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Prudinnik DS, Kussanova A, Vorobjev IA, Tikhonov A, Ataullakhanov FI, Barteneva NS. Deformability of Heterogeneous Red Blood Cells in Aging and Related Pathologies. Aging Dis 2025:AD.2024.0526. [PMID: 39012672 DOI: 10.14336/ad.2024.0526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024] Open
Abstract
Aging is interrelated with changes in red blood cell parameters and functionality. In this article, we focus on red blood cells (RBCs) and provide a review of the known changes associated with the characterization of RBC deformability in aging and related pathologies. The biophysical parameters complement the commonly used biochemical parameters and may contribute to a better understanding of the aging process. The power of the deformability measurement approach is well established in clinical settings. Measuring RBCs' deformability has the advantage of relative simplicity, and it reflects the complex effects developing in erythrocytes during aging. However, aging and related pathological conditions also promote heterogeneity of RBC features and have a certain impact on the variance in erythrocyte cell properties. The possible applications of deformability as an early biophysical biomarker of pathological states are discussed, and modulating PIEZO1 as a therapeutic target is suggested. The changes in RBCs' shape can serve as a proxy for deformability evaluation, leveraging single-cell analysis with imaging flow cytometry and artificial intelligence algorithms. The characterization of biophysical parameters of RBCs is in progress in humans and will provide a better understanding of the complex dynamics of aging.
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Affiliation(s)
- Dmitry S Prudinnik
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Aigul Kussanova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Ivan A Vorobjev
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Alexander Tikhonov
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Fazly I Ataullakhanov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Natasha S Barteneva
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
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Smith TA, Zhou L, Ghergherehchi CL, Mikesh M, Yang CZ, Tucker HO, Allgood J, Bushman JS, Bittner GD. Polyethylene glycol has immunoprotective effects on sciatic allografts, but behavioral recovery and graft tolerance require neurorrhaphy and axonal fusion. Neural Regen Res 2025; 20:1192-1206. [PMID: 38989956 DOI: 10.4103/nrr.nrr-d-23-01220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/29/2024] [Indexed: 07/12/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202504000-00033/figure1/v/2024-07-06T104127Z/r/image-tiff Behavioral recovery using (viable) peripheral nerve allografts to repair ablation-type (segmental-loss) peripheral nerve injuries is delayed or poor due to slow and inaccurate axonal regeneration. Furthermore, such peripheral nerve allografts undergo immunological rejection by the host immune system. In contrast, peripheral nerve injuries repaired by polyethylene glycol fusion of peripheral nerve allografts exhibit excellent behavioral recovery within weeks, reduced immune responses, and many axons do not undergo Wallerian degeneration. The relative contribution of neurorrhaphy and polyethylene glycol-fusion of axons versus the effects of polyethylene glycol per se was unknown prior to this study. We hypothesized that polyethylene glycol might have some immune-protective effects, but polyethylene glycol-fusion was necessary to prevent Wallerian degeneration and functional/behavioral recovery. We examined how polyethylene glycol solutions per se affect functional and behavioral recovery and peripheral nerve allograft morphological and immunological responses in the absence of polyethylene glycol-induced axonal fusion. Ablation-type sciatic nerve injuries in outbred Sprague-Dawley rats were repaired according to a modified protocol using the same solutions as polyethylene glycol-fused peripheral nerve allografts, but peripheral nerve allografts were loose-sutured (loose-sutured polyethylene glycol) with an intentional gap of 1-2 mm to prevent fusion by polyethylene glycol of peripheral nerve allograft axons with host axons. Similar to negative control peripheral nerve allografts not treated by polyethylene glycol and in contrast to polyethylene glycol-fused peripheral nerve allografts, animals with loose-sutured polyethylene glycol peripheral nerve allografts exhibited Wallerian degeneration for all axons and myelin degeneration by 7 days postoperatively and did not recover sciatic-mediated behavioral functions by 42 days postoperatively. Other morphological signs of rejection, such as collapsed Schwann cell basal lamina tubes, were absent in polyethylene glycol-fused peripheral nerve allografts but commonly observed in negative control and loose-sutured polyethylene glycol peripheral nerve allografts at 21 days postoperatively. Loose-sutured polyethylene glycol peripheral nerve allografts had more pro-inflammatory and less anti-inflammatory macrophages than negative control peripheral nerve allografts. While T cell counts were similarly high in loose-sutured-polyethylene glycol and negative control peripheral nerve allografts, loose-sutured polyethylene glycol peripheral nerve allografts expressed some cytokines/chemokines important for T cell activation at much lower levels at 14 days postoperatively. MHCI expression was elevated in loose-sutured polyethylene glycol peripheral nerve allografts, but MHCII expression was modestly lower compared to negative control at 21 days postoperatively. We conclude that, while polyethylene glycol per se reduces some immune responses of peripheral nerve allografts, successful polyethylene glycol-fusion repair of some axons is necessary to prevent Wallerian degeneration of those axons and immune rejection of peripheral nerve allografts, and produce recovery of sensory/motor functions and voluntary behaviors. Translation of polyethylene glycol-fusion technologies would produce a paradigm shift from the current clinical practice of waiting days to months to repair ablation peripheral nerve injuries.
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Affiliation(s)
- Tyler A Smith
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Liwen Zhou
- Department of Neuroscience, University of Texas at Austin, Austin, TX, USA
| | | | - Michelle Mikesh
- Department of Neuroscience, University of Texas at Austin, Austin, TX, USA
| | - Cathy Z Yang
- Department of Neuroscience, University of Texas at Austin, Austin, TX, USA
| | - Haley O Tucker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - JuliAnne Allgood
- Division of Pharmaceutical Sciences, University of Wyoming, Laramie, WY, USA
| | - Jared S Bushman
- Division of Pharmaceutical Sciences, University of Wyoming, Laramie, WY, USA
| | - George D Bittner
- Department of Neuroscience, University of Texas at Austin, Austin, TX, USA
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Wang J, Ran Y, Li Z, Zhao T, Zhang F, Wang J, Liu Z, Chen X. Salsolinol as an RNA m6A methylation inducer mediates dopaminergic neuronal death by regulating YAP1 and autophagy. Neural Regen Res 2025; 20:887-899. [PMID: 38886960 DOI: 10.4103/nrr.nrr-d-23-01592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/18/2024] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00032/figure1/v/2024-06-17T092413Z/r/image-tiff Salsolinol (1-methyl-6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline, Sal) is a catechol isoquinoline that causes neurotoxicity and shares structural similarity with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, an environmental toxin that causes Parkinson's disease. However, the mechanism by which Sal mediates dopaminergic neuronal death remains unclear. In this study, we found that Sal significantly enhanced the global level of N6-methyladenosine (m6A) RNA methylation in PC12 cells, mainly by inducing the downregulation of the expression of m6A demethylases fat mass and obesity-associated protein (FTO) and alkB homolog 5 (ALKBH5). RNA sequencing analysis showed that Sal downregulated the Hippo signaling pathway. The m6A reader YTH domain-containing family protein 2 (YTHDF2) promoted the degradation of m6A-containing Yes-associated protein 1 (YAP1) mRNA, which is a downstream key effector in the Hippo signaling pathway. Additionally, downregulation of YAP1 promoted autophagy, indicating that the mutual regulation between YAP1 and autophagy can lead to neurotoxicity. These findings reveal the role of Sal on m6A RNA methylation and suggest that Sal may act as an RNA methylation inducer mediating dopaminergic neuronal death through YAP1 and autophagy. Our results provide greater insights into the neurotoxic effects of catechol isoquinolines compared with other studies and may be a reference for assessing the involvement of RNA methylation in the pathogenesis of Parkinson's disease.
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Affiliation(s)
- Jianan Wang
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Yuanyuan Ran
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Zihan Li
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Tianyuan Zhao
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Fangfang Zhang
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Juan Wang
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Zongjian Liu
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Xuechai Chen
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
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Hu B, Wang R, Zhang H, Wang X, Zhou S, Ma B, Luan Y, Wang X, Chen X, Zhang Z, Kang Q. Postnatal development of rat retina: a continuous observation and comparison between the organotypic retinal explant model and in vivo development. Neural Regen Res 2025; 20:900-912. [PMID: 38886961 DOI: 10.4103/nrr.nrr-d-23-01557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/22/2024] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00033/figure1/v/2024-06-17T092413Z/r/image-tiff The organotypic retinal explant culture has been established for more than a decade and offers a range of unique advantages compared with in vivo experiments and cell cultures. However, the lack of systematic and continuous comparison between in vivo retinal development and the organotypic retinal explant culture makes this model controversial in postnatal retinal development studies. Thus, we aimed to verify the feasibility of using this model for postnatal retinal development studies by comparing it with the in vivo retina. In this study, we showed that postnatal retinal explants undergo normal development, and exhibit a consistent structure and timeline with retinas in vivo. Initially, we used SOX2 and PAX6 immunostaining to identify retinal progenitor cells. We then examined cell proliferation and migration by immunostaining with Ki-67 and doublecortin, respectively. Ki-67- and doublecortin-positive cells decreased in both in vivo and explants during postnatal retinogenesis, and exhibited a high degree of similarity in abundance and distribution between groups. Additionally, we used Ceh-10 homeodomain-containing homolog, glutamate-ammonia ligase (glutamine synthetase), neuronal nuclei, and ionized calcium-binding adapter molecule 1 immunostaining to examine the emergence of bipolar cells, Müller glia, mature neurons, and microglia, respectively. The timing and spatial patterns of the emergence of these cell types were remarkably consistent between in vivo and explant retinas. Our study showed that the organotypic retinal explant culture model had a high degree of consistency with the progression of in vivo early postnatal retina development. The findings confirm the accuracy and credibility of this model and support its use for long-term, systematic, and continuous observation.
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Affiliation(s)
- Baoqi Hu
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
- Department of Ophthalmology, The First Affiliated Hospital of Northwest University, Xi'an, Shaanxi Province, China
| | - Rui Wang
- Department of Ophthalmology, The First Affiliated Hospital of Northwest University, Xi'an, Shaanxi Province, China
| | - Hanyue Zhang
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi Province, China
| | - Xiou Wang
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Sijia Zhou
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Bo Ma
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Yan Luan
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi Province, China
| | - Xin Wang
- Department of Ophthalmology, The First Affiliated Hospital of Northwest University, Xi'an, Shaanxi Province, China
| | - Xinlin Chen
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi Province, China
| | - Zhichao Zhang
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi Province, China
| | - Qianyan Kang
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
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Zhang Y, Liu Z, Chopp M, Millman M, Li Y, Cepparulo P, Kemper A, Li C, Zhang L, Zhang ZG. Small extracellular vesicles derived from cerebral endothelial cells with elevated microRNA 27a promote ischemic stroke recovery. Neural Regen Res 2025; 20:224-233. [PMID: 38767487 PMCID: PMC11246145 DOI: 10.4103/nrr.nrr-d-22-01292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/22/2024] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00030/figure1/v/2024-05-14T021156Z/r/image-tiff Axonal remodeling is a critical aspect of ischemic brain repair processes and contributes to spontaneous functional recovery. Our previous in vitro study demonstrated that exosomes/small extracellular vesicles (sEVs) isolated from cerebral endothelial cells (CEC-sEVs) of ischemic brain promote axonal growth of embryonic cortical neurons and that microRNA 27a (miR-27a) is an elevated miRNA in ischemic CEC-sEVs. In the present study, we investigated whether normal CEC-sEVs engineered to enrich their levels of miR-27a (27a-sEVs) further enhance axonal growth and improve neurological outcomes after ischemic stroke when compared with treatment with non-engineered CEC-sEVs. 27a-sEVs were isolated from the conditioned medium of healthy mouse CECs transfected with a lentiviral miR-27a expression vector. Small EVs isolated from CECs transfected with a scramble vector (Scra-sEVs) were used as a control. Adult male mice were subjected to permanent middle cerebral artery occlusion and then were randomly treated with 27a-sEVs or Scra-sEVs. An array of behavior assays was used to measure neurological function. Compared with treatment of ischemic stroke with Scra-sEVs, treatment with 27a-sEVs significantly augmented axons and spines in the peri-infarct zone and in the corticospinal tract of the spinal grey matter of the denervated side, and significantly improved neurological outcomes. In vitro studies demonstrated that CEC-sEVs carrying reduced miR-27a abolished 27a-sEV-augmented axonal growth. Ultrastructural analysis revealed that 27a-sEVs systemically administered preferentially localized to the pre-synaptic active zone, while quantitative reverse transcription-polymerase chain reaction and Western Blot analysis showed elevated miR-27a, and reduced axonal inhibitory proteins Semaphorin 6A and Ras Homolog Family Member A in the peri-infarct zone. Blockage of the Clathrin-dependent endocytosis pathway substantially reduced neuronal internalization of 27a-sEVs. Our data provide evidence that 27a-sEVs have a therapeutic effect on stroke recovery by promoting axonal remodeling and improving neurological outcomes. Our findings also suggest that suppression of axonal inhibitory proteins such as Semaphorin 6A may contribute to the beneficial effect of 27a-sEVs on axonal remodeling.
