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Wen J, Tang H, Tian M, Wang L, Yang Q, Zhao Y, Li X, Ren Y, Wang J, Zhou L, Tan Y, Wu H, Cai X, Wang Y, Cao H, Xu J, Yang Q. Fibrotic scar formation after cerebral ischemic stroke: Targeting the Sonic hedgehog signaling pathway for scar reduction. Neural Regen Res 2026; 21:756-768. [PMID: 40183351 DOI: 10.4103/nrr.nrr-d-24-00999] [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: 08/28/2024] [Accepted: 12/30/2024] [Indexed: 04/05/2025] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202602000-00044/figure1/v/2025-05-05T160104Z/r/image-tiff Recent studies have shown that fibrotic scar formation following cerebral ischemic injury has varying effects depending on the microenvironment. However, little is known about how fibrosis is induced and regulated after cerebral ischemic injury. Sonic hedgehog signaling participates in fibrosis in the heart, liver, lung, and kidney. Whether Shh signaling modulates fibrotic scar formation after cerebral ischemic stroke and the underlying mechanisms are unclear. In this study, we found that Sonic Hedgehog expression was upregulated in patients with acute ischemic stroke and in a middle cerebral artery occlusion/reperfusion injury rat model. Both Sonic hedgehog and Mitofusin 2 showed increased expression in the middle cerebral artery occlusion rat model and in vitro fibrosis cell model induced by transforming growth factor-beta 1. Activation of the Sonic hedgehog signaling pathway enhanced the expression of phosphorylated Smad 3 and Mitofusin 2 proteins, promoted the formation of fibrotic scars, protected synapses or promoted synaptogenesis, alleviated neurological deficits following middle cerebral artery occlusion/reperfusion injury, reduced cell apoptosis, facilitated the transformation of meninges fibroblasts into myofibroblasts, and enhanced the proliferation and migration of meninges fibroblasts. The Smad3 phosphorylation inhibitor SIS3 reversed the effects induced by Sonic hedgehog signaling pathway activation. Bioinformatics analysis revealed significant correlations between Sonic hedgehog and Smad3, between Sonic hedgehog and Mitofusin 2, and between Smad3 and Mitofusin 2. These findings suggest that Sonic hedgehog signaling may influence Mitofusin 2 expression by regulating Smad3 phosphorylation, thereby modulating the formation of early fibrotic scars following cerebral ischemic stroke and affecting prognosis. The Sonic Hedgehog signaling pathway may serve as a new therapeutic target for stroke treatment.
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Affiliation(s)
- Jun Wen
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hao Tang
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mingfen Tian
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ling Wang
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qinghuan Yang
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yong Zhao
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Li
- Department of Neurology, Second People's Hospital of Chongqing Banan District, Chongqing, China
| | - Yu Ren
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiani Wang
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Zhou
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongjun Tan
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haiyun Wu
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xinrui Cai
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yilin Wang
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hui Cao
- Department of Neurosurgery, Third Hospital of Mianyang, Mianyang, Sichuan Province, China
| | - Jianfeng Xu
- Department of Neurosurgery, Third Hospital of Mianyang, Mianyang, Sichuan Province, China
| | - Qin Yang
- Department of Neurology, The Frist Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Ren C, Chen M, Ren B, Zeng Y, Tan Q, Li Q, Zhang X, Fang Y, Zhou Y, Zhang W, Chen F, Bian B, Liu Y. Mesenchymal stem cell-derived small extracellular vesicles enhance the therapeutic effect of retinal progenitor cells in retinal degenerative disease rats. Neural Regen Res 2026; 21:821-832. [PMID: 39101643 DOI: 10.4103/nrr.nrr-d-23-02108] [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: 12/30/2023] [Accepted: 06/08/2024] [Indexed: 08/06/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202602000-00050/figure1/v/2025-05-05T160104Z/r/image-tiff Our previous study demonstrated that combined transplantation of bone marrow mesenchymal stem cells and retinal progenitor cells in rats has therapeutic effects on retinal degeneration that are superior to transplantation of retinal progenitor cells alone. Bone marrow mesenchymal stem cells regulate and interact with various cells in the retinal microenvironment by secreting neurotrophic factors and extracellular vesicles. Small extracellular vesicles derived from bone marrow mesenchymal stem cells, which offer low immunogenicity, minimal tumorigenic risk, and ease of transportation, have been utilized in the treatment of various neurological diseases. These vesicles exhibit various activities, including anti-inflammatory actions, promotion of tissue repair, and immune regulation. Therefore, novel strategies using human retinal progenitor cells combined with bone marrow mesenchymal stem cell-derived small extracellular vesicles may represent an innovation in stem cell therapy for retinal degeneration. In this study, we developed such an approach utilizing retinal progenitor cells combined with bone marrow mesenchymal stem cell-derived small extracellular vesicles to treat retinal degeneration in Royal College of Surgeons rats, a genetic model of retinal degeneration. Our findings revealed that the combination of bone marrow mesenchymal stem cell-derived small extracellular vesicles and retinal progenitor cells significantly improved visual function in these rats. The addition of bone marrow mesenchymal stem cell-derived small extracellular vesicles as adjuvants to stem cell transplantation with retinal progenitor cells enhanced the survival, migration, and differentiation of the exogenous retinal progenitor cells. Concurrently, these small extracellular vesicles inhibited the activation of regional microglia, promoted the migration of transplanted retinal progenitor cells to the inner nuclear layer of the retina, and facilitated their differentiation into photoreceptors and bipolar cells. These findings suggest that bone marrow mesenchymal stem cell-derived small extracellular vesicles potentiate the therapeutic efficacy of retinal progenitor cells in retinal degeneration by promoting their survival and differentiation.
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Affiliation(s)
- Chunge Ren
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Min Chen
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Bangqi Ren
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Yuxiao Zeng
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Qiang Tan
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Qiyou Li
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Xue Zhang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Yajie Fang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Yixiao Zhou
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Weitao Zhang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Fang Chen
- Department of Medical Technology, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Baishijiao Bian
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
- Army 953 Hospital, Shigatse Branch of Xinqiao Hospital, Third Military Medical University (Army Medical University), Shigatse, Tibet Autonomous Region, China
- State Key Laboratory of Trauma and Chemical Poisoning, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yong Liu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
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Cercel AM, Boboc IK, Surugiu R, Doeppner TR, Hermann DM, Catalin B, Gresita A, Popa-Wagner A. Grafts of hydrogel-embedded electrically stimulated subventricular stem cells into the stroke cavity improves functional recovery of mice. Neural Regen Res 2026; 21:695-703. [PMID: 39589177 DOI: 10.4103/nrr.nrr-d-23-02092] [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: 12/27/2023] [Accepted: 10/29/2024] [Indexed: 11/27/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202602000-00039/figure1/v/2025-05-05T160104Z/r/image-tiff The major aim of stroke therapy is to stimulate brain repair and improve behavioral recovery after cerebral ischemia. One option is to stimulate endogenous neurogenesis in the subventricular zone and direct the newly formed neurons to the damaged area. However, only a small percentage of these neurons survive, and many do not reach the damaged area, possibly because the corpus callosum impedes the migration of subventricular zone-derived stem cells into the lesioned cortex. A second major obstacle to stem cell therapy is the strong inflammatory reaction induced by cerebral ischemia, whereby the associated phagocytic activity of brain macrophages removes both therapeutic cells and/or cell-based drug carriers. To address these issues, neurogenesis was electrically stimulated in the subventricular zone, followed by isolation of proliferating cells, including newly formed neurons, which were subsequently mixed with a nutritional hydrogel. This mixture was then transferred to the stroke cavity of day 14 post-stroke mice. We found that the performance of the treated animals improved in behavioral tests, including novel object, open field, hole board, grooming, and "time-to-feel" adhesive tape tests. Furthermore, immunostaining revealed that the stem cell marker nestin, the neuroepithelial marker Mash1, and the immature neuronal marker doublecortin-positive cells survived in the transplanted area for 2 weeks, possibly due to reduced phagocytic activity and supportive angiogenesis. These results clearly indicate that the transplantation of committed subventricular zone stem cells combined with a protective nutritional gel directly into the infarct cavity after the peak of stroke-induced neuroinflammation represents a feasible approach to improve neurorestoration after cerebral ischemia.
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Affiliation(s)
- Andreea-Mihaela Cercel
- Experimental Research Center for Normal and Pathological Aging, University of Medicine and Pharmacy Craiova, Craiova, Romania
- Doctoral School, University of Medicine and Pharmacy Craiova, Craiova, Romania
| | - Ianis Ks Boboc
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova, Romania
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Roxana Surugiu
- Experimental Research Center for Normal and Pathological Aging, University of Medicine and Pharmacy Craiova, Craiova, Romania
- Chair of Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
| | - Thorsten R Doeppner
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
- Department of Neurology, University of Giessen Medical School, Giessen, Germany
| | - Dirk M Hermann
- Chair of Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
| | - Bogdan Catalin
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova, Romania
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Andrei Gresita
- Department of Biomedical Sciences, New York Institute of Technology, College of Osteopathic Medicine, Old Westbury, NY, USA
| | - Aurel Popa-Wagner
- Experimental Research Center for Normal and Pathological Aging, University of Medicine and Pharmacy Craiova, Craiova, Romania
- Chair of Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
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Fu H, Li J, Zhang C, Gao G, Ge Q, Guan X, Cui D. Pathological axonal enlargement in connection with amyloidosis, lysosome destabilization, and bleeding is a major defect in Alzheimer's disease. Neural Regen Res 2026; 21:790-799. [PMID: 40326989 DOI: 10.4103/nrr.nrr-d-24-01440] [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: 11/18/2024] [Accepted: 03/17/2025] [Indexed: 05/07/2025] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202602000-00047/figure1/v/2025-05-05T160104Z/r/image-tiff Alzheimer's disease is a multi-amyloidosis disease characterized by amyloid-β deposits in brain blood vessels, microaneurysms, and senile plaques. How amyloid-β deposition affects axon pathology has not been examined extensively. We used immunohistochemistry and immunofluorescence staining to analyze the forebrain tissue slices of Alzheimer's disease patients. Widespread axonal amyloidosis with distinctive axonal enlargement was observed in patients with Alzheimer's disease. On average, amyloid-β-positive axon diameters in Alzheimer's disease brains were 1.72 times those of control brain axons. Furthermore, axonal amyloidosis was associated with microtubule-associated protein 2 reduction, tau phosphorylation, lysosome destabilization, and several blood-related markers, such as apolipoprotein E, alpha-hemoglobin, glycosylated hemoglobin type A1C, and hemin. Lysosome destabilization in Alzheimer's disease was also clearly identified in the neuronal soma, where it was associated with the co-expression of amyloid-β, Cathepsin D, alpha-hemoglobin, actin alpha 2, and collagen type IV. This suggests that exogenous hemorrhagic protein intake influences neural lysosome stability. Additionally, the data showed that amyloid-β-containing lysosomes were 2.23 times larger than control lysosomes. Furthermore, under rare conditions, axonal breakages were observed, which likely resulted in Wallerian degeneration. In summary, axonal enlargement associated with amyloidosis, micro-bleeding, and lysosome destabilization is a major defect in patients with Alzheimer's disease. This finding suggests that, in addition to the well-documented neural soma and synaptic damage, axonal damage is a key component of neuronal defects in Alzheimer's disease.
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Affiliation(s)
- Hualin Fu
- Institute of Nano Biomedicine and Engineering, School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of Marine Equipment, Shanghai Jiao Tong University, Shanghai, China
- National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jilong Li
- Institute of Nano Biomedicine and Engineering, School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chunlei Zhang
- Institute of Nano Biomedicine and Engineering, School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
- National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guo Gao
- Institute of Nano Biomedicine and Engineering, School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
- National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiqi Ge
- Institute of Marine Equipment, Shanghai Jiao Tong University, Shanghai, China
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
| | - Xinping Guan
- Department of Automation, Shanghai Jiao Tong University, Shanghai, China
- The Key Laboratory of System Control and Information Processing, Ministry of Education, Shanghai, China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
- National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
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5
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Eldar D, Albert S, Tatyana A, Galina S, Albert R, Yana M. Optogenetic approaches for neural tissue regeneration: A review of basic optogenetic principles and target cells for therapy. Neural Regen Res 2026; 21:521-533. [PMID: 39995064 DOI: 10.4103/nrr.nrr-d-24-00685] [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: 06/21/2024] [Accepted: 10/17/2024] [Indexed: 02/26/2025] Open
Abstract
Optogenetics has revolutionized the field of neuroscience by enabling precise control of neural activity through light-sensitive proteins known as opsins. This review article discusses the fundamental principles of optogenetics, including the activation of both excitatory and inhibitory opsins, as well as the development of optogenetic models that utilize recombinant viral vectors. A considerable portion of the article addresses the limitations of optogenetic tools and explores strategies to overcome these challenges. These strategies include the use of adeno-associated viruses, cell-specific promoters, modified opsins, and methodologies such as bioluminescent optogenetics. The application of viral recombinant vectors, particularly adeno-associated viruses, is emerging as a promising avenue for clinical use in delivering opsins to target cells. This trend indicates the potential for creating tools that offer greater flexibility and accuracy in opsin delivery. The adaptations of these viral vectors provide advantages in optogenetic studies by allowing for the restricted expression of opsins through cell-specific promoters and various viral serotypes. The article also examines different cellular targets for optogenetics, including neurons, astrocytes, microglia, and Schwann cells. Utilizing specific promoters for opsin expression in these cells is essential for achieving precise and efficient stimulation. Research has demonstrated that optogenetic stimulation of both neurons and glial cells-particularly the distinct phenotypes of microglia, astrocytes, and Schwann cells-can have therapeutic effects in neurological diseases. Glial cells are increasingly recognized as important targets for the treatment of these disorders. Furthermore, the article emphasizes the emerging field of bioluminescent optogenetics, which combines optogenetic principles with bioluminescent proteins to visualize and manipulate neural activity in real time. By integrating molecular genetics techniques with bioluminescence, researchers have developed methods to monitor neuronal activity efficiently and less invasively, enhancing our understanding of central nervous system function and the mechanisms of plasticity in neurological disorders beyond traditional neurobiological methods. Evidence has shown that optogenetic modulation can enhance motor axon regeneration, achieve complete sensory reinnervation, and accelerate the recovery of neuromuscular function. This approach also induces complex patterns of coordinated motor neuron activity and promotes neural reorganization. Optogenetic approaches hold immense potential for therapeutic interventions in the central nervous system. They enable precise control of neural circuits and may offer new treatments for neurological disorders, particularly spinal cord injuries, peripheral nerve injuries, and other neurodegenerative diseases.
