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Yao J, Li Y, Liu X, Liang W, Li Y, Wu L, Wang Z, Song W. FUBP3 mediates the amyloid-β-induced neuronal NLRP3 expression. Neural Regen Res 2025; 20:2068-2083. [PMID: 39254567 DOI: 10.4103/nrr.nrr-d-23-01799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/13/2024] [Indexed: 09/11/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202507000-00028/figure1/v/2024-09-09T124005Z/r/image-tiff Alzheimer's disease is characterized by deposition of amyloid-β, which forms extracellular neuritic plaques, and accumulation of hyperphosphorylated tau, which aggregates to form intraneuronal neurofibrillary tangles, in the brain. The NLRP3 inflammasome may play a role in the transition from amyloid-β deposition to tau phosphorylation and aggregation. Because NLRP3 is primarily found in brain microglia, and tau is predominantly located in neurons, it has been suggested that NLRP3 expressed by microglia indirectly triggers tau phosphorylation by upregulating the expression of pro-inflammatory cytokines. Here, we found that neurons also express NLRP3 in vitro and in vivo, and that neuronal NLRP3 regulates tau phosphorylation. Using biochemical methods, we mapped the minimal NLRP3 promoter and identified FUBP3 as a transcription factor regulating NLRP3 expression in neurons. In primary neurons and the neuroblastoma cell line Neuro2A, FUBP3 is required for endogenous NLRP3 expression and tau phosphorylation only when amyloid-β is present. In the brains of aged wild-type mice and a mouse model of Alzheimer's disease, FUBP3 expression was markedly increased in cortical neurons. Transcriptome analysis suggested that FUBP3 plays a role in neuron-mediated immune responses. We also found that FUBP3 trimmed the 5' end of DNA fragments that it bound, implying that FUBP3 functions in stress-induced responses. These findings suggest that neuronal NLRP3 may be more directly involved in the amyloid-β-to-phospho-tau transition than microglial NLRP3, and that amyloid-β fundamentally alters the regulatory mechanism of NLRP3 expression in neurons. Given that FUBP3 was only expressed at low levels in young wild-type mice and was strongly upregulated in the brains of aged mice and Alzheimer's disease mice, FUBP3 could be a safe therapeutic target for preventing Alzheimer's disease progression.
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Affiliation(s)
- Jing Yao
- The National Clinical Research Center for Geriatric Disease, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yuan Li
- The National Clinical Research Center for Geriatric Disease, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xi Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Wenping Liang
- The National Clinical Research Center for Geriatric Disease, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yu Li
- The National Clinical Research Center for Geriatric Disease, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Liyong Wu
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Zhe Wang
- The National Clinical Research Center for Geriatric Disease, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Weihong Song
- The National Clinical Research Center for Geriatric Disease, Xuanwu Hospital, Capital Medical University, Beijing, China
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children's Hospital, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Oujiang Laboratory (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, Zhejiang Province, China
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Li T, Xing HM, Qian HD, Gao Q, Xu SL, Ma H, Chi ZL. Small extracellular vesicles derived from human induced pluripotent stem cell-differentiated neural progenitor cells mitigate retinal ganglion cell degeneration in a mouse model of optic nerve injury. Neural Regen Res 2025; 20:587-597. [PMID: 38819069 PMCID: PMC11317950 DOI: 10.4103/nrr.nrr-d-23-01414] [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: 08/22/2023] [Revised: 11/14/2023] [Accepted: 12/29/2023] [Indexed: 06/01/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202502000-00034/figure1/v/2024-05-28T214302Z/r/image-tiff Several studies have found that transplantation of neural progenitor cells (NPCs) promotes the survival of injured neurons. However, a poor integration rate and high risk of tumorigenicity after cell transplantation limits their clinical application. Small extracellular vesicles (sEVs) contain bioactive molecules for neuronal protection and regeneration. Previous studies have shown that stem/progenitor cell-derived sEVs can promote neuronal survival and recovery of neurological function in neurodegenerative eye diseases and other eye diseases. In this study, we intravitreally transplanted sEVs derived from human induced pluripotent stem cells (hiPSCs) and hiPSCs-differentiated NPCs (hiPSC-NPC) in a mouse model of optic nerve crush. Our results show that these intravitreally injected sEVs were ingested by retinal cells, especially those localized in the ganglion cell layer. Treatment with hiPSC-NPC-derived sEVs mitigated optic nerve crush-induced retinal ganglion cell degeneration, and regulated the retinal microenvironment by inhibiting excessive activation of microglia. Component analysis further revealed that hiPSC-NPC derived sEVs transported neuroprotective and anti-inflammatory miRNA cargos to target cells, which had protective effects on RGCs after optic nerve injury. These findings suggest that sEVs derived from hiPSC-NPC are a promising cell-free therapeutic strategy for optic neuropathy.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hui-Min Xing
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hai-Dong Qian
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qiao Gao
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Sheng-Lan Xu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hua Ma
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Zai-Long Chi
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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3
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Na J, Tai C, Wang Z, Yang Z, Chen X, Zhang J, Zheng L, Fan Y. Stiff extracellular matrix drives the differentiation of mesenchymal stem cells toward osteogenesis by the multiscale 3D genome reorganization. Biomaterials 2025; 312:122715. [PMID: 39094522 DOI: 10.1016/j.biomaterials.2024.122715] [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: 03/22/2024] [Revised: 07/17/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
Extracellular matrix (ECM) stiffness is a major driver of stem cell fate. However, the involvement of the three-dimensional (3D) genomic reorganization in response to ECM stiffness remains unclear. Here, we generated comprehensive 3D chromatin landscapes of mesenchymal stem cells (MSCs) exposed to various ECM stiffness. We found that there were more long-range chromatin interactions, but less compartment A in MSCs cultured on stiff ECM than those cultured on soft ECM. However, the switch from compartment B in MSCs cultured on soft ECM to compartment A in MSCs cultured on stiff ECM included genes encoding proteins primarily enriched in cytoskeleton organization. At the topologically associating domains (TADs) level, stiff ECM tends to have merged TADs on soft ECM. These merged TADs on stiff ECM include upregulated genes encoding proteins enriched in osteogenesis, such as SP1, ETS1, and DCHS1, which were validated by quantitative real-time polymerase chain reaction and found to be consistent with the increase of alkaline phosphatase staining. Knockdown of SP1 or ETS1 led to the downregulation of osteogenic marker genes, including COL1A1, RUNX2, ALP, and OCN in MSCs cultured on stiff ECM. Our study provides an important insight into the stiff ECM-mediated promotion of MSC differentiation towards osteogenesis, emphasizing the influence of mechanical cues on the reorganization of 3D genome architecture and stem cell fate.