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Affiliation(s)
- Yi Zhang
- Department of Neurology, Henry Ford Hospital, Detroit, MI, USA
| | - Zhongwu Liu
- Department of Neurology, Henry Ford Hospital, Detroit, MI, USA
| | - Michael Chopp
- Department of Neurology, Henry Ford Hospital, Detroit, MI, USA
- Department of Physics, Oakland University, Rochester, MI, USA
| | - Michael Millman
- Department of Neurology, Henry Ford Hospital, Detroit, MI, USA
| | - Yanfeng Li
- Department of Neurology, Henry Ford Hospital, Detroit, MI, USA
| | | | - Amy Kemper
- Department of Pathology, Henry Ford Hospital, Detroit, MI, USA
| | - Chao Li
- Department of Neurology, Henry Ford Hospital, Detroit, MI, USA
| | - Li Zhang
- Department of Neurology, Henry Ford Hospital, Detroit, MI, USA
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Liu J, Qiu S, Xue T, Yuan Y. Physiology and transcriptome of Eucommia ulmoides seeds at different germination stages. PLANT SIGNALING & BEHAVIOR 2024; 19:2329487. [PMID: 38493506 PMCID: PMC10950268 DOI: 10.1080/15592324.2024.2329487] [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: 10/13/2023] [Accepted: 01/03/2024] [Indexed: 03/19/2024]
Abstract
E. ulmoides (Eucommia ulmoides) has significant industrial and medicinal value and high market demand. E. ulmoides grows seedlings through sowing. According to previous studies, plant hormones have been shown to regulate seed germination. To understand the relationship between hormones and E. ulmoides seed germination, we focused on examining the changes in various indicators during the germination stage of E. ulmoides seeds. We measured the levels of physiological and hormone indicators in E. ulmoides seeds at different germination stages and found that the levels of abscisic acid (ABA), gibberellin (GA), and indole acetic acid (IAA) significantly varied as the seeds germinated. Furthermore, we confirmed that ABA, GA, and IAA are essential hormones in the germination of E. ulmoides seeds using Gene Ontology and Kyoto Encyclopedia of Genes and Genomics enrichment analyses of the transcriptome. The discovery of hormone-related synthesis pathways in the control group of Eucommia seeds at different germination stages further confirmed this conclusion. This study provides a basis for further research into the regulatory mechanisms of E. ulmoides seeds at different germination stages and the relationship between other seed germination and plant hormones.
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Affiliation(s)
- Jia Liu
- Department of Civil and Architecture and Engineering, Chuzhou University, Chuzhou, Anhui, China
- Anhui Low Carbon Highway Engineering Research Center, Chuzhou University, Anhui, China
| | - Sumei Qiu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Tingting Xue
- Department of Civil and Architecture and Engineering, Chuzhou University, Chuzhou, Anhui, China
| | - Yingdan Yuan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
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Hu Y, Tian C, Song S, Li R. Insights on the enhancement of chilling tolerance in Rice through over-expression and knock-out studies of OsRBCS3. PLANT SIGNALING & BEHAVIOR 2024; 19:2318514. [PMID: 38375792 PMCID: PMC10880504 DOI: 10.1080/15592324.2024.2318514] [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: 11/09/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
Chilling stress is an important environmental factor that affects rice (Oryza sativa L.) growth and yield, and the booting stage is the most sensitive stage of rice to chilling stress. In this study, we focused on OsRBCS3, a rice gene related to chilling tolerance at the booting stage, which encodes the key enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit in photosynthesis. The aim of this study was to elucidate the role and mechanism of OsRBCS3 in rice chilling tolerance at the booting stage. The expression levels of OsRBCS3 under chilling stress were compared in two japonica rice cultivars with different chilling tolerances: Kongyu131 (KY131) and Longjing11 (LJ11). A positive correlation was found between OsRBCS3 expression and chilling tolerance. Over-expression (OE) and knock-out (KO) lines of OsRBCS3 were constructed using over-expression and CRISPR/Cas9 technology, respectively, and their chilling tolerance was evaluated at the seedling and booting stages. The results showed that OE lines exhibited higher chilling tolerance than wild-type (WT) lines at both seedling and booting stages, while KO lines showed lower chilling tolerance than WT lines. Furthermore, the antioxidant enzyme activities, malondialdehyde (MDA) content and Rubisco activity of four rice lines under chilling stress were measured, and it was found that OE lines had stronger antioxidant and photosynthetic capacities, while KO lines had the opposite effects. This study validated that OsRBCS3 plays an important role in rice chilling tolerance at the booting stage, providing new molecular tools and a theoretical basis for rice chilling tolerance breeding.
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Affiliation(s)
- Yueting Hu
- Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Chongbing Tian
- Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Shiyu Song
- Key Laboratory of Molecular Biology, Heilongjiang University, Harbin, China
| | - Rongtian Li
- Key Laboratory of Molecular Biology, Heilongjiang University, Harbin, China
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Parves MR, Solares MJ, Dearnaley WJ, Kelly DF. Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics. Cancer Biol Ther 2024; 25:2290732. [PMID: 38073067 PMCID: PMC10732606 DOI: 10.1080/15384047.2023.2290732] [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: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Low molecular weight proteins and protein assemblies can now be investigated using cryo-electron microscopy (EM) as a complement to traditional structural biology techniques. It is important, however, to not lose sight of the dynamic information inherent in macromolecules that give rise to their exquisite functionality. As computational methods continue to advance the field of biomedical imaging, so must strategies to resolve the minute details of disease-related entities. Here, we employed combinatorial modeling approaches to assess flexible properties among low molecular weight proteins (~100 kDa or less). Through a blend of rigid body refinement and simulated annealing, we determined new hidden conformations for wild type p53 monomer and dimer forms. Structures for both states converged to yield new conformers, each revealing good stereochemistry and dynamic information about the protein. Based on these insights, we identified fluid parts of p53 that complement the stable central core of the protein responsible for engaging DNA. Molecular dynamics simulations corroborated the modeling results and helped pinpoint the more flexible residues in wild type p53. Overall, the new computational methods may be used to shed light on other small protein features in a vast ensemble of structural data that cannot be easily delineated by other algorithms.
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Affiliation(s)
- Md Rimon Parves
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Biochemistry, Microbiology, and Molecular Biology Graduate Program, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Maria J. Solares
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - William J. Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
| | - Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
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Hidvégi N, Dobránszki J, Tóth B, Gulyás A. Expression responses of XTH genes in tomato and potato to environmental mechanical forces: focus on behavior in response to rainfall, wind and touch. PLANT SIGNALING & BEHAVIOR 2024; 19:2360296. [PMID: 38808631 PMCID: PMC11141476 DOI: 10.1080/15592324.2024.2360296] [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: 04/26/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
Abstract
Rainfall, wind and touch, as mechanical forces, were mimicked on 6-week-old soil-grown tomato and potato under controlled conditions. Expression level changes of xyloglucan endotransglucosylase/hydrolase genes (XTHs) of tomato (Solanum lycopersicum L. cv. Micro Tom; SlXTHs) and potato (Solanum tuberosum L. cv. Desirée; StXTHs) were analyzed in response to these mechanical forces. Transcription intensity of every SlXTHs of tomato was altered in response to rainfall, while the expression intensity of 72% and 64% of SlXTHs was modified by wind and touch, respectively. Ninety-one percent of StXTHs (32 out of 35) in potato responded to the rainfall, while 49% and 66% of the StXTHs were responsive to the wind and touch treatments, respectively. As previously demonstrated, all StXTHs were responsive to ultrasound treatment, and all were sensitive to one or more of the environmental mechanical factors examined in the current study. To our best knowledge, this is the first study to demonstrate that these ubiquitous mechanical environmental cues, such as rainfall, wind and touch, influence the transcription of most XTHs examined in both species.
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Affiliation(s)
- Norbert Hidvégi
- Centre for Agricultural Genomics and Biotechnology, Faculty of the Agricultural and Food Science and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, Faculty of the Agricultural and Food Science and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Bianka Tóth
- Centre for Agricultural Genomics and Biotechnology, Faculty of the Agricultural and Food Science and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Andrea Gulyás
- Centre for Agricultural Genomics and Biotechnology, Faculty of the Agricultural and Food Science and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
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Jiang H, Zhang Y, Li J, Tang R, Liang F, Tang R, Zhou Y, Zhang C. Genome-wide identification of SIMILAR to RCD ONE (SRO) gene family in rapeseed ( Brassica napus L.) reveals their role in drought stress response. PLANT SIGNALING & BEHAVIOR 2024; 19:2379128. [PMID: 39003725 PMCID: PMC11249032 DOI: 10.1080/15592324.2024.2379128] [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: 04/03/2024] [Accepted: 05/22/2024] [Indexed: 07/16/2024]
Abstract
Rapeseed (Brassica napus L.) is an important oilseed crop widely cultivated worldwide, and drought is the main environmental factor limiting its yield enhancement and the expansion of planted areas. SIMILAR TO RCD ONE (SRO) is a plant-specific small gene family that plays a crucial role in plant growth, development, and responses to abiotic stresses such as drought. However, the functional role of SROs in rapeseed remains poorly understood. In this study, 19 BnaSROs were identified from the rapeseed genome, with 9, 10, 10, 18, and 20 members identified from the genomes of Brassica rapa, Brassica nigra, Brassica oleracea, Brassica juncea, and Brassica carinata, respectively. We then analyzed their sequence characteristics, phylogenetic relationships, gene structures, and conserved domains, and explored the collinearity relationships of the SRO members in Brassica napus and Brassica juncea. Next, we focused on the analysis of tissue expression and stress-responsive expression patterns of rapeseed SRO members and examined their expression profiles under ABA, MeJA and water-deficit drought treatments using qPCR. Transcriptome data analysis and qPCR detection indicated that BnaSROs exhibit multiple stress-responsive expression patterns. BnaSRO1 and BnaSRO11, which are likely to function through interactions with NAC transcription factors, were screened as major drought-regulated members. Our results provide a solid foundation for functional analysis of the role of the SRO gene family in abiotic stress responses, especially drought stress responses, in rapeseed.
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Affiliation(s)
- Huanhuan Jiang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yuling Zhang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Jia Li
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Rongzi Tang
- Qianxi'nan Academy of Agricultural and Forestry Sciences, Xingyi, Guizhou, China
| | - Fenghao Liang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Rong Tang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yuyu Zhou
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Chao Zhang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
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11
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Mane V, Mehta R, Alvarez N, Sharma V, Park S, Fox A, DeCarlo C, Yang X, Perlin DS, Powell RLR. In vivo antiviral efficacy of LCTG-002, a pooled, purified human milk secretory IgA product, against SARS-CoV-2 in a murine model of COVID-19. Hum Vaccin Immunother 2024; 20:2303226. [PMID: 38251677 PMCID: PMC10807469 DOI: 10.1080/21645515.2024.2303226] [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: 09/25/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Immunoglobulin A (IgA) is the most abundant antibody (Ab) in human mucosae, with secretory form (sIgA) being dominant and uniquely stable. sIgA is challenging to produce recombinantly but is naturally found in human milk, which could be considered a global resource for this biologic, justifying its development as a mucosal therapeutic. Presently, SARS-CoV-2 was utilized as a model mucosal pathogen, and methods were developed to efficiently extract human milk sIgA from donors who were naïve to SARS-CoV-2 or had recovered from infection that elicited high-titer anti-SARS-CoV-2 Spike sIgA in their milk (pooled to make LCTG-002). Mass spectrometry determined that proteins with a relative abundance of 1% or greater were all associated with sIgA. Western blot demonstrated that all batches consisted predominantly of sIgA. Compared to control IgA, LCTG-002 demonstrated significantly higher Spike binding (mean endpoint of 0.87 versus 5.87). LCTG-002 was capable of blocking the Spike receptor-binding domain - angiotensin-converting enzyme 2 (ACE2) interaction with significantly greater potency compared to control (mean LCTG-002 IC50 154ug/mL versus 50% inhibition not achieved for control), and exhibited significant neutralization activity against Spike-pseudotyped virus infection (mean LCTG-002 IC50 49.8ug/mL versus 114.5ug/mL for control). LCTG-002 was tested for its capacity to reduce viral lung burden in K18+hACE2 transgenic mice inoculated with SARS-CoV-2. LCTG-002 significantly reduced SARS-CoV-2 titers compared to control when administered at 0.25 mg/day or 1 mg/day, with a maximum TCID50 reduction of 4.9 logs. This innovative study demonstrates that LCTG-002 is highly pure and efficacious in vivo, supporting further development of milk-derived, polyclonal sIgA therapeutics.