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Affiliation(s)
- Davletshin Eldar
- OpenLab Gene and Cell Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Sufianov Albert
- Department of Neurosurgery, Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
- Research and Educational Institute of Neurosurgery, Peoples' Friendship University of Russia (RUDN), Moscow, Russia
| | - Ageeva Tatyana
- OpenLab Gene and Cell Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Sufianova Galina
- Department of Pharmacology, Tyumen State Medical University, Tyumen, Russia
| | - Rizvanov Albert
- OpenLab Gene and Cell Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Division of Medical and Biological Sciences, Tatarstan Academy of Sciences, Kazan, Russia
| | - Mukhamedshina Yana
- OpenLab Gene and Cell Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Division of Medical and Biological Sciences, Tatarstan Academy of Sciences, Kazan, Russia
- Department of Histology, Cytology and Embryology, Kazan State Medical University, Kazan, Russia
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Shi R, Ye J, Liu Z, Wang C, Wu S, Shen H, Suo Q, Li W, He X, Zhang Z, Tang Y, Yang GY, Wang Y. Tropism-shifted AAV-PHP.eB-mediated bFGF gene therapy promotes varied neurorestoration after ischemic stroke in mice. Neural Regen Res 2026; 21:704-714. [PMID: 38993123 DOI: 10.4103/nrr.nrr-d-23-01802] [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: 11/02/2023] [Accepted: 03/26/2024] [Indexed: 07/13/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202602000-00040/figure1/v/2025-05-05T160104Z/r/image-tiff AAV-PHP.eB is an artificial adeno-associated virus (AAV) that crosses the blood-brain barrier and targets neurons more efficiently than other AAVs when administered systematically. While AAV-PHP.eB has been used in various disease models, its cellular tropism in cerebrovascular diseases remains unclear. In the present study, we aimed to elucidate the tropism of AAV-PHP.eB for different cell types in the brain in a mouse model of ischemic stroke and evaluate its effectiveness in mediating basic fibroblast growth factor ( bFGF ) gene therapy. Mice were injected intravenously with AAV-PHP.eB either 14 days prior to (pre-stroke) or 1 day following (post-stroke) transient middle cerebral artery occlusion. Notably, we observed a shift in tropism from neurons to endothelial cells with post-stroke administration of AAV-PHP.eB-mNeonGreen (mNG). This endothelial cell tropism correlated strongly with expression of the endothelial membrane receptor lymphocyte antigen 6 family member A (Ly6A). Furthermore, AAV-PHP.eB-mediated overexpression of bFGF markedly improved neurobehavioral outcomes and promoted long-term neurogenesis and angiogenesis post-ischemic stroke. Our findings underscore the significance of considering potential tropism shifts when utilizing AAV-PHP.eB-mediated gene therapy in neurological diseases and suggest a promising new strategy for bFGF gene therapy in stroke treatment.
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Affiliation(s)
- Rubing Shi
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Ye
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ze Liu
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Wang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shengju Wu
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Shen
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Suo
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Wanlu Li
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaosong He
- Department of Emergency, the Second Affiliated Hospital, Department of Human Anatomy, School of Basic Science, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zhijun Zhang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yaohui Tang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Guo-Yuan Yang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yongting Wang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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Chen X, Lai J, Wu Z, Chen J, Yang B, Chen C, Ding C. Fat mass and obesity-mediated N 6 -methyladenosine modification modulates neuroinflammatory responses after traumatic brain injury. Neural Regen Res 2026; 21:730-741. [PMID: 39248160 DOI: 10.4103/nrr.nrr-d-23-01854] [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: 11/11/2023] [Accepted: 05/24/2024] [Indexed: 09/10/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202602000-00042/figure1/v/2025-05-05T160104Z/r/image-tiff The neuroinflammatory response mediated by microglial activation plays an important role in the secondary nerve injury of traumatic brain injury. The post-transcriptional modification of N 6 -methyladenosine is ubiquitous in the immune response of the central nervous system. The fat mass and obesity-related protein catalyzes the demethylation of N 6 -methyladenosine modifications on mRNA and is widely expressed in various tissues, participating in the regulation of multiple diseases' biological processes. However, the role of fat mass and obesity in microglial activation and the subsequent neuroinflammatory response after traumatic brain injury is unclear. In this study, we found that the expression of fat mass and obesity was significantly down-regulated in both lipopolysaccharide-treated BV2 cells and a traumatic brain injury mouse model. After fat mass and obesity interference, BV2 cells exhibited a pro-inflammatory phenotype as shown by the increased proportion of CD11b + /CD86 + cells and the secretion of pro-inflammatory cytokines. Fat mass and obesity-mediated N 6 -methyladenosine demethylation accelerated the degradation of ADAM17 mRNA, while silencing of fat mass and obesity enhanced the stability of ADAM17 mRNA. Therefore, down-regulation of fat mass and obesity expression leads to the abnormally high expression of ADAM17 in microglia. These results indicate that the activation of microglia and neuroinflammatory response regulated by fat mass and obesity-related N 6 -methyladenosine modification plays an important role in the pro-inflammatory process of secondary injury following traumatic brain injury.
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Affiliation(s)
- Xiangrong Chen
- Department of Neurosurgery, Second Clinical Medical College, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Jinqing Lai
- Department of Neurosurgery, Second Clinical Medical College, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Zhe Wu
- Department of Neurosurgery, Second Clinical Medical College, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Jianlong Chen
- Department of Neurosurgery, Second Clinical Medical College, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Baoya Yang
- Department of Neurosurgery, Second Clinical Medical College, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Chunnuan Chen
- Department of Neurology, Second Clinical Medical College, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Chenyu Ding
- Department of Neurosurgery, Neurosurgery Research Institute, National Regional Medical Center, Binhai Campus, First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
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8
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Ma Y, Han Y. Targeting the brain's glymphatic pathway: A novel therapeutic approach for cerebral small vessel disease. Neural Regen Res 2026; 21:433-442. [PMID: 39688573 DOI: 10.4103/nrr.nrr-d-24-00821] [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: 08/24/2024] [Accepted: 11/21/2024] [Indexed: 12/18/2024] Open
Abstract
Cerebral small vessel disease encompasses a group of neurological disorders characterized by injury to small blood vessels, often leading to stroke and dementia. Due to its diverse etiologies and complex pathological mechanisms, preventing and treating cerebral small vessel vasculopathy is challenging. Recent studies have shown that the glymphatic system plays a crucial role in interstitial solute clearance and the maintenance of brain homeostasis. Increasing evidence also suggests that dysfunction in glymphatic clearance is a key factor in the progression of cerebral small vessel disease. This review begins with a comprehensive introduction to the structure, function, and driving factors of the glymphatic system, highlighting its essential role in brain waste clearance. Afterwards, cerebral small vessel disease was reviewed from the perspective of the glymphatic system, after which the mechanisms underlying their correlation were summarized. Glymphatic dysfunction may lead to the accumulation of metabolic waste in the brain, thereby exacerbating the pathological processes associated with cerebral small vessel disease. The review also discussed the direct evidence of glymphatic dysfunction in patients and animal models exhibiting two subtypes of cerebral small vessel disease: arteriolosclerosis-related cerebral small vessel disease and amyloid-related cerebral small vessel disease. Diffusion tensor image analysis along the perivascular space is an important non-invasive tool for assessing the clearance function of the glymphatic system. However, the effectiveness of its parameters needs to be enhanced. Among various nervous system diseases, including cerebral small vessel disease, glymphatic failure may be a common final pathway toward dementia. Overall, this review summarizes prevention and treatment strategies that target glymphatic drainage and will offer valuable insight for developing novel treatments for cerebral small vessel disease.
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Affiliation(s)
- Yuhui Ma
- Department of Neurology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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9
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Yao L, Cai X, Yang S, Song Y, Xing L, Li G, Cui Z, Chen J. A single-cell landscape of the regenerating spinal cord of zebrafish. Neural Regen Res 2026; 21:780-789. [PMID: 40326988 DOI: 10.4103/nrr.nrr-d-24-01163] [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: 09/28/2024] [Accepted: 03/03/2025] [Indexed: 05/07/2025] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202602000-00046/figure1/v/2025-05-05T160104Z/r/image-tiff Unlike mammals, zebrafish possess a remarkable ability to regenerate their spinal cord after injury, making them an ideal vertebrate model for studying regeneration. While previous research has identified key cell types involved in this process, the underlying molecular and cellular mechanisms remain largely unexplored. In this study, we used single-cell RNA sequencing to profile distinct cell populations at different stages of spinal cord injury in zebrafish. Our analysis revealed that multiple subpopulations of neurons showed persistent activation of genes associated with axonal regeneration post injury, while molecular signals promoting growth cone collapse were inhibited. Radial glial cells exhibited significant proliferation and differentiation potential post injury, indicating their intrinsic roles in promoting neurogenesis and axonal regeneration, respectively. Additionally, we found that inflammatory factors rapidly decreased in the early stages following spinal cord injury, creating a microenvironment permissive for tissue repair and regeneration. Furthermore, oligodendrocytes lost maturity markers while exhibiting increased proliferation following injury. These findings demonstrated that the rapid and orderly regulation of inflammation, as well as the efficient proliferation and redifferentiation of new neurons and glial cells, enabled zebrafish to reconstruct the spinal cord. This research provides new insights into the cellular transitions and molecular programs that drive spinal cord regeneration, offering promising avenues for future research and therapeutic strategies.
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Affiliation(s)
- Lei Yao
- Department of Anesthesiology, Affiliated Hospital 2 of Nantong University, Nantong, Jiangsu Province, China
| | - Xinyi Cai
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Saishuai Yang
- Department of Anesthesiology, Affiliated Hospital 2 of Nantong University, Nantong, Jiangsu Province, China
| | - Yixing Song
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Lingyan Xing
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Guicai Li
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Zhiming Cui
- Department of Spine Surgery, Affiliated Hospital 2 of Nantong University, Nantong, Jiangsu Province, China
- Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu Province, China
| | - Jiajia Chen
- Department of Spine Surgery, Affiliated Hospital 2 of Nantong University, Nantong, Jiangsu Province, China
- Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu Province, China
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10
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Gao B, Wang H, Hu S, Zhong K, Liu X, Deng Z, Li Y, Tong A, Zhou L. Sox2-overexpressing neural stem cells alleviate ventricular enlargement and neurological dysfunction in posthemorrhagic hydrocephalus. Neural Regen Res 2026; 21:769-779. [PMID: 40326987 DOI: 10.4103/nrr.nrr-d-24-01491] [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: 11/29/2024] [Accepted: 03/17/2025] [Indexed: 05/07/2025] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202602000-00045/figure1/v/2025-05-05T160104Z/r/image-tiff Neural stem cells (NSCs) have the potential for self-renewal and multidirectional differentiation, and their transplantation has achieved good efficacy in a variety of diseases. However, only 1%-10% of transplanted NSCs survive in the ischemic and hypoxic microenvironment of posthemorrhagic hydrocephalus. Sox2 is an important factor for NSCs to maintain proliferation. Therefore, Sox2-overexpressing NSCs (NSCSox2) may be more successful in improving neurological dysfunction after posthemorrhagic hydrocephalus. In this study, human NSCSox2 was transplanted into a posthemorrhagic hydrocephalus mouse model, and retinoic acid was administered to further promote NSC differentiation. The results showed that NSCSox2 attenuated the ventricular enlargement caused by posthemorrhagic hydrocephalus and improved neurological function. NSCSox2 also promoted nerve regeneration, inhibited neuroinflammation and promoted M2 polarization (anti-inflammatory phenotype), thereby reducing cerebrospinal fluid secretion in choroid plexus. These findings suggest that NSCSox2 rescued ventricular enlargement and neurological dysfunction induced by posthemorrhagic hydrocephalus through neural regeneration and modulation of inflammation.
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Affiliation(s)
- Baocheng Gao
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
- Department of Neurosurgery, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Haoxiang Wang
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shuang Hu
- Department of Otolaryngology & Head and Neck Surgery, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Kunhong Zhong
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Xiaoyin Liu
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Ziang Deng
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yuanyou Li
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Aiping Tong
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Chengdu, Sichuan Province, China
| | - Liangxue Zhou
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
- Department of Neurosurgery, NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital),School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan Province, China
- Department of Neurosurgery, Fifth People's Hospital of Ningxia Hui Autonomous Region, Shizuishan, Ningxia Hui Autonomous Region, China
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11
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Payne JL, Sabunciyan S. Liquid biopsies in psychiatric disorders: Identifying peripheral biomarkers of brain health. Neural Regen Res 2026; 21:691-692. [PMID: 39819865 DOI: 10.4103/nrr.nrr-d-24-00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Accepted: 12/04/2024] [Indexed: 01/19/2025] Open
Affiliation(s)
- Jennifer L Payne
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA, USA (Payne JL)
| | - Sarven Sabunciyan
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA (Sabunciyan S)
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12
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Ayyappan K, Unger L, Kitchen P, Bill RM, Salman MM. Measuring glymphatic function: Assessing the toolkit. Neural Regen Res 2026; 21:534-541. [PMID: 40145955 DOI: 10.4103/nrr.nrr-d-24-01013] [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: 08/31/2024] [Accepted: 01/27/2025] [Indexed: 03/28/2025] Open
Abstract
Glymphatic flow has been proposed to clear brain waste while we sleep. Cerebrospinal fluid moves from periarterial to perivenous spaces through the parenchyma, with subsequent cerebrospinal fluid drainage to dural lymphatics. Glymphatic disruption is associated with neurological conditions such as Alzheimer's disease and traumatic brain injury. Therefore, investigating its structure and function may improve understanding of pathophysiology. The recent controversy on whether glymphatic flow increases or decreases during sleep demonstrates that the glymphatic hypothesis remains contentious. However, discrepancies between different studies could be due to limitations of the specific techniques used and confounding factors. Here, we review the methods used to study glymphatic function and provide a toolkit from which researchers can choose. We conclude that tracer analysis has been useful, ex vivo techniques are unreliable, and in vivo imaging is still limited. Finally, we explore the potential for future methods and highlight the need for in vitro models, such as microfluidic devices, which may address technique limitations and enable progression of the field.
