1
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Mastrorilli V, Farioli-Vecchioli S. p21 as an essential regulator of neurogenic homeostasis in neuropathological conditions. Neural Regen Res 2026; 21:675-676. [PMID: 39820329 DOI: 10.4103/nrr.nrr-d-24-01255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Accepted: 12/02/2024] [Indexed: 01/19/2025] Open
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2
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Lewis EM, Becker O, Symons AN, LaCoss C, Baclig AJ, Guzman A, Sanders C, Gonzalez L, Warner LR, Lewis KA. The LARP6 La module from Tetrabaena socialis reveals structural and functional differences from plant and animal LARP6 homologues. RNA Biol 2025; 22:1-9. [PMID: 40181506 PMCID: PMC11988235 DOI: 10.1080/15476286.2025.2489303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/06/2025] [Accepted: 03/26/2025] [Indexed: 04/05/2025] Open
Abstract
This study identified the LARP6 La Module from Tetrabaena socialis (T. socialis), a four-celled green algae, in an effort to better understand the evolution of LARP6 structure and RNA-binding activity in multicellular eukaryotes. Using a combination of sequence alignments, domain boundary screens, and structural modelling, we recombinantly expressed and isolated the TsLARP6 La Module to > 98% purity for in vitro biochemical characterization. The La Module is stably folded and exerts minimal RNA binding activity against single-stranded homopolymeric RNAs. Surprisingly, it exhibits low micromolar binding affinity for the vertebrate LARP6 cognate ligand, a bulged-stem loop found in the 5'UTR of collagen type I mRNA, but does not bind double-stranded RNAs of similar size. These result suggests that the TsLARP6 La Module may prefer structured RNA ligands. In contrast, however, the TsLARP6 La Module does not exhibit the RNA chaperone activity that is observed in vertebrate homologs. Therefore, we conclude that protist LARP6 may have both distinct RNA ligands and binding mechanisms from the previously characterized LARP6 proteins of animals and vascular plants, thus establishing a distinct third class of the LARP6 protein family.
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Affiliation(s)
- Emily M. Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Olga Becker
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Alexis N. Symons
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Cora LaCoss
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
- San Marcos High School, San Marcos, TX, USA
| | - A. Jasmine Baclig
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID, USA
| | - Avery Guzman
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Charles Sanders
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Leticia Gonzalez
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Lisa R. Warner
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID, USA
| | - Karen A. Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
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Nair A, Khanna J, Kler J, Ragesh R, Sengupta K. Nuclear envelope and chromatin choreography direct cellular differentiation. Nucleus 2025; 16:2449520. [PMID: 39943681 PMCID: PMC11834525 DOI: 10.1080/19491034.2024.2449520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 12/28/2024] [Accepted: 12/30/2024] [Indexed: 02/20/2025] Open
Abstract
The nuclear envelope plays an indispensable role in the spatiotemporal organization of chromatin and transcriptional regulation during the intricate process of cell differentiation. This review outlines the distinct regulatory networks between nuclear envelope proteins, transcription factors and epigenetic modifications in controlling the expression of cell lineage-specific genes during differentiation. Nuclear lamina with its associated nuclear envelope proteins organize heterochromatin via Lamina-Associated Domains (LADs), proximal to the nuclear periphery. Since nuclear lamina is mechanosensitive, we critically examine the impact of extracellular forces on differentiation outcomes. The nuclear envelope is spanned by nuclear pore complexes which, in addition to their central role in transport, are associated with chromatin organization. Furthermore, mutations in the nuclear envelope proteins disrupt differentiation, resulting in developmental disorders. Investigating the underlying nuclear envelope controlled regulatory mechanisms of chromatin remodelling during lineage commitment will accelerate our fundamental understanding of developmental biology and regenerative medicine.
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Affiliation(s)
- Anjitha Nair
- Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
| | - Jayati Khanna
- Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
| | - Jashan Kler
- Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
| | - Rohith Ragesh
- Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
| | - Kundan Sengupta
- Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER) Pune, Maharashtra, India
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4
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Marcela K, Vojtech K, Marie B, Fanny D, Jaroslava Z, Suhanya P, Anna S, Elena N, Hanna P, Ed K, Wiep Klaas S, Gabriela BN. Genomic islands and molecular mechanisms relating to drug-resistance in Clostridioides ( Clostridium) difficile PCR ribotype 176. Emerg Microbes Infect 2025; 14:2482698. [PMID: 40130321 PMCID: PMC11983580 DOI: 10.1080/22221751.2025.2482698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 03/03/2025] [Accepted: 03/17/2025] [Indexed: 03/26/2025]
Abstract
OBJECTIVES To analyse characteristics of Clostridioides difficile PCR ribotype 176 clinical isolates from Poland, the Czech Republic and Slovakia with regard to the differences in its epidemiology. METHODS Antimicrobial susceptibility testing and whole genome sequencing were performed on a selected group of 22 clonally related isolates as determined by multilocus variable-number tandem repeat analysis (n = 509). Heterologous expression and functional analysis of the newly identified methyltransferase were performed. RESULTS Core genome multilocus sequence typing found 10-37 allele differences. All isolates were resistant to fluoroquinolones (gyrA_p. T82I), aminoglycosides with aac(6')-Ie-aph(2'')-Ia in six isolates. Erythromycin resistance was detected in 21/22 isolates and 15 were also resistant to clindamycin with ermB gene. Fourteen isolates were resistant to rifampicin with rpoB_p. R505K or p. R505K/H502N, and five to imipenem with pbp1_p. P491L and pbp3_p. N537K. PnimBG together with nimB_p. L155I were detected in all isolates but only five were resistant to metronidazole on chocolate agar. The cfrE, vanZ1 and cat-like genes were not associated with linezolid, teicoplanin and chloramphenicol resistance, respectively. The genome comparison identified six transposons carrying antimicrobial resistance genes. The ermB gene was carried by new Tn7808, Tn6189 and Tn6218-like. The aac(6')-Ie-aph(2'')-Ia were carried by Tn6218-like and new Tn7806 together with cfrE gene. New Tn7807 carried a cat-like gene. Tn6110 and new Tn7806 contained an RlmN-type 23S rRNA methyltransferase, designated MrmA, associated with high-level macrolide resistance in isolates without ermB gene. CONCLUSIONS Multidrug-resistant C. difficile PCR ribotype 176 isolates carry already described and unique transposons. A novel mechanism for erythromycin resistance in C. difficile was identified.
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Affiliation(s)
- Krutova Marcela
- Department of Medical Microbiology, Charles University Second Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Kovarovic Vojtech
- Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Brajerova Marie
- Department of Medical Microbiology, Charles University Second Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Demay Fanny
- Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Zikova Jaroslava
- Department of Medical Microbiology, Charles University Second Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Prasad Suhanya
- Department of Medical Microbiology, Charles University Second Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Soltesova Anna
- Department of Clinical Microbiology, Unilabs Slovakia Inc., Roznava, Slovakia
| | - Novakova Elena
- Department of Microbiology and Immunology, Comenius University Jessenius Faculty of Medicine in Martin, Martin, Slovakia
| | - Pituch Hanna
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Kuijper Ed
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
- Dutch National Expertise Centre for Clostridioides difficile infections, Leiden University Center for Infectious Diseases, Leiden and Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Experimental Bacteriology, Leiden University Center for Infectious Diseases, Leiden Medical Center, Leiden, Netherlands
| | - Smits Wiep Klaas
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
- Dutch National Expertise Centre for Clostridioides difficile infections, Leiden University Center for Infectious Diseases, Leiden and Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Experimental Bacteriology, Leiden University Center for Infectious Diseases, Leiden Medical Center, Leiden, Netherlands
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5
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Nguyen TD, Winek MA, Rao MK, Dhyani SP, Lee MY. Nuclear envelope components in vascular mechanotransduction: emerging roles in vascular health and disease. Nucleus 2025; 16:2453752. [PMID: 39827403 DOI: 10.1080/19491034.2025.2453752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 01/08/2025] [Accepted: 01/09/2025] [Indexed: 01/22/2025] Open
Abstract
The vascular network, uniquely sensitive to mechanical changes, translates biophysical forces into biochemical signals for vessel function. This process relies on the cell's architectural integrity, enabling uniform responses to physical stimuli. Recently, the nuclear envelope (NE) has emerged as a key regulator of vascular cell function. Studies implicate nucleoskeletal elements (e.g. nuclear lamina) and the linker of nucleoskeleton and cytoskeleton (LINC) complex in force transmission, emphasizing nucleo-cytoskeletal communication in mechanotransduction. The nuclear pore complex (NPC) and its component proteins (i.e. nucleoporins) also play roles in cardiovascular disease (CVD) progression. We herein summarize evidence on the roles of nuclear lamina proteins, LINC complex members, and nucleoporins in endothelial and vascular cell mechanotransduction. Numerous studies attribute NE components in cytoskeletal-related cellular behaviors to insinuate dysregulation of nucleocytoskeletal feedback and nucleocytoplasmic transport as a mechanism of endothelial and vascular dysfunction, and hence implications for aging and vascular pathophysiology.
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Affiliation(s)
- Tung D Nguyen
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
- The Center for Cardiovascular Research, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Michael A Winek
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Mihir K Rao
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Shaiva P Dhyani
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
| | - Monica Y Lee
- Department of Physiology and Biophysics, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
- The Center for Cardiovascular Research, The University of Illinois at Chicago - College of Medicine, Chicago, IL, USA
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6
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Xu Z, Asakawa S. Release and degradation of dissolved environmental RNAs from zebrafish cells. RNA Biol 2025; 22:1-12. [PMID: 40167163 PMCID: PMC12026185 DOI: 10.1080/15476286.2025.2486281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2024] [Revised: 02/27/2025] [Accepted: 03/21/2025] [Indexed: 04/02/2025] Open
Abstract
The sources and degradation profiles of dissolved environmental RNAs from fish in water remain unknown. In this study, laboratory experiments and mathematical modelling were conducted to investigate the permeability of RNA extracted from zebrafish cells through filters, the release of dissolved environmental RNAs from live and dying zebrafish cells, and the degradation of RNA extracted from zebrafish cells in a non-sterile aqueous environment. This research aimed to provide biological and ecological insights into fish RNAs dissolved in water. The results showed that most of the RNA extracted from zebrafish cells was detected in the filtrates after passage through 0.45 µm filters. Over the course of the 6-day experiment, dynamic levels of the RNAs in the liquid environment containing live or dying zebrafish cells were determined. The release and degradation rates of dissolved environmental RNA from zebrafish cells were calculated using mathematical modelling. RNA extracted from zebrafish cells degraded in non-sterile water in the tubes, and after 2 months, more than 15% of the RNAs in the water remained detectable. The half-life of the RNA in the tubes was approximately 20 ~ 43 days. The modelling results suggest that the levels of the dissolved environmental fish RNAs in natural waters or aquariums could be so low that it would be difficult to detect them using current techniques. The results obtained in this study will help develop new methods for measuring the dynamics of dissolved environmental fish RNAs in water and determining their significance.
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Affiliation(s)
- Zhongneng Xu
- Department of Ecology, Jinan University, Guangzhou, China
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
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Kim H, Bell T, Lee K, Jeong J, Bardwell JCA, Lee C. Identification of host genetic factors modulating β-lactam resistance in Escherichia coli harbouring plasmid-borne β-lactamase through transposon-sequencing. Emerg Microbes Infect 2025; 14:2493921. [PMID: 40231449 PMCID: PMC12024506 DOI: 10.1080/22221751.2025.2493921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 03/28/2025] [Accepted: 04/11/2025] [Indexed: 04/16/2025]
Abstract
Since β-lactam antibiotics are widely used, emergence of bacteria with resistance to them poses a significant threat to society. In particular, acquisition of genes encoding β-lactamase, an enzyme that degrades β-lactam antibiotics, has been a major contributing factor in the emergence of bacteria that are resistant to β-lactam antibiotics. However, relatively few genetic targets for killing these resistant bacteria have been identified to date. Here, we used a systematic approach called transposon-sequencing (Tn-Seq), to screen the Escherichia coli genome for host genetic factors that, when mutated, affect resistance to ampicillin, one of the β-lactam antibiotics, in a strain carrying a plasmid that encodes β-lactamase. This approach enabled not just the isolation of genes previously known to affect β-lactam resistance, but the additional loci skp, gshA, phoPQ and ypfN. Individual mutations in these genes modestly but consistently affected antibiotic resistance. We have identified that these genes are not only implicated in β-lactam resistance by itself but also play a crucial role in conditions associated with the expression of β-lactamase. GshA and phoPQ appear to contribute to β-lactam resistance by regulating membrane integrity. Notably, the overexpression of the uncharacterized membrane-associated protein, ypfN, has been shown to significantly enhance β-lactam resistance. We applied the genes identified from the screening into Salmonella Typhimurium and Pseudomonas aeruginosa strains, both critical human pathogens with antibiotic resistance, and observed their significant impact on β-lactam resistance. Therefore, these genes can potentially be utilized as therapeutic targets to control the survival of β-lactamase-producing bacteria.