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Affiliation(s)
- Jing Na
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Chengzheng Tai
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Ziyi Wang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zhijie Yang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Xinyuan Chen
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Jing Zhang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100083, China.
| | - Lisha Zheng
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Yubo Fan
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
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Kaistha BP, Kar G, Dannhorn A, Watkins A, Opoku-Ansah G, Ilieva K, Mullins S, Anderton J, Galvani E, Garcon F, Lapointe JM, Brown L, Hair J, Slidel T, Luheshi N, Ryan K, Hardaker E, Dovedi S, Kumar R, Wilkinson RW, Hammond SA, Eyles J. Efficacy and pharmacodynamic effect of anti-CD73 and anti-PD-L1 monoclonal antibodies in combination with cytotoxic therapy: observations from mouse tumor models. Cancer Biol Ther 2024; 25:2296048. [PMID: 38206570 PMCID: PMC10793677 DOI: 10.1080/15384047.2023.2296048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
CD73 is a cell surface 5'nucleotidase (NT5E) and key node in the catabolic process generating immunosuppressive adenosine in cancer. Using a murine monoclonal antibody surrogate of Oleclumab, we investigated the effect of CD73 inhibition in concert with cytotoxic therapies (chemotherapies as well as fractionated radiotherapy) and PD-L1 blockade. Our results highlight improved survival in syngeneic tumor models of colorectal cancer (CT26 and MC38) and sarcoma (MCA205). This therapeutic outcome was in part driven by cytotoxic CD8 T-cells, as evidenced by the detrimental effect of CD8 depleting antibody treatment of MCA205 tumor bearing mice treated with anti-CD73, anti-PD-L1 and 5-Fluorouracil+Oxaliplatin (5FU+OHP). We hypothesize that the improved responses are tumor microenvironment (TME)-driven, as suggested by the lack of anti-CD73 enhanced cytopathic effects mediated by 5FU+OHP on cell lines in vitro. Pharmacodynamic analysis, using imaging mass cytometry and RNA-sequencing, revealed noteworthy changes in specific cell populations like cytotoxic T cells, B cells and NK cells in the CT26 TME. Transcriptomic analysis highlighted treatment-related modulation of gene profiles associated with an immune response, NK and T-cell activation, T cell receptor signaling and interferon (types 1 & 2) pathways. Inclusion of comparator groups representing the various components of the combination allowed deconvolution of contribution of the individual therapeutic elements; highlighting specific effects mediated by the anti-CD73 antibody with respect to immune-cell representation, chemotaxis and myeloid biology. These pre-clinical data reflect complementarity of adenosine blockade with cytotoxic therapy, and T-cell checkpoint inhibition, and provides new mechanistic insights in support of combination therapy.
