 | DOI:10.1016/j.xpro.2025.103649

Cell Mol Life Sci. 2025 Feb 22;82(1):84. doi: 10.1007/s00018-025-05576-1.

ABSTRACT

Coenzyme A (CoA) is a crucial metabolite involved in various biological processes, encompassing lipid metabolism, regulation of mitochondrial function, and membrane modeling. CoA deficiency is associated with severe human diseases, such as Pantothenate Kinase-Associated Neurodegeneration (PKAN) and CoASY protein-associated neurodegeneration (CoPAN), which are linked to genetic mutations in Pantothenate Kinase 2 (PANK2) and CoA Synthase (CoASY). Although the association between CoA deficiency and mitochondrial dysfunction has been established, the underlying molecular alterations and mechanisms remain largely elusive. In this study, we investigated the detailed changes resulting from the functional decline of CoASY using the Drosophila model. Our findings revealed that a reduction of CoASY in muscle and brain led to degenerative phenotypes and apoptosis, accompanied by impaired mitochondrial integrity. The release of mitochondrial DNA was notably augmented, while the assembly and activity of mitochondrial electron transport chain (ETC) complexes, particularly complex I and III, were diminished. Consequently, this resulted in decreased ATP generation, rendering the fly more susceptible to energy insufficiency. Our findings suggest that compromised mitochondrial integrity and energy supply play a crucial role in the pathogenesis associated with CoA deficiency, thereby implying that enhancing mitochondrial integrity can be considered a potential therapeutic strategy in future interventions.

PMID:39985665 | DOI:10.1007/s00018-025-05576-1

J Agric Food Chem. 2025 Feb 22. doi: 10.1021/acs.jafc.4c12616. Online ahead of print.

ABSTRACT

Vibrio natriegens, a fast-growing bacterium, is an emerging chassis of next-generation industrial biotechnology capable of thriving under open and continuous culture conditions. Cadaverine, a valuable industrial C5 platform chemical, has various chemical and biological activities. This study found that V. natriegens exhibited superior tolerance to lysine, the substrate of cadaverine production. For the first time, a cadaverine synthesis pathway was introduced into V. natriegens for whole-cell catalysis of cadaverine from lysine. A high-efficiency cadaverine-producing strain harboring a toxin-antitoxin system, V. natriegens (pSEVA341-pTac-ldcC-pHbpBC-hbpBC) with lysE (PN96_RS17440) inactivation, was constructed. In 7 L bioreactors, the cadaverine titer increased from 115 g/L in the original strain to 158 g/L within 11 h of biotransformation, exhibiting a 37% increase in production. Its productivity reached 14.4 g/L/h with a conversion rate as high as 90%. These results confirm V. natriegens as an exceptional chassis for effective cadaverine bioproduction.

PMID:39985470 | DOI:10.1021/acs.jafc.4c12616

Exp Oncol. 2025 Feb 20;46(4):408-409. doi: 10.15407/exp-oncology.2024.04.408.

ABSTRACT

The Conference was organized on the initiative of the R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology of the National Academy of Sciences of Ukraine, the State Institution "SP Grigoriev Institute of Medical Radiology and Oncology of the National Academy of Medical Sciences of Ukraine", and public organizations "National Association of Oncologists of Ukraine" and "Ukrainian Society for Cancer Research". The cancer patient's health and the quality of life (QoL) was put in the focus of this conference. Various edges of cancer research were discussed by researchers together with medical doctors, clinical scientists, specialists in demography, economics, law, and the general public.

PMID:39985343 | DOI:10.15407/exp-oncology.2024.04.408

Nat Commun. 2025 Feb 21;16(1):1862. doi: 10.1038/s41467-025-57153-6.

ABSTRACT

Genetically engineered commensal bacteria are promising living drugs, however, their therapeutic molecules are frequently confined to their colonization sites. Herein, we report an oral protein delivery technology utilizing an engineered bacterial type zero secretion system (T0SS) via outer membrane vesicles (OMVs). We find that OMVs produced in situ by Escherichia coli Nissle 1917 (EcN) can penetrate the intact gut epithelial barrier to enter the circulation and that epithelial transcytosis involves pinocytosis and dynamin-dependent pathways. EcN is engineered to endogenously load various enzymes into OMVs, and the secreted enzyme-loaded OMVs are able to stably catalyze diverse detoxification reactions against digestive fluid and even enter the circulation. Using hyperuricemic mice and uricase delivery as a demonstration, we demonstrate that the therapeutic efficacy of our engineered EcN with a modified T0SS outperforms that with a direct protein secretion apparatus. The enzyme-loaded OMVs also effectively detoxify human serum samples, highlighting the potential for the clinical treatment of metabolic disorders.