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Affiliation(s)
- Viraj Mane
- Lactiga US, Inc. 675 US-1, North Brunswick, NJ, USA
| | - Rikin Mehta
- Lactiga US, Inc. 675 US-1, North Brunswick, NJ, USA
| | - Nadine Alvarez
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Vijeta Sharma
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Steven Park
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Alisa Fox
- Icahn School of Medicine at Mount Sinai, Department of Medicine, Division of Infectious Diseases, New York, NY, USA
| | - Claire DeCarlo
- Icahn School of Medicine at Mount Sinai, Department of Medicine, Division of Infectious Diseases, New York, NY, USA
| | - Xiaoqi Yang
- Icahn School of Medicine at Mount Sinai, Department of Medicine, Division of Infectious Diseases, New York, NY, USA
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Rebecca L. R. Powell
- Icahn School of Medicine at Mount Sinai, Department of Medicine, Division of Infectious Diseases, New York, NY, USA
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12
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Portilla Llerena JP, Kiyota E, dos Santos FRC, Garcia JC, de Lima RF, Mayer JLS, dos Santos Brito M, Mazzafera P, Creste S, Nobile PM. ShF5H1 overexpression increases syringyl lignin and improves saccharification in sugarcane leaves. GM CROPS & FOOD 2024; 15:67-84. [PMID: 38507337 PMCID: PMC10956634 DOI: 10.1080/21645698.2024.2325181] [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: 10/21/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
The agricultural sugarcane residues, bagasse and straws, can be used for second-generation ethanol (2GE) production by the cellulose conversion into glucose (saccharification). However, the lignin content negatively impacts the saccharification process. This polymer is mainly composed of guaiacyl (G), hydroxyphenyl (H), and syringyl (S) units, the latter formed in the ferulate 5-hydroxylase (F5H) branch of the lignin biosynthesis pathway. We have generated transgenic lines overexpressing ShF5H1 under the control of the C4H (cinnamate 4-hydroxylase) rice promoter, which led to a significant increase of up to 160% in the S/G ratio and 63% in the saccharification efficiency in leaves. Nevertheless, the content of lignin was unchanged in this organ. In culms, neither the S/G ratio nor sucrose accumulation was altered, suggesting that ShF5H1 overexpression would not affect first-generation ethanol production. Interestingly, the bagasse showed a significantly higher fiber content. Our results indicate that the tissue-specific manipulation of the biosynthetic branch leading to S unit formation is industrially advantageous and has established a foundation for further studies aiming at refining lignin modifications. Thus, the ShF5H1 overexpression in sugarcane emerges as an efficient strategy to improve 2GE production from straw.
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Affiliation(s)
- Juan Pablo Portilla Llerena
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Academic Department of Biology, Professional and Academic School of Biology, Universidad Nacional de San Agustín de Arequipa, Arequipa, Perú
| | - Eduardo Kiyota
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Julio C. Garcia
- Centro de Cana, Instituto Agronômico (IAC), Ribeirão Preto, Brazil
| | | | | | - Michael dos Santos Brito
- Centro de Cana, Instituto Agronômico (IAC), Ribeirão Preto, Brazil
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Paulo Mazzafera
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Silvana Creste
- Centro de Cana, Instituto Agronômico (IAC), Ribeirão Preto, Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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13
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Cogno N, Axenie C, Bauer R, Vavourakis V. Agent-based modeling in cancer biomedicine: applications and tools for calibration and validation. Cancer Biol Ther 2024; 25:2344600. [PMID: 38678381 PMCID: PMC11057625 DOI: 10.1080/15384047.2024.2344600] [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: 10/30/2023] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
Computational models are not just appealing because they can simulate and predict the development of biological phenomena across multiple spatial and temporal scales, but also because they can integrate information from well-established in vitro and in vivo models and test new hypotheses in cancer biomedicine. Agent-based models and simulations are especially interesting candidates among computational modeling procedures in cancer research due to the capability to, for instance, recapitulate the dynamics of neoplasia and tumor - host interactions. Yet, the absence of methods to validate the consistency of the results across scales can hinder adoption by turning fine-tuned models into black boxes. This review compiles relevant literature that explores strategies to leverage high-fidelity simulations of multi-scale, or multi-level, cancer models with a focus on verification approached as simulation calibration. We consolidate our review with an outline of modern approaches for agent-based models' validation and provide an ambitious outlook toward rigorous and reliable calibration.
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Affiliation(s)
- Nicolò Cogno
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Institute for Condensed Matter Physics, Technische Universit¨at Darmstadt, Darmstadt, Germany
| | - Cristian Axenie
- Computer Science Department and Center for Artificial Intelligence, Technische Hochschule Nürnberg Georg Simon Ohm, Nuremberg, Germany
| | - Roman Bauer
- Nature Inspired Computing and Engineering Research Group, Computer Science Research Centre, University of Surrey, Guildford, UK
| | - Vasileios Vavourakis
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
- Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus
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14
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Yao R, Xie C, Xia X. Recent progress in mRNA cancer vaccines. Hum Vaccin Immunother 2024; 20:2307187. [PMID: 38282471 PMCID: PMC10826636 DOI: 10.1080/21645515.2024.2307187] [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: 09/28/2023] [Accepted: 01/16/2024] [Indexed: 01/30/2024] Open
Abstract
The research and development of messenger RNA (mRNA) cancer vaccines have gradually overcome numerous challenges through the application of personalized cancer antigens, structural optimization of mRNA, and the development of alternative RNA-based vectors and efficient targeted delivery vectors. Clinical trials are currently underway for various cancer vaccines that encode tumor-associated antigens (TAAs), tumor-specific antigens (TSAs), or immunomodulators. In this paper, we summarize the optimization of mRNA and the emergence of RNA-based expression vectors in cancer vaccines. We begin by reviewing the advancement and utilization of state-of-the-art targeted lipid nanoparticles (LNPs), followed by presenting the primary classifications and clinical applications of mRNA cancer vaccines. Collectively, mRNA vaccines are emerging as a central focus in cancer immunotherapy, offering the potential to address multiple challenges in cancer treatment, either as standalone therapies or in combination with current cancer treatments.
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Affiliation(s)
- Ruhui Yao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chunyuan Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaojun Xia
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
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15
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Wang J, Wang Z, Wang P, Wu J, Kong L, Ma L, Jiang S, Ren W, Liu W, Guo Y, Ma W, Liu X. Genome-wide identification of YABBY gene family and its expression pattern analysis in Astragalus mongholicus. PLANT SIGNALING & BEHAVIOR 2024; 19:2355740. [PMID: 38776425 PMCID: PMC11123558 DOI: 10.1080/15592324.2024.2355740] [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: 03/12/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
During plant growth and development, the YABBY gene plays a crucial role in the morphological structure, hormone signaling, stress resistance, crop breeding, and agricultural production of plant lateral organs, leaves, flowers, and fruits. Astragalus mongholicus is a perennial herbaceous plant in the legume family, widely used worldwide due to its high medicinal and edible value. However, there have been no reports of the YABBY gene family in A. mongholicus. This study used bioinformatics methods, combined with databases and analysis websites, to systematically analyze the AmYABBY gene family in the entire genome of A. mongholicus and verified its expression patterns in different tissues of A. mongholicus through transcriptome data and qRT-PCR experiments. A total of seven AmYABBY genes were identified, which can be divided into five subfamilies and distributed on three chromosomes. Two pairs of AmYABBY genes may be involved in fragment duplication on three chromosomes. All AmYABBY proteins have a zinc finger YABBY domain, and members of the same group have similar motif composition and intron - exon structure. In the promoter region of the genes, light-responsive and MeJa-response cis-elements are dominant. AmYABBY is highly expressed in stems and leaves, especially AmYABBY1, AmYABBY2, and AmYABBY3, which play important roles in the growth and development of stems and leaves. The AmYABBY gene family regulates the growth and development of A. mongholicus. In summary, this study provides a theoretical basis for in-depth research on the function of the AmYABBY gene and new insights into the molecular response mechanism of the growth and development of the traditional Chinese medicine A. mongholicus.
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Affiliation(s)
- Jiamei Wang
- Equipment Department, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhen Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Panpan Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jianhao Wu
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lingyang Kong
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lengleng Ma
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Shan Jiang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Weichao Ren
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Weili Liu
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yanli Guo
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wei Ma
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiubo Liu
- College of Jiamusi, Heilongjiang University of Chinese Medicine, Jiamusi, China
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16
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Lv L, Yang C, Zhang X, Chen T, Luo M, Yu G, Chen Q. Autophagy-related protein PlATG2 regulates the vegetative growth, sporangial cleavage, autophagosome formation, and pathogenicity of peronophythora litchii. Virulence 2024; 15:2322183. [PMID: 38438325 PMCID: PMC10913709 DOI: 10.1080/21505594.2024.2322183] [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: 08/23/2023] [Accepted: 02/18/2024] [Indexed: 03/06/2024] Open
Abstract
Autophagy is an intracellular degradation process that is important for the development and pathogenicity of phytopathogenic fungi and for the defence response of plants. However, the molecular mechanisms underlying autophagy in the pathogenicity of the plant pathogenic oomycete Peronophythora litchii, the causal agent of litchi downy blight, have not been well characterized. In this study, the autophagy-related protein ATG2 homolog, PlATG2, was identified and characterized using a CRISPR/Cas9-mediated gene replacement strategy in P. litchii. A monodansylcadaverine (MDC) staining assay indicated that deletion of PlATG2 abolished autophagosome formation. Infection assays demonstrated that ΔPlatg2 mutants showed significantly impaired pathogenicity in litchi leaves and fruits. Further studies have revealed that PlATG2 participates in radial growth and asexual/sexual development of P. litchii. Moreover, zoospore release and cytoplasmic cleavage of sporangia were considerably lower in the ΔPlatg2 mutants than in the wild-type strain by FM4-64 staining. Taken together, our results revealed that PlATG2 plays a pivotal role in vegetative growth, sporangia and oospore production, zoospore release, sporangial cleavage, and plant infection of P. litchii. This study advances our understanding of the pathogenicity mechanisms of the phytopathogenic oomycete P. litchii and is conducive to the development of effective control strategies.
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Affiliation(s)
- Lin Lv
- Hainan Yazhou Bay Seed Laboratory, College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chengdong Yang
- Hainan Yazhou Bay Seed Laboratory, College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xue Zhang
- Hainan Yazhou Bay Seed Laboratory, College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Taixu Chen
- Hainan Yazhou Bay Seed Laboratory, College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Manfei Luo
- Hainan Yazhou Bay Seed Laboratory, College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Ge Yu
- Hainan Yazhou Bay Seed Laboratory, College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Qinghe Chen
- Hainan Yazhou Bay Seed Laboratory, College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
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17
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Moeckel C, Mareboina M, Konnaris MA, Chan CS, Mouratidis I, Montgomery A, Chantzi N, Pavlopoulos GA, Georgakopoulos-Soares I. A survey of k-mer methods and applications in bioinformatics. Comput Struct Biotechnol J 2024; 23:2289-2303. [PMID: 38840832 PMCID: PMC11152613 DOI: 10.1016/j.csbj.2024.05.025] [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: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
The rapid progression of genomics and proteomics has been driven by the advent of advanced sequencing technologies, large, diverse, and readily available omics datasets, and the evolution of computational data processing capabilities. The vast amount of data generated by these advancements necessitates efficient algorithms to extract meaningful information. K-mers serve as a valuable tool when working with large sequencing datasets, offering several advantages in computational speed and memory efficiency and carrying the potential for intrinsic biological functionality. This review provides an overview of the methods, applications, and significance of k-mers in genomic and proteomic data analyses, as well as the utility of absent sequences, including nullomers and nullpeptides, in disease detection, vaccine development, therapeutics, and forensic science. Therefore, the review highlights the pivotal role of k-mers in addressing current genomic and proteomic problems and underscores their potential for future breakthroughs in research.