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Affiliation(s)
- Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, South Korea
- Research Institute of Basic Sciences, Ajou University, Suwon, South Korea
| | - Travis Bell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jeongyun Jeong
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - James C. A. Bardwell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
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Sall I, Foxall R, Felth L, Maret S, Rosa Z, Gaur A, Calawa J, Pavlik N, Whistler JL, Whistler CA. Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic morphine. Gut Microbes 2025; 17:2446423. [PMID: 39800714 PMCID: PMC11730370 DOI: 10.1080/19490976.2024.2446423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 11/24/2024] [Accepted: 12/18/2024] [Indexed: 01/16/2025] Open
Abstract
The therapeutic benefits of opioids are compromised by the development of analgesic tolerance, which necessitates higher dosing for pain management thereby increasing the liability for drug dependence and addiction. Rodent models indicate opposing roles of the gut microbiota in tolerance: morphine-induced gut dysbiosis exacerbates tolerance, whereas probiotics ameliorate tolerance. Not all individuals develop tolerance, which could be influenced by differences in microbiota, and yet no study design has capitalized upon this natural variation. We leveraged natural behavioral variation in a murine model of voluntary oral morphine self-administration to elucidate the mechanisms by which microbiota influences tolerance. Although all mice shared similar morphine-driven microbiota changes that largely masked informative associations with variability in tolerance, our high-resolution temporal analyses revealed a divergence in the progression of dysbiosis that best explained sustained antinociception. Mice that did not develop tolerance maintained a higher capacity for production of the short-chain fatty acid (SCFA) butyrate known to bolster intestinal barriers and promote neuronal homeostasis. Both fecal microbial transplantation (FMT) from donor mice that did not develop tolerance and dietary butyrate supplementation significantly reduced the development of tolerance independently of suppression of systemic inflammation. These findings could inform immediate therapies to extend the analgesic efficacy of opioids.
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Affiliation(s)
- Izabella Sall
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Graduate program in Molecular and Evolutionary Systems Biology, University of New Hampshire, Durham, NH, USA
| | - Randi Foxall
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Lindsey Felth
- Center for Neuroscience, University of California–Davis, Davis, CA, USA
| | - Soren Maret
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Zachary Rosa
- Center for Neuroscience, University of California–Davis, Davis, CA, USA
| | - Anirudh Gaur
- Center for Neuroscience, University of California–Davis, Davis, CA, USA
| | - Jennifer Calawa
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Microbiology Graduate Program, University of New Hampshire, Durham, NH, USA
| | - Nadia Pavlik
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Jennifer L. Whistler
- Center for Neuroscience, University of California–Davis, Davis, CA, USA
- Department of Physiology and Membrane Biology, UC Davis School of Medicine, Davis, CA, USA
| | - Cheryl A. Whistler
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
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9
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Boukili M, Zmerli O, Fenollar F, Bellali S, Bou Khalil J. Tips and tricks for gut microbiota investigation using scanning electron microscopy (SEM): going from sample preparation to imaging and landscape analysis. Gut Microbes 2025; 17:2512016. [PMID: 40491126 DOI: 10.1080/19490976.2025.2512016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Revised: 05/19/2025] [Accepted: 05/22/2025] [Indexed: 06/11/2025] Open
Abstract
The Gut Microbiota (GM) remains a complex microbial ecosystem with many unknown facets despite significant technologic advancement. This study introduces a novel rapid technique using tabletop scanning electron microscopy (SEM) for investigating GM composition, focusing on Clostridioides difficile infection (CDI) as a representative model for dysbiosis-related diseases. Six stool sample preparation protocols were tested on 40 stool samples to develop an optimized SEM protocol. Protocol stability was evaluated after four-month storage. The optimized protocol produced high-resolution micrographs while maintaining sample integrity over time. SEM investigation of GM was done by analyzing ten stool samples (5-control and 5-C. difficile groups), imaged at low and high magnifications. Object detection analysis generated a SEM-based GM components database helping describe and compare microbial diversity variation between the groups. CDI group revealed a reduction in microbial diversity, compared to the controls. Epithelial and red blood cells were more prevalent in CDI group. Statistical analyses of objects proved clear clustering of samples into CDI and control groups. This study pioneers the proof-of-concept for using tabletop SEM to investigate GM components in a dysbiosis-related disease model. This concept emerges as a complementary technique capable of providing deeper insight to describe GM components previously elusive with other methods.
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Affiliation(s)
| | - Omar Zmerli
- Aix Marseille Univ, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, Marseille, France
- Aix Marseille Univ, APHM, SSA, RITMES, Marseille, France
| | | | - Jacques Bou Khalil
- IHU Méditerranée Infection, Marseille, France
- Aix Marseille Univ, APHM, MEPHI, Marseille, France
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10
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Hartasánchez DA, Dumond M, Dubrulle N, Monéger F, Boudaoud A. Highly expressed cell wall genes contribute to robustness of sepal size. PLANT SIGNALING & BEHAVIOR 2025; 20:2446858. [PMID: 39739543 DOI: 10.1080/15592324.2024.2446858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 12/18/2024] [Accepted: 12/19/2024] [Indexed: 01/02/2025]
Abstract
Reproducibility in organ size and shape is a fascinating trait of living organisms. The mechanisms underlying such robustness remain, however, to be elucidated. Taking the sepal of Arabidopsis as a model, we investigated whether variability of gene expression plays a role in variation of organ size and shape. Previous work from our team identified cell-wall related genes as being enriched among the genes whose expression is highly variable. We then hypothesized that the variation of measured morphological parameters in cell-wall related single knockout mutants could be correlated with the variation in gene expression of the corresponding gene (the knocked-out gene) in wild-type plants. We analyzed sepal size and shape from 16 cell-wall mutants and found that sepal size variability correlates positively, not with gene expression variation, but with mean gene expression of the corresponding gene in wild type. These findings support a contribution of cell-wall related genes to the robustness of sepal size.
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Affiliation(s)
- Diego A Hartasánchez
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Mathilde Dumond
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
| | - Nelly Dubrulle
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
| | - Françoise Monéger
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
| | - Arezki Boudaoud
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau Cedex, France
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11
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Chang TM, Fang WY, Hsu HP, Chu PY, Jiang SS, Huang KW, Hung WC, Lin HY, Tsai HJ. PCK2 promotes invasion and epithelial-to-mesenchymal transition in triple-negative breast cancer by promoting TGF-β/SMAD3 signaling through inhibiting TRIM67-mediated SMAD3 ubiquitination. Cancer Biol Ther 2025; 26:2478670. [PMID: 40081967 PMCID: PMC11913380 DOI: 10.1080/15384047.2025.2478670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 01/22/2025] [Accepted: 03/07/2025] [Indexed: 03/16/2025] Open
Abstract
PCK2, which encodes mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M), is upregulated in various cancers. We demonstrated high expression of PEPCK-M in approximately half of triple-negative breast cancers (TNBCs) previously. TNBC is associated with an aggressive phenotype and a high metastasis rate. In this study, we investigated the role of PCK2 in TNBC. PCK2 knockdown suppressed proliferation and mTOR signaling in TNBC cells. In addition, cell invasion/migration ability and the expression of epithelial-to-mesenchymal transition (EMT) markers were positively correlated with PCK2 expression in TNBC cells via regulation of transforming growth factor-β (TGF-β)/SMAD3 signaling. SMAD3 was positively regulated by PCK2 in TNBC cells. Knockdown of SMAD3 in PCK2-overexpressing TNBC cells reduced the expression levels of EMT markers, Snail and Slug, and suppressed cell invasion/migration. In addition, PCK2 knockdown attenuated the stimulatory effect of TGF-β on SMAD3 phosphorylation in TNBC cells. PEPCK-M promotes the protein and mRNA expression of SMAD3 via competitive binding to tripartite motif-containing 67 (TRIM67), an E3 ubiquitin ligase, to reduce SMAD3 ubiquitination, which leads to promoting nuclear translocation of SMAD3 and autoregulation of SMAD3 transcription. Moreover, high PCK2 mRNA expression was significantly associated with poor survival in TNBC patients. In conclusion, our study revealed for the first time that PCK2 activates TGF-β/SMAD3 signaling by regulating the expression and phosphorylation of SMAD3 by inhibiting TRIM67-mediated SMAD3 ubiquitination and promoting the stimulatory effect of TGF-β to promote TNBC invasion. The regulatory effect of PCK2 on mTOR and TGF-β/SMAD3 signaling suggests that PCK2 is a potential therapeutic target for suppressing TNBC progression.
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Affiliation(s)
- Tsung-Ming Chang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
- Department of Medical Laboratory Science, College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
| | - Wei-Yu Fang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Hui-Ping Hsu
- Department of Surgery, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Pei-Yi Chu
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Shih Sheng Jiang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Kuo-Wei Huang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Hui-You Lin
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Hui-Jen Tsai
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
- Department of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
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12
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Boulund U, Thorsen J, Trivedi U, Tranæs K, Jiang J, Shah SA, Stokholm J. The role of the early-life gut microbiome in childhood asthma. Gut Microbes 2025; 17:2457489. [PMID: 39882630 PMCID: PMC11784655 DOI: 10.1080/19490976.2025.2457489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 12/05/2024] [Accepted: 01/17/2025] [Indexed: 01/31/2025] Open
Abstract
Asthma is a chronic disease affecting millions of children worldwide, and in severe cases requires hospitalization. The etiology of asthma is multifactorial, caused by both genetic and environmental factors. In recent years, the role of the early-life gut microbiome in relation to asthma has become apparent, supported by an increasing number of population studies, in vivo research, and intervention trials. Numerous early-life factors, which for decades have been associated with the risk of developing childhood asthma, are now being linked to the disease through alterations of the gut microbiome. These factors include cesarean birth, antibiotic use, breastfeeding, and having siblings or pets, among others. Association studies have highlighted several specific microbes that are altered in children developing asthma, but these can vary between studies and disease phenotype. This demonstrates the importance of the gut microbial ecosystem in asthma, and the necessity of well-designed studies to validate the underlying mechanisms and guide future clinical applications. In this review, we examine the current literature on the role of the gut microbiome in childhood asthma and identify research gaps to allow for future microbial-focused therapeutic applications in asthma.
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Affiliation(s)
- Ulrika Boulund
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Urvish Trivedi
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Tranæs
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jie Jiang
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Shiraz A. Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
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13
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Zheng XQ, Wang DB, Jiang YR, Song CL. Gut microbiota and microbial metabolites for osteoporosis. Gut Microbes 2025; 17:2437247. [PMID: 39690861 DOI: 10.1080/19490976.2024.2437247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 11/13/2024] [Accepted: 11/26/2024] [Indexed: 12/19/2024] Open
Abstract
Osteoporosis is an age-related bone metabolic disease. As an essential endocrine organ, the skeletal system is intricately connected with extraosseous organs. The crosstalk between bones and other organs supports this view. In recent years, the link between the gut microecology and bone metabolism has become an important research topic, both in preclinical studies and in clinical trials. Many studies have shown that skeletal changes are accompanied by changes in the composition and structure of the gut microbiota (GM). At the same time, natural or artificial interventions targeting the GM can subsequently affect bone metabolism. Moreover, microbiome-related metabolites may have important effects on bone metabolism. We aim to review the relationships among the GM, microbial metabolites, and bone metabolism and to summarize the potential mechanisms involved and the theory of the gut‒bone axis. We also describe existing bottlenecks in laboratory studies, as well as existing challenges in clinical settings, and propose possible future research directions.