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Affiliation(s)
| | - Gozde Kar
- Oncology R & D, AstraZeneca, Cambridge, UK
| | | | | | | | - Kristina Ilieva
- Oncology R & D, AstraZeneca, Cambridge, UK
- Immunooncology, MorphoSys AG, Planegg, Germany
| | - Stefanie Mullins
- Oncology R & D, AstraZeneca, Cambridge, UK
- Translational Science, F-Star, Cambridge, UK
| | | | | | | | | | - Lee Brown
- Imaging Sciences, AstraZeneca, Cambridge, UK
| | - James Hair
- Oncology R & D, AstraZeneca, Cambridge, UK
| | - Tim Slidel
- Oncology R & D, AstraZeneca, Cambridge, UK
| | | | - Kelli Ryan
- Oncology R & D, AstraZeneca, Cambridge, UK
| | | | | | - Rakesh Kumar
- Oncology R & D, AstraZeneca, Gaithersburg, MD, USA
| | | | | | - Jim Eyles
- Oncology R & D, AstraZeneca, Cambridge, UK
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Kuczyńska A, Michałek M, Ogrodowicz P, Kempa M, Witaszak N, Dziurka M, Gruszka D, Daszkowska-Golec A, Szarejko I, Krajewski P, Mikołajczak K. Drought-induced molecular changes in crown of various barley phytohormone mutants. PLANT SIGNALING & BEHAVIOR 2024; 19:2371693. [PMID: 38923879 PMCID: PMC11210921 DOI: 10.1080/15592324.2024.2371693] [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: 02/26/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
One of the main signal transduction pathways that modulate plant growth and stress responses, including drought, is the action of phytohormones. Recent advances in omics approaches have facilitated the exploration of plant genomes. However, the molecular mechanisms underlying the response in the crown of barley, which plays an essential role in plant performance under stress conditions and regeneration after stress treatment, remain largely unclear. The objective of the present study was the elucidation of drought-induced molecular reactions in the crowns of different barley phytohormone mutants. We verified the hypothesis that defects of gibberellins, brassinosteroids, and strigolactones action affect the transcriptomic, proteomic, and hormonal response of barley crown to the transitory drought influencing plant development under stress. Moreover, we assumed that due to the strong connection between strigolactones and branching the hvdwarf14.d mutant, with dysfunctional receptor of strigolactones, manifests the most abundant alternations in crowns and phenotype under drought. Finally, we expected to identify components underlying the core response to drought which are independent of the genetic background. Large-scale analyses were conducted using gibberellins-biosynthesis, brassinosteroids-signaling, and strigolactones-signaling mutants, as well as reference genotypes. Detailed phenotypic evaluation was also conducted. The obtained results clearly demonstrated that hormonal disorders caused by mutations in the HvGA20ox2, HvBRI1, and HvD14 genes affected the multifaceted reaction of crowns to drought, although the expression of these genes was not induced by stress. The study further detected not only genes and proteins that were involved in the drought response and reacted specifically in mutants compared to the reaction of reference genotypes and vice versa, but also the candidates that may underlie the genotype-universal stress response. Furthermore, candidate genes involved in phytohormonal interactions during the drought response were identified. We also found that the interplay between hormones, especially gibberellins and auxins, as well as strigolactones and cytokinins may be associated with the regulation of branching in crowns exposed to drought. Overall, the present study provides novel insights into the molecular drought-induced responses that occur in barley crowns.
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Affiliation(s)
- Anetta Kuczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Martyna Michałek
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Piotr Ogrodowicz
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Kempa
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Natalia Witaszak
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Dziurka
- Faculty of Natural Sciences, The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Krakow, Poland
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Aljani B, Lindner A, Weigelt M, Zhao M, Sharma V, Bonifacio E, Jones P, Eugster A. Small RNA-Seq and real time rt-qPCR reveal islet miRNA released under stress conditions. Islets 2024; 16:2392343. [PMID: 39154325 PMCID: PMC11332650 DOI: 10.1080/19382014.2024.2392343] [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: 04/29/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024] Open
Abstract
Replacement of beta cells through transplantation is a potential therapeutic approach for individuals with pancreas removal or poorly controllable type 1 diabetes. However, stress and death of beta cells pose significant challenges. Circulating miRNA has emerged as potential biomarkers reflecting early beta cell stress and death, allowing for timely intervention. The aim of this study was to identify miRNAs as potential biomarkers for beta cell health. Literature review combined with small RNA sequencing was employed to select islet-enriched miRNA. The release of those miRNA was assessed by RT-qPCR in vivo, using a streptozotocin induced diabetes mouse model and in vitro, through mouse and human islets exposed to varying degrees of hypoxic and cytokine stressors. Utilizing the streptozotocin induced model, we identified 18 miRNAs out of 39 candidate islet-enriched miRNA to be released upon islet stress in vivo. In vitro analysis of culture supernatants from cytokine and/or hypoxia stressed islets identified the release of 45 miRNAs from mouse and 8 miRNAs from human islets. Investigation into the biological pathways targeted by the cytokine- and/or hypoxia-induced miRNA suggested the involvement of MAPK and PI3K-Akt signaling pathways in both mouse and human islets. We have identified miRNAs associated with beta cell health and stress. The findings allowed us to propose a panel of 47 islet-related human miRNA that is potentially valuable for application in clinical contexts of beta cell transplantation and presymptomatic early-stage type 1 diabetes.