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Affiliation(s)
- Koushikk Ayyappan
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Lucas Unger
- College of Health and Life Sciences, Aston University, Birmingham, UK
- Aston Institute for Membrane Excellence and the School of Biosciences, Aston University, Birmingham, UK
| | - Philip Kitchen
- College of Health and Life Sciences, Aston University, Birmingham, UK
- Aston Institute for Membrane Excellence and the School of Biosciences, Aston University, Birmingham, UK
| | - Roslyn M Bill
- College of Health and Life Sciences, Aston University, Birmingham, UK
- Aston Institute for Membrane Excellence and the School of Biosciences, Aston University, Birmingham, UK
| | - Mootaz M Salman
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
- BHF Oxford Centre of Research Excellence, University of Oxford, Oxford, UK
- Kavli Institute for NanoScience Discovery, University of Oxford, Oxford, UK
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13
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Vidi PA, Liu J, Bonin K, Bloom K. Closing the loops: chromatin loop dynamics after DNA damage. Nucleus 2025; 16:2438633. [PMID: 39720924 DOI: 10.1080/19491034.2024.2438633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 11/29/2024] [Accepted: 11/30/2024] [Indexed: 12/26/2024] Open
Abstract
Chromatin is a dynamic polymer in constant motion. These motions are heterogeneous between cells and within individual cell nuclei and are profoundly altered in response to DNA damage. The shifts in chromatin motions following genomic insults depend on the temporal and physical scales considered. They are also distinct in damaged and undamaged regions. In this review, we emphasize the role of chromatin tethering and loop formation in chromatin dynamics, with the view that pulsing loops are key contributors to chromatin motions. Chromatin tethers likely mediate micron-scale chromatin coherence predicted by polymer models and measured experimentally, and we propose that remodeling of the tethers in response to DNA breaks enables uncoupling of damaged and undamaged chromatin regions.
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Affiliation(s)
| | - Jing Liu
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN, USA
| | - Keith Bonin
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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14
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Islam S, Chauhan VM, Pantazes RJ. Analysis of how antigen mutations disrupt antibody binding interactions toward enabling rapid and reliable antibody repurposing. MAbs 2025; 17:2440586. [PMID: 39690439 DOI: 10.1080/19420862.2024.2440586] [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: 06/26/2024] [Revised: 12/04/2024] [Accepted: 12/05/2024] [Indexed: 12/19/2024] Open
Abstract
Antibody repurposing is the process of changing a known antibody so that it binds to a mutated antigen. One of the findings to emerge from the Coronavirus Disease 2019 (COVID-19) pandemic was that it was possible to repurpose neutralizing antibodies for Severe Acute Respiratory Syndrome, a related disease, to work for COVID-19. Thus, antibody repurposing is a possible pathway to prepare for and respond to future pandemics, as well as personalizing cancer therapies. For antibodies to be successfully repurposed, it is necessary to know both how antigen mutations disrupt their binding and how they should be mutated to recover binding, with this work describing an analysis to address the first of these topics. Every possible antigen point mutation in the interface of 246 antibody-protein complexes were analyzed using the Rosetta molecular mechanics force field. The results highlight a number of features of how antigen mutations affect antibody binding, including the effects of mutating critical hotspot residues versus other positions, how many mutations are necessary to be likely to disrupt binding, the prevalence of indirect effects of mutations on binding, and the relative importance of changing attractive versus repulsive energies. These data are expected to be useful in guiding future antibody repurposing experiments.
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Affiliation(s)
- Sumaiya Islam
- Department of Chemical Engineering, Auburn University, Auburn, AL, USA
| | - Varun M Chauhan
- Department of Chemical Engineering, Auburn University, Auburn, AL, USA
| | - Robert J Pantazes
- Department of Chemical Engineering, Auburn University, Auburn, AL, USA
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15
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Thibaut MM, Roumain M, Piron E, Gillard J, Loriot A, Neyrinck AM, Rodriguez J, Massart I, Thissen JP, Huot JR, Pin F, Bonetto A, Delzenne NM, Muccioli GG, Bindels LB. The microbiota-derived bile acid taurodeoxycholic acid improves hepatic cholesterol levels in mice with cancer cachexia. Gut Microbes 2025; 17:2449586. [PMID: 39780051 PMCID: PMC11730681 DOI: 10.1080/19490976.2025.2449586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 11/20/2024] [Accepted: 12/30/2024] [Indexed: 01/11/2025] Open
Abstract
Alterations in bile acid profile and pathways contribute to hepatic inflammation in cancer cachexia, a syndrome worsening the prognosis of cancer patients. As the gut microbiota impinges on host metabolism through bile acids, the current study aimed to explore the functional contribution of gut microbial dysbiosis to bile acid dysmetabolism and associated disorders in cancer cachexia. Using three mouse models of cancer cachexia (the C26, MC38 and HCT116 models), we evidenced a reduction in the hepatic levels of several secondary bile acids, mainly taurodeoxycholic (TDCA). This reduction in hepatic TDCA occurred before the appearance of cachexia. Longitudinal analysis of the gut microbiota pinpointed an ASV, identified as Xylanibacter rodentium, as a bacterium potentially involved in the reduced production of TDCA. Coherently, stable isotope-based experiments highlighted a robust decrease in the microbial 7α-dehydroxylation (7α-DH) activity with no changes in the bile salt hydrolase (BSH) activity in cachectic mice. This approach also highlighted a reduced microbial 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 12α-hydroxysteroid dehydrogenase (12α-HSDH) activities in these mice. The contribution of the lower production of TDCA to cancer cachexia was explored in vitro and in vivo. In vitro, TDCA prevented myotube atrophy, whereas in vivo hepatic whole transcriptome analysis revealed that TDCA administration to cachectic mice improved the unfolded protein response and cholesterol homeostasis pathways. Coherently, TDCA administration reversed hepatic cholesterol accumulation in these mice. Altogether, this work highlights the contribution of the gut microbiota to bile acid dysmetabolism and the therapeutic interest of the secondary bile acid TDCA for hepatic cholesterol homeostasis in the context of cancer cachexia. Such discovery may prove instrumental in the understanding of other metabolic diseases characterized by microbial dysbiosis. More broadly, our work demonstrates the interest and relevance of microbial activity measurements using stable isotopes, an approach currently underused in the microbiome field.
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Affiliation(s)
- Morgane M. Thibaut
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Martin Roumain
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Edwige Piron
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Justine Gillard
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Laboratory of Hepato-Gastroenterology, Institut de Recherche Expérimentale et Clinique, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Axelle Loriot
- Computational Biology and Bioinformatics Unit (CBIO), de Duve Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Audrey M. Neyrinck
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Julie Rodriguez
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Isabelle Massart
- Endocrinology, Diabetology and Nutrition Department, Institut de Recherches Expérimentales et Cliniques, UCLouvain, Université catholique de Louvain, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Jean-Paul Thissen
- Endocrinology, Diabetology and Nutrition Department, Institut de Recherches Expérimentales et Cliniques, UCLouvain, Université catholique de Louvain, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Joshua R. Huot
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Fabrizio Pin
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrea Bonetto
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nathalie M. Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Giulio G. Muccioli
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Laure B. Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Welbio Department, WEL Research Institute, Wavre, Belgium
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16
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Hart M, Diener C, Rheinheimer S, Kehl T, Keller A, Lenhof HP, Meese E. Expanding the immune-related targetome of miR-155-5p by integrating time-resolved RNA patterns into miRNA target prediction. RNA Biol 2025; 22:1-9. [PMID: 39760255 PMCID: PMC11730359 DOI: 10.1080/15476286.2025.2449775] [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: 08/30/2024] [Revised: 12/14/2024] [Accepted: 12/27/2024] [Indexed: 01/07/2025] Open
Abstract
The lack of a sufficient number of validated miRNA targets severely hampers the understanding of their biological function. Even for the well-studied miR-155-5p, there are only 239 experimentally validated targets out of 42,554 predicted targets. For a more complete assessment of the immune-related miR-155 targetome, we used an inverse correlation of time-resolved mRNA profiles and miR-155-5p expression of early CD4+ T cell activation to predict immune-related target genes. Using a high-throughput miRNA interaction reporter (HiTmIR) assay we examined 90 target genes and confirmed 80 genes as direct targets of miR-155-5p. Our study increases the current number of verified miR-155-5p targets approximately threefold and exemplifies a method for verifying miRNA targetomes as a prerequisite for the analysis of miRNA-regulated cellular networks.
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Affiliation(s)
- Martin Hart
- Institute of Human Genetics, Saarland University (USAAR), Homburg, Germany
- Center of Human and Molecular Biology (ZHMB), Saarland University (USAAR), Saarbrücken, Germany
| | - Caroline Diener
- Institute of Human Genetics, Saarland University (USAAR), Homburg, Germany
| | | | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University (USAAR), Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University (USAAR), Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University (USAAR), Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University (USAAR), Homburg, Germany
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17
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Xu H, Cao L, Chen Y, Zhou C, Xu J, Zhang Z, Li X, Liu L, Lu J. Single-cell RNA sequencing reveals the heterogeneity and interactions of immune cells and Müller glia during zebrafish retina regeneration. Neural Regen Res 2025; 20:3635-3648. [PMID: 38934409 PMCID: PMC11974639 DOI: 10.4103/nrr.nrr-d-23-02083] [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: 12/26/2023] [Revised: 04/17/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202512000-00031/figure1/v/2025-01-31T122243Z/r/image-tiff Inflammation plays a crucial role in the regeneration of fish and avian retinas. However, how inflammation regulates Müller glia (MG) reprogramming remains unclear. Here, we used single-cell RNA sequencing to investigate the cell heterogeneity and interactions of MG and immune cells in the regenerating zebrafish retina. We first showed that two types of quiescent MG (resting MG1 and MG2) reside in the uninjured retina. Following retinal injury, resting MG1 transitioned into an activated state expressing known reprogramming genes, while resting MG2 gave rise to rod progenitors. We further showed that retinal microglia can be categorized into three subtypes (microglia-1, microglia-2, and proliferative) and pseudotime analysis demonstrated dynamic changes in microglial status following retinal injury. Analysis of cell-cell interactions indicated extensive crosstalk between immune cells and MG, with many interactions shared among different immune cell types. Finally, we showed that inflammation activated Jak1-Stat3 signaling in MG, promoting their transition from a resting to an activated state. Our study reveals the cell heterogeneity and crosstalk of immune cells and MG in zebrafish retinal repair, and may provide valuable insights into future mammalian retina regeneration.
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Affiliation(s)
- Hui Xu
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Key Lab of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Lining Cao
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yuxi Chen
- Key Lab of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Cuiping Zhou
- Key Lab of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Jie Xu
- Key Lab of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Zhuolin Zhang
- Key Lab of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Xiangyu Li
- Key Lab of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Lihua Liu
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jianfeng Lu
- Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
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18
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Moutsoglou D, Ramakrishnan P, Vaughn BP. Microbiota transplant therapy in inflammatory bowel disease: advances and mechanistic insights. Gut Microbes 2025; 17:2477255. [PMID: 40062406 PMCID: PMC11901402 DOI: 10.1080/19490976.2025.2477255] [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: 11/06/2024] [Revised: 01/27/2025] [Accepted: 03/04/2025] [Indexed: 03/14/2025] Open
Abstract
Microbiota transplant therapy is an emerging therapy for inflammatory bowel disease, but factors influencing its efficacy and mechanism remain poorly understood. In this narrative review, we outline key elements affecting therapeutic outcomes, including donor factors (such as age and patient relationship), recipient factors, control selection, and elements impacting engraftment and its correlation with clinical response. We also examine potential mechanisms through inflammatory bowel disease trials, focusing on the interplay between the microbiota, host, and immune system. Finally, we briefly explore potential future directions for microbiota transplant therapy and promising emerging treatments.
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Affiliation(s)
- Daphne Moutsoglou
- Gastroenterology Section, Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | - Byron P. Vaughn
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, MN, USA
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19
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Alhnaity HM, Shraim AS, Abumsimir B, Hattab D, Ghazzy AM, Abdelhalim M, Abdel Majeed BA, Daoud E, Jarrar Y. Genetic variants in QRICH2 gene among Jordanians with sperm motility disorders. Libyan J Med 2025; 20:2481741. [PMID: 40107860 PMCID: PMC11924270 DOI: 10.1080/19932820.2025.2481741] [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: 12/23/2024] [Accepted: 03/15/2025] [Indexed: 03/22/2025] Open
Abstract
Sperm motility, a key determinant of male fertility, is often impaired by genetic variations affecting flagellar formation. The glutamine-rich protein 2 (QRICH2) gene encodes a protein essential for sperm flagella biogenesis and structural integrity. This study investigates genetic variations within exon 3 of the QRICH2 gene, identifying novel heterozygous variants associated with sperm tail-specific abnormalities and motility impairments. Among 34 individuals diagnosed with asthenozoospermia (ASZ) and 26 individuals with normal sperm parameters (NZ) from Jordan, eight unique heterozygous variants (c.123 G>T, c.133 G>C, c.138A>G, c.170A>C, c.189C>G, c.190T>C, c.195A>T, and c.204A>T) were exclusive to the ASZ group, while four variants (c.136 G>A, c.145A>C, c.179T>G, and c.180T>G) were found only in NZ. These variants were absent from major genetic databases, suggesting their potential novelty, while two variants (c.206C>T and c.189C>T) were linked to known SNP cluster IDs rs73996306 and rs1567790525, respectively. Four non-synonymous SNPs (c.136 G>A, c.145A>C, c.170A>C, and c.204A>T) were predicted to be functionally and structurally damaging, underscoring their significance. Additionally, five variants overlapped with previously reported mutation sites, indicating potential mutation hotspots. Statistical analysis revealed a significant association between QRICH2 mutations and tail defects (p < 0.021). These findings highlight the critical role of heterozygous QRICH2 mutations in mild-to-moderate ASZ, even in NZ individuals. Despite some carriers meeting WHO criteria for NZ, notable morphological abnormalities suggest the need for refined diagnostic benchmarks. Screening for QRICH2 mutations is essential for accurate molecular diagnosis and should be integrated into genetic counseling, particularly in regions like Jordan. Further research into the cumulative effects of heterozygous mutations and their environmental interactions is needed to expand our understanding of idiopathic male infertility and to enhance diagnostic and therapeutic strategies for male infertility.