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Affiliation(s)
- Camille Moeckel
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Manvita Mareboina
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Maxwell A. Konnaris
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Candace S.Y. Chan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ioannis Mouratidis
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
| | - Austin Montgomery
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikol Chantzi
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | | | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
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18
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Zhao Z, Yang T, Xiang G, Zhang S, Cai Y, Zhong G, Pu J, Shen C, Zeng J, Chen C, Huang B. A novel small RNA PhaS contributes to polymyxin B-heteroresistance in carbapenem-resistant Klebsiella pneumoniae. Emerg Microbes Infect 2024; 13:2366354. [PMID: 38979571 PMCID: PMC11238654 DOI: 10.1080/22221751.2024.2366354] [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: 01/04/2024] [Accepted: 06/05/2024] [Indexed: 07/10/2024]
Abstract
In recent years, polymyxin has been used as a last-resort therapy for carbapenem-resistant bacterial infections. The emergence of heteroresistance (HR) to polymyxin hampers the efficacy of polymyxin treatment by amplifying resistant subpopulation. However, the mechanisms behind polymyxin HR remain unclear. Small noncoding RNAs (sRNAs) play an important role in regulating drug resistance. The purpose of this study was to investigate the effects and mechanisms of sRNA on polymyxin B (PB)-HR in carbapenem-resistant Klebsiella pneumoniae. In this study, a novel sRNA PhaS was identified by transcriptome sequencing. PhaS expression was elevated in the PB heteroresistant subpopulation. Overexpression and deletion of PhaS were constructed in three carbapenem-resistant K. pneumoniae strains. Population analysis profiling, growth curve, and time-killing curve analysis showed that PhaS enhanced PB-HR. In addition, we verified that PhaS directly targeted phoP through the green fluorescent protein reporter system. PhaS promoted the expression of phoP, thereby encouraging the expression of downstream genes pmrD and arnT. This upregulation of arnT promoted the 4-amino-4-deoxyL-arabinosaccharide (L-Ara4N) modification of lipid A in PhaS overexpressing strains, thus enhancing PB-HR. Further, within the promoter region of PhaS, specific PhoP recognition sites were identified. ONPG assays and RT-qPCR analysis confirmed that PhaS expression was positively modulated by PhoP and thus up-regulated by PB stimulation. To sum up, a novel sRNA enhancing PB-HR was identified and a positive feedback regulatory pathway of sRNA-PhoP/Q was demonstrated in the study. This helps to provide a more comprehensive and clear understanding of the underlying mechanisms behind polymyxin HR in carbapenem-resistant K. pneumoniae.
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Affiliation(s)
- Zhiwei Zhao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Tingting Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Guoxiu Xiang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shebin Zhang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Yimei Cai
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Guosheng Zhong
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jieying Pu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, People’s Republic of China
| | - Cong Shen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, People’s Republic of China
| | - Jianming Zeng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, People’s Republic of China
| | - Cha Chen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
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19
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Kubitscheck U, Siebrasse JP. Pre-ribosomal particles from nucleoli to cytoplasm. Nucleus 2024; 15:2373052. [PMID: 38940456 PMCID: PMC11216097 DOI: 10.1080/19491034.2024.2373052] [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: 04/02/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024] Open
Abstract
The analysis of nucleocytoplasmic transport of proteins and messenger RNA has been the focus of advanced microscopic approaches. Recently, it has been possible to identify and visualize individual pre-ribosomal particles on their way through the nuclear pore complex using both electron and light microscopy. In this review, we focused on the transport of pre-ribosomal particles in the nucleus on their way to and through the pores.
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Affiliation(s)
- Ulrich Kubitscheck
- Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Jan Peter Siebrasse
- Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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20
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Korhonen J, Siiskonen H, Haimakainen S, Harvima RJ, Harvima IT. Expression of mast cell tryptase and immunoglobulin E is increased in cutaneous photodamage: implications for carcinogenesis. J DERMATOL TREAT 2024; 35:2307488. [PMID: 38291602 DOI: 10.1080/09546634.2024.2307488] [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: 09/08/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
Purpose: Mast cells, their serine proteinase tryptase, and immunoglobulin E (IgE) can be involved in cutaneous carcinogenesis.Materials and methods: To study the association of tryptase+ and IgE+ cells with photodamage and skin cancers 385 adult patients (201 males, 184 females, 75 with immunosuppression) at risk of any type of skin cancer were examined. Skin biopsies were taken from the sun-protected medial arm and from the photodamaged dorsal forearm skin followed by immunohistochemical staining for tryptase and IgE.Results: The results show that tryptase+ and IgE+ cells are significantly higher in number in the photodamaged than sun-protected skin, both in immunocompetent and -compromised subjects, and there is a strong correlation between tryptase+ and IgE+ cells. The numbers of forearm tryptase+ and especially IgE+ cells associated significantly with the forearm photodamage severity. In the logistic regression analysis, the forearm to upper arm ratio of IgE+ cells produced a univariate odds ratio of 1.521 (p = .010) and a multivariate one of 3.875 (p = .047) for the history of squamous cell carcinoma. The serum level of total IgE correlated significantly to the IgE to tryptase ratio in both skin sites.Conclusions: Therefore, IgE+ mast cells participate in photodamage and carcinogenesis, though it is unclear whether they are tumor-protective or -causative.
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Affiliation(s)
- Jenni Korhonen
- Department of Dermatology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Hanna Siiskonen
- Department of Dermatology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Salla Haimakainen
- Department of Dermatology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Rauno J Harvima
- Department of Dermatology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Ilkka T Harvima
- Department of Dermatology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
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Mazetyte-Godiene A, Vailionyte A, Jelinskas T, Denkovskij J, Usas A. Promotion of hMDSC differentiation by combined action of scaffold material and TGF-β superfamily growth factors. Regen Ther 2024; 27:307-318. [PMID: 38633416 PMCID: PMC11021853 DOI: 10.1016/j.reth.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/08/2024] [Accepted: 03/17/2024] [Indexed: 04/19/2024] Open
Abstract
Objective Herein we propose a combined action of collagen type I (CA) or synthetic collagen-like-peptide functionalized with the cell adhesive RGD motif (PEG-CLP-RGD) hydrogels and selected growth factors to promote chondrogenic differentiation of human muscle-derived stem cells (hMDSCs) under normal and reduced oxygen conditions. Methods hMDSCs were set for differentiation towards chondrogenic lineage using BMP-7 and TGF-β3. Cells were seeded onto hydrogels loaded with growth factors (75ng/scaffold) and cultured for 28 days under normal (21%) and severe hypoxic (1%) conditions. Chondrogenesis was evaluated by monitoring collagen type II and GAG deposition, and quantification of ACAN expression by RT-PCR. Results Sustained release of TGFβ3 from the hydrogels was observed, 8.7 ± 0.5% of the initially loaded amount diffused out after 24 h from both substrates. For the BMP-7 growth factor, 14.8 ± 0.3% and 18.2 ± 0.6% of the initially loaded amount diffused out after 24 h from CA and CLP-RGD, respectively. The key findings of this study are: i) the self-supporting hydrogels themselves can stimulate hMDSC chondrogenesis by inducing gene expression of cartilage-specific proteoglycan aggrecan and ECM production; ii) the effect of dual BMP-7 and TGF-β3 loading was more pronounced on CA hydrogel under normal oxygen conditions; iii) dual loading on PEG-CLP-RGD hydrogels did not have the synergistic effect, TGF-β3 was more effective under both oxygen conditions; iv) BMP-7 can improve chondrogenic effect of TGF-β3 on CA scaffolds, and hydrogels loaded with both growth factors can induce cartilage formation in hMDSC cultures. Conclusion Our results support the potential strategy of combining implantable hydrogels functionalized with differentiation factors toward improving cartilaginous repair.
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Affiliation(s)
- Airina Mazetyte-Godiene
- Institute of Physiology and Pharmacology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
- UAB Ferentis, Savanoriu ave. 235, Vilnius, Lithuania
- Department of Nanoengineering, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | | | - Tadas Jelinskas
- Department of Nanoengineering, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Jaroslav Denkovskij
- Department of Regenerative Medicine, Centre for Innovative Medicine, Vilnius, Lithuania
| | - Arvydas Usas
- Institute of Physiology and Pharmacology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
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22
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Ni K, Lu X, Li S, Li F, Zhang Y, Cui R, Fan Y, Huang H, Chen X, Wang J, Wang S, Guo L, Zhao L, He Y, Ye W. GhLCYε-3 characterized as a lycopene cyclase gene responding to drought stress in cotton. Comput Struct Biotechnol J 2024; 23:384-395. [PMID: 38226314 PMCID: PMC10788185 DOI: 10.1016/j.csbj.2023.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024] Open
Abstract
Drought stress significantly affects crop productivity. Carotenoids are essential photosynthetic pigment for plants, bacteria, and algae, with signaling and antioxidant functions. Lutein is a crucial branch product in the carotenoid synthesis pathway, which effectively improves the stress tolerance of higher plants. lycopene cyclase, a central enzyme for lutein synthesis, holds great significance in regulating lutein production. This research establishes a correlation between lutein content and stress resistance by measuring the drought resistance and lutein content of various cotton materials. To identify which crucial genes are associated with lutein, the lycopene cyclase family (LCYs) was analyzed. The research found that LCYs form a highly conserved family divided into two subfamilies, LCY-ε (lycopene ε-cyclase) and LCY-β (lycopene β-cyclase). Most members of the LCY family contain photoresponsive elements and abscisic acid elements. qRT-PCR demonstrates showed that most genes responded positively to drought stress, and GhLCYε-3 was expressed significantly differently under drought stress. Virus-induced gene silencing (VIGS) assay showed that the content of GhLCYε-3 was significantly increased with MDA and PRO, and the contents of chlorophyll and lutein were significantly decreased in pYL156 plants. The decrease in GhLCYε-3 expression is speculated to lead to reduced lutein content in vivo, resulting in the accumulation of reactive oxygen species (ROS) and decreased drought tolerance. This research enriched the understanding of LCY gene family and lutein function, and provided a new reference for cotton planting in arid areas. Synopsis Lycopene cyclase plays an important role in enhancing the ability of scavenging ROS and drought resistance of plants.
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Affiliation(s)
- Kesong Ni
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Shuyan Li
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Fei Li
- Hunan Institute of Cotton Science, Changde 415101, Hunan China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Ruifeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
| | - Yunxin He
- Hunan Institute of Cotton Science, Changde 415101, Hunan China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang 455000, Henan, China
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Sahoo K, Sundararajan V. Methods in DNA methylation array dataset analysis: A review. Comput Struct Biotechnol J 2024; 23:2304-2325. [PMID: 38845821 PMCID: PMC11153885 DOI: 10.1016/j.csbj.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the intricate relationships between gene expression levels and epigenetic modifications in a genome is crucial to comprehending the pathogenic mechanisms of many diseases. With the advancement of DNA Methylome Profiling techniques, the emphasis on identifying Differentially Methylated Regions (DMRs/DMGs) has become crucial for biomarker discovery, offering new insights into the etiology of illnesses. This review surveys the current state of computational tools/algorithms for the analysis of microarray-based DNA methylation profiling datasets, focusing on key concepts underlying the diagnostic/prognostic CpG site extraction. It addresses methodological frameworks, algorithms, and pipelines employed by various authors, serving as a roadmap to address challenges and understand changing trends in the methodologies for analyzing array-based DNA methylation profiling datasets derived from diseased genomes. Additionally, it highlights the importance of integrating gene expression and methylation datasets for accurate biomarker identification, explores prognostic prediction models, and discusses molecular subtyping for disease classification. The review also emphasizes the contributions of machine learning, neural networks, and data mining to enhance diagnostic workflow development, thereby improving accuracy, precision, and robustness.
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Affiliation(s)
| | - Vino Sundararajan
- Correspondence to: Department of Bio Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India.
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24
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Bręborowicz A, Umezawa K. Effect of NF-κβ inhibitor - dehydroxymethylepoxyquinomicin on iron isomaltoside toxicity toward peritoneal mesothelial cells. Ren Fail 2024; 46:2304647. [PMID: 38240039 PMCID: PMC10802802 DOI: 10.1080/0886022x.2024.2304647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Affiliation(s)
- Andrzej Bręborowicz
- Department of Pathophysiology, Poznan University Medical School, Poznan, Poland
- Collegium Medicum, University of Zielona Góra, Góra, Poland
| | - Kazuo Umezawa
- Department of Molecular Target Medicine Screening, Aichi Medical University School of Medicine, Nagakute, Japan
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Zhang Z, Bao C, Li Z, He C, Jin W, Li C, Chen Y. Integrated omics analysis reveals the alteration of gut microbiota and fecal metabolites in Cervus elaphus kansuensis. Appl Microbiol Biotechnol 2024; 108:125. [PMID: 38229330 DOI: 10.1007/s00253-023-12841-5] [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: 04/13/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 01/18/2024]
Abstract
The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host's dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer (Cervus elaphus kansuensis), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis. The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. KEY POINTS: • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer.
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Affiliation(s)
- Zhenxiang Zhang
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Changhong Bao
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Zhaonan Li
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Caixia He
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Wenjie Jin
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China
| | - Changzhong Li
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China.
| | - Yanxia Chen
- College of Eco-Environmental Engineering, Qinghai University, No. 251 Ningda Road, Xining, 810016, China.