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Affiliation(s)
- Bssam Aljani
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Annett Lindner
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Marc Weigelt
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Min Zhao
- German Center for Environmental Health, Institute of Diabetes Research, Helmholtz Munich, Munich, Germany
| | - Virag Sharma
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Ezio Bonifacio
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
- Faculty of Medicine, German Center for Diabetes Research (DZD), Paul Langerhans Institute Dresden of Helmholtz Centre Munich at University Clinic Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Peter Jones
- Department of Diabetes, School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London, London, UK
| | - Anne Eugster
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
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Yang Y, Shen J, Deng P, Chen P. Mechanism investigation of Forsythoside A against esophageal squamous cell carcinoma in vitro and in vivo. Cancer Biol Ther 2024; 25:2380023. [PMID: 39046082 PMCID: PMC11271126 DOI: 10.1080/15384047.2024.2380023] [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: 12/29/2023] [Revised: 06/21/2024] [Accepted: 07/10/2024] [Indexed: 07/25/2024] Open
Abstract
CONTEXT Forsythoside A (FSA) was extracted from Forsythia suspensa, a traditional Chinese medicine, which has been demonstrated to exert anti-inflammatory, antibacterial, and other pharmacological effects. However, the anticancer effect of FSA in esophageal squamous cell carcinoma (ESCC) has not been documented. OBJECTIVE The present study aimed to elucidate the mechanism of FSA against ESCC. MATERIALS AND METHODS Network pharmacology and molecular docking were employed to predict the mechanism. FSA was utilized to treat ESCC cell lines KYSE450 and KYSE30, followed by CCK-8 assay, cell cloning formation assay, flow cytometry, Western blot, RNA-seq analysis, and subsequent in vivo experiments. RESULTS Network pharmacology and molecular docking predicted that the therapeutic effect of FSA in ESCC is mediated through proteins such as BCL2 and BAX, influencing KEGG pathways associated with apoptosis. In vitro experiments showed that FSA inhibited cell proliferation and plate clone formation, promoted cell apoptosis and impacted the cell cycle distribution of G2/M phase by regulating BCL2, BAX, and p21. Further RNA-seq in KYSE450 cells showed that FSA regulated the expression of 223 genes, specifically affecting the biological process of epidermal development. In vivo experiments showed that gastric administration of FSA resulted in notable reductions in both tumor volume and weight by regulating BCL2, BAX, and p21. 16S rRNA sequencing showed that FSA led to significant changes of beta diversity. Abundance of 11 specific bacterial taxa were considerably changed following administration of FSA. CONCLUSIONS This study presents a novel candidate drug against ESCC and establishes a foundation for future clinical application.
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Affiliation(s)
- Yingying Yang
- School of Life Sciences, Zhengzhou Normal University, Zhengzhou, People’s Republic of China
| | - Junru Shen
- School of Life Sciences, Zhengzhou Normal University, Zhengzhou, People’s Republic of China
| | - Peiyuan Deng
- School of Life Sciences, Zhengzhou Normal University, Zhengzhou, People’s Republic of China
| | - Ping Chen
- Academy of Medical Sciences, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, People’s Republic of China
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Li T, Jia W, Peng S, Guo Y, Liu J, Zhang X, Li P, Zhang H, Xu R. Endogenous cAMP elevation in Brassica napus causes changes in phytohormone levels. PLANT SIGNALING & BEHAVIOR 2024; 19:2310963. [PMID: 38314783 PMCID: PMC10854363 DOI: 10.1080/15592324.2024.2310963] [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: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024]
Abstract
In higher plants, the regulatory roles of cAMP (cyclic adenosine 3',5'-monophosphate) signaling remain elusive until now. Cellular cAMP levels are generally much lower in higher plants than in animals and transiently elevated for triggering downstream signaling events. Moreover, plant adenylate cyclase (AC) activities are found in different moonlighting multifunctional proteins, which may pose additional complications in distinguishing a specific signaling role for cAMP. Here, we have developed rapeseed (Brassica napus L.) transgenic plants that overexpress an inducible plant-origin AC activity for generating high AC levels much like that in animal cells, which served the genetic model disturbing native cAMP signaling as a whole in plants. We found that overexpression of the soluble AC activity had significant impacts on the contents of indole-3-acetic acid (IAA) and stress phytohormones, i.e. jasmonic acid (JA), abscisic acid (ABA), and salicylic acid (SA) in the transgenic plants. Acute induction of the AC activity caused IAA overaccumulation, and upregulation of TAA1 and CYP83B1 in the IAA biosynthesis pathways, but also simultaneously the hyper-induction of PR4 and KIN2 expression indicating activation of JA and ABA signaling pathways. We observed typical overgrowth phenotypes related to IAA excess in the transgenic plants, including significant increases in plant height, internode length, width of leaf blade, petiole length, root length, and fresh shoot biomass, as well as the precocious seed development, as compared to wild-type plants. In addition, we identified a set of 1465 cAMP-responsive genes (CRGs), which are most significantly enriched in plant hormone signal transduction pathway, and function mainly in relevance to hormonal, abiotic and biotic stress responses, as well as growth and development. Collectively, our results support that cAMP elevation impacts phytohormone homeostasis and signaling, and modulates plant growth and development. We proposed that cAMP signaling may be critical in configuring the coordinated regulation of growth and development in higher plants.
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Affiliation(s)
- Tianming Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenjing Jia
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Song Peng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yanhui Guo
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Jinrui Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xue Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Panyu Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Hanfeng Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Ruqiang Xu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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9
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Liu Y, Qi L, Ye B, Wang A, Lu J, Qu L, Luo P, Wang L, Jiang A. MOICS, a novel classier deciphering immune heterogeneity and aid precise management of clear cell renal cell carcinoma at multiomics level. Cancer Biol Ther 2024; 25:2345977. [PMID: 38659199 PMCID: PMC11057626 DOI: 10.1080/15384047.2024.2345977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
Recent studies have indicated that the tumor immune microenvironment plays a pivotal role in the initiation and progression of clear cell renal cell carcinoma (ccRCC). However, the characteristics and heterogeneity of tumor immunity in ccRCC, particularly at the multiomics level, remain poorly understood. We analyzed immune multiomics datasets to perform a consensus cluster analysis and validate the clustering results across multiple internal and external ccRCC datasets; and identified two distinctive immune phenotypes of ccRCC, which we named multiomics immune-based cancer subtype 1 (MOICS1) and subtype 2 (MOICS2). The former, MOICS1, is characterized by an immune-hot phenotype with poor clinical outcomes, marked by significant proliferation of CD4+ and CD8+ T cells, fibroblasts, and high levels of immune inhibitory signatures; the latter, MOICS2, exhibits an immune-cold phenotype with favorable clinical characteristics, characterized by robust immune activity and high infiltration of endothelial cells and immune stimulatory signatures. Besides, a significant negative correlation between immune infiltration and angiogenesis were identified. We further explored the mechanisms underlying these differences, revealing that negatively regulated endopeptidase activity, activated cornification, and neutrophil degranulation may promote an immune-deficient phenotype, whereas enhanced monocyte recruitment could ameliorate this deficiency. Additionally, significant differences were observed in the genomic landscapes between the subtypes: MOICS1 exhibited mutations in TTN, BAP1, SETD2, MTOR, MUC16, CSMD3, and AKAP9, while MOICS2 was characterized by notable alterations in the TGF-β pathway. Overall, our work demonstrates that multi-immune omics remodeling analysis enhances the understanding of the immune heterogeneity in ccRCC and supports precise patient management.