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Affiliation(s)
- Haneen M Alhnaity
- Medical Laboratory Sciences Department, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Ala'a S Shraim
- Medical Laboratory Sciences Department, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Berjas Abumsimir
- Medical Laboratory Sciences Department, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Dima Hattab
- School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Asma M Ghazzy
- Pharmaceutical Sciences Department, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, Jordan
| | - May Abdelhalim
- Medical Laboratory Sciences Department, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Bayan A Abdel Majeed
- Medical Laboratory Sciences Department, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Enas Daoud
- Pharmaceutics and Pharmaceutical Technology Department, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, Jordan
| | - Yazun Jarrar
- Department of Basic Medical Sciences, Faculty of Medicine, Al-Balqa Applied University, Al-Salt, Jordan
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20
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Joshi AS. Advancing in vitro cell migration studies: a review of open-source analytical platforms for cancer and wound healing research. Cell Adh Migr 2025; 19:2488116. [PMID: 40241248 PMCID: PMC12006941 DOI: 10.1080/19336918.2025.2488116] [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: 11/23/2024] [Revised: 03/27/2025] [Accepted: 03/30/2025] [Indexed: 04/18/2025] Open
Abstract
A single cell or cell population exhibits the fundamental phenomenon of cell migration during developmental processes or disease progression. Vast literature suggests that, in vitro 2-dimensional or 3-dimensional cell migration assay is one of the most commonly used assays in cancer, wound healing research, and developmental biology research. The data obtained from this assay are often analyzed using various proprietary or open-source programs. Proprietary software are costly and not always accessible to everyone. Whereas the open-source programs are free, easy to access, and user friendly. However, not all researchers are aware of these open-source programs. Despite the increasing availability of these programs, many researchers still rely on proprietary software, due to a lack of comparative analyses and practical guidance on their implementation. Hence, this review aims to provide insights into these open-source tools and serves as a practical guide to both biologists and computational researchers for their specific analytical needs.
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Affiliation(s)
- Abhayraj S. Joshi
- Manipal Centre for Biotherapeutics Research (MCBR), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
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21
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Ren X, Qu Y, Shari A, Li G. Transcriptome-wide study of mRNAs modified by m 6A RNA methylation in the testis development of dairy goats. Anim Biotechnol 2025; 36:2496641. [PMID: 40306318 DOI: 10.1080/10495398.2025.2496641] [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: 10/14/2024] [Accepted: 04/14/2025] [Indexed: 05/02/2025]
Abstract
N6-methyladenosine (m6A) is an important epigenetic modification in RNA, playing a crucial role in regulating the production and aging of animal testicular sperm. This study extracted mRNA from the testicular tissue of male goats before and after sexual maturity, generating a methylation map through preliminary experiments and methylation immunoprecipitation sequencing. The results showed that during the development of dairy goats, the expression levels of marker genes related to testicular development and methylation-related enzymes changed significantly. A total of 36,602 peaks and 11,223 genes were identified in the two groups, including 2989 differential peaks (427 upregulated and 2562 downregulated) and 1457 differentially expressed genes (833 upregulated and 624 downregulated). The abundance of m6A was positively correlated with gene expression levels. This study reports for the first time the mRNA profiles of m6A modifications across the entire transcriptome during testicular development in Guanzhong dairy goats, providing a new perspective for genetic improvement in goats.
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Affiliation(s)
- Xinyang Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, PR China
| | - Yingxin Qu
- College of Animal Science and Technology, Northwest A&F University, Yangling, PR China
| | - Akang Shari
- College of Animal Science and Technology, Northwest A&F University, Yangling, PR China
| | - Guang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, PR China
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22
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O’Sullivan J, Patel S, Leventhal GE, Fitzgerald RS, Laserna-Mendieta EJ, Huseyin CE, Konstantinidou N, Rutherford E, Lavelle A, Dabbagh K, DeSantis TZ, Shanahan F, Temko A, Iwai S, Claesson MJ. Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease. Gut Microbes 2025; 17:2450207. [PMID: 39812341 PMCID: PMC11740686 DOI: 10.1080/19490976.2025.2450207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 11/07/2024] [Accepted: 01/02/2025] [Indexed: 01/16/2025] Open
Abstract
Crohn's disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury and environmental influences, most of which appear to act via the gut microbiome. We hypothesized that host-microbe alterations could be used to prognostically stratify patients experiencing relapses up to four years after endoscopy. We therefore examined multiple omics data, including published and new datasets, generated from paired inflamed and non-inflamed mucosal biopsies from 142 patients with IBD (54 CD; 88 UC) and from 34 control (non-diseased) biopsies. The relapse-predictive potential of 16S rRNA gene and transcript amplicons (standing and active microbiota) were investigated along with host transcriptomics, epigenomics and genetics. While standard single-omics analysis could not distinguish between patients who relapsed and those that remained in remission within four years of colonoscopy, we did find an association between the number of flares and a patient's succinotype. Our multi-omics machine learning approach was also able to predict relapse when combining features from the microbiome and human host. Therefore multi-omics, rather than single omics, better predicts relapse within 4 years of colonoscopy, while a patient's succinotype is associated with a higher frequency of relapses.
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Affiliation(s)
- Jill O’Sullivan
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway, Ireland
| | - Shriram Patel
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- SeqBiome Ltd, Cork, Ireland
| | | | - Rachel S. Fitzgerald
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Emilio J. Laserna-Mendieta
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Chloe E. Huseyin
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Nina Konstantinidou
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Informatics, Second Genome Inc, South San Francisco, California, USA
| | - Erica Rutherford
- Department of Informatics, Second Genome Inc, South San Francisco, California, USA
| | - Aonghus Lavelle
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
| | - Karim Dabbagh
- Department of Informatics, Second Genome Inc, South San Francisco, California, USA
| | - Todd Z. DeSantis
- Department of Informatics, Second Genome Inc, South San Francisco, California, USA
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Andriy Temko
- Department of Electrical and Electronic Engineering, University College Cork, Cork, Ireland
| | - Shoko Iwai
- Department of Informatics, Second Genome Inc, South San Francisco, California, USA
| | - Marcus J. Claesson
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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23
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Dong X, Xiang Y, Li L, Zhang Y, Wu T. Genomic insights into the rapid rise of Pseudomonas aeruginosa ST463: A high-risk lineage's adaptive strategy in China. Virulence 2025; 16:2497901. [PMID: 40320374 PMCID: PMC12051580 DOI: 10.1080/21505594.2025.2497901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 12/19/2024] [Accepted: 04/17/2025] [Indexed: 05/08/2025] Open
Abstract
High-risk lineages of Pseudomonas aeruginosa pose a serious threat to public health, causing severe infections with high mortality rates and limited treatment options. The emergence and rapid spread of the high-risk lineage ST463 in China have further exacerbated this issue. However, the basis of its success in China remains unidentified. In this study, we analyzed a comprehensive dataset of ST463 strains from 2000 to 2023 using whole genome sequencing to unravel the epidemiological characteristics, evolutionary trajectory, and antibiotic resistance profiles. Our findings suggest that ST463 likely originated from a single introduction from North America in 2007, followed by widespread domestic dissemination. Since its introduction, the lineage has undergone significant genomic changes, including the acquisition of three unique regions that enhanced its metabolism and adaptability. Frequent recombination events, along with the burden of bacteriophages, antibiotic resistance genes, and the spread of c1-type (blaKPC-2) plasmid-carrying strains, have played crucial roles in its expansion in China. Mutation analysis reveals adaptive responses to antibiotics and selective pressures on key virulence factors, indicating that ST463 is evolving toward a more pathogenic lifestyle.
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Affiliation(s)
- Xu Dong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanghui Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Tiantian Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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24
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Sweet-Jones J, Martin AC. An antibody developability triaging pipeline exploiting protein language models. MAbs 2025; 17:2472009. [PMID: 40038849 PMCID: PMC11901365 DOI: 10.1080/19420862.2025.2472009] [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: 10/31/2024] [Revised: 02/17/2025] [Accepted: 02/20/2025] [Indexed: 03/06/2025] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) are a successful class of biologic drugs that are frequently selected from phage display libraries and transgenic mice that produce fully human antibodies. However, binding affinity to the correct epitope is necessary, but not sufficient, for a mAb to have therapeutic potential. Sequence and structural features affect the developability of an antibody, which influences its ability to be produced at scale and enter trials, or can cause late-stage failures. Using data on paired human antibody sequences, we introduce a pipeline using a machine learning approach that exploits protein language models to identify antibodies which cluster with antibodies that have entered the clinic and are therefore expected to have developability features similar to clinically acceptable antibodies, and triage out those without these features. We propose this pipeline as a useful tool in candidate selection from large libraries, reducing the cost of exploration of the antibody space, and pursuing new therapeutics.
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Affiliation(s)
- James Sweet-Jones
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Andrew C.R. Martin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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25
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Xue J, Allaband C, Zuffa S, Poulsen O, Meadows J, Zhou D, Dorrestein PC, Knight R, Haddad GG. Gut microbiota and derived metabolites mediate obstructive sleep apnea induced atherosclerosis. Gut Microbes 2025; 17:2474142. [PMID: 40025767 PMCID: PMC11881840 DOI: 10.1080/19490976.2025.2474142] [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: 12/04/2024] [Revised: 02/03/2025] [Accepted: 02/25/2025] [Indexed: 03/04/2025] Open
Abstract
Obstructive sleep apnea (OSA) is characterized by intermittent hypoxia/hypercapnia (IHC), affects predominantly obese individuals, and increases atherosclerosis risk. Since we and others have implicated gut microbiota and metabolites in atherogenesis, we dissected their contributions to OSA-induced atherosclerosis. Atherosclerotic lesions were compared between conventionally-reared specific pathogen free (SPF) and germ-free (GF) Apoe-/- mice following a high fat high cholesterol diet (HFHC), with and without IHC conditions. The fecal microbiota and metabolome were profiled using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry (LC-MS/MS) respectively. Phenotypic data showed that HFHC significantly increased atherosclerosis as compared to regular chow (RC) in both aorta and pulmonary artery (PA) of SPF mice. IHC exacerbated lesions in addition to HFHC. Differential abundance analysis of gut microbiota identified an enrichment of Akkermansiaceae and a depletion of Muribaculaceae (formerly S24-7) family members in the HFHC-IHC group. LC-MS/MS showed a dysregulation of bile acid profiles with taurocholic acid, taurodeoxycholic acid, and 12-ketodeoxycholic acid enriched in the HFHC-IHC group, long-chain N-acyl amides, and phosphatidylcholines. Interestingly, GF Apoe-/- mice markedly reduced atherosclerotic formation relative to SPF Apoe-/- mice in the aorta under HFHC/IHC conditions. In contrast, microbial colonization did not show a significant impact on the atherosclerotic progression in PA. In summary, this research demonstrated that (1) IHC acts cooperatively with HFHC to induce atherosclerosis; (2) gut microbiota modulate atherogenesis, induced by HFHC/IHC, in the aorta not in PA; (3) different analytical methods suggest that a specific imbalance between Akkermansiaceae and Muribaculaceae bacterial families mediate OSA-induced atherosclerosis; and (4) derived bile acids, such as deoxycholic acid and lithocholic acid, regulate atherosclerosis in OSA. The knowledge obtained provides novel insights into the potential therapeutic approaches to prevent and treat OSA-induced atherosclerosis.
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Affiliation(s)
- Jin Xue
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Celeste Allaband
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, San Diego, CA, USA
| | - Orit Poulsen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jason Meadows
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Dan Zhou
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pieter C. Dorrestein
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Gabriel G. Haddad
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- The Division of Respiratory Medicine, Rady Children’s Hospital, San Diego, CA, USA
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26
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Floor E, Su J, Chatterjee M, Kuipers ES, IJssennagger N, Heidari F, Giordano L, Wubbolts RW, Mihăilă SM, Stapels DAC, Vercoulen Y, Strijbis K. Development of a Caco-2-based intestinal mucosal model to study intestinal barrier properties and bacteria-mucus interactions. Gut Microbes 2025; 17:2434685. [PMID: 39714032 DOI: 10.1080/19490976.2024.2434685] [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: 04/03/2024] [Revised: 11/15/2024] [Accepted: 11/21/2024] [Indexed: 12/24/2024] Open
Abstract
The intestinal mucosal barrier is a dynamic system that allows nutrient uptake, stimulates healthy microbe-host interactions, and prevents invasion by pathogens. The mucosa consists of epithelial cells connected by cellular junctions that regulate the passage of nutrients covered by a mucus layer that plays an important role in host-microbiome interactions. Mimicking the intestinal mucosa for in vitro assays, particularly the generation of a mucus layer, has proven to be challenging. The intestinal cell-line Caco-2 is widely used in academic and industrial laboratories due to its capacity to polarize, form an apical brush border, and reproducibly grow into confluent cell layers in different culture systems. However, under normal culture conditions, Caco-2 cultures lack a mucus layer. Here, we demonstrate for the first time that Caco-2 cultures can form a robust mucus layer when cultured under air-liquid interface (ALI) conditions on Transwell inserts with addition of vasointestinal peptide (VIP) in the basolateral compartment. We demonstrate that unique gene clusters are regulated in response to ALI and VIP single stimuli, but the ALI-VIP combination treatment resulted in a significant upregulation of multiple mucin genes and proteins, including secreted MUC2 and transmembrane mucins MUC13 and MUC17. Expression of tight junction proteins was significantly altered in the ALI-VIP condition, leading to increased permeability to small molecules. Commensal Lactiplantibacillus plantarum bacteria closely associated with the Caco-2 mucus layer and differentially colonized the surface of the ALI cultures. Pathogenic Salmonella enterica were capable of invading beyond the mucus layer and brush border. In conclusion, Caco-2 ALI-VIP cultures provide an accessible and straightforward way to culture an in vitro intestinal mucosal model with improved biomimetic features. This novel in vitro intestinal model can facilitate studies into mucus and epithelial barrier functions and in-depth molecular characterization of pathogenic and commensal microbe-mucus interactions.