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Affiliation(s)
- Xuan-Qi Zheng
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
| | - Ding-Ben Wang
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
| | - Yi-Rong Jiang
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
| | - Chun-Li Song
- Department of Orthopaedics, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Spinal Disease Research, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Beijing, China
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14
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Park JH, Cho YR. Draw+: network-based computational drug repositioning with attention walking and noise filtering. Health Inf Sci Syst 2025; 13:14. [PMID: 39764174 PMCID: PMC11700073 DOI: 10.1007/s13755-024-00326-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Accepted: 12/11/2024] [Indexed: 02/02/2025] Open
Abstract
Purpose Drug repositioning, a strategy that repurposes already-approved drugs for novel therapeutic applications, provides a faster and more cost-effective alternative to traditional drug discovery. Network-based models have been adopted by many computational methodologies, especially those that use graph neural networks to predict drug-disease associations. However, these techniques frequently overlook the quality of the input network, which is a critical factor for achieving accurate predictions. Methods We present a novel network-based framework for drug repositioning, named DRAW+, which incorporates noise filtering and feature extraction using graph neural networks and attention mechanisms. The proposed model first constructs a heterogeneous network that integrates the drug-disease association network with the similarity networks of drugs and diseases, which are upgraded through reduced-rank singular value decomposition. Next, a subgraph surrounding the targeted drug-disease node pair is extracted, allowing the model to focus on local structures. Graph neural networks are then applied to extract structural representation, followed by attention walking to capture key features of the subgraph. Finally, a multi-layer perceptron classifies the subgraph as positive or negative, which indicates the presence of the link between the target node pair. Results Experimental validation across three benchmark datasets showed that DRAW+ outperformed seven state-of-the-art methods, achieving the highest average AUROC and AUPRC, 0.963 and 0.564, respectively. Moreover, DRAW+ demonstrated its robustness by achieving the best performance across two additional datasets, further confirming its generalizability and effectiveness in diverse settings. Conclusions The proposed network-based computational approach, DRAW+, demonstrates exceptional accuracy and robustness, confirming its effectiveness in drug repositioning tasks.
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Affiliation(s)
- Jong-Hoon Park
- Division of Software, Yonsei University, Mirae Campus, Yeonsedae-gil 1, Wonju-si, 26493 Gangwon-do Korea
| | - Young-Rae Cho
- Division of Software, Yonsei University, Mirae Campus, Yeonsedae-gil 1, Wonju-si, 26493 Gangwon-do Korea
- Division of Digital Healthcare, Yonsei University, Mirae Campus, Yeonsedae-gil 1, Wonju-si, Gangwon-do 26493 Korea
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15
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Su F, Su M, Wei W, Wu J, Chen L, Sun X, Liu M, Sun S, Mao R, Bourgonje AR, Hu S. Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease. Gut Microbes 2025; 17:2476570. [PMID: 40063366 PMCID: PMC11901428 DOI: 10.1080/19490976.2025.2476570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 02/14/2025] [Accepted: 03/03/2025] [Indexed: 03/14/2025] Open
Abstract
Numerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors. In this review, we introduce the interactome concept to systematically summarize how intestinal dysbiosis is involved in IBD pathogenesis in terms of microbial composition, functionality, genomic structure, transcriptional activity, and downstream proteins and metabolites. Meanwhile, this review also aims to present an updated overview of the relevant mechanisms, high-throughput multi-omics methodologies, different types of multi-omics cohort resources, and computational methods used to understand host-microbiota interactions in the context of IBD. Finally, we discuss the challenges pertaining to the integration of multi-omics data in order to reveal host-microbiota cross-talk and offer insights into relevant future research directions.
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Affiliation(s)
- Fengyuan Su
- Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Meng Su
- The First Clinical Medical School, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Wenting Wei
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jiayun Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Leyan Chen
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Xiqiao Sun
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Moyan Liu
- Amsterdam UMC location Academic Medical Center, Department of Experimental Vascular Medicine, Amsterdam, The Netherlands
| | - Shiqiang Sun
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ren Mao
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Arno R. Bourgonje
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shixian Hu
- Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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16
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Watkins L, Li M, Wu B. Translation elongation: measurements and applications. RNA Biol 2025; 22:1-10. [PMID: 40377059 PMCID: PMC12087489 DOI: 10.1080/15476286.2025.2504727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/22/2025] [Accepted: 05/06/2025] [Indexed: 05/18/2025] Open
Abstract
Translation converts genetic information in mRNAs into functional proteins. This process occurs in four major steps: initiation, elongation, termination and ribosome recycling; each of which profoundly impacts mRNA stability and protein yield. Over recent decades, regulatory mechanisms governing these aspects of translation have been identified. In this review, we focus on the elongation phase, reviewing the experimental methods used to measure elongation rates and discussing how the measurements shed light on the factors that regulate elongation and ultimately gene expression.
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Affiliation(s)
- Leslie Watkins
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mulin Li
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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17
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Li Y, Bai R, Zhu Y, Shi P, Wang T, Zhou D, Zhou J, Zhu T, Zhang X, Gu R, Ding X, Chen H, Wang X, Zhu Z. Genetic variation in gut microbe as a key regulator of host social behavior in C. elegans. Gut Microbes 2025; 17:2490828. [PMID: 40223740 PMCID: PMC12005443 DOI: 10.1080/19490976.2025.2490828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 02/25/2025] [Accepted: 03/25/2025] [Indexed: 04/15/2025] Open
Abstract
Gut microbiota have been shown to influence the social behaviors of their hosts, while variations in host genetics can affect the composition of the microbiome. Nonetheless, the degree to which genetic variations in microbial populations impact host behavior, as well as any potential transgenerational effects, remains inadequately understood. Utilizing C. elegans as a model organism, we identified 77 strains of E. coli from a total of 3,983 mutants that significantly enhanced aggregation behavior through various neurobehavioral pathways. This discovery underscores a collaborative regulatory mechanism between microbial genetics and host behavior. Notably, we observed that some mutant bacteria might affect social behavior via the mitochondrial pathway. Additionally, the modulation of social behavior has been identified as a heritable trait in offspring. Our results provide a novel perspective on the regulatory role of microbial genetic variation in host behavior, which may have significant implications for human studies and the development of genetically engineered probiotics aimed at enhancing well-being across generations.
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Affiliation(s)
- Ying Li
- Jiangsu Engineering Center for Precision Diagnosis and Treatment Research of Polygenic Diseases, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
- Medical Technology College, Xuzhou Medical University, Xuzhou, China
| | - Ruijie Bai
- The First Clinical College, Xuzhou Medical University, Xuzhou, China
| | - Yao Zhu
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Peng Shi
- Jiangsu Engineering Center for Precision Diagnosis and Treatment Research of Polygenic Diseases, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Tao Wang
- Jiangsu Engineering Center for Precision Diagnosis and Treatment Research of Polygenic Diseases, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Dianshuang Zhou
- Jiangsu Engineering Center for Precision Diagnosis and Treatment Research of Polygenic Diseases, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Jianteng Zhou
- Jiangsu Engineering Center for Precision Diagnosis and Treatment Research of Polygenic Diseases, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Tao Zhu
- Jiangsu Engineering Center for Precision Diagnosis and Treatment Research of Polygenic Diseases, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Xinrong Zhang
- Jiangsu Engineering Center for Precision Diagnosis and Treatment Research of Polygenic Diseases, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Rongrong Gu
- Jiangsu Engineering Center for Precision Diagnosis and Treatment Research of Polygenic Diseases, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Xiaoyue Ding
- Jiangsu Engineering Center for Precision Diagnosis and Treatment Research of Polygenic Diseases, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Hao Chen
- Department of Neurology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiangming Wang
- Department of Cell Biology, Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Capital Medical University, Beijing, China
| | - Zuobin Zhu
- Jiangsu Engineering Center for Precision Diagnosis and Treatment Research of Polygenic Diseases, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
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18
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Schlicht K, Pape L, Rohmann N, Knappe C, Epe J, Geisler C, Pohlschneider D, Brodesser S, Kruse L, Rohlfing ME, Hartmann K, Türk K, Marquardt J, Beckmann J, von Schönfels W, Beckmann A, Wietzke-Braun P, Schulte DM, Hollstein T, Demetrowitsch T, Jensen-Kroll J, Brix F, Schreiber S, Franke A, Schwarz K, Waschina S, Laudes M. Prediabetes and type 2 diabetes but not obesity are associated with alterations in bile acid related gut microbe-microbe and gut microbe-host community metabolism. Gut Microbes 2025; 17:2474143. [PMID: 40045464 PMCID: PMC11901388 DOI: 10.1080/19490976.2025.2474143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 01/20/2025] [Accepted: 02/25/2025] [Indexed: 03/14/2025] Open
Abstract
The interplay between bile acids (BAs) and metabolic diseases has gained importance in recent years, with a variety of studies investigating their relationship with diverging results. Therefore, in the present study we performed a detailed analysis of BA metabolism in 492 subjects with different metabolic phenotypes. Besides microbiomics and metabolomics this investigation included in silico analysis of community metabolism to examine metabolic interchange between different microbes as well as microbes and the human host. Our findings revealed distinct changes in the BA profiles of patients with diabetes and prediabetes, whereas obesity alone had no influence on circulating BAs. Impaired glycemic control led to increased circulating BAs, a shift toward more secondary BAs, and an increase in the ratio of glycine to taurine-conjugated BAs. Additional analyses revealed that the ratio of glycine to taurine conjugation demonstrated variations between the single BAs, cholic acid (CA), chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA), regardless of the metabolic status, with CA having a higher fraction of taurine conjugation. Furthermore, we found that microbiome alterations are associated with BAs, independent of diabetes or obesity. Analysis of microbial community metabolism revealed differential relative pathway abundance in relation to diabetes, particularly those related to membrane and polyamine synthesis. Increased bacterial cross-feeding of polyamines, galactose, and D-arabinose also coincided with an increase in BA. Notably, our serum metabolome analysis mirrored several of the previously in silico predicted exchanged metabolites, especially amino acid metabolism. Therefore, targeting BA metabolism may be a future approach for the treatment of metabolic diseases, especially prediabetes and type 2 diabetes.
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Affiliation(s)
- Kristina Schlicht
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Lea Pape
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Nathalie Rohmann
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Carina Knappe
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Johannes Epe
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Corinna Geisler
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Daniela Pohlschneider
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Susanne Brodesser
- Faculty of Medicine and University Hospital of Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Lucy Kruse
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Maria-Elisabeth Rohlfing
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Katharina Hartmann
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Kathrin Türk
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jens Marquardt
- Department of Internal Medicine 1, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Jan Beckmann
- Department of General and Abdominal Surgery, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Witigo von Schönfels
- Department of General and Abdominal Surgery, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Alexia Beckmann
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Perdita Wietzke-Braun
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Dominik M. Schulte
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Tim Hollstein
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Tobias Demetrowitsch
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Julia Jensen-Kroll
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Fynn Brix
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Karin Schwarz
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Silvio Waschina
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
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19
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Famà V, Coscujuela Tarrero L, Albanese R, Calviello L, Biffo S, Pelizzola M, Furlan M. Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle. RNA Biol 2025; 22:1-12. [PMID: 40116043 PMCID: PMC11934187 DOI: 10.1080/15476286.2025.2483001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2024] [Revised: 03/06/2025] [Accepted: 03/13/2025] [Indexed: 03/23/2025] Open
Abstract
Gene expression involves a series of consequential processes, beginning with mRNA synthesis and culminating in translation. Traditionally studied as a linear sequence of events, recent findings challenge this perspective, revealing coupling mechanisms that coordinate key steps of gene expression, even when spatially and temporally distant. In this review, we focus on translation, the final stage of gene expression, and examine its coupling with key stages of mRNA metabolism: synthesis, processing, export, and decay. For each of these processes, we provide an overview of known instances of coupling with translation. Furthermore, we discuss the role of high-throughput technologies in uncovering these intricate interactions on a genome-wide scale. Finally, we highlight key challenges and propose future directions to advance our understanding of how coupling mechanisms orchestrate robust and adaptable gene expression programs.
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Affiliation(s)
- Valeria Famà
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
- Department of Oncology and Emato-Oncology, University of Milan, Milan, Italy
| | | | | | | | - Stefano Biffo
- National Institute of Molecular Genetics, Fondazione Romeo ed Enrica Invernizzi, INGM, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Mattia Furlan
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
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20
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Osnaya VG, Gómez-Romero L, Moreno-Hagelsieb G, Hernández G. AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes. RNA Biol 2025; 22:1-5. [PMID: 39936323 PMCID: PMC11834415 DOI: 10.1080/15476286.2025.2465196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 02/05/2025] [Accepted: 02/06/2025] [Indexed: 02/13/2025] Open
Abstract
The mRNA translation defines the composition of the cell proteome in all forms of life and diseases. In this process, precise selection of the mRNA translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for triplet decoding. We have gathered and curated all published TIS consensus context sequences. We also included the TIS consensus context from novel 538 fungal genomes available from NCBI's RefSeq database. To do so, we wrote ad hoc programs in PERL to find and extract the TIS for each annotated gene, plus ten bases upstream and three downstream. For each genome, the sequences around the TIS of each gene were obtained, and the consensus was further calculated according to the Cavener rules and by the LOGOS algorithm. We created AUGcontext DB, a portal with a comprehensive collection of TIS context sequences across eukaryotes in a range from -10 to + 6. The compilation covers species of 30 vertebrates, 17 invertebrates, 25 plants, 14 fungi, and 11 protists studied in silico; 23 experimental studies; data on biotechnology; and the discovery of 8 diseases associated with specific mutations. Additionally, TIS context sequences of cellular IRESs were included. AUGcontext DB belongs to the National Institute of Cancer (Instituto Nacional de Cancerología, INCan), Mexico, and is freely available at http://108.161.138.77:8096/. Our catalogue allows us to do comparative studies between species, may help improve the diagnosis of certain diseases, and will be key to maximize the production of recombinant proteins.