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Affiliation(s)
- Ying Liu
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Lin Qi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, Hunan, China
| | - Bicheng Ye
- School of Clinical Medicine, Medical College of Yangzhou Polytechnic College, Yangzhou, China
| | - Anbang Wang
- Department of Urology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Juan Lu
- Vocational Education Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Le Qu
- Department of Urology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
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10
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Huang J, Wang X, Zeng Y, Xu H, Zhang S, Ding Z, Guo R. Identification of key mitochondria-related genes and their potential crosstalk role with immune pattern in Idiopathic pulmonary fibrosis. Gene 2024; 930:148840. [PMID: 39147114 DOI: 10.1016/j.gene.2024.148840] [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: 06/02/2024] [Revised: 07/29/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) stands out as a life-threatening and one of the most severe interstitial lung diseases. The pathogenesis of IPF is not fully understood, while recent studies have highlighted the association of mitochondrial dysfunction with IPF. This study is dedicated to pinpointing crucial genes related to mitochondria that potentially impact the advancement of IPF, thereby offering new perspectives on the pathogenesis of this condition. METHODS The Gene Expression Omnibus (GEO) database was utilized to download three datasets (GSE32537, GSE92592, and GSE150910), following which a comprehensive analysis was conducted to identify differentially expressed mitochondria-related genes (DEMTRGs) in the IPF lung tissues. Subsequently, GO and KEGG enrichment analysis of the DEMTRGs was performed. Next, external datasets and in vivo experiments were performed to validate their expression. Additionally, a Logistic regression model based on key DEMTRGs was constructed, and the model's ability to distinguish between IPF and controls was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC). Finally, gene set enrichment analysis (GSEA) and CIBERSORT algorithm were conducted. RESULTS We identified five key DEMTRGs (ALDH18A1, ALDH1B1, MCCC1, ACAT1, and PDHA1), ALDH18A1 and ALDH1B1 exhibited upregulated expression levels, whereas MCCC1, ACAT1, and PDHA1 showed downregulation in the lung tissue of individuals with IPF. The expression levels of these key DEMTRGs were validated by an independent external dataset (GSE53845) and the bleomycin-induced pulmonary fibrosis mice. In addition, the ROCs indicated that the diagnostic model constructed based on key DEMTRGs could effectively distinguish between IPF and controls (AUC>0.8). GSEA analysis and immune-related analysis shed light on the potential mechanisms through which these key DEMTRGs influence IPF. CONCLUSION Our research has pinpointed key genes associated with mitochondria that may ultimately contribute to the progression of IPF by exerting regulatory effects on mitochondrial function, thereby influencing multiple cellular processes.
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Affiliation(s)
- Jun Huang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Xia Wang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Youjie Zeng
- Department of Anesthesiology, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Huilin Xu
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Siyi Zhang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Zhigang Ding
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Ren Guo
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China.
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11
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Xing F, Xiao Q, Gul H, Liu T, Cao W, Zhang Y, Duan H, Li Y, Liang J, Zhang X, Xu D, Liu Z. Comparative global profiling of Perilla leaf and stem via transcriptomics and metabolomics. Gene 2024; 929:148828. [PMID: 39122229 DOI: 10.1016/j.gene.2024.148828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Perilla (Perilla frutescens L.) is a time-honored herbal plant with widespread applications in both medicine and culinary practices around the world. Profiling the essential organs and tissues with medicinal significance on a global scale offers valuable insights for enhancing the yield of desirable compounds in Perilla and other medicinal plants. In the present study, genome-wide RNA-sequencing (RNA-seq) and assessing the global spectrum of metabolites were carried out in the two major organs/tissues of stem (PfST) and leaf (PfLE) in Perilla. The results showed a total of 18,490 transcripts as the DEGs (differentially expressed genes) and 144 metabolites as the DAMs (differentially accumulated metabolites) through the comparative profiling of PfST vs PfLE, and all the DEGs and DAMs exhibited tissue-specific trends. An association analysis between the transcriptomics and metabolomics revealed 14 significantly enriched pathways for both DEGs and DAMs, among which the pathways of Glycine, serine and threonine metabolism (ko00260), Glyoxylate and dicarboxylate metabolism (ko00630), and Glucagon signaling pathway (ko04922) involved relatively more DEGs and DAMs. The results of qRT-PCR assays of 18 selected DEGs confirmed the distinct tissue-specific characteristics of all identified DEGs between PfST and PfLE. Notably, all eight genes associated with the flavonoid biosynthesis/metabolism pathways exhibited significantly elevated expression levels in PfLE compared to PfST. This observation suggests a heightened accumulation of metabolites related to flavonoids in Perilla leaves. The findings of this study offer a comprehensive overview of the organs and tissues in Perilla that have medicinal significance.