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Affiliation(s)
- Evelien Floor
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jinyi Su
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Maitrayee Chatterjee
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- The TIM Company, Delft, the Netherlands
| | - Elise S Kuipers
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Noortje IJssennagger
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Danone Research and Innovation Center, Utrecht, The Netherlands
| | - Faranak Heidari
- Div. Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Laura Giordano
- Div. Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Richard W Wubbolts
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Silvia M Mihăilă
- Div. Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Daphne A C Stapels
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Yvonne Vercoulen
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Karin Strijbis
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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27
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Ramon A, Ni M, Predeina O, Gaffey R, Kunz P, Onuoha S, Sormanni P. Prediction of protein biophysical traits from limited data: a case study on nanobody thermostability through NanoMelt. MAbs 2025; 17:2442750. [PMID: 39772905 PMCID: PMC11730357 DOI: 10.1080/19420862.2024.2442750] [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: 10/04/2024] [Revised: 12/10/2024] [Accepted: 12/11/2024] [Indexed: 01/11/2025] Open
Abstract
In-silico prediction of protein biophysical traits is often hindered by the limited availability of experimental data and their heterogeneity. Training on limited data can lead to overfitting and poor generalizability to sequences distant from those in the training set. Additionally, inadequate use of scarce and disparate data can introduce biases during evaluation, leading to unreliable model performances being reported. Here, we present a comprehensive study exploring various approaches for protein fitness prediction from limited data, leveraging pre-trained embeddings, repeated stratified nested cross-validation, and ensemble learning to ensure an unbiased assessment of the performances. We applied our framework to introduce NanoMelt, a predictor of nanobody thermostability trained with a dataset of 640 measurements of apparent melting temperature, obtained by integrating data from the literature with 129 new measurements from this study. We find that an ensemble model stacking multiple regression using diverse sequence embeddings achieves state-of-the-art accuracy in predicting nanobody thermostability. We further demonstrate NanoMelt's potential to streamline nanobody development by guiding the selection of highly stable nanobodies. We make the curated dataset of nanobody thermostability freely available and NanoMelt accessible as a downloadable software and webserver.
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Affiliation(s)
- Aubin Ramon
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Mingyang Ni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Olga Predeina
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Rebecca Gaffey
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Patrick Kunz
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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28
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Kim H, Bell T, Lee K, Jeong J, Bardwell JCA, Lee C. Identification of host genetic factors modulating β-lactam resistance in Escherichia coli harbouring plasmid-borne β-lactamase through transposon-sequencing. Emerg Microbes Infect 2025; 14:2493921. [PMID: 40231449 PMCID: PMC12024506 DOI: 10.1080/22221751.2025.2493921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 03/28/2025] [Accepted: 04/11/2025] [Indexed: 04/16/2025]
Abstract
Since β-lactam antibiotics are widely used, emergence of bacteria with resistance to them poses a significant threat to society. In particular, acquisition of genes encoding β-lactamase, an enzyme that degrades β-lactam antibiotics, has been a major contributing factor in the emergence of bacteria that are resistant to β-lactam antibiotics. However, relatively few genetic targets for killing these resistant bacteria have been identified to date. Here, we used a systematic approach called transposon-sequencing (Tn-Seq), to screen the Escherichia coli genome for host genetic factors that, when mutated, affect resistance to ampicillin, one of the β-lactam antibiotics, in a strain carrying a plasmid that encodes β-lactamase. This approach enabled not just the isolation of genes previously known to affect β-lactam resistance, but the additional loci skp, gshA, phoPQ and ypfN. Individual mutations in these genes modestly but consistently affected antibiotic resistance. We have identified that these genes are not only implicated in β-lactam resistance by itself but also play a crucial role in conditions associated with the expression of β-lactamase. GshA and phoPQ appear to contribute to β-lactam resistance by regulating membrane integrity. Notably, the overexpression of the uncharacterized membrane-associated protein, ypfN, has been shown to significantly enhance β-lactam resistance. We applied the genes identified from the screening into Salmonella Typhimurium and Pseudomonas aeruginosa strains, both critical human pathogens with antibiotic resistance, and observed their significant impact on β-lactam resistance. Therefore, these genes can potentially be utilized as therapeutic targets to control the survival of β-lactamase-producing bacteria.
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Affiliation(s)
- Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, South Korea
- Research Institute of Basic Sciences, Ajou University, Suwon, South Korea
| | - Travis Bell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jeongyun Jeong
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - James C. A. Bardwell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
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Wang S, Li X, Ma J, Duan X, Wang H, Wang L, Hu D, Jiang W, Li X, Qian P. Structural and functional analysis reveals the catalytic mechanism and substrate binding mode of the broad-spectrum endolysin Ply2741. Virulence 2025; 16:2449025. [PMID: 39810299 PMCID: PMC11740692 DOI: 10.1080/21505594.2024.2449025] [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: 02/26/2024] [Revised: 12/09/2024] [Accepted: 12/29/2024] [Indexed: 01/16/2025] Open
Abstract
The emergence of antibiotic-resistant bacteria has attracted interest in the field of endolysins. Here, we analyzed the diversity of Streptococcus endolysins and identified a new endolysin, Ply2741, that exhibited broad-spectrum bactericidal activity. Our results demonstrated that Ply2741 could effectively eradicate multidrug-resistant gram-positive pathogens in vitro and in vivo. Structural analysis revealed that the bactericidal activity of Ply2741 depends on the classic "Cys-His-Asn" catalytic triad. Site-directed mutagenesis results further identified that the conserved residue Gln29, located near the catalytic triad, also contributes to the lytic activity of Ply2741. Furthermore, the key residues (R189 and W250) in the Ply2741 cell wall binding domain (CBD) responsible for binding to peptidoglycan were revealed by molecular docking and fluorescence-activated cell sorting (FACS) analysis. Ply2741 demonstrates a broad lytic spectrum, with significant bactericidal activity against Enterococcus, Staphylococcus, and Streptococcus and species. To the best of our knowledge, we found that residue Gln29 participated in the lytic activity of endolysin for the first time. Additionally, we systematically elucidate the binding mode and key residues of the Ply2741CBD. This study proposes Ply2741 as a potential antibiotic substitute and provides a structural basis for the modification and design of endolysins.
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Affiliation(s)
- Shuang Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xinxin Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jiahui Ma
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaochao Duan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Haiyan Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Linkang Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Dayue Hu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wenwu Jiang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiangmin Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ping Qian
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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Chen C, Ma Y, Gao Y, Ge H, Zhang X. Prognostic significance of neutrophil extracellular trap-related genes in childhood acute lymphoblastic leukemia: insights from multi-omics and in vitro experiment. Hematology 2025; 30:2452701. [PMID: 39829399 DOI: 10.1080/16078454.2025.2452701] [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: 07/28/2024] [Accepted: 01/08/2025] [Indexed: 01/22/2025] Open
Abstract
BACKGROUND This study aimed to develop a prognostic model based on extracellular trap-related genes (NETRGs) for patients with cALL. METHODS Data from the TARGET-ALL-P2 and TARGET-ALL-P3 cohorts in the Genomic Data Commons database, the transcriptome dataset GSE26713, the single-cell transcriptome dataset GSE130116 from the Gene Expression Omnibus database and 306 NETRGs identified were analysed. Differentially expressed genes (DEGs) were identified from GSE26713 and differentially expressed NETRGs (DE-NETRGs) were obtained by overlapping DEGs with NETRGs. Functional analyses were conducted. Key feature genes were identified through univariate and least absolute shrinkage and selection operator (LASSO) regression. Prognostic genes were determined via multivariate Cox regression analysis, followed by the construction and validation of a risk model and nomogram. Additional analyses included immune profiling, drug sensitivity, functional differences, cell-type-specific expression, enrichment analysis and RT-qPCR. RESULTS A total of 1,270 DEGs were identified in GSE26713, of which 74 overlapped with NETRGs. Seven prognostic genes were identified using univariate, LASSO and multivariate Cox regression analyses. Survival analysis revealed lower survival rates in the high-risk group. Independent prognostic analysis identified risk scores and primary diagnosis as independent predictors of prognosis. Immune cell profiling showed significant differences in cell populations such as aDCs, eosinophils and Th2 cells between risk groups. Six cell subtypes were annotated, with prognostic genes predominantly expressed in myeloid cells. RT-qPCR revealed that PTAFR, FCGR2A, RETN and CAT were significantly downregulated, while TLR2 and S100A12 were upregulated in cALL. CONCLUSION TLR2, PTAFR, FCGR2A, RETN, S100A12 and CAT may serve as potential therapeutic targets.
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Affiliation(s)
- Cheng Chen
- Department of Pediatrics, Peking University First Hospital Ningxia Women and Children's Hospital (Ningxia Hui Autonomous Region Maternal and Child Health Hospital), Yinchuan, People's Republic of China
| | - Yu Ma
- Department of Pediatrics, Peking University First Hospital Ningxia Women and Children's Hospital (Ningxia Hui Autonomous Region Maternal and Child Health Hospital), Yinchuan, People's Republic of China
| | - Yadai Gao
- Department of Pediatrics, Yinchuan Women and Children Healthcare Hospital, Yinchuan, People's Republic of China
| | - Huiqing Ge
- Department of Pediatrics, Peking University First Hospital Ningxia Women and Children's Hospital (Ningxia Hui Autonomous Region Maternal and Child Health Hospital), Yinchuan, People's Republic of China
| | - Xiaochun Zhang
- Department of Pediatrics, Peking University First Hospital Ningxia Women and Children's Hospital (Ningxia Hui Autonomous Region Maternal and Child Health Hospital), Yinchuan, People's Republic of China
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Nepal S, Shi N, Hoyd R, Spakowicz DJ, Orwoll E, Shikany JM, Napoli N, Tabung FK. Role of insulinemic and inflammatory dietary patterns on gut microbial composition and circulating biomarkers of metabolic health among older American men. Gut Microbes 2025; 17:2497400. [PMID: 40296253 PMCID: PMC12045561 DOI: 10.1080/19490976.2025.2497400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Revised: 03/25/2025] [Accepted: 04/17/2025] [Indexed: 04/30/2025] Open
Abstract
Chronic low-grade inflammation and hyperinsulinemia are linked with metabolic dysfunction and dysbiosis. This study investigated the role of dietary inflammatory and insulinemic potential on gut microbiome and circulating health biomarkers in older men. Data from the Osteoporotic Fractures in Men (MrOS) study were analyzed. Reversed Empirical Dietary Inflammatory Pattern (rEDIP), Empirical Dietary Index for Hyperinsulinemia (rEDIH), and Healthy Eating Index (HEI)-2020 scores were computed from food frequency questionnaire data. Stool samples were profiled using 16S rRNA sequencing. Elastic net regression identified diet-associated microbial profiles and multivariable-adjusted linear regression assessed diet-biomarker associations. Higher rEDIP, rEDIH, and HEI-2020 scores were positively associated with gut microbiota alpha diversity. Specific genera, including Intestinibacter and Lachnospira, associated positively, while Dielma, Peptococcus, Feacalitalea, and Negativibaccilus associated inversely with healthier dietary patterns. When evaluating changes in dietary patterns between baseline and visit 4 ( ~ 14 years), these genera tended to define rEDIP, rEDIH more than HEI-2020. In addition, higher dietary quality was linked to better biomarker profiles, including lower creatinine, sodium, triglycerides, and insulin resistance. Beneficial effects of higher dietary quality on health may be mediated by the ability of diet to regulate gut microbial composition and metabolic biomarker profiles.
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Affiliation(s)
- Sushma Nepal
- Interdisciplinary Ph.D. Program in Nutrition, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Ni Shi
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rebecca Hoyd
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Daniel J. Spakowicz
- Interdisciplinary Ph.D. Program in Nutrition, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Eric Orwoll
- Department of Medicine, Oregon Health & Sciences University, Portland, OR, USA
| | - James M. Shikany
- Division of General Internal Medicine and Population Science, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicola Napoli
- Unit of Endocrinology and Diabetes, Department of Medicine, Campus Bio-Medico University of Rome, Rome, Italy
- Division of Bone and Mineral Diseases, Washington University, St Louis, MO, USA
| | - Fred K. Tabung
- Interdisciplinary Ph.D. Program in Nutrition, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, OH, USA
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Cong R, Lu C, Li X, Xu Z, Wang Y, Sun S. Tumor organoids in cancer medicine: from model systems to natural compound screening. PHARMACEUTICAL BIOLOGY 2025; 63:89-109. [PMID: 39893515 PMCID: PMC11789228 DOI: 10.1080/13880209.2025.2458149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 12/04/2024] [Accepted: 01/17/2025] [Indexed: 02/04/2025]
Abstract
CONTEXT The advent of tissue engineering and biomedical techniques has significantly advanced the development of three-dimensional (3D) cell culture systems, particularly tumor organoids. These self-assembled 3D cell clusters closely replicate the histopathological, genetic, and phenotypic characteristics of primary tissues, making them invaluable tools in cancer research and drug screening. OBJECTIVE This review addresses the challenges in developing in vitro models that accurately reflect tumor heterogeneity and explores the application of tumor organoids in cancer research, with a specific focus on the screening of natural products for antitumor therapies. METHODS This review synthesizes information from major databases, including Chemical Abstracts, Medicinal and Aromatic Plants Abstracts, ScienceDirect, Google Scholar, Scopus, PubMed and Springer Link. Publications were selected without date restrictions, using terms such as 'organoid', 'natural product', 'pharmacological', 'extract', 'nanomaterial' and 'traditional uses'. Articles related to agriculture, ecology, synthetic work or published in languages other than English were excluded. RESULTS AND CONCLUSIONS The review identifies key challenges related to the efficiency and variability of organoid generation and discusses ongoing efforts to enhance their predictive capabilities in drug screening and personalized medicine. Recent studies utilizing patient-derived organoid models for natural compound screening are highlighted, demonstrating the potential of these models in developing new classes of anticancer agents. The integration of natural products with patient-derived organoid models presents a promising approach for discovering novel anticancer compounds and elucidating their mechanisms of action.