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Affiliation(s)
- Vincent G. Osnaya
- mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City, Mexico
| | - Laura Gómez-Romero
- Bioinformatics Department, National Institute of Genomic Medicine, Mexico City, Mexico
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Mexico City, Mexico
| | | | - Greco Hernández
- mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City, Mexico
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Mexico City, Mexico
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21
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Li P, Li M, Chen WH. Best practices for developing microbiome-based disease diagnostic classifiers through machine learning. Gut Microbes 2025; 17:2489074. [PMID: 40186338 PMCID: PMC11980492 DOI: 10.1080/19490976.2025.2489074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 03/13/2025] [Accepted: 03/28/2025] [Indexed: 04/07/2025] Open
Abstract
The human gut microbiome, crucial in various diseases, can be utilized to develop diagnostic models through machine learning (ML). The specific tools and parameters used in model construction such as data preprocessing, batch effect removal and modeling algorithms can impact model performance and generalizability. To establish an generally applicable workflow, we divided the ML process into three above-mentioned steps and optimized each sequentially using 83 gut microbiome cohorts across 20 diseases. We tested a total of 156 tool-parameter-algorithm combinations and benchmarked them according to internal- and external- AUCs. At the data preprocessing step, we identified four data preprocessing methods that performed well for regression-type algorithms and one method that excelled for non-regression-type algorithms. At the batch effect removal step, we identified the "ComBat" function from the sva R package as an effective batch effect removal method and compared the performance of various algorithms. Finally, at the ML algorithm selection step, we found that Ridge and Random Forest ranked the best. Our optimized work flow performed similarly comparing with previous exhaustive methods for disease-specific optimizations, thus is generally applicable and can provide a comprehensive guideline for constructing diagnostic models for a range of diseases, potentially serving as a powerful tool for future medical diagnostics.
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Affiliation(s)
- Peikun Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Min Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- School of Biological Science, Jining Medical University, Rizhao, China
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22
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Zhang Y, Mo C, Ai P, He X, Xiao Q, Yang X. Pharmacomicrobiomics: a new field contributing to optimizing drug therapy in Parkinson's disease. Gut Microbes 2025; 17:2454937. [PMID: 39875349 PMCID: PMC11776486 DOI: 10.1080/19490976.2025.2454937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 11/19/2024] [Accepted: 01/13/2025] [Indexed: 01/30/2025] Open
Abstract
Gut microbiota, which act as a determinant of pharmacokinetics, have long been overlooked. In recent years, a growing body of evidence indicates that the gut microbiota influence drug metabolism and efficacy. Conversely, drugs also exert a substantial influence on the function and composition of the gut microbiota. Pharmacomicrobiomics, an emerging field focusing on the interplay of drugs and gut microbiota, provides a potential foundation for making certain advances in personalized medicine. Understanding the communication between gut microbiota and antiparkinsonian drugs is critical for precise treatment of Parkinson's disease. Here, we provide a historical overview of the interplay between gut microbiota and antiparkinsonian drugs. Moreover, we discuss potential mechanistic insights into the complex associations between gut microbiota and drug metabolism. In addition, we also draw attention to microbiota-based biomarkers for predicting antiparkinsonian drug efficacy and examine current state-of-the-art knowledge of microbiota-based strategies to optimize drug therapy in Parkinson's disease.
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Affiliation(s)
- Yi Zhang
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chengjun Mo
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Penghui Ai
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqin He
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qin Xiao
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaodong Yang
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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23
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Dong H, Wang X, Zheng Y, Li J, Liu Z, Wang A, Shen Y, Wu D, Cui H. Mapping the rapid growth of multi-omics in tumor immunotherapy: Bibliometric evidence of technology convergence and paradigm shifts. Hum Vaccin Immunother 2025; 21:2493539. [PMID: 40275437 PMCID: PMC12026087 DOI: 10.1080/21645515.2025.2493539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 04/01/2025] [Accepted: 04/11/2025] [Indexed: 04/26/2025] Open
Abstract
This study aims to fill the knowledge gap in systematically mapping the evolution of omics-driven tumor immunotherapy research through a bibliometric lens. While omics technologies (genomics, transcriptomics, proteomics, metabolomics)provide multidimensional molecular profiling, their synergistic potential with immunotherapy remains underexplored in large-scale trend analyses. A comprehensive search was conducted using the Web of Science Core Collection for literature related to omics in tumor immunotherapy, up to August 2024. Bibliometric analyses, conducted using R version 4.3.3, VOSviewer 1.6.20, and Citespace 6.2, examined publication trends, country and institutional contributions, journal distributions, keyword co-occurrence, and citation bursts. This analysis of 9,494 publications demonstrates rapid growth in omics-driven tumor immunotherapy research since 2019, with China leading in output (63% of articles) yet exhibiting limited multinational collaboration (7.9% vs. the UK's 61.8%). Keyword co-occurrence and citation burst analyses reveal evolving frontiers: early emphasis on "PD-1/CTLA-4 blockade" has transitioned toward "machine learning," "multi-omics," and "lncRNA," reflecting a shift to predictive modeling and biomarker discovery. Multi-omics integration has facilitated the development of immune infiltration-based prognostic models, such as TIME subtypes, which have been validated across multiple tumor types, which inform clinical trial design (e.g. NCT06833723). Additionally, proteomic analysis of melanoma patients suggests that metabolic biomarkers, particularly oxidative phosphorylation and lipid metabolism, may stratify responders to PD-1 blockade therapy. Moreover, spatial omics has confirmed ENPP1 as a potential novel therapeutic target in Ewing sarcoma. Citation trends underscore clinical translation, particularly mutation-guided therapies. Omics technologies are transforming tumor immunotherapy by enhancing biomarker discovery and improving therapeutic predictions. Future advancements will necessitate longitudinal omics monitoring, AI-driven multi-omics integration, and international collaboration to accelerate clinical translation. This study presents a systematic framework for exploring emerging research frontiers and offers insights for optimizing precision-driven immunotherapy.
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Affiliation(s)
- Huijing Dong
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Xinmeng Wang
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Yumin Zheng
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Jia Li
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Zhening Liu
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Aolin Wang
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Yulei Shen
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Daixi Wu
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Huijuan Cui
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing, China
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24
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Chen L, Gao X, Liu X, Zhu Y, Wang D. Translational regulation of PKD1 by evolutionarily conserved upstream open reading frames. RNA Biol 2025; 22:1-12. [PMID: 39757590 PMCID: PMC11810096 DOI: 10.1080/15476286.2024.2448387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/17/2024] [Accepted: 12/24/2024] [Indexed: 01/07/2025] Open
Abstract
Mutations in PKD1 coding sequence and abnormal PKD1 expression levels contribute to the development of autosomal-dominant polycystic kidney disease, the most common genetic disorder. Regulation of PKD1 expression by factors located in the promoter and 3´ UTR have been extensively studied. Less is known about its regulation by 5´ UTR elements. In this study, we investigated the effects of uORFs and uORF-affecting variants by combining bioinformatic analyses, luciferase reporter assays, RT-qPCR and immunoblotting experiments. Our analyses demonstrate that PKD1 mRNA contains two evolutionarily conserved translation-inhibitory uORFs. uORF1 is translatable, and uORF2 is likely not translatable. The 5´ UTR and uORFs do not modulate downstream protein output under endoplasmic reticulum stress and oxidative stress conditions. Some of uORF-perturbing variants in the SNP database are predicted to affect gene translation. Luciferase reporter assays and RT-qPCR results reveal that rs2092942382 and rs1596636969 increase, while rs2092942900 decreases main gene translation without affecting transcription. Antisense oligos targeting the uORFs reduce luciferase protein levels without altering luciferase mRNA levels. Our results establish PKD1 as a novel target of uORF-mediated translational regulation and mutations that perturb uORFs may dysregulate PKD1 protein level.
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Affiliation(s)
- Lei Chen
- Department of Urology, Fuzong Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Xia Gao
- Department of Urology, Fuzong Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Xiangshen Liu
- Department of Urology, Fuzong Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Ye Zhu
- Department of Nephrology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Dong Wang
- Department of Urology, Fuzong Clinical Medical College, Fujian Medical University, Fuzhou, China
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25
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Wu J, Xu S, Li Z, Cong B, Yang Z, Yang Z, Gao W, Liu S, Yu Z, Xu S, Li N, Hou J, Wang G, Cao X, Liu S. SARS-CoV-2 enhances complement-mediated endothelial injury via the suppression of membrane complement regulatory proteins. Emerg Microbes Infect 2025; 14:2467781. [PMID: 39945674 PMCID: PMC11873982 DOI: 10.1080/22221751.2025.2467781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 01/29/2025] [Accepted: 02/11/2025] [Indexed: 03/01/2025]
Abstract
Complement hyperactivation and thrombotic microangiopathy are closely associated with severe COVID-19. Endothelial dysfunction is a key mechanism underlying thrombotic microangiopathy. To address the relationship between endothelial injury, complement activation and thrombotic microangiopathy of severe COVID-19, we wonder whether, and if so, what and how SARS-CoV-2 factors make endothelial cells (ECs) sensitive to complement-mediated cytotoxicity. We revealed that multiple SARS-CoV-2 proteins enhanced complement-mediated cytotoxicity to ECs by inhibiting membrane complement regulatory proteins (CRPs) and enhancing the deposition of complement-recognizing component FCN1. By screening with CRISPR/Cas9-gRNA libraries, we identified that ADAMTS9, SYAP1, and HIGD1A as intrinsic regulators of CD59 on ECs, which were inhibited by the SARS-CoV-2 M, NSP16, and ORF9b proteins. IFN-γ, GM-CSF, and IFN-α upregulated CD55 and CD59, while IFN-γ antagonized the inhibition of CD59 by the three SARS-CoV-2 proteins. So, the deficiency of IFN-γ weakened the protection of ECs by CRPs against complement-mediated injury which may be enhanced during infection. Our findings illustrated the regulation of protection against complement-mediated attack on self-cells by SARS-CoV-2 infection and immune responses, providing insights into endothelial injury, thrombotic microangiopathy, and potential targets for treating severe COVID-19.
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Affiliation(s)
- Jian Wu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai, People’s Republic of China
| | - Sanpeng Xu
- Department of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, People’s Republic of China
| | - Zhiqing Li
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai, People’s Republic of China
| | - Boyi Cong
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Zongheng Yang
- Department of Immunology, Center for Immunotherapy, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Zhichao Yang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai, People’s Republic of China
| | - Wanfeng Gao
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Shuo Liu
- Department of Immunology, Center for Immunotherapy, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Zhou Yu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai, People’s Republic of China
| | - Sheng Xu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai, People’s Republic of China
| | - Nan Li
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai, People’s Republic of China
| | - Jin Hou
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai, People’s Republic of China
| | - Guoping Wang
- Department of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, People’s Republic of China
| | - Xuetao Cao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai, People’s Republic of China
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
- Department of Immunology, Center for Immunotherapy, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Shuxun Liu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai, People’s Republic of China
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26
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Zhang D, Wang Q, Li D, Chen S, Chen J, Zhu X, Bai F. Gut microbiome composition and metabolic activity in metabolic-associated fatty liver disease. Virulence 2025; 16:2482158. [PMID: 40122128 PMCID: PMC11959907 DOI: 10.1080/21505594.2025.2482158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Revised: 01/24/2025] [Accepted: 03/12/2025] [Indexed: 03/25/2025] Open
Abstract
Metabolic Associated Fatty Liver Disease (MAFLD) impacts approximately 25% of the global population. Between April 2023 and July 2023, 60 patients with MAFLD, along with 60 age, ethnicity, and sex-matched healthy controls (HCs), were enrolled from the Inner Mongolia Autonomous Region, China. Analysis of gut microbiota composition and plasma metabolic profiles was conducted using metagenome sequencing and LC-MS. LEfSe analysis identified five pivotal species: Eubacterium rectale, Dialister invisus, Pseudoruminococcus massiliensis, GGB3278 SGB4328, and Ruminococcaceae bacteria. In subgroup analysis, Eubacterium rectale tended to increase by more than 2 times and more than double in the non-obese MAFLD group, and MAFLD with moderate hepatic steatosis (HS), respectively. Plasma samples identified 172 metabolites mainly composed of fatty acid metabolites such as propionic acid and butyric acid analogues. Ruminococcaceae bacteria have a strong positive correlation with β-alanine, uric acid, and L-valine. Pseudoruminococcus massiliensis has a strong positive correlation with β-alanine. Combinations of phenomics and metabolomics yielded the highest accuracy (AUC = 0.97) in the MAFLD diagnosis. Combinations of phenomics and metagenomics yielded the highest accuracy (AUC = 0.94) in the prediction of the MAFLD HS progress. Increases in Eubacterium rectale and decreases in Dialister invisus seem to be indicative of MAFLD patients. Eubacterium rectale may predict HS degree of MAFLD and play an important role in the development of non-obese MAFLD. Eubacterium rectale can generate more propionic acid and butyric acid analogues to absorb energy and increase lipid synthesis and ultimately cause MAFLD.