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Affiliation(s)
- Fangyu Xing
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Qianlin Xiao
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Hameed Gul
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Tingting Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Wan Cao
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Yingyi Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Hong Duan
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Yongjun Li
- Qianzhongdao Perilla Planting Professional Cooperative, Chongqing Houli Biotechnology Co., Ltd, Chongqing 409600, PR China
| | - Jiahong Liang
- Qianzhongdao Perilla Planting Professional Cooperative, Chongqing Houli Biotechnology Co., Ltd, Chongqing 409600, PR China
| | - Xingcui Zhang
- Qianzhongdao Perilla Planting Professional Cooperative, Chongqing Houli Biotechnology Co., Ltd, Chongqing 409600, PR China
| | - Delin Xu
- Department of Cell Biology, Zunyi Medical University, Guizhou 563099, PR China.
| | - Zhizhai Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, PR China.
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12
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Rosati D, Palmieri M, Brunelli G, Morrione A, Iannelli F, Frullanti E, Giordano A. Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review. Comput Struct Biotechnol J 2024; 23:1154-1168. [PMID: 38510977 PMCID: PMC10951429 DOI: 10.1016/j.csbj.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
In recent years, the role of bioinformatics and computational biology together with omics techniques and transcriptomics has gained tremendous importance in biomedicine and healthcare, particularly for the identification of biomarkers for precision medicine and drug discovery. Differential gene expression (DGE) analysis is one of the most used techniques for RNA-sequencing (RNA-seq) data analysis. This tool, which is typically used in various RNA-seq data processing applications, allows the identification of differentially expressed genes across two or more sample sets. Functional enrichment analyses can then be performed to annotate and contextualize the resulting gene lists. These studies provide valuable information about disease-causing biological processes and can help in identifying molecular targets for novel therapies. This review focuses on differential gene expression (DGE) analysis pipelines and bioinformatic techniques commonly used to identify specific biomarkers and discuss the advantages and disadvantages of these techniques.
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Affiliation(s)
- Diletta Rosati
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Maria Palmieri
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Giulia Brunelli
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Andrea Morrione
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Frullanti
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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13
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Xia W, Shi N, Li C, Tang A. RNA-Seq and miRNA-Seq data from Epstein-Barr virus-infected tree shrews reveal a ceRNA network contributing to immune microenvironment regulation. Virulence 2024; 15:2306795. [PMID: 38251668 PMCID: PMC10826628 DOI: 10.1080/21505594.2024.2306795] [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: 10/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Epstein-Barr virus (EBV) infection in humans is ubiquitous and associated with various diseases. Remodeling of the immune microenvironment is the primary cause of EBV infection and pathogenesis; however, the underlying mechanism has not been fully elucidated. In this study, we used whole-transcriptome RNA-Seq to detect mRNAs, long non-coding RNAs (lncRNA), and microRNA (miRNA) profiles in the control group, 3 days, and 28 days after EBV infection, based on the tree shrew model that we reported previously. First, we estimated the proportion of 22 cell types in each sample using CIBERSORT software and identified 18 high-confidence DElncRNAs related to immune microenvironment regulation after EBV infection. Functional enrichment analysis of these differentially expressed lncRNAs primarily focused on the autophagy, endocytosis, and ferroptosis signalling pathways. Moreover, EBV infection affects miRNA expression patterns, and many miRNAs are silenced. Finally, three competing endogenous RNA regulatory networks were built using lncRNAs that significantly correlated with immune cell types, miRNAs that responded to EBV infection, and potentially targeted the mRNA of the miRNAs. Among them, MRPL42-AS-5 might act as an hsa-miR-296-5p "sponge" and compete with target mRNAs, thus increasing mRNA expression level, which could induce immune cell infiltration through the cellular senescence signalling pathway against EBV infection. Overall, we conducted a complete transcriptomic analysis of EBV infection in vivo for the first time and provided a novel perspective for further investigation of EBV-host interactions.
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Affiliation(s)
- Wei Xia
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
| | - Nan Shi
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
| | - Chaoqian Li
- Department of Emergency, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Anzhou Tang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
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14
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Doloman A, Besteman MS, Sanders MG, Sousa DZ. Methanogenic partner influences cell aggregation and signalling of Syntrophobacterium fumaroxidans. Appl Microbiol Biotechnol 2024; 108:127. [PMID: 38229305 DOI: 10.1007/s00253-023-12955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/18/2024]
Abstract
For several decades, the formation of microbial self-aggregates, known as granules, has been extensively documented in the context of anaerobic digestion. However, current understanding of the underlying microbial-associated mechanisms responsible for this phenomenon remains limited. This study examined morphological and biochemical changes associated with cell aggregation in model co-cultures of the syntrophic propionate oxidizing bacterium Syntrophobacterium fumaroxidans and hydrogenotrophic methanogens, Methanospirillum hungatei or Methanobacterium formicicum. Formerly, we observed that when syntrophs grow for long periods with methanogens, cultures tend to form aggregates visible to the eye. In this study, we maintained syntrophic co-cultures of S. fumaroxidans with either M. hungatei or M. formicicum for a year in a fed-batch growth mode to stimulate aggregation. Millimeter-scale aggregates were observed in both co-cultures within the first 5 months of cultivation. In addition, we detected quorum sensing molecules, specifically N-acyl homoserine lactones, in co-culture supernatants preceding the formation of macro-aggregates (with diameter of more than 20 μm). Comparative transcriptomics revealed higher expression of genes related to signal transduction, polysaccharide secretion and metal transporters in the late-aggregation state co-cultures, compared to the initial ones. This is the first study to report in detail both biochemical and physiological changes associated with the aggregate formation in syntrophic methanogenic co-cultures. KEYPOINTS: • Syntrophic co-cultures formed mm-scale aggregates within 5 months of fed-batch cultivation. • N-acyl homoserine lactones were detected during the formation of aggregates. • Aggregated co-cultures exhibited upregulated expression of adhesins- and polysaccharide-associated genes.