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Affiliation(s)
- Rong Cong
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Can Lu
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yaqin Wang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Shusen Sun
- College of Pharmacy and Health Sciences, Western New England University, Springfield, MA, USA
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Ma Y, Zhang M, Wang Z, Cao L, Li Y, Wan Z, Kane Y, Wang G, Li X, Zhang C. Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection. Virulence 2025; 16:2467168. [PMID: 39950859 PMCID: PMC11866967 DOI: 10.1080/21505594.2025.2467168] [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: 10/14/2024] [Revised: 12/09/2024] [Accepted: 02/09/2025] [Indexed: 02/28/2025] Open
Abstract
An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1 but had positive correlations with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effects of ART on virome and cytokine profiles in HIV-1-infected individuals.
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Affiliation(s)
- Yingying Ma
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Min Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhenyan Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Le Cao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yanpeng Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhenzhou Wan
- Medical Laboratory,Taizhou Fourth People’s Hospital, Taizhou, China
| | - Yakhouba Kane
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Gang Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xin Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Zheng X, Liu B, Ni P, Cai L, Shi X, Ke Z, Zhang S, Hu B, Yang B, Xu Y, Long W, Fang Z, Wang Y, Zhang W, Xu Y, Wang Z, Pan K, Zhou K, Wang H, Geng H, Hu H, Liu B. Development and application of an uncapped mRNA platform. Ann Med 2025; 57:2437046. [PMID: 39648715 PMCID: PMC11632943 DOI: 10.1080/07853890.2024.2437046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/28/2023] [Accepted: 06/01/2024] [Indexed: 12/10/2024] Open
Abstract
BACKGROUND A novel uncapped mRNA platform was developed. METHODS Five lipid nanoparticle (LNP)-encapsulated mRNA constructs were made to evaluate several aspects of our platform, including transfection efficiency and durability in vitro and in vivo and the activation of humoral and cellular immunity in several animal models. The constructs were eGFP-mRNA-LNP (for enhanced green fluorescence mRNA), Fluc-mRNA-LNP (for firefly luciferase mRNA), SδT-mRNA-LNP (for Delta strain SARS-CoV-2 spike protein trimer mRNA), gDED-mRNA-LNP (for truncated glycoprotein D mRNA coding ectodomain from herpes simplex virus type 2 (HSV2)) and gDFR-mRNA-LNP (for truncated HSV2 glycoprotein D mRNA coding amino acids 1-400). RESULTS Quantifiable target protein expression was achieved in vitro and in vivo with eGFP- and Fluc-mRNA-LNP. SδT-mRNA-LNP, gDED-mRNA-LNP and gDFR-mRNA-LNP induced both humoral and cellular immune responses comparable to those obtained by previously reported capped mRNA-LNP constructs. Notably, SδT-mRNA-LNP elicited neutralizing antibodies in hamsters against the Omicron and Delta strains. Additionally, gDED-mRNA-LNP and gDFR-mRNA-LNP induced potent neutralizing antibodies in rabbits and mice. The mRNA constructs with uridine triphosphate (UTP) outperformed those with N1-methylpseudouridine triphosphate (N1mψTP) in the induction of antibodies via SδT-mRNA-LNP. CONCLUSIONS Our uncapped, process-simplified and economical mRNA platform may have broad utility in vaccines and protein replacement drugs.KEY MESSAGESThe mRNA platform described in our paper uses internal ribosome entry site (IRES) (Rapid, Amplified, Capless and Economical, RACE; Register as BH-RACE platform) instead of caps and uridine triphosphate (UTP) instead of N1-methylpseudouridine triphosphate (N1mψTP) to synthesize mRNA.Through the self-developed packaging instrument and lipid nanoparticle (LNP) delivery system, mRNA can be expressed in cells more efficiently, quickly and economically.Particularly exciting is that potent neutralizing antibodies against Delta and Omicron real viruses were induced with the new coronavirus S protein mRNA vaccine from the BH-RACE platform.
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Affiliation(s)
- Xiaodi Zheng
- College of Bioengineering, National ‘‘111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, China
| | - Biao Liu
- College of Bioengineering, National ‘‘111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, China
| | - Peng Ni
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Linkang Cai
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Xiaotai Shi
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Zonghuang Ke
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Siqi Zhang
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Bing Hu
- Hubei Provincial Centre for Disease Control and Prevention, Wuhan, China
| | - Binfeng Yang
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Yiyan Xu
- College of Bioengineering, National ‘‘111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, China
| | - Wei Long
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Zhizheng Fang
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Yang Wang
- College of Bioengineering, National ‘‘111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, China
| | - Wen Zhang
- Department of Immunology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Xu
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Zhong Wang
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Kai Pan
- Hubei Provincial Centre for Disease Control and Prevention, Wuhan, China
| | - Kangping Zhou
- Hubei Provincial Centre for Disease Control and Prevention, Wuhan, China
| | - Hanming Wang
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
| | - Hui Geng
- School of Life Science, Huazhong Normal University, Wuhan, China
| | - Han Hu
- College of Bioengineering, National ‘‘111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, China
| | - Binlei Liu
- College of Bioengineering, National ‘‘111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, China
- Wuhan Binhui Biopharmaceutical Co., Ltd., Wuhan, China
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Masaadeh AH, Eletrebi M, Parajuli B, De Jager N, Bosch DE. Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts. Gut Microbes 2025; 17:2479774. [PMID: 40094201 PMCID: PMC11917176 DOI: 10.1080/19490976.2025.2479774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 02/14/2025] [Accepted: 03/10/2025] [Indexed: 03/19/2025] Open
Abstract
Dysbiosis and pathobionts contribute to inflammation and the risk of colitis-associated carcinoma (CAC) in animal models, but their roles in humans with this uncommon disease are unknown. We identified microbiome differences in human CAC compared with longstanding inflammatory bowel disease (IBD) and sporadic colorectal carcinoma (CRC). Twenty-four CAC resections were matched with CRC and IBD controls. Methods included histopathology, 16S rDNA metagenomics, and pathobiont-specific qPCR. Beta diversity differed by diagnosis (PERMANOVA p = 0.007). The distinguishing taxa included Akkermansia enriched in CRC, and Bacteroides spp. enriched in IBD. The non-neoplastic mucosae presented distinct beta diversity (p = 0.005), but the CAC/CRC tumor microbiomes were similar (p = 0.7). Within metastases and margins, Enterobacteriaceae were enriched in CAC, and Bacteroidales in CRC. Pathobiont-specific qPCR confirmed a greater frequency of pks+ E. coli and enterotoxigenic Bacteroides fragilis in CAC than IBD. High alpha diversity was associated with active inflammation, advanced cancer stage, and shorter overall survival (log-rank p = 0.008). Mucosal microbiomes distinguish CAC from longstanding IBD, implicating pathobionts as markers for disease progression. Integrating our findings with prior animal model research, pathobionts promote carcinogenesis in IBD patients through genotoxicity and host cell signaling.
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Affiliation(s)
- Amr H Masaadeh
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Mohamed Eletrebi
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Bishal Parajuli
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nicola De Jager
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Dustin E Bosch
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, Iowa City, IA, USA
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Workman VL, Giblin AV, Green NH, MacNeil S, Hearnden V. Adipose tissue and adipose-derived stromal cells can reduce skin contraction in an in vitro tissue engineered full thickness skin model. Adipocyte 2025; 14:2473367. [PMID: 40104883 DOI: 10.1080/21623945.2025.2473367] [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: 08/21/2024] [Revised: 02/10/2025] [Accepted: 02/17/2025] [Indexed: 03/20/2025] Open
Abstract
Skin contracts during wound healing to facilitate wound closure. In some patients, skin contraction can lead to the formation of skin contractures that limit movement, impair function, and significantly impact well-being. Current treatment options for skin contractures are burdensome for patients, and there is a high risk of recurrence. Autologous fat grafting can improve the structure and function of scarred skin; however, relatively little is known about the effect of fat on skin contraction. In this study, an in vitro tissue-engineered model of human skin was used to test the effects of adipose tissue and adipose-derived stromal cells on skin contraction. Untreated tissue-engineered skin contracted to approximately 60% of the original area over 14 days in culture. The addition of adipose tissue reduced this contraction by 50%. Adipose tissue, which was emulsified or concentrated and high doses of adipose-derived stromal cells (ADSC) were able to inhibit contraction to a similar degree; however, lower doses of ADSC did not show the same effect. In conclusion, the subcutaneous application of adipose tissue has the potential to inhibit skin contraction. This study provides in vitro evidence to support the use of autologous fat grafting to prevent skin contraction in patients most at risk.
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Affiliation(s)
- Victoria L Workman
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK
| | - Anna-Victoria Giblin
- Department of Plastic Surgery, Sheffield Teaching Hospitals, NHS Foundation Trust, Sheffield, UK
| | - Nicola H Green
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK
- INSIGNEO Institute, University of Sheffield, Sheffield, UK
| | - Sheila MacNeil
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK
| | - Vanessa Hearnden
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK
- INSIGNEO Institute, University of Sheffield, Sheffield, UK
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Cheng W, Yi L, Xu T, Xie Y, Zhu J, Guan X, Li Q, Huang Y, Zhao Y, Zhao S. The stems and leaves of Panax notoginseng reduce the abundance of antibiotic resistance genes by regulating intestinal microbiota in Duzang pigs. Anim Biotechnol 2025; 36:2471785. [PMID: 40094563 DOI: 10.1080/10495398.2025.2471785] [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: 07/25/2024] [Accepted: 02/20/2025] [Indexed: 03/19/2025]
Abstract
In order to study the distribution characteristics of intestinal microbiota and antibiotic resistance genes (ARGs) in Duzang pigs after adding stems and leaves of Panax notoginseng to the feed, the characteristics of intestinal microbiota were explored by metagenomic sequencing, and 14 ARGs and 2 integrase genes were detected by qPCR. The results showed that the addition of stems and leaves of P. notoginseng increased the relative abundance of Firmicutes, Lactobacillus and Pediococcus in the cecum of Duzang pigs. A total of 10 ARGs and 2 integrase genes were detected in the cecal contents of pigs. The addition of stems and leaves of P. notoginseng reduced the relative abundance of total ARGs, ermB, tetO and tetW in the cecum of Duzang pigs. The results of network analysis showed that multiple genera were potential hosts of ARGs. The addition of stems and leaves of P. notoginseng may reduce the relative abundance of ARGs by reducing the relative abundance of genera such as Corynebacterium and Flavonifractor, thereby reducing the risk of ARGs spread. This study provides a theoretical basis for the rational use of stems and leaves of P. notoginseng to control ARGs.
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Affiliation(s)
- Wenjie Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Lanlan Yi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Taojie Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yuxiao Xie
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
- College of Biology and Agriculture, Zunyi Normal University, Zunyi, China
| | - Junhong Zhu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xuancheng Guan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Qiuyan Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Ying Huang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yanguang Zhao
- Shanghai Laboratory Animal Research Center, Shanghai, China
| | - Sumei Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
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Li X, Zhu L. Comprehensive profiling of cell type-specific expression and distribution of complement genes in mouse and human kidneys: insights into normal physiology and response to kidney transplantations. Ren Fail 2025; 47:2471568. [PMID: 40015727 PMCID: PMC11869339 DOI: 10.1080/0886022x.2025.2471568] [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: 07/24/2024] [Revised: 01/24/2025] [Accepted: 02/15/2025] [Indexed: 03/01/2025] Open
Abstract
BACKGROUND Recent studies innovatively revealed the localized expression of complement genes in kidneys and shed light on the vital roles of the intracellular complement system in the physiologic function and pathological conditions. However, a comprehensive analysis of the expression of complement genes in the context of the evolving cellular landscape of the kidney is not available. METHODS We analyzed single-cell RNA sequencing data from healthy human subjects, C57BL/6 mice, and kidney transplant-rejected mice. The data were sourced from the NCBI Gene Expression Omnibus and processed using quality control measures and unsupervised clustering. Differential gene analyses were based on expression levels. RESULTS In total, 50 complement genes were categorized into pattern recognition molecules, proteases, complement components, receptors, and regulators. In normal mice kidneys, complement genes were expressed at relatively low levels. Among different complement gene categories, receptor genes were most widely expressed in kidney cells. Comparatively, macrophages and mesangial cells are the most abundant immune and nonimmune cell types for complement gene expression. A comparison of human and mouse data showed similar expression patterns, but human kidney complement gene expression was more abundant. Comparative analysis between mouse transplant-rejected and normal kidneys demonstrated stronger complement gene expression in transplant-rejected kidneys. CONCLUSIONS This study illustrated significant similarities in complement gene expression between murine and human kidneys and highlighted the responsive nature of complement genes to kidney injury, underscoring the dynamic nature of local complement regulation. These findings enhance our understanding of the complex regulation of the complement system within the kidney, offering insights into its role in renal disease pathogenesis.
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Affiliation(s)
- Xianzhi Li
- Renal Division, Department of Medicine, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease (Peking University), National Health Commission, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
| | - Li Zhu
- Renal Division, Department of Medicine, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease (Peking University), National Health Commission, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing, China
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Jiao Y, Ren J, Xie S, Yuan N, Shen J, Yin H, Wang J, Guo H, Cao J, Wang X, Wu D, Zhou Z, Qi X. Raffinose-metabolizing bacteria impair radiation-associated hematopoietic recovery via the bile acid/FXR/NF-κB signaling pathway. Gut Microbes 2025; 17:2488105. [PMID: 40192235 PMCID: PMC11980471 DOI: 10.1080/19490976.2025.2488105] [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: 12/20/2024] [Revised: 03/23/2025] [Accepted: 03/28/2025] [Indexed: 04/11/2025] Open
Abstract
Radiation-associated hematopoietic recovery (RAHR) is critical for mitigating lethal complications of acute radiation syndrome (ARS), yet therapeutic strategies remain limited. Through integrated multi-omics analysis of a total body irradiation (TBI) mouse model, we identify Bacteroides acidifaciens-dominated gut microbiota as key mediators of RAHR impairment. 16S ribosomal rRNA sequencing revealed TBI-induced dysbiosis characterized by Bacteroidaceae enrichment, while functional metagenomics identified raffinose metabolism as the most significantly perturbed pathway. Notably, raffinose supplementation (10% w/v) recapitulated radiation-induced microbiota shifts and delayed bone marrow recovery. Fecal microbiota transplantation (FMT) revealed a causative role for raffinose-metabolizing microbiota, particularly Bacteroides acidifaciens, in delaying RAHR progression. Mechanistically, B. acidifaciens-mediated bile acid deconjugation activated FXR, subsequently suppressing NF-κB-dependent hematopoietic recovery. Therapeutic FXR inhibition via ursodeoxycholic acid (UDCA) had been shown to be a viable method for rescuing RAHR. Our results delineated a microbiome-bile acid-FXR axis as a master regulator of post-irradiation hematopoiesis. Targeting B. acidifaciens or its metabolic derivatives could represent a translatable strategy to mitigate radiation-induced hematopoietic injury.