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Kishawy AT, Abd El-Wahab RA, Eldemery F, Abdel Rahman MMI, Altuwaijri S, Ezz-Eldin RM, Abd-Allah EM, Zayed S, Mulla ZS, El Sharkawy RB, Badr S, Youssef W, Ibrahim D. Insights of early feeding regime supplemented with glutamine and various levels of omega-3 in broiler chickens: growth performance, muscle building, antioxidant capacity, intestinal barriers health and defense against mixed Eimeria spp infection. Vet Q 2024; 44:1-20. [PMID: 38961536 PMCID: PMC11225632 DOI: 10.1080/01652176.2024.2373287] [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: 02/05/2024] [Accepted: 06/22/2024] [Indexed: 07/05/2024] Open
Abstract
Early nutritional management approach greatly impacts broilers' performance and resistance against coccidiosis. The current study explored the impact of post-hatch feeding with a combination of glutamine (Glut) and different levels of omega-3 on broiler chickens' growth performance, muscle building, intestinal barrier, antioxidant ability and protection against avian coccidiosis. A total of six hundred Cobb 500 was divided into six groups: first group (fed basal diet and unchallenged (control) and challenged (negative control, NC) groups were fed a basal diet without additives, and the other groups were infected with Eimeria spp and supplemented with 1.5% Glut alone or with three different levels of omega-3 (0.25, 0.5 and 1%) during the starter period. Notable improvement in body weight gain was observed in the group which fed basal diet supplemented with glut and 1% omega 3 even after coccidia infection (increased by 25% compared challenged group) while feed conversion ratio was restored to control. Myogeneis was enhanced in the group supplemented with Glut and omega-3 (upregulation of myogenin, MyoD, mechanistic target of rapamycin kinase and insulin like growth factor-1 and downregulating of myostatin genes). Groups supplemented with Glut and higher levels of omega-3 highly expressed occluding, mucin-2, junctional Adhesion Molecule 2, b-defensin-1 and cathelicidins-2 genes. Group fed 1% Glut + omega-3 showed an increased total antioxidant capacity and glutathione peroxidase and super oxide dismutase enzymes activities with reduced levels of malondialdehyde, reactive oxygen species and H2O2. Post-infection, dietary Glut and 1% omega-3 increased intestinal interleukin-10 (IL) and secretory immunoglobulin-A and serum lysozyme, while decreased the elevated inflammatory mediators comprising interleukin IL-6, tumor necrosis factor-alpha, nitric oxide (NO) and inducible NO synthase. Fecal oocyst excretion and lesions score severity were lowered in the group fed 1% Glut and omega 3. Based on these findings, dietary Glut and omega-3 supplementation augmented restored overall broilers' performance after coccidial challenge.
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Affiliation(s)
- Asmaa T.Y Kishawy
- Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Reham A. Abd El-Wahab
- Biochemistry Department, Animal Health Research Institute (AHRI), Mansoura Branch, Agriculture Research Center (ARC), Giza, Egypt
| | - Fatma Eldemery
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | | | - Saleh Altuwaijri
- Department of Pathology and laboratory diagnosis, College of Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Rasha M.M. Ezz-Eldin
- Department of Biochemistry, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Ehab M. Abd-Allah
- Veterinary Educational Hospital, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Shimaa Zayed
- Biochemistry Department, Animal Health Research Institute (AHRI), Mansoura Branch, Agriculture Research Center (ARC), Giza, Egypt
| | - Zohair S. Mulla
- Department of Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudia Arabia
| | - Rasha B. El Sharkawy
- Department of Clinical Pathology, Zagazig Branch, Animal Health Research Institute (AHRI), Agriculture Research Center, Zagazig, Egypt
| | - Shereen Badr
- Department of Clinical Pathology, Animal Health Research Institute (AHRI), Mansoura Branch, Agricultural Research Center (ARC), Giza, Egypt
| | - Wessam Youssef
- Department of Biotechnology, Animal Health Research Institute (AHRI), Giza, Egypt
| | - Doaa Ibrahim
- Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
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27
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Zhang H, Ye Y, Zhao Y, Li S, Jiao P, Yang Y, Jin Y, Zeng L, Zhang H, Chen M, Jiang H, Zhou L, Li J, Li D, Li R. Obesity is associated with lower levels of negative emotions in polycystic ovary syndrome in clinical and animal studies. Ann Med 2024; 56:2373199. [PMID: 38956857 PMCID: PMC11225633 DOI: 10.1080/07853890.2024.2373199] [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: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Polycystic ovary syndrome (PCOS) is one of the most common endocrine and metabolic disorders in women of reproductive age. It is frequently comorbid with obesity and negative emotions. Currently, there are few reports on the relationship between obesity and negative emotions in patients with PCOS. Here we performed both basic and clinical studies to study the relationship between obesity and negative emotions in PCOS. METHODS We performed a cross-sectional study including 608 patients with PCOS and 184 healthy participants to assess the mental health status of people with different body mass indices (BMI). Self-rated anxiety, depression, and perceived stress scales were used for subjective mood evaluations. Rat PCOS models fed 45 and 60% high-fat diets were used to confirm the results of the clinical study. Elevated plus maze and open field tests were used to assess anxiety- and depression-like behaviors in rats. RESULTS We observed overweight/obesity, increased depression, anxiety, and perceived stress in women with PCOS, and found that anxiety and depression were negatively correlated with BMI in patients with severe obesity and PCOS. Similar results were confirmed in the animal study; the elevated plus maze test and open field test demonstrated that only 60% of high fat diet-induced obesity partly reversed anxiety- and depression-like behaviors in PCOS rats. A high-fat diet also modulated rat hypothalamic and hippocampal luteinizing hormone and testosterone levels. CONCLUSION These results reveal a potential relationship between obesity and negative emotions in PCOS and prompt further investigation. The interactions between various symptoms of PCOS may be targeted to improve the overall well-being of patients.
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Affiliation(s)
- Haolin Zhang
- Department of Traditional Chinese Medicine, Peking University Third Hospital, Beijing, China
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yang Ye
- Department of Traditional Chinese Medicine, Peking University Third Hospital, Beijing, China
| | - Yue Zhao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Shi Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Peijie Jiao
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Yang Yang
- Department of Traditional Chinese Medicine, Peking University Third Hospital, Beijing, China
| | - Yuxin Jin
- Department of Traditional Chinese Medicine, Peking University Third Hospital, Beijing, China
| | - Lin Zeng
- Research Centre of Clinical Epidemiology, Peking University Third Hospital, Beijing, China
| | - Hua Zhang
- Research Centre of Clinical Epidemiology, Peking University Third Hospital, Beijing, China
| | - Meishuang Chen
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Hong Jiang
- Department of Neurobiology, School of Basic Medical Sciences, Neuroscience Research Institute, Peking University, Beijing, China
| | - Lifei Zhou
- Department of Traditional Chinese Medicine, Peking University Third Hospital, Beijing, China
| | - Jiayi Li
- Department of Traditional Chinese Medicine, Peking University Third Hospital, Beijing, China
| | - Dong Li
- Department of Traditional Chinese Medicine, Peking University Third Hospital, Beijing, China
| | - Rong Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
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Chen Q, Zheng Y, Jiang X, Wang Y, Chen Z, Wu D. Nature's carriers: leveraging extracellular vesicles for targeted drug delivery. Drug Deliv 2024; 31:2361165. [PMID: 38832506 DOI: 10.1080/10717544.2024.2361165] [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: 08/07/2023] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
With the rapid development of drug delivery systems, extracellular vesicles (EVs) have emerged as promising stars for improving targeting abilities and realizing effective delivery. Numerous studies have shown when compared to conventional strategies in targeted drug delivery (TDD), EVs-based strategies have several distinguished advantages besides targeting, such as participating in cell-to-cell communications and immune response, showing high biocompatibility and stability, penetrating through biological barriers, etc. In this review, we mainly focus on the mass production of EVs including the challenges and strategies for scaling up EVs production in a cost-effective and reproducible manner, the loading and active targeting methods, and examples of EVs as vehicles for TDD in consideration of potential safety and regulatory issues associated. We also conclude and discuss the rigor and reproducibility of EVs production, the current research status of the application of EVs-based strategies to targeted drug delivery, clinical conversion prospects, and existing chances and challenges.
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Affiliation(s)
- Qi Chen
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou, P. R. China
| | - Yuyi Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xuhong Jiang
- Epilepsy Center, Department of Neurology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, PR China
| | - Yi Wang
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- Zhejiang Rehabilitation Medical Center, The Third Affiliated Hospital of Zhejiang, Chinese Medical University, Hangzhou, PR China
| | - Zhong Chen
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- Epilepsy Center, Department of Neurology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, PR China
| | - Di Wu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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Liang Q, Fu C, Liu Y, Liu W, Guo W. Association of plasma microRNA-16-5p and abdominal aortic calcification in maintenance hemodialysis patients. Ren Fail 2024; 46:2368091. [PMID: 39049724 DOI: 10.1080/0886022x.2024.2368091] [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: 11/08/2023] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 07/27/2024] Open
Abstract
Recent studies have shown that microRNA-16-5p (miR-16-5p) plays a crucial role in the pathological mechanism of vascular calcification. Nevertheless, the expression profile of miR-16-5p in maintenance hemodialysis (MHD) patients who are predisposed to vascular calcification remains unknown. This study aims to investigate the potential associations between calcification risk and serum miR-16-5p expression among MHD patients. This cross-sectional study involved 132 MHD patients from the Dialysis Center of Beijing Friendship Hospital between 1 January 2019 and 31 December 2020. The degree of calcification in MHD patients was assessed using the Abdominal aortic calcification (AAC) score, and miR-16-5p expression was quantified using quantitative real-time polymerase chain reaction (qRT-PCR) with the 2-ΔΔCT method. Statistical analyses, including spearman correlation, linear regression and logistic regression analysis were used to explore the associations between laboratory parameters and AAC score. Calcifications were observed in 79(59.80%) patients. The linear regression showed a one-quartile decrease in miR-16-5p expression led to a significant increase in the AAC score by 5.336 (95% CI: 2.670-10.662, p = 0.000). Multivariate logistic regression analyses revealed that decreased miR-16-5p expression, reduced serum urea nitrogen, elevated white blood cell count, and longer dialysis vintage were significantly associated with an increased incidence of vascular calcification. The Area Under the Curve (AUC) of the Receiver Operating Characteristic (ROC) of the miR-16-5p-based logistic regression model was 0.842 (95% CI: 0.771-0.913, p = 0.000). There was an independent association between miR-16-5p expression and calcification degree. Lower miR-16-5p expression levels seem to be a potential risk factor of vascular calcification in MHD patients.
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Affiliation(s)
- Qiaojing Liang
- Department of Nephrology, Faculty of Kidney Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Chen Fu
- Department of Nephrology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, China
| | - Yingjie Liu
- Department of Nephrology, Faculty of Kidney Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Wenhu Liu
- Department of Nephrology, Faculty of Kidney Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Weikang Guo
- Department of Nephrology, Faculty of Kidney Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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Fang J, Zhou G, Zhao H, Xie D, Zhang J, Kües U, Xiao Y, Fang Z, Liu J. An apoptosis-inducing factor controls programmed cell death and laccase expression during fungal interactions. Appl Microbiol Biotechnol 2024; 108:135. [PMID: 38229306 DOI: 10.1007/s00253-023-12988-1] [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: 10/24/2023] [Revised: 12/15/2023] [Accepted: 12/24/2023] [Indexed: 01/18/2024]
Abstract
Apoptotic-like programmed cell death (PCD) is one of the main strategies for fungi to resist environmental stresses and maintain homeostasis. The apoptosis-inducing factor (AIF) has been shown in different fungi to trigger PCD through upregulating reactive oxygen species (ROS). This study identified a mitochondrial localized AIF homolog, CcAIF1, from Coprinopsis cinerea monokaryon Okayama 7. Heterologous overexpression of CcAIF1 in Saccharomyces cerevisiae caused apoptotic-like PCD of the yeast cells. Ccaif1 was increased in transcription when C. cinerea interacted with Gongronella sp. w5, accompanied by typical apoptotic-like PCD in C. cinerea, including phosphatidylserine externalization and DNA fragmentation. Decreased mycelial ROS levels were observed in Ccaif1 silenced C. cinerea transformants during cocultivation, as well as reduction of the apoptotic levels, mycelial growth, and asexual sporulation. By comparison, Ccaif1 overexpression led to the opposite phenotypes. Moreover, the transcription and expression levels of laccase Lcc9 decreased by Ccaif1 silencing but increased firmly in Ccaif1 overexpression C. cinerea transformants in coculture. Thus, in conjunction with our previous report that intracellular ROS act as signal molecules to stimulate defense responses, we conclude that CcAIF1 is a regulator of ROS to promote apoptotic-like PCD and laccase expression in fungal-fungal interactions. In an axenic culture of C. cinerea, CcAIF1 overexpression and H2O2 stimulation together increased laccase secretion with multiplied production yield. The expression of two other normally silent isozymes, Lcc8 and Lcc13, was unexpectedly triggered along with Lcc9. KEY POINTS: • Mitochondrial CcAIF1 induces PCD during fungal-fungal interactions • CcAIF1 is a regulator of ROS to trigger the expression of Lcc9 for defense • CcAIF1 overexpression and H2O2 stimulation dramatically increase laccase production.
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Affiliation(s)
- Junnan Fang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Gang Zhou
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Huifang Zhao
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Dengdeng Xie
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Jingna Zhang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Büsgen‑Institute, University of Goettingen, Büsgenweg 2, 37077, Goettingen, Germany
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China.
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China.
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China.
| | - Juanjuan Liu
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China.