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Affiliation(s)
- Daya Zhang
- The Second School of Clinical Medicine, Hainan Medical University, Haikou, China
| | - Qi Wang
- The Second School of Clinical Medicine, Hainan Medical University, Haikou, China
| | - Da Li
- The Second School of Clinical Medicine, Hainan Medical University, Haikou, China
| | - Shiju Chen
- The Second School of Clinical Medicine, Hainan Medical University, Haikou, China
| | - Jinrun Chen
- Department of Gastroenterology, Otog Front Banner People 's Hospital, Otog Front Banner, China
| | - Xuli Zhu
- Department of Gastroenterology, Otog Front Banner People 's Hospital, Otog Front Banner, China
| | - Feihu Bai
- Department of Gastroenterology, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
- Department of Gastroenterology, The Gastroenterology Clinical Medical Center of Hainan Province, Haikou, China
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27
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Maor M, Levy Barazany H, Kolodkin-Gal I. The ladder of regulatory stringency and balance: an application to the US FDA's regulation of bacterial live therapeutics. Gut Microbes 2025; 17:2517377. [PMID: 40501442 PMCID: PMC12164374 DOI: 10.1080/19490976.2025.2517377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Revised: 04/30/2025] [Accepted: 06/03/2025] [Indexed: 06/16/2025] Open
Abstract
The three main types of live bacterial therapies - probiotics, fecal/microbiome transplants, and engineered bacterial therapies - hold immense potential to revolutionize medicine. While offering targeted and personalized treatments for various diseases, these therapies also carry risks such as adverse immune reactions, antibiotic resistance, and the potential for unintended consequences. Therefore, developing and deploying these therapies necessitates a robust regulatory framework to protect public health while fostering innovation. In this paper, we propose a novel conceptual tool - the Ladder of Regulatory Stringency and Balance-which can assist in the design of robust regulatory regimes which encompass medicine practices based not only on definitive Randomized Controlled Trials (RCTs), but also on meta-analyses, observational studies, and clinicians experience. Regulatory stringency refers to the strictness of regulations, while regulatory balance concerns the degree of alignment between the regulatory framework governing a technology and the actual risks posed by specific products within that technology. Focusing on the US regulatory environment, we subsequently position the three types of live bacterial therapies on the Ladder. The insight gained from this exercise demonstrates that probiotics are generally positioned at the bottom of the Ladder, corresponding to low-stringency regulation, with a proportionate regulatory balance. However, probiotics intended for high-risk populations are currently subject to low-stringency regulations, resulting in under-regulation. Our analysis also supports the conclusion that fecal microbiota transplants (FMT) for recurrent Clostridium difficile infection should be positioned close to but below the threshold for under regulation by the U.S. Food and Drug Administration (FDA), and we recommend improved donor screening procedures, preservation and processing, storage, and distribution. Our framework can serve as a scale to assess regulatory gaps for live bacterial therapies and to identify potential solutions where such gaps exist.
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Affiliation(s)
- Moshe Maor
- Lauder School of Government, Diplomacy & Strategy, Reichman University, Herzliya, Israel
| | - Hilit Levy Barazany
- Scojen Institute for Synthetic Biology, Dina Recanati School of Medicine, Reichman University, Herzliya, Israel
| | - Ilana Kolodkin-Gal
- Scojen Institute for Synthetic Biology, Dina Recanati School of Medicine, Reichman University, Herzliya, Israel
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28
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Yi LX, Woon HR, Saw G, Zeng L, Tan EK, Zhou ZD. Induced pluripotent stem cell-related approaches to generate dopaminergic neurons for Parkinson's disease. Neural Regen Res 2025; 20:3193-3206. [PMID: 39665833 PMCID: PMC11881713 DOI: 10.4103/nrr.nrr-d-24-00771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 09/25/2024] [Accepted: 10/23/2024] [Indexed: 12/13/2024] Open
Abstract
The progressive loss of dopaminergic neurons in affected patient brains is one of the pathological features of Parkinson's disease, the second most common human neurodegenerative disease. Although the detailed pathogenesis accounting for dopaminergic neuron degeneration in Parkinson's disease is still unclear, the advancement of stem cell approaches has shown promise for Parkinson's disease research and therapy. The induced pluripotent stem cells have been commonly used to generate dopaminergic neurons, which has provided valuable insights to improve our understanding of Parkinson's disease pathogenesis and contributed to anti-Parkinson's disease therapies. The current review discusses the practical approaches and potential applications of induced pluripotent stem cell techniques for generating and differentiating dopaminergic neurons from induced pluripotent stem cells. The benefits of induced pluripotent stem cell-based research are highlighted. Various dopaminergic neuron differentiation protocols from induced pluripotent stem cells are compared. The emerging three-dimension-based brain organoid models compared with conventional two-dimensional cell culture are evaluated. Finally, limitations, challenges, and future directions of induced pluripotent stem cell-based approaches are analyzed and proposed, which will be significant to the future application of induced pluripotent stem cell-related techniques for Parkinson's disease.
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Affiliation(s)
| | | | | | - Li Zeng
- National Neuroscience Institute, Singapore
- Department of Neurology, Singapore General Hospital, Singapore
- Signature Research Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore
| | - Eng King Tan
- National Neuroscience Institute, Singapore
- Department of Neurology, Singapore General Hospital, Singapore
- Signature Research Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore
| | - Zhi Dong Zhou
- National Neuroscience Institute, Singapore
- Signature Research Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore
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29
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Deshpande P, Chimata AV, Singh A. Exploring the role of N-acetyltransferases in diseases: a focus on N-acetyltransferase 9 in neurodegeneration. Neural Regen Res 2025; 20:2862-2871. [PMID: 39435604 PMCID: PMC11826463 DOI: 10.4103/nrr.nrr-d-24-00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 09/04/2024] [Accepted: 09/23/2024] [Indexed: 10/23/2024] Open
Abstract
Acetyltransferases, required to transfer an acetyl group on protein are highly conserved proteins that play a crucial role in development and disease. Protein acetylation is a common post-translational modification pivotal to basic cellular processes. Close to 80%-90% of proteins are acetylated during translation, which is an irreversible process that affects protein structure, function, life, and localization. In this review, we have discussed the various N-acetyltransferases present in humans, their function, and how they might play a role in diseases. Furthermore, we have focused on N-acetyltransferase 9 and its role in microtubule stability. We have shed light on how N-acetyltransferase 9 and acetylation of proteins can potentially play a role in neurodegenerative diseases. We have specifically discussed the N-acetyltransferase 9-acetylation independent function and regulation of c-Jun N-terminal kinase signaling and microtubule stability during development and neurodegeneration.
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Affiliation(s)
| | | | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, USA
- Premedical Program, University of Dayton, Dayton, OH, USA
- Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, OH, USA
- Integrative Science and Engineering Center, University of Dayton, Dayton, OH, USA
- Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA
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30
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Wang Z, Wang S, Liu X, Shi H, Zhang W, Yang Z, Feng L, Ji A, Liang Z, Liu J, Zhang L, Zhang Y. Discovery of specific protein markers in multiple body fluids and their application in forensic science. Talanta 2025; 293:128032. [PMID: 40187281 DOI: 10.1016/j.talanta.2025.128032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 03/24/2025] [Accepted: 03/25/2025] [Indexed: 04/07/2025]
Abstract
Identification of multiple body fluids is crucial for the reconstruction and corroboration of crime event. However, for the body fluids with high component similarities, such as peripheral blood and menstrual blood, reliable distinguishing markers are still lacking. Furthermore, a comprehensive protein marker assay for multiple body fluids is urgently necessary for complex crime events. Herein, we established a highly specific and detectable method for discovering protein markers in peripheral blood, menstrual blood, saliva, semen and vaginal fluid through integrating in-depth discovery proteomics and a two-step targeted screening approach. Four menstrual blood markers with high endometrial specificities were identified for differentiation from peripheral blood and exhibited moderate protein concentrations for reproducible analysis with a protein quantitation CV value of 8.66%. Finally, a targeted discrimination method with 16 protein markers was established. We successfully identified 47 blind samples with 100% specificity and detection rate, sourced from five types of body fluids and presented on matrices such as cotton, tissues, slides or fluid. Overall, this work developed an effective method for discovering body fluid biomarkers, obtained specific protein markers to identify five kinds of body fluids and their targeted monitoring will show great significance for forensic science.
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Affiliation(s)
- Zhiting Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Songduo Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xinxin Liu
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Huixia Shi
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Weijie Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; DP Technology, Beijing, 100089, China
| | - Zhiyuan Yang
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Lei Feng
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Anquan Ji
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Zhen Liang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jianhui Liu
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Lihua Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yukui Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
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31
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Hu P, Miao H, Li M, Zhou R, Lou Q, Wang D, Gao J, Guo F. Identification of plasma biomarkers for non-invasive diagnosis of hepatitis B cirrhosis. J Pharm Biomed Anal 2025; 263:116909. [PMID: 40300315 DOI: 10.1016/j.jpba.2025.116909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 04/15/2025] [Accepted: 04/16/2025] [Indexed: 05/01/2025]
Abstract
Hepatitis B virus (HBV) infection represents a major public health challenge due to its potential progression to liver cirrhosis and hepatocellular carcinoma, underscoring the importance of early diagnosis for effective management. This study aimed to identify plasma biomarkers for the non-invasive diagnosis of hepatitis B cirrhosis (HBC). We employed quantitative proteomic analysis via liquid chromatography-tandem mass spectrometry on plasma samples from 27 individuals, including 13 patients with HBC and 14 with chronic hepatitis B (CHB). Bioinformatics analysis of 963 identified proteins revealed 234 differential expressed proteins, comprising 115 upregulated and 119 downregulated proteins. Four candidate biomarkers-CHI3L1, IGFBP1, SHBG, and TIMP2-were subsequently selected and validated using ELISA in a cohort of 158 patients, all demonstrating elevated levels in HBC patients. The four-biomarker panel (4MP) demonstrated superior diagnostic performance, achieving an area under the curve (AUC) of 0.902 for distinguishing HBC from CHB. For differentiating decompensated HBC from CHB, the 4MP achieved an AUC of 0.993, with a sensitivity of 93.75 % and specificity of 98.73 %. Mostly, the 4MP also performed well in identifying severe HBC from non-severe HBC, achieving an AUC of 0.911, with a sensitivity of 81.25% and specificity of 93.65%. In conclusion, this study identifies four novel plasma biomarkers for HBC, highlighting their potential to enhance non-invasive diagnostic strategies for monitoring HBC progression.
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Affiliation(s)
- Piao Hu
- Department of Infectious Diseases, The First People's Hospital of Xiaoshan District, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou 311200, China
| | - Haifeng Miao
- Department of Infectious Diseases, The First People's Hospital of Xiaoshan District, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou 311200, China
| | - Mei Li
- Department of Infectious Diseases, The First People's Hospital of Xiaoshan District, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou 311200, China
| | - Ruxue Zhou
- Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, Hangzhou 311200, China; Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affliated Hospital of Jiaxing University, Jiaxing 314000, China
| | - Qinqin Lou
- Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, Hangzhou 311200, China; Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affliated Hospital of Jiaxing University, Jiaxing 314000, China
| | - Dezhen Wang
- Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, Hangzhou 311200, China; Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affliated Hospital of Jiaxing University, Jiaxing 314000, China
| | - Junli Gao
- Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, Hangzhou 311200, China; Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affliated Hospital of Jiaxing University, Jiaxing 314000, China.
| | - Feng Guo
- Department of Gastroenterology, The First People's Hospital of Xiaoshan District, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou 311200, China.