PMID:39984501 | DOI:10.1038/s41467-025-57153-6

Nat Commun. 2025 Feb 21;16(1):1839. doi: 10.1038/s41467-025-56334-7.

ABSTRACT

Shaping embryonic tissues requires spatiotemporal changes in genetic and signaling activity as well as in tissue mechanics. Studies linking specific molecular perturbations to changes in the tissue physical state remain sparse. Here we study how specific genetic perturbations affecting different posterior tissues during zebrafish body axis elongation change their physical state, the resulting large-scale tissue flows, and posterior elongation. Using a custom analysis software to reveal spatiotemporal variations in tissue fluidity, we show that dorsal tissues are most fluid at the posterior end, rigidify anterior of this region, and become more fluid again yet further anteriorly. In the absence of notochord (noto mutants) or when the presomitic mesoderm is substantially reduced (tbx16 mutants), dorsal tissues elongate normally. Perturbations of posterior-directed morphogenetic flows in dorsal tissues (vangl2 mutants) strongly affect the speed of elongation, highlighting the essential role of dorsal cell flows in delivering the necessary material to elongate the axis.

PMID:39984461 | DOI:10.1038/s41467-025-56334-7

Nat Commun. 2025 Feb 21;16(1):1842. doi: 10.1038/s41467-025-56934-3.

ABSTRACT

Antibiotics that target multiple cellular functions are anticipated to be less prone to bacterial resistance. Here we hypothesize that while dual targeting is crucial, it is not sufficient in preventing resistance. Only those antibiotics that simultaneously target membrane integrity and block another cellular pathway display reduced resistance development. To test the hypothesis, we focus on three antibiotic candidates, POL7306, Tridecaptin M152-P3 and SCH79797, all of which fulfill the above criteria. Here we show that resistance evolution against these antibiotics is limited in ESKAPE pathogens, including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, while dual-target topoisomerase antibiotics are prone to resistance. We discover several mechanisms restricting resistance. First, de novo mutations result in only a limited elevation in resistance, including those affecting the molecular targets and efflux pumps. Second, resistance is inaccessible through gene amplification. Third, functional metagenomics reveal that mobile resistance genes are rare in human gut, soil and clinical microbiomes. Finally, we detect rapid eradication of bacterial populations upon toxic exposure to membrane targeting antibiotics. We conclude that resistance mechanisms commonly found in natural bacterial pathogens provide only limited protection to these antibiotics. Our work provides guidelines for the future development of antibiotics.

PMID:39984459 | DOI:10.1038/s41467-025-56934-3

J Proteome Res. 2025 Feb 21. doi: 10.1021/acs.jproteome.4c00677. Online ahead of print.

ABSTRACT

Many factors negatively affect a generalization of the findings in discovery proteomics. They include differentiation between patient cohorts, a variety of experimental conditions, etc. We presented a machine-learning-based workflow for proteomics data analysis, aiming at improving generalizability across multiple data sets. In particular, we customized the decision tree model by introducing a new parameter, min_groups_leaf, which regulates the presence of the samples from each data set inside the model's leaves. Further, we analyzed a trend for the feature importance's curve as a function of the novel parameter for feature selection to a list of proteins with significantly improved generalization. The developed workflow was tested using five proteomic data sets obtained for post-mortem human brain samples of Alzheimer's disease. The data sets consisted of 535 LC-MS/MS acquisition files. The results were obtained for two different pipelines of data processing: (1) MS1-only processing based on DirectMS1 search engine and (2) a standard MS/MS-based one. Using the developed workflow, we found seven proteins with expression patterns that were unique for asymptomatic Alzheimer patients. Two of them, Serotransferrin TRFE and DNA repair nuclease APEX1, may be potentially important for explaining the lack of dementia in patients with the presence of neuritic plaques and neurofibrillary tangles.

PMID:39984290 | DOI:10.1021/acs.jproteome.4c00677

Drug Discov Today. 2025 Feb 19:104315. doi: 10.1016/j.drudis.2025.104315. Online ahead of print.

ABSTRACT

Fucoidan, a polysaccharide from seaweed, holds promise as a drug delivery system and immune modulator; however, its exact mechanism of action remains unclear. As various carbohydrates play key roles in immune responses by binding to carbohydrate-binding proteins like lectins, fucoidan is hypothesized to interact with immune receptors, potentially driving its anticancer activities. However, structural variability, extraction-induced heterogeneity, and weak binding affinities pose challenges to research. Computational tools offer valuable insights into fucoidan-receptor interactions, addressing these challenges and enabling the design of more effective therapies. This review examines fucoidan's therapeutic activities, drug delivery potential, and receptor interactions, emphasizing computational approaches to advance immune modulation and anticancer applications using carbohydrate polymers.

PMID:39984116 | DOI:10.1016/j.drudis.2025.104315