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China.
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China.
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Li X, Liang Q, Liu L, Chen S, Li Y, Pu Y. FTO attenuates TNF-α-induced damage of proximal tubular epithelial cells in acute pancreatitis-induced acute kidney injury via targeting AQP3 in an N6-methyladenosine-dependent manner. Ren Fail 2024; 46:2322037. [PMID: 38445367 PMCID: PMC10919303 DOI: 10.1080/0886022x.2024.2322037] [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: 08/17/2023] [Accepted: 02/17/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Acute kidney injury (AKI) is a frequent complication of severe acute pancreatitis (SAP). Previous investigations have revealed the involvement of FTO alpha-ketoglutarate-dependent dioxygenase (FTO) and aquaporin 3 (AQP3) in AKI. Therefore, the aim of this study is to explore the association of FTO and AQP3 on proximal tubular epithelial cell damage in SAP-induced AKI. METHODS An in-vitro AKI model was established in human proximal tubular epithelial cells (PTECs) HK-2 via tumor necrosis factor-α (TNF-α) induction (20 ng/mL), after which FTO and AQP3 expression was manipulated and quantified by quantitative real-time PCR and Western blotting. The viability and apoptosis of PTECs under various conditions, and reactive oxygen species (ROS), superoxide dismutase (SOD), and malonaldehyde (MDA) levels within these cells were measured using commercial assay kits and flow cytometry. Methylated RNA immunoprecipitation and mRNA stability assays were performed to elucidate the mechanism of FTO-mediated N6-methyladenosine (m6A) modification. Western blotting was performed to quantify β-catenin protein levels in the PTECs. RESULTS FTO overexpression attenuated the TNF-α-induced decrease in viability and SOD levels, elevated apoptosis, increased levels of ROS and MDA, and diminished TNF-α-induced AQP3 expression and reduced β-catenin expression, but its silencing led to contradictory results. FTO negatively modulates AQP3 levels in RTECs in an m6A-depednent manner and compromises AQP3 stability. In addition, all FTO overexpression-induced effects in TNF-α-induced PTECs were neutralized following AQP3 upregulation. CONCLUSION FTO alleviates TNF-α-induced damage to PTECs in vitro by targeting AQP3 in an m6A-dependent manner.
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Affiliation(s)
- Xinghui Li
- Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Medical Imaging Key Laboratory of Sichuan Province, Nanchong, Sichuan Province, China
| | - Qi Liang
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Lu Liu
- Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Medical Imaging Key Laboratory of Sichuan Province, Nanchong, Sichuan Province, China
| | - Shujun Chen
- Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Medical Imaging Key Laboratory of Sichuan Province, Nanchong, Sichuan Province, China
| | - Yong Li
- Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Medical Imaging Key Laboratory of Sichuan Province, Nanchong, Sichuan Province, China
| | - Yu Pu
- Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Medical Imaging Key Laboratory of Sichuan Province, Nanchong, Sichuan Province, China
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Onuzulu CD, Lee S, Basu S, Comte J, Hai Y, Hizon N, Chadha S, Fauni MS, Halayko AJ, Pascoe CD, Jones MJ. Novel DNA methylation changes in mouse lungs associated with chronic smoking. Epigenetics 2024; 19:2322386. [PMID: 38436597 PMCID: PMC10913724 DOI: 10.1080/15592294.2024.2322386] [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: 11/14/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Smoking is a potent cause of asthma exacerbations, chronic obstructive pulmonary disease (COPD) and many other health defects, and changes in DNA methylation (DNAm) have been identified as a potential link between smoking and these health outcomes. However, most studies of smoking and DNAm have been done using blood and other easily accessible tissues in humans, while evidence from more directly affected tissues such as the lungs is lacking. Here, we identified DNAm patterns in the lungs that are altered by smoking. We used an established mouse model to measure the effects of chronic smoke exposure first on lung phenotype immediately after smoking and then after a period of smoking cessation. Next, we determined whether our mouse model recapitulates previous DNAm patterns observed in smoking humans, specifically measuring DNAm at a candidate gene responsive to cigarette smoke, Cyp1a1. Finally, we carried out epigenome-wide DNAm analyses using the newly released Illumina mouse methylation microarrays. Our results recapitulate some of the phenotypes and DNAm patterns observed in human studies but reveal 32 differentially methylated genes specific to the lungs which have not been previously associated with smoking. The affected genes are associated with nicotine dependency, tumorigenesis and metastasis, immune cell dysfunction, lung function decline, and COPD. This research emphasizes the need to study CS-mediated DNAm signatures in directly affected tissues like the lungs, to fully understand mechanisms underlying CS-mediated health outcomes.
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Affiliation(s)
- Chinonye Doris Onuzulu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Samantha Lee
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sujata Basu
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jeannette Comte
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Yan Hai
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nikho Hizon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Shivam Chadha
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Maria Shenna Fauni
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew J. Halayko
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Christopher D. Pascoe
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Meaghan J. Jones
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
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Guan J, Chen X, Li Z, Deng S, Wumaier A, Ma Y, Xie L, Huang S, Zhu Y, Zhuo Y. Role of N6-methyladenosine-related lncRnas in pseudoexfoliation glaucoma. Epigenetics 2024; 19:2348840. [PMID: 38716769 PMCID: PMC11086004 DOI: 10.1080/15592294.2024.2348840] [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: 12/03/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
To explore the role of lncRNA m6A methylation modification in aqueous humour (AH) of patients with pseudoexfoliation glaucoma (PXG). Patients with open-angle PXG under surgery from June 2021 to December 2021 were selected. Age- and gender-matched patients with age-related cataract (ARC) were chosen as control. Patients underwent detailed ophthalmic examinations. 0.05-0.1 ml AH were extracted during surgery for MeRIP-Seq and RNA-Seq. Joint analysis was used to screen lncRNAs with differential m6A methylation modification and expression. Online software tools were used to draw lncRNA-miRNA-mRNA network (ceRNA). Expression of lncRNAs and mRNAs was confirmed using quantitative real-time PCR. A total of 4151 lncRNAs and 4386 associated m6A methylation modified peaks were identified in the PXG group. Similarly, 2490 lncRNAs and 2595 associated m6A methylation modified peaks were detected in the control. Compared to the ARC group, the PXG group had 234 hypermethylated and 402 hypomethylated m6A peaks, with statistically significant differences (| Fold Change (FC) |≥2, p < 0.05). Bioinformatic analysis revealed that these differentially methylated lncRNA enriched in extracellular matrix formation, tight adhesion, TGF- β signalling pathway, AMPK signalling pathway, and MAPK signalling pathway. Joint analysis identified 10 lncRNAs with differential m6A methylation and expression simultaneously. Among them, the expression of ENST000000485383 and ROCK1 were confirmed downregulated in the PXG group by RT-qPCR. m6A methylation modification may affect the expression of lncRNA and participate in the pathogenesis of PXG through the ceRNA network. ENST000000485383-hsa miR592-ROCK1 May be a potential target pathway for further investigation in PXG m6A methylation.
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Affiliation(s)
- Jieying Guan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaohong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Zhidong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Shuifeng Deng
- The Department of Ophthalmology, Huizhou Hospital Affiliated to Guangzhou Medical University (Huizhou Third People’s Hospital), Huizhou, China
| | - Aizezi Wumaier
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Yuncheng Ma
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Lingling Xie
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Shengsong Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yingting Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
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Yu M, Song T, Yu J, Cao H, Pan X, Qi Z, Du Y, Liu W, Liu Y. UvVelC is important for conidiation and pathogenicity in the rice false smut pathogen Ustilaginoidea virens. Virulence 2024; 15:2301243. [PMID: 38240294 PMCID: PMC10802205 DOI: 10.1080/21505594.2023.2301243] [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: 04/29/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Rice false smut disease is one of the most significant rice diseases worldwide. Ustilaginoidea virens is the causative agent of this disease. Although several developmental and pathogenic genes have been identified and functionally analyzed, the pathogenic molecular mechanisms of U. virens remain elusive. The velvet family regulatory proteins are involved in fungal development, conidiation, and pathogenicity. In this study, we demonstrated the function of the VelC homolog UvVELC in U. virens. We identified the velvet family protein UvVELC and characterized its functions using a target gene deletion-strategy. Deletion of UvVELC resulted in conidiation failure and pathogenicity. The UvVELC expression levels during infection suggested that this gene might be involved in the early infection process. UvVELC is also important in resistance to abiotic stresses, the utilization efficiency of glucose, stachyose, raffinose, and other sugars, and the expression of transport-related genes. Moreover, UvVELC could physically interact with UvVEA in yeast, and UvVELC/UvVEA double-knockout mutants also failed in conidiation and pathogenicity. These results indicate that UvVELC play a critical role in the conidiation and pathogenicity in U. virens. Functional analysis indicated that UvVELC-mediated conidiation and nutrient acquisition from rice regulates the pathogenicity of U. virens. Understanding the function of the UvVELC homolog could provide a potential molecular target for controlling rice false smut disease.
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Affiliation(s)
- Mina Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tianqiao Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junjie Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Huijuan Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiayan Pan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhongqiang Qi
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yan Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Insistant of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Picard M, Scott-Boyer MP, Bodein A, Leclercq M, Prunier J, Périn O, Droit A. Target repositioning using multi-layer networks and machine learning: The case of prostate cancer. Comput Struct Biotechnol J 2024; 24:464-475. [PMID: 38983753 PMCID: PMC11231507 DOI: 10.1016/j.csbj.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
The discovery of novel therapeutic targets, defined as proteins which drugs can interact with to induce therapeutic benefits, typically represent the first and most important step of drug discovery. One solution for target discovery is target repositioning, a strategy which relies on the repurposing of known targets for new diseases, leading to new treatments, less side effects and potential drug synergies. Biological networks have emerged as powerful tools for integrating heterogeneous data and facilitating the prediction of biological or therapeutic properties. Consequently, they are widely employed to predict new therapeutic targets by characterizing potential candidates, often based on their interactions within a Protein-Protein Interaction (PPI) network, and their proximity to genes associated with the disease. However, over-reliance on PPI networks and the assumption that potential targets are necessarily near known genes can introduce biases that may limit the effectiveness of these methods. This study addresses these limitations in two ways. First, by exploiting a multi-layer network which incorporates additional information such as gene regulation, metabolite interactions, metabolic pathways, and several disease signatures such as Differentially Expressed Genes, mutated genes, Copy Number Alteration, and structural variants. Second, by extracting relevant features from the network using several approaches including proximity to disease-associated genes, but also unbiased approaches such as propagation-based methods, topological metrics, and module detection algorithms. Using prostate cancer as a case study, the best features were identified and utilized to train machine learning algorithms to predict 5 novel promising therapeutic targets for prostate cancer: IGF2R, C5AR, RAB7, SETD2 and NPBWR1.
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Affiliation(s)
- Milan Picard
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Antoine Bodein
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Julien Prunier
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Olivier Périn
- Digital Transformation and Innovation Department, L'Oréal Advanced Research, Aulnay-sous-bois, France
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
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Lai TH, Hwang JS, Ngo QN, Lee DK, Kim HJ, Kim DR. A comparative assessment of reference genes in mouse brown adipocyte differentiation and thermogenesis in vitro. Adipocyte 2024; 13:2330355. [PMID: 38527945 PMCID: PMC10965104 DOI: 10.1080/21623945.2024.2330355] [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: 11/15/2023] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
Adipogenic differentiation and thermogenesis in brown adipose tissue (BAT) undergo dynamic processes, altering phenotypes and gene expressions. Proper reference genes in gene expression analysis are crucial to mitigate experimental variances and ensure PCR efficacy. Unreliable reference genes can lead to erroneous gene expression quantification, resulting in data misinterpretation. This study focused on identifying suitable reference genes for mouse brown adipocyte research, utilizing brown adipocytes from the Ucp1-luciferase ThermoMouse model. Comparative analysis of gene expression data under adipogenesis and thermogenesis conditions was conducted, validating 13 housekeeping genes through various algorithms, including DeltaCq, BestKeeper, geNorm, Normfinder, and RefFinder. Tbp and Rer1 emerged as optimal references for Ucp1 and Pparg expression in brown adipogenesis, while Tbp and Ubc were ideal for the expression analysis of these target genes in thermogenesis. Conversely, certain conventional references, including Actb, Tubb5, and Gapdh, proved unstable as reference genes under both conditions. These findings stress the critical consideration of reference gene selection in gene expression analysis within specific biological systems to ensure accurate conclusions.