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Morgan KJ, Carley E, Coyne AN, Rothstein JD, Lusk CP, King MC. Visualizing nuclear pore complex plasticity with pan-expansion microscopy. J Cell Biol 2025; 224:e202409120. [PMID: 40504117 PMCID: PMC12162248 DOI: 10.1083/jcb.202409120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Revised: 04/09/2025] [Accepted: 05/30/2025] [Indexed: 06/16/2025] Open
Abstract
The exploration of cell-type and environmentally responsive nuclear pore complex (NPC) plasticity requires new, accessible tools. Using pan-expansion microscopy (pan-ExM), NPCs were identified by machine learning-facilitated segmentation. They exhibited a large range of diameters with a bias for dilated NPCs at the basal nuclear surface in clusters suggestive of local islands of nuclear envelope tension. Whereas hyperosmotic shock constricted NPCs analogously to those found in annulate lamellae, depletion of LINC complexes specifically eliminated the modest nuclear surface diameter biases. Therefore, LINC complexes may contribute locally to nuclear envelope tension to toggle NPC diameter between dilated, but not constricted, states. Lastly, POM121 shifts from the nuclear ring to the inner ring of the NPC specifically in induced pluripotent stem cell-derived neurons from a patient with C9orf72 amyotrophic lateral sclerosis. Thus, pan-ExM is a powerful tool to visualize NPC plasticity in physiological and pathological contexts at single NPC resolution.
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Affiliation(s)
| | - Emma Carley
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Alyssa N. Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey D. Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Megan C. King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, CT, USA
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33
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Zhang W, Zhao S, Wang M, Lou C, Xiang Y, Wu Q. Programming anti-ribozymes to sense trigger RNAs for modulating gene expression in mammalian cells. Synth Syst Biotechnol 2025; 10:827-834. [PMID: 40291978 PMCID: PMC12033390 DOI: 10.1016/j.synbio.2025.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2025] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 04/30/2025] Open
Abstract
Synthetic RNA-based switches provide distinctive merits in modulating gene expression. Simple and flexible RNA-based switches are crucial for advancing the field of gene regulation, paving the way for innovative tools that can sense and manipulate cellular processes. In this research, we have developed programmable ribozymes that are capable of suppressing gene expression in response to specific, endogenously expressed trigger RNAs. We engineer ribozymes by introducing upstream antisense sequences (anti-ribozymes) to inhibit the self-cleaving activity of the hammerhead ribozyme and open the expression of the target gene. The trigger RNA is designed to recognize and bind to complementary sequences within the anti-ribozymes, thereby inhibiting their ability to direct protein synthesis. The anti-ribozyme performance is optimized by regulating the essential sequence modules that play a crucial role in determining the specificity and efficiency of the anti-ribozyme's interaction with its trigger RNA. By applying this switch mechanism to various ribozyme designs, we have shown that it is possible to achieve control over gene expression across a wide range of trigger RNAs. By exploiting these programmable anti-ribozymes, we aim to create a powerful tool for controlling gene expression in mammalian cells, which could have important implications for basic research, disease diagnosis, and therapeutic interventions.
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Affiliation(s)
- Wenhui Zhang
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- State Key Laboratory of Green Biomanufacturing, MOE Key Lab. Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shi Zhao
- State Key Laboratory of Green Biomanufacturing, MOE Key Lab. Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mengyuan Wang
- State Key Laboratory of Green Biomanufacturing, MOE Key Lab. Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chunbo Lou
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yanhui Xiang
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qiong Wu
- State Key Laboratory of Green Biomanufacturing, MOE Key Lab. Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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34
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Liu C, Yi F, Niu C, Li Q. Unravelling microbial interactions in a synthetic broad bean paste microbial community. Food Microbiol 2025; 130:104767. [PMID: 40210396 DOI: 10.1016/j.fm.2025.104767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 12/12/2024] [Accepted: 03/04/2025] [Indexed: 04/12/2025]
Abstract
The biotic factors governing the assembly and functionality of broad bean paste microbiota remain largely unexplored due to its highly complex fermentation ecosystem. This study constructed a synthetic community comprising Zygosaccharomyces rouxii, Staphylococcus carnosus, Bacillus subtilis, Bacillus amyloliquefaciens, Tetragenococcus halophilus and Weissella confusa, representing key microorganisms involved in broad bean paste fermentation. The generalized Lotka-Volterra (gLV) model revealed that the microbial interaction network among the six species was dominated by pairwise interactions. The abundances of most species in the multi-species communities at 2 and 4 days were accurately predicted using the gLV model, based on pairwise species combinations outcomes. Among pairwise interactions, negative interactions (57 %) were significantly more prevalent than positive interactions (37 %), with the former generally being stronger. Subsequent investigations demonstrated that the tested Z. rouxii inhibited acid accumulation by acid-producing bacteria, while the two strains belonging to the genus Bacillus stimulated lactic acid bacteria growth and lactic acid accumulation. The sequential inoculation strategy, informed by the interaction network, enhanced the synthetic community's bioaugmentation in broad bean paste, significantly improving ester and mellow flavors, reducing unpleasant odors, and increasing volatile flavor substances to 9.43 times that of natural fermentation. Overall, this study revealed the interaction network of six key microorganisms in broad bean paste using the gLV model and guided the application of the synthetic community in its fermentation, significantly enhancing flavor quality.
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Affiliation(s)
- Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Feng Yi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
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35
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Arvaniti M, Balomenos A, Tsakanikas P, Skandamis P. VBNC induction and persistence of Listeria monocytogenes Scott A as a defence mechanism against free chlorine stress. Food Microbiol 2025; 130:104781. [PMID: 40210404 DOI: 10.1016/j.fm.2025.104781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 03/23/2025] [Accepted: 03/25/2025] [Indexed: 04/12/2025]
Abstract
Sodium hypochlorite (SH) belongs to the chlorine-releasing agents (CRAs) and is widely used as a disinfectant or a bleaching agent for sanitizing in the food processing environment and fresh-cut industry. In the present study, the potential induction of dormancy states, i.e. the VBNC state and persistence, in Listeria monocytogenes, Scott A strain, was evaluated after exposure to SH for 3 h at 20 °C. Our results showed that the concentration of free chlorine after cells (109.5 CFU/mL) resuspension into the working solution decreased down to 3.7 ppm (SD ± 0.4 ppm; pH 6.64 ± 0.1). To detect VBNC fractions we evaluated comparatively the results of plate counting with fluorescence microscopy, using 5(6)-carboxy-fluorescein diacetate (CFDA; metabolic activity) and propidium iodide (PI; death) staining. The resuscitation capacity of L. monocytogenes stressed single cells was monitored real-time on TSAYE at 37°C, using time-lapse microscopy. Thus, colony outgrowth kinetics were estimated and non-diving fractions were detected. Furthermore, variability in the division time per generation was examined. Our analyses showed that SH induces the VBNC state and persistence in L. monocytogenes. Phenotypic variants of "high" fitness, i.e. size colony variations (SCVs) were also detected in response to SH stress. L. monocytogenes cells presented a prolonged lag time after exposure to SH. This phenomenon is a defence mechanism that allows cells to tolerate stress and maximize population fitness. The investigation of the VBNC state is of high importance for the food industry, as the impacts of VBNC induction and single cell outgrowth heterogeneity can contribute to false-negative detection outcomes.
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Affiliation(s)
- Marianna Arvaniti
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece.
| | - Athanasios Balomenos
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Panagiotis Tsakanikas
- Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Panagiotis Skandamis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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36
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Zhang H, Tong H, Yin Q, Qiu Y, Xu H, Li S. Efficient production of ectoine from Jerusalem artichoke using engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2025; 431:132589. [PMID: 40288656 DOI: 10.1016/j.biortech.2025.132589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 01/24/2025] [Accepted: 04/24/2025] [Indexed: 04/29/2025]
Abstract
In this study, a recombinant Escherichia coli strain was constructed to produce ectoine from Jerusalem artichoke through modular pathway engineering. First, a promoter-optimized ectoine synthesis module was integrated into the chromosome using multiple copies. Then, the introduction and expression of inulin hydrolase was optimized because inulin cannot be directly utilized. Subsequently, Fructose transport and phosphorylation, glycolysis, and oxaloacetate supply module were enhanced separately and in combination to improve ectoine production and substrate utilization. The strain ETC16 (co-expression of gapA, ppc, and fruK, ΔiclR) produced 6.51 g/L ectoine with 0.13 g/g inulin. Furthermore, the raw inulin extract and monosodium glutamate (MSG) residue were optimized for ectoine production. Finally, 35.60 g/L of ectoine with a yield of 0.36 g/g inulin was achieved in a 7.5 L fermenter. This study revealed a potential method of non-food fermentation to produce high-value products.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Hairui Tong
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Qiang Yin
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yibin Qiu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China.
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37
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Anderson A, Kinahan MW, Gonzalez AH, Udekwu K, Hernandez-Vargas EA. Invariant set theory for predicting potential failure of antibiotic cycling. Infect Dis Model 2025; 10:897-908. [PMID: 40297503 PMCID: PMC12036053 DOI: 10.1016/j.idm.2025.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Revised: 01/22/2025] [Accepted: 04/01/2025] [Indexed: 04/30/2025] Open
Abstract
Collateral sensitivity, where resistance to one drug confers heightened sensitivity to another, offers a promising strategy for combating antimicrobial resistance, yet predicting resultant evolutionary dynamics remains a significant challenge. We propose here a mathematical model that integrates fitness trade-offs and adaptive landscapes to predict the evolution of collateral sensitivity pathways, providing insights into optimizing sequential drug therapies. Our approach embeds collateral information into a network of switched systems, allowing us to abstract the effects of sequential antibiotic exposure on antimicrobial resistance. We analyze the system stability at disease-free equilibrium and employ set-control theory to tailor therapeutic windows. Consequently, we propose a computational algorithm to identify effective sequential therapies to counter antibiotic resistance. By leveraging our theory with data on collateral sensivity interactions, we predict scenarios that may prevent bacterial escape for chronic Pseudomonas aeruginosa infections.
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Affiliation(s)
- Alejandro Anderson
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, USA
| | - Matthew W. Kinahan
- Department of Biological Sciences, Bioinformatics and Computational Biology, University of Idaho, Moscow, ID, USA
| | - Alejandro H. Gonzalez
- University of Littoral (UNL), Institute of Technological Development for the Chemical Industry (INTEC) and National Scientific and Technical Research Council (CONICET), Santa Fe, Argentina
| | - Klas Udekwu
- Department of Biological Sciences, Bioinformatics and Computational Biology, University of Idaho, Moscow, ID, USA
| | - Esteban A. Hernandez-Vargas
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, 83844–1103, Idaho, USA
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38
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Qiao J, Guo X, Jin J, Wang D, Li K, Gao W, Cui F, Zhang Z, Shi H, Wei L. Taco-DDI: accurate prediction of drug-drug interaction events using graph transformer-based architecture and dynamic co-attention matrices. Neural Netw 2025; 189:107655. [PMID: 40446573 DOI: 10.1016/j.neunet.2025.107655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Revised: 05/11/2025] [Accepted: 05/19/2025] [Indexed: 06/11/2025]
Abstract
Drug-drug interactions (DDIs) are critical in pharmaceutical research, as adverse interactions can pose significant risks for patient treatment plans. Accurate prediction of DDI events risk levels can provide valuable guidance for designing safer and more effective medical regimens. However, existing approaches often focus on interaction networks while overlooking the inherent molecular properties of drugs. In this study, we present Taco-DDI, a novel drug representation learning framework that utilizes a graph transformer-based model combined with a dynamic co-attention mechanism. Taco-DDI leverages the transformer architecture to derive atom-level feature encodings, capturing comprehensive molecular representations. Furthermore, it employs an adaptive co-attention matrix to identify essential substructures in drug molecules solely from structural information. Our results demonstrate that Taco-DDI achieves a 6.59 % relative accuracy improvement in DDI events risk levels prediction. Additionally, interpretability analysis confirms that Taco-DDI provides meaningful insights into DDI mechanisms, highlighting its practical utility as a robust tool for identifying DDI events risk levels.
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Affiliation(s)
- Jianbo Qiao
- School of Software, Shandong University, Jinan, China
| | - Xu Guo
- School of Software, Shandong University, Jinan, China
| | - Junru Jin
- School of Software, Shandong University, Jinan, China
| | - Ding Wang
- School of Software, Shandong University, Jinan, China
| | - Kefei Li
- School of Software, Shandong University, Jinan, China
| | - Wenjia Gao
- School of Software, Shandong University, Jinan, China
| | - Feifei Cui
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Zilong Zhang
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Hua Shi
- School of Opto-electronic and Communication Engineering, Xiamen University of Technology, Xiamen, China
| | - Leyi Wei
- School of Information, Xiamen University, Xiamen, China; Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China; Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan, China.