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Affiliation(s)
- Yang Jiao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, Suzhou, China
| | - Jiawei Ren
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Shichang Xie
- Key Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China
| | - Nan Yuan
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Jiaqi Shen
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Huafang Yin
- The Affiliated Jiangyin People’s Hospital of Nantong University, Jiangyin, China
| | - Jian Wang
- The Affiliated Jiangyin People’s Hospital of Nantong University, Jiangyin, China
| | - Hongjuan Guo
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Jianping Cao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Xin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Depei Wu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, Suzhou, China
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Zhemin Zhou
- Key Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China
- Cancer Institute, Suzhou Medical College, The Second Affiliated Hospital of Soochow University, Suzhou, China
- National Center of Technology Innovation for Biopharmaceuticals, Suzhou Biomedical Industry Innovation Center, Suzhou, China
| | - Xiaofei Qi
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, Suzhou, China
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
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He Y, Zhao G, Ouyang X, Wang S, Chen Y, Li C, He Y, Gao J, Han S, Zhao J, Wang J, Wang C. Creatine-mediated ferroptosis inhibition is involved in the intestinal radioprotection of daytime-restricted feeding. Gut Microbes 2025; 17:2489072. [PMID: 40205678 PMCID: PMC11988229 DOI: 10.1080/19490976.2025.2489072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2024] [Revised: 03/11/2025] [Accepted: 03/31/2025] [Indexed: 04/11/2025] Open
Abstract
Ionizing radiation-induced intestinal injury (IRIII) is a catastrophic disease lack of sufficient medical countermeasures currently. Regulation of the gut microbiota through dietary adjustments is a potential strategy to mitigate IRIII. Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention with pleiotropic health benefits. Whether this dietary pattern influences the pathogenesis of IRIII remains vague. We evaluated the impact of TRF on intestinal radiosensitivity in this study and discovered that only daytime TRF (DTRF), not nighttime TRF, could ameliorate intestinal damage in mice that received a high dose of IR. Faecal metagenomic and metabolomic studies revealed that the intestinal creatine level was increased by approximate 9 times by DTRF, to which the Bifidobacterium pseudolongum enrichment contribute. Further investigations showed that creatine could activate the energy sensor AMP-activated protein kinase in irradiated enterocytes and induce phosphorylation of acetyl-CoA carboxylase, resulting in reduced production of polyunsaturated fatty acids and reduced ferroptosis after IR. The administration of creatine mitigated IRIII and reduced bacteremia and proinflammatory responses. Blockade of creatine import compromised the ferroptosis inhibition and mitigation of DTRF on IRIII. Our study demonstrates a radioprotective dietary mode that can reshape the gut microbiota and increase intestinal creatine, which can suppress IR-induced ferroptosis, thereby providing effective countermeasures for IRIII prevention.
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Affiliation(s)
- Yingjuan He
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury of PLA, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Gaomei Zhao
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury of PLA, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Xue Ouyang
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury of PLA, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Shaobo Wang
- Department of Nephrology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yin Chen
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury of PLA, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Chenwenya Li
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury of PLA, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Yongwu He
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury of PLA, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Jining Gao
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury of PLA, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Songling Han
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury of PLA, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Jinghong Zhao
- Department of Nephrology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Junping Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury of PLA, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Cheng Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury of PLA, College of Preventive Medicine, Army Medical University, Chongqing, China
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Hoops SL, Moutsoglou D, Vaughn BP, Khoruts A, Knights D. Metagenomic source tracking after microbiota transplant therapy. Gut Microbes 2025; 17:2487840. [PMID: 40229213 PMCID: PMC12005403 DOI: 10.1080/19490976.2025.2487840] [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: 12/13/2024] [Revised: 03/07/2025] [Accepted: 03/28/2025] [Indexed: 04/16/2025] Open
Abstract
Reliable engraftment assessment of donor microbial communities and individual strains is an essential component of characterizing the pharmacokinetics of microbiota transplant therapies (MTTs). Recent methods for measuring donor engraftment use whole-genome sequencing and reference databases or metagenome-assembled genomes (MAGs) to track individual bacterial strains but lack the ability to disambiguate DNA that matches both donor and patient microbiota. Here, we describe a new, cost-efficient analytic pipeline, MAGEnTa, which compares post-MTT samples to a database comprised MAGs derived directly from donor and pre-treatment metagenomic data, without relying on an external database. The pipeline uses Bayesian statistics to determine the likely sources of ambiguous reads that align with both the donor and pre-treatment samples. MAGEnTa recovers engrafted strains with minimal type II error in a simulated dataset and is robust to shallow sequencing depths in a downsampled dataset. Applying MAGEnTa to a dataset from a recent MTT clinical trial for ulcerative colitis, we found the results to be consistent with 16S rRNA gene SourceTracker analysis but with added MAG-level specificity. MAGEnTa is a powerful tool to study community and strain engraftment dynamics in the development of MTT-based treatments that can be integrated into frameworks for functional and taxonomic analysis.
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Affiliation(s)
- Susan L. Hoops
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA
| | - Daphne Moutsoglou
- Gastroenterology Section, Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Byron P. Vaughn
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
- Division of Gastroenterology, University of Minnesota, Minneapolis, MN, USA
| | - Alexander Khoruts
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
- Division of Gastroenterology, University of Minnesota, Minneapolis, MN, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA
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Liu Y, Dong K, Yao Y, Lu B, Wang L, Ji G, Zhang H, Zhao Z, Yang X, Huang R, Zhou W, Pan X, Cui X. Construction and validation of renal cell carcinoma tumor cell differentiation-related prognostic classification (RCC-TCDC): an integrated bioinformatic analysis and clinical study. Ann Med 2025; 57:2490830. [PMID: 40248945 PMCID: PMC12010653 DOI: 10.1080/07853890.2025.2490830] [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: 12/16/2024] [Revised: 02/28/2025] [Accepted: 03/08/2025] [Indexed: 04/19/2025] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is a heterogeneous malignancy with diverse gene expression patterns, molecular landscapes, and differentiation characteristics of tumor cells. It is imperative to develop molecular RCC classification based on tumor cell differentiation for precise risk stratification and personalized therapy. METHODS We obtained scRNA-seq profiles from GSE159115 and bulk RNA-seq profiles from TCGA-KIRC cohort. We then performed scRNA-seq cluster analysis, monocle2 pseudotime analysis, and prognostic analysis to obtain tumor cell differentiation-related prognostic genes (TCDGs). Subsequently, we conducted consensus clustering to construct the RCC tumor cell differentiation-related prognostic classification (RCC-TCDC) and implemented prognostic and multi-omics analyses. Moreover, we utilized Lasso regression to help develop a multivariable prognostic model. In addition, we performed correlation analysis and Cmap algorithm for regulatory network establishment and candidate inhibitor prediction. We eventually included 370 kidney neoplasm patients in Xinhua cohort to undergo immunohistochemical staining and scoring for classification and comprehensive statistical analyses, including Chi-square tests, Kaplan-Meier survival analyses, and multivariable Cox regression analysis . RESULTS 32 TCDGs were identifiedand RCC-TCDC was constructed to classify TCGA-KIRC patients into RCC-low differentiation (RCC-LD) (S100A11+ SH3BGRL3+, high risk), RCC-moderate differentiation (TSPAN7+, medium risk), and RCC-high differentiation (RCC-HD) (AQP1+ NPR3+, low risk). Notably, RCC-LD was validated as anindependent risk factor for both OS (p = 0.015, HR = 14.0, 95%CI = 1.67-117.8) and PFS (p = 0.010, HR = 4.0, 95%CI = 1.39-11.7) of RCC patients in Xinhua cohort, taking RCC-HD as reference. CONCLUSIONS We constructed and validated a robust molecular classification system, RCC-TCDC, elucidating three distinct RCC subtypes.
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Affiliation(s)
- Yifan Liu
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Keqin Dong
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuntao Yao
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingnan Lu
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Wang
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guo Ji
- Department of Pathology, Shanghai Tenth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Haoyu Zhang
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zihui Zhao
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyue Yang
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Runzhi Huang
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Wang Zhou
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiuwu Pan
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingang Cui
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Vlasac IM, Stolrow HG, Thayer ZM, Christensen BC, Rivera L. DNA-based cell typing in menstrual effluent identifies cell type variation by sample collection method: toward noninvasive biomarker development for women's health. Epigenetics 2025; 20:2453275. [PMID: 39825876 DOI: 10.1080/15592294.2025.2453275] [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: 08/28/2024] [Revised: 01/06/2025] [Accepted: 01/08/2025] [Indexed: 01/20/2025] Open
Abstract
Menstrual effluent cell profiles have potential as noninvasive biomarkers of female reproductive and gynecological health and disease. We used DNA methylation-based cell type deconvolution (methylation cytometry) to identify cell type profiles in self-collected menstrual effluent. During the second day of their menstrual cycle, healthy participants collected menstrual effluent using a vaginal swab, menstrual cup, and pad. Immune cell proportions were highest in menstrual cup samples, and epithelial cells were highest in swab samples. Our work demonstrates the feasibility and utility of menstrual effluent cell profiling in population-level research using remotely collected samples and DNA methylation.
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Affiliation(s)
- Irma M Vlasac
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Hannah G Stolrow
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Zaneta M Thayer
- Department of Anthropology, Dartmouth College, Hanover, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Luisa Rivera
- Department of Anthropology, Dartmouth College, Hanover, NH, USA
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Rosati D, Valentine M, Bruno M, Pradhan A, Dietschmann A, Jaeger M, Leaves I, van de Veerdonk FL, Joosten LA, Roy S, Stappers MHT, Gow NA, Hube B, Brown AJ, Gresnigt MS, Netea MG. Lactic acid in the vaginal milieu modulates the Candida-host interaction. Virulence 2025; 16:2451165. [PMID: 39843417 PMCID: PMC11760238 DOI: 10.1080/21505594.2025.2451165] [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: 08/19/2024] [Revised: 11/07/2024] [Accepted: 12/28/2024] [Indexed: 01/24/2025] Open
Abstract
Vulvovaginal candidiasis (VVC) is one of the most common infections caused by Candida albicans. VVC is characterized by an inadequate hyperinflammatory response and clinical symptoms associated with Candida colonization of the vaginal mucosa. Compared to other host niches in which C. albicans can cause infection, the vaginal environment is extremely rich in lactic acid that is produced by the vaginal microbiota. We examined how lactic acid abundance in the vaginal niche impacts the interaction between C. albicans and the human immune system using an in vitro culture in vaginal simulative medium (VSM). The presence of lactic acid in VSM (VSM+LA) increased C. albicans proliferation, hyphal length, and its ability to cause damage during subsequent infection of vaginal epithelial cells. The cell wall of C. albicans cells grown in VSM+LA displayed a robust mannan fibrillar structure, β-glucan exposure, and low chitin content. These cell wall changes were associated with altered immune responses and an increased ability of the fungus to induce trained immunity. Neutrophils were compromised in clearing C. albicans grown in VSM+LA conditions, despite mounting stronger oxidative responses. Collectively, we found that fungal adaptation to lactic acid in a vaginal simulative context increases its immunogenicity favouring a pro-inflammatory state. This potentially contributes to the immune response dysregulation and neutrophil recruitment observed during recurrent VVC.
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Affiliation(s)
- Diletta Rosati
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, T
he Netherlands
| | - Marisa Valentine
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Mariolina Bruno
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, T
he Netherlands
| | - Arnab Pradhan
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Axel Dietschmann
- Junior Research Group Adaptive Pathogenicity Strategies, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, T
he Netherlands
| | - Ian Leaves
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Frank L. van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, T
he Netherlands
| | - Leo A.B. Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, T
he Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Sumita Roy
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Mark H. T. Stappers
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Neil A.R. Gow
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
- Institute of Microbiology, Friedrich-Schiller-University, Jena, Germany
| | - Alistair J.P. Brown
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Mark S. Gresnigt
- Junior Research Group Adaptive Pathogenicity Strategies, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, T
he Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
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Fumagalli A, Castells-Nobau A, Trivedi D, Garre-Olmo J, Puig J, Ramos R, Ramió-Torrentà L, Pérez-Brocal V, Moya A, Swann J, Martin-Garcia E, Maldonado R, Fernández-Real JM, Mayneris-Perxachs J. Archaea methanogens are associated with cognitive performance through the shaping of gut microbiota, butyrate and histidine metabolism. Gut Microbes 2025; 17:2455506. [PMID: 39910065 PMCID: PMC11810085 DOI: 10.1080/19490976.2025.2455506] [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: 09/30/2024] [Revised: 12/28/2024] [Accepted: 01/13/2025] [Indexed: 02/07/2025] Open
Abstract
The relationship between bacteria, cognitive function and obesity is well established, yet the role of archaeal species remains underexplored. We used shotgun metagenomics and neuropsychological tests to identify microbial species associated with cognition in a discovery cohort (IRONMET, n = 125). Interestingly, methanogen archaeas exhibited the strongest positive associations with cognition, particularly Methanobrevibacter smithii (M. smithii). Stratifying individuals by median-centered log ratios (CLR) of M. smithii (low and high M. smithii groups: LMs and HMs) revealed that HMs exhibited better cognition and distinct gut bacterial profiles (PERMANOVA p = 0.001), characterized by increased levels of Verrucomicrobia, Synergistetes and Lentisphaerae species and reduced levels of Bacteroidetes and Proteobacteria. Several of these species were linked to the cognitive test scores. These findings were replicated in a large-scale validation cohort (Aging Imageomics, n = 942). Functional analyses revealed an enrichment of energy, butyrate, and bile acid metabolism in HMs in both cohorts. Global plasma metabolomics by CIL LC-MS in IRONMET identified an enrichment of methylhistidine, phenylacetate, alpha-linolenic and linoleic acid, and secondary bile acid metabolism associated with increased levels of 3-methylhistidine, phenylacetylgluamine, adrenic acid, and isolithocholic acid in the HMs group. Phenylacetate and linoleic acid metabolism also emerged in the Aging Imageomics cohort performing untargeted HPLC-ESI-MS/MS metabolic profiling, while a targeted bile acid profiling identified again isolithocholic acid as one of the most significant bile acid increased in the HMs. 3-Methylhistidine levels were also associated with intense physical activity in a second validation cohort (IRONMET-CGM, n = 116). Finally, FMT from HMs donors improved cognitive flexibility, reduced weight, and altered SCFAs, histidine-, linoleic acid- and phenylalanine-related metabolites in the dorsal striatum of recipient mice. M. smithii seems to interact with the bacterial ecosystem affecting butyrate, histidine, phenylalanine, and linoleic acid metabolism with a positive impact on cognition, constituting a promising therapeutic target to enhance cognitive performance, especially in subjects with obesity.