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Affiliation(s)
- Trang Huyen Lai
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Jin Seok Hwang
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Quang Nhat Ngo
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Dong-Kun Lee
- Department of Physiology and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Hyun Joon Kim
- Department of Anatomy and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
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Jian Y, Chen T, Yang Z, Xiang G, Xu K, Wang Y, Zhao N, He L, Liu Q, Li M. Small regulatory RNA RSaX28 promotes virulence by reinforcing the stability of RNAIII in community-associated ST398 clonotype Staphylococcus aureus. Emerg Microbes Infect 2024; 13:2341972. [PMID: 38597192 PMCID: PMC11034457 DOI: 10.1080/22221751.2024.2341972] [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: 12/28/2023] [Accepted: 04/06/2024] [Indexed: 04/11/2024]
Abstract
Staphylococcus aureus (S. aureus) is a notorious pathogen that cause metastatic or complicated infections. Hypervirulent ST398 clonotype strains, remarkably increased in recent years, dominated Community-associated S. aureus (CA-SA) infections in the past decade in China. Small RNAs like RNAIII have been demonstrated to play important roles in regulating the virulence of S. aureus, however, the regulatory roles played by many of these sRNAs in the ST398 clonotype strains are still unclear. Through transcriptome screening and combined with knockout phenotype analysis, we have identified a highly transcribed sRNA, RSaX28, in the ST398 clonotype strains. Sequence analysis revealed that RSaX28 is highly conserved in the most epidemic clonotypes of S. aureus, but its high transcription level is particularly prominent in the ST398 clonotype strains. Characterization of RSaX28 through RACE and Northern blot revealed its length to be 533nt. RSaX28 is capable of promoting the hemolytic ability, reducing biofilm formation capacity, and enhancing virulence of S. aureus in the in vivo murine infection model. Through IntaRNA prediction and EMSA validation, we found that RSaX28 can specifically interact with RNAIII, promoting its stability and positively regulating the translation of downstream alpha-toxin while inhibiting the translation of Sbi, thereby regulating the virulence and biofilm formation capacity of the ST398 clonotype strains. RSaX28 is an important virulence regulatory factor in the ST398 clonotype S. aureus and represents a potential important target for future treatment and immune intervention against S. aureus infections.
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Affiliation(s)
- Ying Jian
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Tianchi Chen
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Ziyu Yang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Guoxiu Xiang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Kai Xu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yanan Wang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Na Zhao
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Lei He
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Qian Liu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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Basu S, Kurgan L. Taxonomy-specific assessment of intrinsic disorder predictions at residue and region levels in higher eukaryotes, protists, archaea, bacteria and viruses. Comput Struct Biotechnol J 2024; 23:1968-1977. [PMID: 38765610 PMCID: PMC11098722 DOI: 10.1016/j.csbj.2024.04.059] [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: 02/05/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Intrinsic disorder predictors were evaluated in several studies including the two large CAID experiments. However, these studies are biased towards eukaryotic proteins and focus primarily on the residue-level predictions. We provide first-of-its-kind assessment that comprehensively covers the taxonomy and evaluates predictions at the residue and disordered region levels. We curate a benchmark dataset that uniformly covers eukaryotic, archaeal, bacterial, and viral proteins. We find that predictive performance differs substantially across taxonomy, where viruses are predicted most accurately, followed by protists and higher eukaryotes, while bacterial and archaeal proteins suffer lower levels of accuracy. These trends are consistent across predictors. We also find that current tools, except for flDPnn, struggle with reproducing native distributions of the numbers and sizes of the disordered regions. Moreover, analysis of two variants of disorder predictions derived from the AlphaFold2 predicted structures reveals that they produce accurate residue-level propensities for archaea, bacteria and protists. However, they underperform for higher eukaryotes and generally struggle to accurately identify disordered regions. Our results motivate development of new predictors that target bacteria and archaea and which produce accurate results at both residue and region levels. We also stress the need to include the region-level assessments in future assessments.
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Affiliation(s)
- Sushmita Basu
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
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Xu C, Li X, Zhang X, Wu R, Zhou Y, Zhao Q, Zhang Y, Geng S, Gu Y, Hong S. Cardiac murmur grading and risk analysis of cardiac diseases based on adaptable heterogeneous-modality multi-task learning. Health Inf Sci Syst 2024; 12:2. [PMID: 38045019 PMCID: PMC10692066 DOI: 10.1007/s13755-023-00249-4] [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: 08/01/2023] [Accepted: 09/20/2023] [Indexed: 12/05/2023] Open
Abstract
Cardiovascular disease (CVDs) has become one of the leading causes of death, posing a significant threat to human life. The development of reliable Artificial Intelligence (AI) assisted diagnosis algorithms for cardiac sounds is of great significance for early detection and treatment of CVDs. However, there is scarce research in this field. Existing research mainly faces three major challenges: (1) They mainly limited to murmur classification and cannot achieve murmur grading, but attempting both classification and grading may lead to negative effects between different multi-tasks. (2) They mostly pay attention to unstructured cardiac sound modality and do not consider the structured demographic modality, as it is difficult to balance the influence of heterogeneous modalities. (3) Deep learning methods lack interpretability, which makes it challenging to apply them clinically. To tackle these challenges, we propose a method for cardiac murmur grading and cardiac risk analysis based on heterogeneous modality adaptive multi-task learning. Specifically, a Hierarchical Multi-Task learning-based cardiac murmur detection and grading method (HMT) is proposed to prevent negative interference between different tasks. In addition, a cardiac risk analysis method based on Heterogeneous Multi-modal feature impact Adaptation (HMA) is also proposed, which transforms unstructured modality into structured modality representation, and utilizes an adaptive mode weight learning mechanism to balance the impact between unstructured modality and structured modality, thus enhancing the performance of cardiac risk prediction. Finally, we propose a multi-task interpretability learning module that incorporates an important evaluation using random masks. This module utilizes SHAP graphs to visualize crucial murmur segments in cardiac sound and employs a multi-factor risk decoupling model based on nomograms. And then we gain insights into the cardiac disease risk in both pre-decoupled multi-modality and post-decoupled single-modality scenarios, thus providing a solid foundation for AI assisted cardiac murmur grading and risk analysis. Experimental results on a large real-world CirCor DigiScope PCG dataset demonstrate that the proposed method outperforms the state-of-the-art (SOTA) method in murmur detection, grading, and cardiac risk analysis, while also providing valuable diagnostic evidence.
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Affiliation(s)
- Chenyang Xu
- Department of Computer Science, Tianjin University of Technology, Tianjin, China
| | - Xin Li
- Department of Rehabilitation Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Xinyue Zhang
- Department of Computer Science, Tianjin University of Technology, Tianjin, China
| | - Ruilin Wu
- Department of Computer Science, Tianjin University of Technology, Tianjin, China
| | - Yuxi Zhou
- Department of Computer Science, Tianjin University of Technology, Tianjin, China
- DCST, BNRist, RIIT, Institute of Internet Industry, Tsinghua University, Beijing, China
| | - Qinghao Zhao
- Department of Cardiology, Peking University People’s Hospital, Beijing, China
| | - Yong Zhang
- DCST, BNRist, RIIT, Institute of Internet Industry, Tsinghua University, Beijing, China
| | | | - Yue Gu
- Department of Computer Science, Tianjin University of Technology, Tianjin, China
| | - Shenda Hong
- National Institute of Health Data Science, Peking University, Beijing, China
- Institute of Medical Technology, Peking University, Beijing, China
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Li X, Yang Y, Xu S, Gui Y, Chen J, Xu J. Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning. Neural Regen Res 2024; 19:2723-2734. [PMID: 38595290 PMCID: PMC11168503 DOI: 10.4103/1673-5374.391306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/15/2023] [Accepted: 11/06/2023] [Indexed: 04/11/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202412000-00028/figure1/v/2024-04-08T165401Z/r/image-tiff Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal cord injury. They can greatly affect nerve regeneration and functional recovery. However, there is still limited understanding of the peripheral immune inflammatory response in spinal cord injury. In this study, we obtained microRNA expression profiles from the peripheral blood of patients with spinal cord injury using high-throughput sequencing. We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus (GEO) database (GSE151371). We identified 54 differentially expressed microRNAs and 1656 differentially expressed genes using bioinformatics approaches. Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways, such as neutrophil extracellular trap formation pathway, T cell receptor signaling pathway, and nuclear factor-κB signal pathway, were abnormally activated or inhibited in spinal cord injury patient samples. We applied an integrated strategy that combines weighted gene co-expression network analysis, LASSO logistic regression, and SVM-RFE algorithm and identified three biomarkers associated with spinal cord injury: ANO10, BST1, and ZFP36L2. We verified the expression levels and diagnostic performance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve. Quantitative polymerase chain reaction results showed that ANO10 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients. We also constructed a small RNA-mRNA interaction network using Cytoscape. Additionally, we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal cord injury patients using the CIBERSORT tool. The proportions of naïve B cells, plasma cells, monocytes, and neutrophils were increased while the proportions of memory B cells, CD8+ T cells, resting natural killer cells, resting dendritic cells, and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects, and ANO10, BST1 and ZFP26L2 were closely related to the proportion of certain immune cell types. The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal cord injury and suggest that ANO10, BST1, and ZFP36L2 are potential biomarkers for spinal cord injury. The study was registered in the Chinese Clinical Trial Registry (registration No. ChiCTR2200066985, December 12, 2022).
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Affiliation(s)
- Xiaolu Li
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Ye Yang
- Department of Rehabilitation Medicine, Guilin People’s Hospital, Guilin, Guangxi Zhuang Autonomous Region, China
| | - Senming Xu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Yuchang Gui
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Jianmin Chen
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jianwen Xu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
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Liu Y, Koo JS, Zhang H. Chronic intermittent ethanol exposure-induced m6A modifications around mRNA stop codons of opioid receptor genes. Epigenetics 2024; 19:2294515. [PMID: 38118075 PMCID: PMC10761033 DOI: 10.1080/15592294.2023.2294515] [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: 08/05/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Chronic alcohol consumption may alter mRNA methylation and expression levels of genes related to addiction and reward in the brain, potentially contributing to alcohol tolerance and dependence. Neuron-like (SH-SY5Y) and non-neuronal (SW620) cells were utilized as models to examine chronic intermittent ethanol (CIE) exposure-induced global m6A RNA methylation changes, as well as m6A mRNA methylation changes around the stop codon of three opioid receptor genes (OPRM1, OPRD1, and OPRK1), which are known to regulate pain, reward, and addiction behaviours. CIE exposure for three weeks significantly increased global RNA methylation levels in both SH-SY5Y (t = 3.98, P = 0.007) and SW620 (t = 2.24, P = 0.067) cells. However, a 3-week CIE exposure resulted in hypomethylation around mRNA stop codon regions of OPRM1 and OPRD1 in both cell lines [OPRM1(SH-SY5Y): t = -5.05, P = 0.0005; OPRM1(SW620): t = -3.19, P = 0.013; OPRD1(SH-SY5Y): t = -13.43, P < 0.00001; OPRD1(SW620): t = -4.00, P = 0.003]. Additionally, mRNA expression levels of OPRM1, OPRD1, and OPRK1 were downregulated (corresponding to mRNA hypomethylation) in both SH-SY5Y and SW620 cells after a 3-week CIE exposure. The present study demonstrated that chronic ethanol exposure altered global RNA methylation levels, as well as mRNA methylation and expression levels of opioid receptor genes in both neuron-like and non-neuronal cells. Our findings suggest a potential epitranscriptomic mechanism by which chronic alcohol consumption remodels the expression of reward-related and alcohol responsive genes in the brain, thus increasing the risk of alcohol use disorder development.Abbreviations: OPRM1: the μ-opioid receptor; OPRD1: the δ-opioid receptor; OPRK1: the κ-opioid receptor; CIE: chronic intermittent ethanol exposure; CIE+WD: chronic intermittent ethanol exposure followed by a 24-hr withdrawal; SH-SY5Y: human neuroblastoma cell Line; SW620: human colon carcinoma cell line; RT-qPCR: reverse transcription followed by quantitative polymerase reaction; MazF-RT-qPCR: MazF digestion followed by RT-qPCR.
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Affiliation(s)
- Ying Liu
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, USA
| | - Ji Sun Koo
- Department of Biology, Boston University, Boston, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, USA
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Hasan MK, Jeannine Brady L. Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes. J Struct Biol X 2024; 10:100106. [PMID: 39040530 PMCID: PMC11261784 DOI: 10.1016/j.yjsbx.2024.100106] [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: 02/23/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein-protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.
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Affiliation(s)
- Md Kamrul Hasan
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
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Nguyen LTT, Park AR, Van Le V, Hwang I, Kim JC. Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight. Appl Microbiol Biotechnol 2024; 108:49. [PMID: 38183485 DOI: 10.1007/s00253-023-12874-w] [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: 06/14/2023] [Revised: 10/17/2023] [Accepted: 11/05/2023] [Indexed: 01/08/2024]
Abstract
Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.
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Affiliation(s)
- Loan Thi Thanh Nguyen
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ae Ran Park
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Inmin Hwang
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea.
- JAN153 Biotech Incorporated, Gwangju, 61186, Republic of Korea.