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39
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Yu H, Wang Y, Yang Z, Ying J, Guan F, Liu B, Miao M, Mohamed A, Wei X, Yang Y, Liu X, Sun L, Jiang Z, Yang S, Xin F. Enhancing the synthesis efficiency of galacto-oligosaccharides of a β-galactosidase from Paenibacillus barengoltzii by engineering the active and distal sites. Food Chem 2025; 483:144208. [PMID: 40220440 DOI: 10.1016/j.foodchem.2025.144208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 03/20/2025] [Accepted: 04/03/2025] [Indexed: 04/14/2025]
Abstract
Previously, a glycoside hydrolase (GH) family 2 β-galactosidase (PbBGal2A) from Paenibacillus barengoltzii is characterized for its high transglycosylation capability. Here, the cryo-electron microscopy (cryo-EM) structure of PbBGal2A was determined, revealing an enlarged acidic catalytic pocket that facilitate the binding of carbohydrate substrates. Three structure-based strategies as well as machine learning MECE platform (method for enhancing the catalytic efficiency) were employed to identify active and distal mutations with enhanced galacto-oligosaccharides (GOS) synthesis and their synergistic effects were evaluated. The best H331V mutation yielded a maximum GOS production of 76.57 % at 4 h when 35 % (w/v) of lactose was used as a substrate. Molecular dynamics (MD) simulation analysis further indicated that distal mutations increase the rigidity of the loops surrounding the catalytic pocket. This research sheds light on the structural and catalytic mechanisms of PbBGal2A, highlighting the importance of both active and distal mutations in the efficient design of customized β-galactosidases.
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Affiliation(s)
- Haiyan Yu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulu Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Institute of Food Science Technology Nutrition and Health (Cangzhou), Chinese Academy of Agricultural Sciences, Cangzhou 061001, China
| | - Zhisen Yang
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jiabao Ying
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Feifei Guan
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bolin Liu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Miao Miao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Abeer Mohamed
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Wei
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuji Yang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xin Liu
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Linfeng Sun
- Department of Neurology of The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Zhengqiang Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Shaoqing Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Institute of Food Science Technology Nutrition and Health (Cangzhou), Chinese Academy of Agricultural Sciences, Cangzhou 061001, China.
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40
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Sena-Torralba A, Banguera-Ordoñez YD, Carrascosa J, Maquieira Á, Morais S. Portable electrophoretic lateral flow biosensing for ultra-sensitive human lactate dehydrogenase detection in serum samples. Biosens Bioelectron 2025; 282:117504. [PMID: 40273775 DOI: 10.1016/j.bios.2025.117504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 03/29/2025] [Accepted: 04/21/2025] [Indexed: 04/26/2025]
Abstract
Lateral flow immunoassays are globally recognized for their simplicity, cost-effectiveness, and rapid qualitative and semiquantitative analyses, making them indispensable as point-of-care screening tools. However, their limited sensitivity restricts their application in clinical settings, requiring the detection of ultralow analyte concentrations in complex sample matrices. To address these challenges, we present a portable biosensing platform integrating battery-powered electrokinetic-driven microfluidics to enhance sensitivity while preserving point-of-care functionality. Our lightweight (151 g), 3D-printed electrophoretic device (€82) supports the simultaneous analysis of three samples and operates with an ultra-low power consumption of 225 mAh-1, enabling 44 h of operation on a single charge. By optimizing key parameters such as Joule heating, buffer evaporation, and electroosmotic flow, the device enables iterative incubation and washing steps directly on the nitrocellulose strip, capabilities unattainable with conventional capillarity-driven LFIAs. This advanced biosensing platform achieves a detection limit of 70 pg mL-1 for human lactate dehydrogenase (h-LDH), a key cancer biomarker, using gold nanoparticles as signal transducers. This result means a 367-fold improvement in sensitivity. Offering rapid, cost-effective, and ultra-sensitive biomarker quantification, this approach holds significant promise for transforming precision medicine, particularly in monitoring LDH-related cancer therapies.
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Affiliation(s)
- Amadeo Sena-Torralba
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - Yulieth D Banguera-Ordoñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain; Grupo de Investigación y Desarrollo en Ciencias, Tecnología e Innovación (BioGRID), Sociedad de Doctores e Investigadores de Colombia (SoPhIC), Bogotá, Colombia
| | - Javier Carrascosa
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Ángel Maquieira
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain; Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain; Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, IIS La Fe, Av. Fernando Abril Martorell, 46026, Valencia, Spain.
| | - Sergi Morais
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain; Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain; Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, IIS La Fe, Av. Fernando Abril Martorell, 46026, Valencia, Spain.
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Liu Q, Ye YY, Yang S, Cui CY, Du H, Ye JC, Cheng JL, Hu RW, Xiang L, Liu BL, Li YW, Cai QY, Zhang M, Mo CH, Zhao HM. Sustainable remediation of butyl xanthate-contaminated mine wastewater by combining emergent macrophyte Cyperus alternifolius with a versatile bacterial isolate. JOURNAL OF HAZARDOUS MATERIALS 2025; 493:138345. [PMID: 40280067 DOI: 10.1016/j.jhazmat.2025.138345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 03/25/2025] [Accepted: 04/18/2025] [Indexed: 04/29/2025]
Abstract
Butyl xanthate (BuX) is an emerging pollutant due to wide use as flotation collector, posing a serious threat to ecosystem health in mining areas. Here we develop a combinational plant-microbe remediation strategy for restoration of BuX-contaminated mining areas. A novel bacterial strain that completely degraded up to 1000 mg/L of BuX within 12 h was isolated and identified as Pseudomonas monteilii W50. It was found to harbor good tolerance to extreme environmental conditions and multiple plant growth-promoting traits such as phosphate and potassium solubilization, indole-3-acetic acid and gibberellin production, and cellulose degradation. This strain can colonize in the rhizosphere of an emergent macrophyte Cyperus alternifolius, improving removal of BuX and chemical oxygen demand (COD) from simulated wastewater. Compared to the phytoremediation alone, the removal of BuX and COD increased from 70 % to 98 % and from 21 % to 46 % respectively in the combined remediation The strain W50 protected the macrophyte from the phytotoxicity of BuX and the macrophyte provided it with a suitable habitat for return, benefiting each other. Compared to the individual treatment using C. alternifolius or strain W50, the combinational treatment significantly improved the plant growth and the residence of inoculated bacteria. Overall, C. alternifolius and strain W50 are the perfect combination for efficient and sustainable remediation of BuX-contaminated mine wastewater, overcoming the constraints of individual phytoremediation or bioaugmentation methods.
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Affiliation(s)
- Qi Liu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yao-Yao Ye
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Sha Yang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Cheng-Yu Cui
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Huan Du
- Guangzhou Customs Technology Center, Guangzhou 510632, China
| | - Jin-Cheng Ye
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ji-Liang Cheng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Rui-Wen Hu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Bai-Lin Liu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Miaoyue Zhang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China.
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Ameen ZS, Mubarak AS, Hamad M, Hamoudi R, Jemimah S, Ozsahin DU, Hamad M. Incorporating time as a third dimension in transcriptomic analysis using machine learning and explainable AI. Comput Biol Chem 2025; 117:108432. [PMID: 40132403 DOI: 10.1016/j.compbiolchem.2025.108432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 03/03/2025] [Accepted: 03/14/2025] [Indexed: 03/27/2025]
Abstract
Transcriptomic data analysis entails the measurement of RNA transcript (gene expression products) abundance in a cell or a cell population at a single point in time. In other words, transcriptomics as it is currently practiced is two-dimensional (2DTA). Gene expression profiling by 2DTA has proven invaluable in furthering our understanding of numerous biological processes in health and disease. That said, shortcomings including technical variability, small sample size, differential rates of transcript decay, and the lack of linearity between transcript abundance and functionality or the formation of functional proteins limit the interpretive utility and generalizability of transcriptomic data. 2DTA utility may also be constrained by its reliance on RNA extracts obtained at a single time point. In other words, much like judging a movie by a single frame, 2DTA can only provide a snapshot of the transcriptome at time of RNA extraction. Whether this perceived "temporality" problem is real and whether it has any bearing on transcriptomic data interpretation have yet to be addressed. To investigate this problem, 25 publicly available datasets relating to MCF-7 cells, where RNA extracts obtained at 12- or 48-hours post-culture were subjected to transcriptomic analysis. The individual datasets were downloaded and compiled into two separate datasets (MCF-7 U12hr and MCF-7 U48hr). To comparatively analyze the two compiled datasets, three machine learning approaches (decision trees (DT), random forests (RF), and XGBoost (Extreme Gradient Boosting)) were used as classifiers to search for genes with distinct expression patterns between the two groups. Shapley additive explanation (SHAP), an explainable AI method, was used to assess the fundamental principles of the DT, RF, and XGBoost models. Coefficient of Determination (DC), Mean Absolute Error (MAE), and Mean Squared Error (MSE) were used to evaluate the models. The results show that the two datasets exhibited very significant gene expression patterns. The XGBoost model performed better than the DT or RF models with MSE, MAE, and DC values of 0.00028, 0.00028, and 0.95778 respectively. These observations suggest that time, as a third dimension, can impact transcriptomic data interpretation and that machine learning and explainable AI are useful tools in resolving the temporality problem in transcriptomics.
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Affiliation(s)
- Zubaida Said Ameen
- Operational Research Center in Healthcare, Near East University, Mersin 99138, Turkey
| | - Auwalu Saleh Mubarak
- Operational Research Center in Healthcare, Near East University, Mersin 99138, Turkey
| | - Mohamed Hamad
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, UAE; Research Institute of Medical and Health Sciences, University of Sharjah, UAE
| | - Rifat Hamoudi
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, UAE; BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, UAE; Division of Surgery and Interventional Science, University College London, London NW3 2QG, UK
| | - Sherlyn Jemimah
- Department of Biology, College of Science, American University of Sharjah, UAE
| | - Dilber Uzun Ozsahin
- Operational Research Center in Healthcare, Near East University, Mersin 99138, Turkey; Research Institute of Medical and Health Sciences, University of Sharjah, UAE; Department of Diagnostic Medical Imaging, College of Health Sciences, University of Sharjah, UAE.
| | - Mawieh Hamad
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, UAE; Research Institute of Medical and Health Sciences, University of Sharjah, UAE.
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Wong DPH, Wong KH, Park S, Boël G, Hunt JF, Aalberts DP. OPT: Codon optimize gene sequences for E. coli protein overexpression. J Mol Biol 2025; 437:168965. [PMID: 40133777 PMCID: PMC12145263 DOI: 10.1016/j.jmb.2025.168965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Revised: 01/23/2025] [Accepted: 01/23/2025] [Indexed: 03/27/2025]
Abstract
The ability to overexpress proteins is valuable for biotechnology, but not all sequences are compatible with high yield. We previously analyzed the sequence features and mRNA folding stability of a large data set of 6,384 distinct gene constructs, and developed a model for protein yield. Our OPT.williams.edu server (1) predicts the probability an input sequence will produce protein at a high level when overexpressed in E. coli, and (2) returns optimized synonymous sequences designed to boost protein expression. Here we also present experimental evidence of the high yields of our OPT constructs for eight commercially produced proteins.
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Affiliation(s)
- Daniel P H Wong
- Physics Department, Williams College, Williamstown, MA 01267, USA
| | - Kam-Ho Wong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Sunjae Park
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Universite Paris Cite, Institut de Biologie Physio-Chimique, F-75005 Paris, France.
| | - John F Hunt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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Liu J, Zhang WG, Rao ZM. Transcriptional regulator-based biosensors for biomanufacturing in Corynebacterium glutamicum. Microbiol Res 2025; 297:128169. [PMID: 40209574 DOI: 10.1016/j.micres.2025.128169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 03/10/2025] [Accepted: 04/02/2025] [Indexed: 04/12/2025]
Abstract
Intracellular biosensors based on transcriptional regulators have become essential instruments in biomanufacturing, extensively employed for the semi-quantitative assessment of intracellular metabolites, high-throughput screening of production strains, and the directed evolution of enzymes. Corynebacterium glutamicum serves as an industrial chassis for the production of amino acids and a variety of high-value-added chemicals. This paper discusses the varieties and modes of action of transcriptional regulators employed in the construction of intracellular biosensors in C. glutamicum. It also reviews the design principles and progress in the application of transcriptional regulator-based biosensors. Furthermore, measures designed to improve the efficacy of these biosensors are delineated. The challenges and future prospects of biosensors based on transcriptional regulators in practical applications are analyzed. This review seeks to offer theoretical direction for the systematic design and development of transcriptional regulator-based biosensors and to aid researchers in enhancing the growth and productivity of microbial production strains.
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Affiliation(s)
- Jie Liu
- School of Biological and Food Engineering, Anhui Polytechnic University, 18# Beijing Middle Road, WuHu 241000, PR China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi 214122, PR China.