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Affiliation(s)
- Anna Doloman
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands.
| | - Maaike S Besteman
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Mark G Sanders
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Princetonlaan 6, 3584, CB, Utrecht, The Netherlands
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15
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Mahdavi M, Prévost K, Balthazar P, Hus IFP, Duchesne É, Dumont N, Gagné-Ouellet V, Gagnon C, Laforest-Lapointe I, Massé E. Disturbance of the human gut microbiota in patients with Myotonic Dystrophy type 1. Comput Struct Biotechnol J 2024; 23:2097-2108. [PMID: 38803516 PMCID: PMC11128782 DOI: 10.1016/j.csbj.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a rare autosomal dominant genetic disorder. Although DM1 is primarily characterized by progressive muscular weakness, it exhibits many multisystemic manifestations, such as cognitive deficits, cardiac conduction abnormalities, and cataracts, as well as endocrine and reproductive issues. Additionally, the gastrointestinal (GI) tract is frequently affected, encompassing the entire digestive tract. However, the underlying causes of these GI symptoms remain uncertain, whether it is biomechanical problems of the intestine, involvement of bacterial communities, or both. The primary objective of this study is to investigate the structural changes in the gut microbiome of DM1 patients. To achieve this purpose, 35 patients with DM1 were recruited from the DM-Scope registry of the neuromuscular clinic in the Saguenay-Lac-St-Jean region of the province of Québec, Canada. Stool samples from these 35 patients, including 15 paired samples with family members living with them as controls, were collected. Subsequently, these samples were sequenced by 16S MiSeq and were analyzed with DADA2 to generate taxonomic signatures. Our analysis revealed that the DM1 status correlated with changes in gut bacterial community. Notably, there were differences in the relative abundance of Bacteroidota, Euryarchaeota, Fusobacteriota, and Cyanobacteria Phyla compared to healthy controls. However, no significant shift in gut microbiome community structure was observed between DM1 phenotypes. These findings provide valuable insights into how the gut bacterial community, in conjunction with biomechanical factors, could potentially influence the gastrointestinal tract of DM1 patients.
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Affiliation(s)
- Manijeh Mahdavi
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Karine Prévost
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Philippe Balthazar
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Isabelle Fisette-Paul Hus
- Department of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Élise Duchesne
- Physiotherapy teaching unit, Université du Québec à Chicoutimi, Chicoutimi, G7H 2B1, Canada
| | - Nicolas Dumont
- School of Rehabilitation, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Valérie Gagné-Ouellet
- Department of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Cynthia Gagnon
- Department of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | | | - Eric Massé
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
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16
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Ziemann M, Abeysooriya M, Bora A, Lamon S, Kasu MS, Norris MW, Wong YT, Craig JM. Direction-aware functional class scoring enrichment analysis of infinium DNA methylation data. Epigenetics 2024; 19:2375022. [PMID: 38967555 PMCID: PMC11229754 DOI: 10.1080/15592294.2024.2375022] [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: 02/22/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
Infinium Methylation BeadChip arrays remain one of the most popular platforms for epigenome-wide association studies, but tools for downstream pathway analysis have their limitations. Functional class scoring (FCS) is a group of pathway enrichment techniques that involve the ranking of genes and evaluation of their collective regulation in biological systems, but the implementations described for Infinium methylation array data do not retain direction information, which is important for mechanistic understanding of genomic regulation. Here, we evaluate several candidate FCS methods that retain directional information. According to simulation results, the best-performing method involves the mean aggregation of probe limma t-statistics by gene followed by a rank-ANOVA enrichment test using the mitch package. This method, which we call 'LAM,' outperformed an existing over-representation analysis method in simulations, and showed higher sensitivity and robustness in an analysis of real lung tumour-normal paired datasets. Using matched RNA-seq data, we examine the relationship of methylation differences at promoters and gene bodies with RNA expression at the level of pathways in lung cancer. To demonstrate the utility of our approach, we apply it to three other contexts where public data were available. First, we examine the differential pathway methylation associated with chronological age. Second, we investigate pathway methylation differences in infants conceived with in vitro fertilization. Lastly, we analyse differential pathway methylation in 19 disease states, identifying hundreds of novel associations. These results show LAM is a powerful method for the detection of differential pathway methylation complementing existing methods. A reproducible vignette is provided to illustrate how to implement this method.