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44
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Lai J, Zhou Z, Hu K, Yu H, Su X, Niu X, Li H, Mao S. N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells. Epigenetics 2024; 19:2298058. [PMID: 38145548 PMCID: PMC10761136 DOI: 10.1080/15592294.2023.2298058] [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: 07/03/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
N6 methyladenosine (m6A), methylation at the sixth N atom of adenosine, is the most common and abundant modification in mammalian mRNAs and non-coding RNAs. Increasing evidence shows that the alteration of m6A modification level could regulate tumour proliferation, metastasis, self-renewal, and immune infiltration by regulating the related expression of tumour genes. However, the role of m6A modification in colorectal cancer (CRC) drug resistance is unclear. Here, MeRIP-seq and RNA-seq techniques were utilized to obtain mRNA, lncRNA expression, and their methylation profiles in 5-Fluorouracil (5-FU)-resistant colon cancer HCT-15 cells and control cells. In addition, we performed detailed bioinformatics analysis as well as in vitro experiments of lncRNA to explore the function of lncRNA with differential m6A in CRC progression and drug resistance. In this study, we obtained the m6A methylomic landscape of CRC cells and resistance group cells by MeRIP-seq and RNA-seq. We identified 3698 differential m6A peaks, of which 2224 were hypermethylated, and 1474 were hypomethylated. Among the lncRNAs, 60 were hypermethylated, and 38 were hypomethylated. GO and KEGG analysis annotations showed significant enrichment of endocytosis and MAPK signalling pathways. Moreover, knockdown of lncRNA ADIRF-AS1 and AL139035.1 promoted CRC proliferation and invasive metastasis in vitro. lncRNA- mRNA network showed that ADIRF-AS1 and AL139035.1 May play a key role in regulating drug resistance formation. We provide the first m6A methylation profile in 5-FU resistance CRC cells and analyse the functions of differential m6A-modified mRNAs and lncRNAs. Our results indicated that differential m6A RNAs were significantly associated with MAPK signalling and endocytosis after induction of 5-FU resistance. Knockdown of LncRNA ADIRF-AS1 and AL139035.1 promotes CRC progression and might be critical in regulating drug resistance formation.
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Affiliation(s)
- Jie Lai
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - Zhiyong Zhou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kan Hu
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - HongLong Yu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xingyao Su
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaoqiang Niu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Huizi Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shengxun Mao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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Mendes F, Miranda E, Amaral L, Carvalho C, Castro BB, Sousa MJ, Chaves SR. Novel yeast-based biosensor for environmental monitoring of tebuconazole. Appl Microbiol Biotechnol 2024; 108:10. [PMID: 38170307 PMCID: PMC10764535 DOI: 10.1007/s00253-023-12944-z] [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: 08/07/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 01/05/2024]
Abstract
Due to increasing demand for high and stable crop production, human populations are highly dependent on pesticide use for growing and storing food. Environmental monitoring of these agrochemicals is therefore of utmost importance, because of their collateral effects on ecosystem and human health. Even though most current-use analytical methods achieve low detection limits, they require procedures that are too complex and costly for routine monitoring. As such, there has been an increased interest in biosensors as alternative or complementary tools to streamline detection and quantification of environmental contaminants. In this work, we developed a biosensor for environmental monitoring of tebuconazole (TEB), a common agrochemical fungicide. For that purpose, we engineered S. cerevisiae cells with a reporter gene downstream of specific promoters that are expressed after exposure to TEB and characterized the sensitivity and specificity of this model system. After optimization, we found that this easy-to-use biosensor consistently detects TEB at concentrations above 5 μg L-1 and does not respond to realistic environmental concentrations of other tested azoles, suggesting it is specific. We propose the use of this system as a complementary tool in environmental monitoring programs, namely, in high throughput scenarios requiring screening of numerous samples. KEY POINTS: • A yeast-based biosensor was developed for environmental monitoring of tebuconazole. •The biosensor offers a rapid and easy method for tebuconazole detection ≥ 5 μg L-1. •The biosensor is specific to tebuconazole at environmentally relevant concentrations.
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Affiliation(s)
- Filipa Mendes
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
| | - Eduarda Miranda
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
| | - Leslie Amaral
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
| | - Carla Carvalho
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
- Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Bruno B Castro
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), School of Sciences, University of Minho, 4710-057, Braga, Portugal
| | - Maria João Sousa
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), School of Sciences, University of Minho, 4710-057, Braga, Portugal
| | - Susana R Chaves
- CBMA - Centre of Molecular and Environmental Biology/ARNET - Aquatic Research Network, Department of Biology, School of Sciences, University of Minho, 4710-057, Braga, Portugal.
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Alotaibi B, Elekhnawy E, El-Masry TA, Saleh A, Alosaimi ME, Alotaibi KN, Negm WA. Antibacterial potential of Euphorbia canariensis against Pseudomonas aeruginosa bacteria causing respiratory tract infections. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:261-269. [PMID: 38696143 DOI: 10.1080/21691401.2024.2345891] [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: 10/24/2023] [Accepted: 04/14/2024] [Indexed: 05/14/2024]
Abstract
The widespread dissemination of bacterial resistance has led to great attention being paid to finding substitutes for traditionally used antibiotics. Plants are rich in various phytochemicals that could be used as antibacterial therapies. Here, we elucidate the phytochemical profile of Euphorbia canariensis ethanol extract (EMEE) and then elucidate the antibacterial potential of ECEE against Pseudomonas aeruginosa clinical isolates. ECEE showed minimum inhibitory concentrations ranging from 128 to 512 µg/mL. The impact of ECEE on the biofilm-forming ability of the tested isolates was elucidated using crystal violet assay and qRT-PCR to study its effect on the gene expression level. ECEE exhibited antibiofilm potential, which resulted in a downregulation of the expression of the biofilm genes (algD, pelF, and pslD) in 39.13% of the tested isolates. The antibacterial potential of ECEE was studied in vivo using a lung infection model in mice. A remarkable improvement was observed in the ECEE-treated group, as revealed by the histological and immunohistochemical studies. Also, ELISA showed a noticeable decrease in the oxidative stress markers (nitric oxide and malondialdehyde). The gene expression of the proinflammatory marker (interleukin-6) was downregulated, while the anti-inflammatory biomarker was upregulated (interleukin-10). Thus, clinical trials should be performed soon to explore the potential antibacterial activity of ECEE, which could help in our battle against resistant pathogenic bacteria.
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Affiliation(s)
- Badriyah Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh 84428, Saudi Arabia
| | - Engy Elekhnawy
- Pharmaceutical Microbiology Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Thanaa A El-Masry
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Asmaa Saleh
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh 84428, Saudi Arabia
| | - Manal E Alosaimi
- Department of Basic Health Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh 84428, Saudi Arabia
| | | | - Walaa A Negm
- Department of Pharmacognosy, Faculty of Pharmacy, Tanta University, Tanta
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Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [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: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
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Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
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48
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Lalsangpuii F, Rokhum SL, Nghakliana F, V L Ruatpuia J, Tochhawng L, Trivedi AK, Lalfakzuala R, Siama Z. Mikania micrantha silver nanoparticles exhibit anticancer activities against human lung adenocarcinoma via caspase-mediated apoptotic cell death. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:186-200. [PMID: 38465883 DOI: 10.1080/21691401.2024.2325942] [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: 01/04/2024] [Accepted: 02/27/2024] [Indexed: 03/12/2024]
Abstract
Green-mediated synthesis of nanoparticles has earned a promising role in the area of nanotechnology due to their biomedical applications. This study describes the synthesis of silver nanoparticles (AgNPs) using Mikania micrantha leaf extract and its functional activities against cancer. The synthesis of AgNPs was confirmed using Ultraviolet-Visible (UV-Vis) spectrum that exhibited an absorption band at 459 nm. The bioactive compounds of M. micrantha leaf extract that functioned as reducing and capping agents were confirmed by a shift in the absorption bands in Fourier Transform Infra-red Spectroscopy (FT-IR). Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) studies validated the spherical shape and size of AgNPs, respectively. Energy Dispersive Spectroscopy (EDS) analysis revealed the presence of elemental silver. The crystalline nature of AgNPs was confirmed by the X-ray Diffraction Analysis (XRD). AgNPs effectively induced cytotoxicity and prevented A549 cell colony formation in a dose-dependent manner. Treatment of A549 cells with AgNPs also increased DNA damage, which was coupled with elevated lipid peroxidation and decreased antioxidant enzymes such as glutathione (GSH), glutathione-s-transferase (GST), and superoxide dismutase (SOD). Following AgNPs treatment, the mRNA expression levels of the pro-apoptotic genes as well as the activities of caspases were significantly elevated in A549 cells while the expression levels of anti-apoptotic genes were downregulated. Our study demonstrates the potential of the synthesised AgNPs for cancer therapy possibly targeting the apoptotic pathway.
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Affiliation(s)
| | | | | | - Joseph V L Ruatpuia
- Department of Chemistry, National Institute of Technology Silchar, Silchar, India
| | | | | | | | - Zothan Siama
- Department of Zoology, Mizoram University, Aizawl, India
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49
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Nocentini A, Di Porzio A, Bonardi A, Bazzicalupi C, Petreni A, Biver T, Bua S, Marzano S, Amato J, Pagano B, Iaccarino N, De Tito S, Amente S, Supuran CT, Randazzo A, Gratteri P. Development of a multi-targeted chemotherapeutic approach based on G-quadruplex stabilisation and carbonic anhydrase inhibition. J Enzyme Inhib Med Chem 2024; 39:2366236. [PMID: 38905127 PMCID: PMC11195807 DOI: 10.1080/14756366.2024.2366236] [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: 02/23/2024] [Accepted: 06/02/2024] [Indexed: 06/23/2024] Open
Abstract
A novel class of compounds designed to hit two anti-tumour targets, G-quadruplex structures and human carbonic anhydrases (hCAs) IX and XII is proposed. The induction/stabilisation of G-quadruplex structures by small molecules has emerged as an anticancer strategy, disrupting telomere maintenance and reducing oncogene expression. hCAs IX and XII are well-established anti-tumour targets, upregulated in many hypoxic tumours and contributing to metastasis. The ligands reported feature a berberine G-quadruplex stabiliser scaffold connected to a moiety inhibiting hCAs IX and XII. In vitro experiments showed that our compounds selectively stabilise G-quadruplex structures and inhibit hCAs IX and XII. The crystal structure of a telomeric G-quadruplex in complex with one of these ligands was obtained, shedding light on the ligand/target interaction mode. The most promising ligands showed significant cytotoxicity against CA IX-positive HeLa cancer cells in hypoxia, and the ability to stabilise G-quadruplexes within tumour cells.
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Affiliation(s)
- Alessio Nocentini
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Alessandro Bonardi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Carla Bazzicalupi
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Andrea Petreni
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Silvia Bua
- Research Institute of the University of Bucharest (ICUB), Bucharest, Romania
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Stefano De Tito
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Claudiu T. Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Paola Gratteri
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
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50
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Yang X, Zeng J, Wang D, Zhou Q, Yu X, Wang Z, Bai T, Luan G, Xu Y. NagZ modulates the virulence of E. cloacae by acting through the gene of unknown function, ECL_03795. Virulence 2024; 15:2367652. [PMID: 38912723 PMCID: PMC11197897 DOI: 10.1080/21505594.2024.2367652] [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: 02/19/2024] [Accepted: 06/09/2024] [Indexed: 06/25/2024] Open
Abstract
β-N-acetylglucosaminidase (NagZ), a cytosolic glucosaminidase, plays a pivotal role in peptidoglycan recycling. Previous research demonstrated that NagZ knockout significantly eradicated AmpC-dependent β-lactam resistance in Enterobacter cloacae. However, NagZ's role in the virulence of E. cloacae remains unclear. Our study, incorporating data on mouse and Galleria mellonella larval mortality rates, inflammation markers, and histopathological examinations, revealed a substantial reduction in the virulence of E. cloacae following NagZ knockout. Transcriptome sequencing uncovered differential gene expression between NagZ knockout and wild-type strains, particularly in nucleotide metabolism pathways. Further investigation demonstrated that NagZ deletion led to a significant increase in cyclic diguanosine monophosphate (c-di-GMP) levels. Additionally, transcriptome sequencing and RT-qPCR confirmed significant differences in the expression of ECL_03795, a gene with an unknown function but speculated to be involved in c-di-GMP metabolism due to its EAL domain known for phosphodiesterase activity. Interestingly, in ECL_03795 knockout strains, a notable reduction in the virulence was observed, and virulence was rescued upon complementation with ECL_03795. Consequently, our study suggests that NagZ's function on virulence is partially mediated through the ECL_03795→c-di-GMP pathway, providing insight into the development of novel therapies and strongly supporting the interest in creating highly efficient NagZ inhibitors.
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Affiliation(s)
- Xianggui Yang
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Zeng
- Division of Pulmonary and Critical Care Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Dan Wang
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Qin Zhou
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Xuejing Yu
- Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhenguo Wang
- Department of Stomatology, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Tingting Bai
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Guangxin Luan
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Ying Xu
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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