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Affiliation(s)
- Andrea Fumagalli
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Salt, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III; Madrid, Spain
| | - Anna Castells-Nobau
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Salt, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III; Madrid, Spain
| | - Dakshat Trivedi
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Josep Garre-Olmo
- serra-hunter program Department of Nursing, University of Girona, Girona, Spain
| | - Josep Puig
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Institute of Diagnostic Imaging (IDI)-Research Unit (IDIR), Parc Sanitari Pere Virgili, Barcelona, Spain
- Medical Imaging, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- Department of Radiology (IDI), Dr. Josep Trueta University Hospital, Girona, Spain
| | - Rafel Ramos
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Vascular Health Research Group of Girona (ISV-Girona), Jordi Gol Institute for Primary Care Research (Institut Universitari per a la Recerca en Atenció Primària Jordi Gol I Gorina -IDIAPJGol), Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud-RICAPPS- ISCIII Girona Biomedical Research Institute (IDIBGI), Dr. Josep Trueta University Hospital, Girona, Catalonia, Spain
- Research in Vascular Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Dr. Josep Trueta University Hospital, Girona, Spain
| | - Lluís Ramió-Torrentà
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
- Neurodegeneration and Neuroinflammation Research Group, IDIBGI-CERCA, Girona, Spain
| | - Vicente Pérez-Brocal
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Andrés Moya
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), Valencia, Spain
| | - Jonathan Swann
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Elena Martin-Garcia
- Laboratory of Neuropharmacology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III; Madrid, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Salt, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III; Madrid, Spain
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An L, Li S, Chang Z, Lei M, He Z, Xu P, Zhang S, Jiang Z, Iqbal MS, Sun X, Liu H, Duan X, Wu W. Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet. Gut Microbes 2025; 17:2457490. [PMID: 39873191 PMCID: PMC11776474 DOI: 10.1080/19490976.2025.2457490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 12/16/2024] [Accepted: 01/17/2025] [Indexed: 01/30/2025] Open
Abstract
Hyperoxaluria, including primary and secondary hyperoxaluria, is a disorder characterized by increased urinary oxalate excretion and could lead to recurrent calcium oxalate kidney stones, nephrocalcinosis and eventually end stage renal disease. For secondary hyperoxaluria, high dietary oxalate (HDOx) or its precursors intake is a key reason. Recently, accumulated studies highlight the important role of gut microbiota in the regulation of oxalate homeostasis. However, the underlying mechanisms involving gut microbiota and metabolite disruptions in secondary hyperoxaluria remain poorly understood. Here, we investigated the therapeutic efficacy of fecal microbiota transplantation (FMT) sourced from healthy rats fed with standard pellet diet against urinary oxalate excretion, renal damage and calcium oxalate (CaOx) crystal depositions via using hyperoxaluria rat models. We observed dose-dependent increases in urinary oxalate excretion and CaOx crystal depositions due to hyperoxaluria, accompanied by significant reductions in gut microbiota diversity characterized by shifts in Ruminococcaceae_UCG-014 and Parasutterella composition. Metabolomic analysis validated these findings, revealing substantial decreases in key metabolites associated with these microbial groups. Transplanting microbes from healthy rats effectively reduced HDOx-induced urinary oxalate excretion and CaOx crystal depositions meanwhile restoring Ruminococcaceae_UCG-014 and Parasutterella populations and their associated metabolites. Furthermore, FMT treatment could significantly decrease the urinary oxalate excretion and CaOx crystal depositions in rat kidneys via, at least in part, upregulating the expressions of intestinal barrier proteins and oxalate transporters in the intestine. In conclusion, our study emphasizes the effectiveness of FMT in countering HDOx-induced hyperoxaluria by restoring gut microbiota and related metabolites. These findings provide insights on the complex connection between secondary hyperoxaluria caused by high dietary oxalate and disruptions in gut microbiota, offering promising avenues for targeted therapeutic strategies.
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Affiliation(s)
- Lingyue An
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Shujue Li
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhenglin Chang
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min Lei
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhican He
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Peng Xu
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shike Zhang
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zheng Jiang
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Muhammad Sarfaraz Iqbal
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xinyuan Sun
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hongxing Liu
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaolu Duan
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenqi Wu
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Rodrigues CS, Gaifem J, Pereira MS, Alves MF, Silva M, Padrão N, Cavadas B, Moreira-Barbosa C, Alves I, Marcos-Pinto R, Torres J, Lavelle A, Colombel JF, Sokol H, Pinho SS. Alterations in mucosa branched N-glycans lead to dysbiosis and downregulation of ILC3: a key driver of intestinal inflammation. Gut Microbes 2025; 17:2461210. [PMID: 39918275 PMCID: PMC11810091 DOI: 10.1080/19490976.2025.2461210] [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: 08/29/2024] [Revised: 11/29/2024] [Accepted: 01/13/2025] [Indexed: 02/12/2025] Open
Abstract
The perturbation of the symbiotic relationship between microbes and intestinal immune system contributes to gut inflammation and Inflammatory Bowel Disease (IBD) development. The host mucosa glycans (glycocalyx) creates a major biological interface between gut microorganisms and host immunity that remains ill-defined. Glycans are essential players in IBD immunopathogenesis, even years before disease onset. However, how changes in mucosa glycosylation shape microbiome and how this impact gut immune response and inflammation remains to be clarified. Here, we revealed that alterations in the expression of complex branched N-glycans at gut mucosa surface, modeled in glycoengineered mice, resulted in dysbiosis, with a deficiency in Firmicutes bacteria. Concomitantly, this mucosa N-glycan switch was associated with a downregulation of type 3 innate lymphoid cells (ILC3)-mediated immune response, leading to the transition of ILC3 toward an ILC1 proinflammatory phenotype and increased TNFα production. In addition, we demonstrated that the mucosa glycosylation remodeling through prophylactic supplementation with glycans at steady state was able to restore microbial-derived short-chain fatty acids and microbial sensing (by NOD2 expression) alongside the rescue of the expression of ILC3 module, suppressing intestinal inflammation and controlling disease onset. In a complementary approach, we further showed that IBD patients, often displaying dysbiosis, exhibited a tendency of decreased MGAT5 expression at epithelial cells that was accompanied by reduced ILC3 expression in gut mucosa. Altogether, these results unlock the effects of alterations in mucosa glycome composition in the regulation of the bidirectional crosstalk between microbiota and gut immune response, revealing host branched N-glycans/microbiota/ILC3 axis as an essential pathway in gut homeostasis and in preventing health to intestinal inflammation transition.
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Affiliation(s)
- Cláudia S. Rodrigues
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Joana Gaifem
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
| | - Márcia S. Pereira
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Maria Francisca Alves
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Mariana Silva
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Nuno Padrão
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Bruno Cavadas
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
| | | | - Inês Alves
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
| | - Ricardo Marcos-Pinto
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
- Department of Gastroenterology, Centro Hospitalar do Porto, Porto, Portugal
- Centro de Investigação em Tecnologias e Serviços de Saúde, University of Porto, Porto, Portugal
| | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
- Faculty of Medicine, University of Lisbon, Lisbon, Portugal
- Division of Gastroenterology, Hospital da Luz, Lisbon, Portugal
| | - Aonghus Lavelle
- Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Gastroenterology Department, Sorbonne Université, INSERM, Paris, France
| | - Jean-Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harry Sokol
- Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Gastroenterology Department, Sorbonne Université, INSERM, Paris, France
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Salomé S. Pinho
- Institute for Research and Innovation in Health (i3S), Immunology, Cancer & Glycomedicine Group, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
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Meza-Torres J, Tinevez JY, Crouzols A, Mary H, Kim M, Hunault L, Chamorro-Rodriguez S, Lejal E, Altamirano-Silva P, Groussard D, Gobaa S, Peltier J, Chassaing B, Dupuy B. Clostridioides difficile binary toxin CDT induces biofilm-like persisting microcolonies. Gut Microbes 2025; 17:2444411. [PMID: 39719371 DOI: 10.1080/19490976.2024.2444411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 11/07/2024] [Accepted: 12/09/2024] [Indexed: 12/26/2024] Open
Abstract
Clinical symptoms of Clostridioides difficile infection (CDI) range from diarrhea to pseudomembranous colitis. A major challenge in managing CDI is the high rate of relapse. Several studies correlate the production of CDT binary toxin by clinical strains of C. difficile with higher relapse rates. Although the mechanism of action of CDT on host cells is known, its exact contribution to CDI is still unclear. To understand the physiological role of CDT during CDI, we established two hypoxic relevant intestinal models, Transwell and Microfluidic Intestine-on-Chip systems. Both were challenged with the epidemic strain UK1 CDT+ and its isogenic CDT- mutant. We report that CDT induces mucin-associated microcolonies that increase C. difficile colonization and display biofilm-like properties by enhancing C. difficile resistance to vancomycin. Importantly, biofilm-like microcolonies were also observed in the cecum and colon of infected mice. Hence, our study shows that CDT induces biofilm-like microcolonies, increasing C. difficile persistence and risk of relapse.
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Affiliation(s)
- Jazmin Meza-Torres
- Pathogenesis of Bacterial Anaerobes, Department of Microbiology, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Jean-Yves Tinevez
- Image Analysis Hub, Department of Cell Biology and Infection, Institut Pasteur, Université Paris Cité, Paris, France
| | - Aline Crouzols
- Pathogenesis of Bacterial Anaerobes, Department of Microbiology, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Héloïse Mary
- Biomaterials and Microfluidics Core Facility, Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Minhee Kim
- Biomaterials and Microfluidics Core Facility, Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Lise Hunault
- Antibodies in Therapy and Pathology, Department of Immunology, Institut Pasteur, Paris, France
| | - Susan Chamorro-Rodriguez
- Pathogenesis of Bacterial Anaerobes, Department of Microbiology, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Emilie Lejal
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Pamela Altamirano-Silva
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | | | - Samy Gobaa
- Biomaterials and Microfluidics Core Facility, Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Johann Peltier
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Benoit Chassaing
- Microbiome-Host Interactions, Department of Microbiology, Institut Pasteur, Université Paris Cité, INSERM U1306, Paris, France
- Mucosal Microbiota in Chronic Inflammatory Diseases, INSERM U1016, CNRS UMR 8104, Université Paris Cité, Paris, France
| | - Bruno Dupuy
- Pathogenesis of Bacterial Anaerobes, Department of Microbiology, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
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49
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Zhang M, Lu Z. tRNA modifications: greasing the wheels of translation and beyond. RNA Biol 2025; 22:1-25. [PMID: 39723662 DOI: 10.1080/15476286.2024.2442856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/29/2024] [Accepted: 12/11/2024] [Indexed: 12/28/2024] Open
Abstract
Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.
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Affiliation(s)
- Minjie Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Medical Epigenetics, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
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50
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Cantu-Jungles TM, Agamennone V, Van den Broek TJ, Schuren FHJ, Hamaker B. Systematically-designed mixtures outperform single fibers for gut microbiota support. Gut Microbes 2025; 17:2442521. [PMID: 39704614 DOI: 10.1080/19490976.2024.2442521] [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: 05/15/2024] [Revised: 10/03/2024] [Accepted: 12/09/2024] [Indexed: 12/21/2024] Open
Abstract
Dietary fiber interventions to modulate the gut microbiota have largely relied on isolated fibers or specific fiber sources. We hypothesized that fibers systematically blended could promote more health-related bacterial groups. Initially, pooled in vitro fecal fermentations were used to design dietary fiber mixtures to support complementary microbial groups related to health. Then, microbial responses were compared for the designed mixtures versus their single fiber components in vitro using fecal samples from a separate cohort of 10 healthy adults. The designed fiber mixtures outperformed individual fibers in supporting bacterial taxa across donors resulting in superior alpha diversity and unexpected higher SCFA production. Moreover, unique shifts in community structure and specific taxa were observed for fiber mixtures that were not observed for single fibers, suggesting a synergistic effect when certain fibers are put together. Fiber mixture responses were remarkably more consistent than individual fibers across donors in promoting several taxa, especially butyrate producers from the Clostridium cluster XIVa. This is the first demonstration of synergistic fiber interactions for superior support of a diverse group of important beneficial microbes consistent across people, and unexpectedly high SCFA production. Overall, harnessing the synergistic potential of designed fiber mixtures represents a promising and more efficacious avenue for future prebiotic development.
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Affiliation(s)
- T M Cantu-Jungles
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - V Agamennone
- Microbiology and Systems Biology Group, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, the Netherlands
| | - T J Van den Broek
- Microbiology and Systems Biology Group, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, the Netherlands
| | - F H J Schuren
- Microbiology and Systems Biology Group, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, the Netherlands
| | - B Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA
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