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi 214122, PR China
| | - Zhi-Ming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi 214122, PR China
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45
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Tan L, Yang J, He Z, Wan Y, Li Z, Song J, Zhang W, Yang X. Inhibitory effects of extracts from Prunella vulgaris on biofilm formation of Staphylococcus aureus. Microb Pathog 2025; 205:107694. [PMID: 40355056 DOI: 10.1016/j.micpath.2025.107694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 05/07/2025] [Accepted: 05/09/2025] [Indexed: 05/14/2025]
Abstract
Staphylococcus aureus (S. aureus) is a highly prevalent pathogen capable of strongly adhering to food processing equipment and the contact surfaces, where it forms resilient biofilms that are difficult to eliminate. Prunella vulgaris (P. vulgaris), a traditional Chinese herbal medicine, has demonstrated strong potential in inhibiting S. aureus biofilm formation. This study investigated the inhibitory mechanisms of P. vulgaris extracts against S. aureus growth and biofilm formation, evaluating the biofilm inhibitory concentration, bactericidal concentration and their effects on ica operon gene expression. The P. vulgaris extracts exhibited a minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of 1.25 mg/mL. At the MIC level, the extracts not only suppressed S. aureus growth and metabolic viability but also inhibited polysaccharide intercellular adhesion (PIA), prevented biofilm formation and disrupted mature biofilms. Furthermore, P. vulgaris extracts demonstrated concentration-dependent effects on extracellular polymeric substances (EPS) production: while 1/2 MIC concentrations stimulated EPS synthesis, double-MIC concentrations markedly suppressed it. Notably, the extracts consistently downregulated icaA and icaD expression at both MIC and 2 × MIC concentrations. Therefore, P. vulgaris exhibits significant potential against S. aureus-induced foodborne diseases, demonstrating promise as a novel antibacterial agent for future applications in both pharmaceutical development and food safety enhancement.
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Affiliation(s)
- Luyi Tan
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong-Hongkong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, PR China; Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong, 510632, PR China
| | - Jiani Yang
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong-Hongkong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, PR China; Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong, 510632, PR China
| | - Zhini He
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong-Hongkong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, PR China
| | - Yu Wan
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong-Hongkong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, PR China
| | - Ziyin Li
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong-Hongkong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, PR China
| | - Jia Song
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong-Hongkong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, PR China
| | - Wenjuan Zhang
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong, 510632, PR China.
| | - Xingfen Yang
- Food Safety and Health Research Center, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong-Hongkong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, PR China.
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Ak B, Akısü M, Durmaz A, Yalaz M, Terek D, Sönmezler E, Oktay Y, Akın H, Aykut A. Expanding the genetic spectrum of short rib polydactyly syndrome: Novel DYNC2H1 variants and functional insights. Bone 2025; 197:117511. [PMID: 40339774 DOI: 10.1016/j.bone.2025.117511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2025] [Revised: 04/28/2025] [Accepted: 05/02/2025] [Indexed: 05/10/2025]
Abstract
INTRODUCTION Short rib polydactyly syndrome (SRPS), with or without polydactyly, also known as Verma-Naumoff/Saldino-Noonan syndrome, is a type of skeletal ciliopathy. Initially, variants in the IFT80 gene were implicated; however, approximately half of the SRPS cases are associated with variants in the DYNC2H1 gene. Additionally, digenic variants involving DYNC2H1 and NEK1 can contribute to the syndrome. MATERIALS AND METHODS This case report describes a male patient presenting with characteristic SRPS features, including a constricted thorax and shortened limbs. Exome sequencing was performed to identify causative variants, followed by functional analyses to assess the pathogenicity of the identified variants, including a synonymous variant. RESULTS Exome sequencing identified compound heterozygous variants in the DYNC2H1 gene: a novel missense variant c.6439G>T p.(Asp2147Tyr) and a synonymous variant c.6477G>A p.(Gln2159=). Functional analyses confirmed that the synonymous variant triggers nonsense-mediated decay of the affected allele. CONCLUSION This study expands the spectrum of DYNC2H1 variants associated with SRPS and emphasizes the importance of functional analyses in genetic diagnostics. Demonstrating pathogenicity for a synonymous variant highlights the necessity for comprehensive variant assessments to improve diagnostic accuracy and enable early intervention. These findings have significant implications for molecular diagnostics and personalized therapy strategies in skeletal ciliopathies.
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Affiliation(s)
- Bilgesu Ak
- Department of Medical Genetics, Ege University Hospital, Izmir, Turkey
| | - Mete Akısü
- Department of Neonatology, Ege University Hospital, Izmir, Turkey.
| | - Asude Durmaz
- Department of Medical Genetics, Ege University Hospital, Izmir, Turkey.
| | - Mehmet Yalaz
- Department of Neonatology, Ege University Hospital, Izmir, Turkey.
| | - Demet Terek
- Department of Neonatology, Ege University Hospital, Izmir, Turkey.
| | | | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Izmir, Turkey.
| | - Haluk Akın
- Department of Medical Genetics, Ege University Hospital, Izmir, Turkey.
| | - Ayça Aykut
- Department of Medical Genetics, Ege University Hospital, Izmir, Turkey.
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Jiang Y, Tian Y, Han J, Wang X, Zhang R, Xu X, Ma X, Zhang W, Man C. CircITSN2-miR-17-5p/20a-5p/20b-5p- PD-L1 regulatory network is a potential molecular mechanism of PD-L1 gene involving in immune response to IBDV. Avian Pathol 2025; 54:512-520. [PMID: 39980444 DOI: 10.1080/03079457.2025.2470754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 09/11/2024] [Accepted: 11/26/2024] [Indexed: 02/22/2025]
Abstract
RESEARCH HIGHLIGHTS PD-L1 gene is correlated with IBDV immune response in chickens.PD-L1 is a key gene regulating the immune functions of the heart, lung, and proventriculus.CircITSN2-miR-17-5p/20a-5p/20b-5p-PD-L1 is a potential mechanism in IBDV immunity.
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Affiliation(s)
- Yi Jiang
- College of Life Science and Technology, Harbin Normal University, Harbin, People's Republic of China
| | - Yufei Tian
- College of Life Science and Technology, Harbin Normal University, Harbin, People's Republic of China
| | - Jianwei Han
- College of Life Science and Technology, Harbin Normal University, Harbin, People's Republic of China
| | - Xiangnan Wang
- College of Life Science and Technology, Harbin Normal University, Harbin, People's Republic of China
| | - Rui Zhang
- College of Life Science and Technology, Harbin Normal University, Harbin, People's Republic of China
| | - Xinxin Xu
- College of Life Science and Technology, Harbin Normal University, Harbin, People's Republic of China
| | - Xiaoli Ma
- College of Life Science and Technology, Harbin Normal University, Harbin, People's Republic of China
| | - Wei Zhang
- College of Life Science and Technology, Harbin Normal University, Harbin, People's Republic of China
| | - Chaolai Man
- College of Life Science and Technology, Harbin Normal University, Harbin, People's Republic of China
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Zhang Y, Deng J, Dong M, Wu J, Zhao Q, Gao X, Xiong D. PILOT: Deep Siamese network with hybrid attention improves prediction of mutation impact on protein stability. Neural Netw 2025; 188:107476. [PMID: 40252373 DOI: 10.1016/j.neunet.2025.107476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Revised: 02/13/2025] [Accepted: 04/07/2025] [Indexed: 04/21/2025]
Abstract
Evaluating the mutation impact on protein stability (ΔΔG) is essential in the study of protein engineering and understanding molecular mechanisms of disease-associated mutations. Here, we propose a novel deep learning framework, PILOT, for improved prediction of ΔΔG using a Siamese network with hybrid attention mechanism. The PILOT framework leverages multiple attention modules to effectively extract representations for amino acids, atoms, and protein sequences, respectively. This approach significantly ensures the deep fusion of structural information at both residue and atom levels, the seamless integration of structural and sequence representations, and the effective capture of both long-range and short-range dependencies among amino acids. Our extensive evaluations demonstrate that PILOT greatly outperforms other state-of-the-art methods. We also showcase that PILOT identifies exceptional patterns for different mutation types. Moreover, we illustrate the clinical applicability of PILOT in highlighting pathogenic variants from benign variants and VUS (variants of uncertain significance), and distinguishing de novo mutations in disease cases and controls. In summary, PILOT presents a robust deep learning tool that could offer significant insights into drug design, medical applications, and protein engineering studies.
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Affiliation(s)
- Yuan Zhang
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China
| | - Junsheng Deng
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China
| | - Mingyuan Dong
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China
| | - Jiafeng Wu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China
| | - Qiuye Zhao
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Xieping Gao
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, Hunan Normal University, Changsha 410081, China.
| | - Dapeng Xiong
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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Dar AI, Randhawa S, Verma M, Saini TC, Acharya A. Debugging the dynamics of protein corona: Formation, composition, challenges, and applications at the nano-bio interface. Adv Colloid Interface Sci 2025; 342:103535. [PMID: 40319752 DOI: 10.1016/j.cis.2025.103535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 04/25/2025] [Accepted: 04/25/2025] [Indexed: 05/07/2025]
Abstract
The intricate interplay between nanomaterials and the biological molecules has garnered considerable interest in understanding the dynamics of protein corona formation at the nano-bio interface. This review provides an in-depth exploration of protein-nanoparticle interactions, elucidating their structural dynamics and thermodynamics at the nano-Bio interface and further on emphasizing its formation, composition, challenges, and applications in the biomedical and nanotechnological domains, such as drug delivery, theranostics, and the translational medicine. We delve the nuanced mechanisms governing protein corona formation on nanoparticle surfaces, highlighting the influence of nanoparticle and biological factors, and review the impact of corona formation on the biological identity and functionality of nanoparticles. Notably, emerging applications of artificial intelligence and machine learning have begun to revolutionize this field, enabling accurate prediction of corona composition and related biological outcomes. These tools not only enhance efficiency over traditional experimental methods but also help decode complex protein-nanoparticle interaction patterns, offering new insights into corona-driven cellular responses and disease diagnostics. Additionally, it discusses recent advancements in the field of protein corona, particularly in translational nanomedicine and associated applications entailing current and future strategies which are aimed at mitigating the adverse effects of protein-nanoparticle interactions at the biological interface, for tailoring the protein coronas by engineering of the nanomaterials. This comprehensive assessment from chemical, technological, and biological aspects serves as a guiding beacon for the development of future nanomedicine, enabling the more effective emulation of the biological milieu and the design of protein-NP systems for enhanced biomedical applications.
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Affiliation(s)
- Aqib Iqbal Dar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shiwani Randhawa
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohini Verma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Trilok Chand Saini
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amitabha Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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50
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Hashem HR, Amin BH, Yosri M. Elucidation of the possible synergistic effect of Torulaspora delbrueckii and ciprofloxacin in a rat model of induced pulmonary fibrosis and infected with Klebsiella pneumonia: An in vivo study. Tissue Cell 2025; 95:102865. [PMID: 40120428 DOI: 10.1016/j.tice.2025.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 02/13/2025] [Accepted: 03/14/2025] [Indexed: 03/25/2025]
Abstract
The lungs are constantly subjected to enormous amounts of air and potentially transmitted agents, leading to a high incidence of severe and complex ailments urging the demand for defensive actions to maintain their regular function. Numerous studies have demonstrated how certain probiotics have many advantages including hindering pulmonary exacerbations in individuals with cystic fibrosis, which encourages the idea of combining them with approved antibiotics as a therapeutic choice for treatment patients with lung fibrosis who also have bacterial infections. This investigation aimed to test the possibility of a combination of Torulaspora delbrueckii as a probiotic with ciprofloxacin in an animal model having pulmonary fibrosis with a moderate load of Klebsiella pneumonia. Ninety adult male rats were split into six groups (15 rats/each): GI (control), GII (lung fibrosis), GIII (lung fibrosis infected by K. pneumonia), GIV (lung fibrosis infected by K. pneumonia then treated with ciprofloxacin), GV (lung fibrosis infected by K. pneumonia and fed with T. delbrueckii) and GVI (lung fibrosis infected by K. pneumonia then treated with combined therapy of ciprofloxacin and T. delbrueckii) for 28 days. Survival rate and bacterial load were determined in various experimental animal groups. Histological variations were examined as well as scanning electron microscopy. Gene expression, various levels of cytokines, redox enzymes, and oxidative stress markers were assessed and compared in different tested groups. The treatment using a combination of T. delbrueckii and ciprofloxacin is suggested as a new method to treat induced lung fibrosis in animals and infected with K. pneumonia as a possible option in complicated infection.
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Affiliation(s)
- Heba R Hashem
- Anatomy and Embryology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Basma H Amin
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo 11787, Egypt
| | - Mohammed Yosri
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo 11787, Egypt.
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