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Affiliation(s)
- Mark Ziemann
- Bioinformatics Working Group, Burnet Institute, Melbourne, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Mandhri Abeysooriya
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University, Geelong, Australia
| | - Anusuiya Bora
- Bioinformatics Working Group, Burnet Institute, Melbourne, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Séverine Lamon
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University, Geelong, Australia
| | - Mary Sravya Kasu
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Mitchell W. Norris
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Yen Ting Wong
- School of Medicine, Deakin University, Geelong, Australia
- Murdoch Children’s Research Institute, Melbourne, Australia
| | - Jeffrey M. Craig
- School of Medicine, Deakin University, Geelong, Australia
- Murdoch Children’s Research Institute, Melbourne, Australia
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17
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Wang L, Yin N, Shi W, Xie Y, Yi J, Tang Z, Tang J, Xiang J. Splicing inhibition mediated by reduced splicing factors and helicases is associated with the cellular response of lung cancer cells to cisplatin. Comput Struct Biotechnol J 2024; 23:648-658. [PMID: 38283853 PMCID: PMC10819863 DOI: 10.1016/j.csbj.2023.12.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024] Open
Abstract
Lung cancer's mortality is predominantly linked to post-chemotherapy recurrence, driven by the reactivation of dormant cancer cells. Despite the critical role of these reactivated cells in cancer recurrence and metastasis, the molecular mechanisms governing their therapeutic selection remain poorly understood. In this study, we conducted an integrative analysis by combining PacBio single molecule real-time (SMRT) sequencing with short reads Illumina RNA-seq. Our study revealed that cisplatin-induced dormant and reactivated cancer cells exhibited a noteworthy reduction in gene transcripts and alternative splicing events. Particularly, the differential alternative splicing events were found to be overlapping with the differentially expression genes and enriched in genes related to cell cycle and cell division. Utilizing ENCORI database and correlation analysis, we identified key splicing factors, including SRSF7, SRSF3, PRPF8, and HNRNPC, as well as RNA helicase such as EIF4A3, DDX39A, DDX11, and BRIP1, which were associated with the observed reduction in alternative splicing and subsequent decrease in gene expression. Our study demonstrated that lung cancer cells reduce gene transcripts through diminished alternative splicing events mediated by specific splicing factors and RNA helicase in response to the chemotherapeutic stress. These findings provide insights into the molecular mechanisms underlying the therapeutic selection and reactivation of dormant cancer cells. This discovery opens a potential avenue for the development of therapeutic strategies aimed at preventing cancer recurrence following chemotherapy.
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Affiliation(s)
- Lujuan Wang
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Na Yin
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Wenhua Shi
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yaohuan Xie
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Junqi Yi
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Ziying Tang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Jingqun Tang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Juanjuan Xiang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
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18
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Foong YH, Caldwell B, Thorvaldsen JL, Krapp C, Mesaros CA, Zhou W, Kohli RM, Bartolomei MS. TET1 displays catalytic and non-catalytic functions in the adult mouse cortex. Epigenetics 2024; 19:2374979. [PMID: 38970823 PMCID: PMC11229741 DOI: 10.1080/15592294.2024.2374979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024] Open
Abstract
TET1/2/3 dioxygenases iteratively demethylate 5-methylcytosine, beginning with the formation of 5-hydroxymethylcytosine (5hmC). The post-mitotic brain maintains higher levels of 5hmC than most peripheral tissues, and TET1 ablation studies have underscored the critical role of TET1 in brain physiology. However, deletion of Tet1 precludes the disentangling of the catalytic and non-catalytic functions of TET1. Here, we dissect these functions of TET1 by comparing adult cortex of Tet1 wildtype (Tet1 WT), a novel Tet1 catalytically dead mutant (Tet1 HxD), and Tet1 knockout (Tet1 KO) mice. Using DNA methylation array, we uncover that Tet1 HxD and KO mutations perturb the methylation status of distinct subsets of CpG sites. Gene ontology (GO) analysis on specific differential 5hmC regions indicates that TET1's catalytic activity is linked to neuronal-specific functions. RNA-Seq further shows that Tet1 mutations predominantly impact the genes that are associated with alternative splicing. Lastly, we performed High-performance Liquid Chromatography Mass-Spectrometry lipidomics on WT and mutant cortices and uncover accumulation of lysophospholipids lysophosphatidylethanolamine and lysophosphatidylcholine in Tet1 HxD cortex. In summary, we show that Tet1 HxD does not completely phenocopy Tet1 KO, providing evidence that TET1 modulates distinct cortical functions through its catalytic and non-catalytic roles.
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Affiliation(s)
- Yee Hoon Foong
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Blake Caldwell
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Joanne L. Thorvaldsen
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Christopher Krapp
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Clementina A. Mesaros
- Translational Biomarkers Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wanding Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Children’s Hospital of Philadelphia (CHOP), University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Smilow Center for Translational Rsearch, Philadelphia, PA, USA
| | - Rahul M. Kohli
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Smilow Center for Translational Rsearch, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
- Penn Epigenetics Institute, Smilow Center for Translational Rsearch, Philadelphia, PA, USA
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19
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Saito T, Espe M, Vikeså V, Bock C, Thomsen TH, Adam AC, Fernandes JMO, Skjaerven KH. One-carbon metabolism nutrients impact the interplay between DNA methylation and gene expression in liver, enhancing protein synthesis in Atlantic salmon. Epigenetics 2024; 19:2318517. [PMID: 38404006 PMCID: PMC10900267 DOI: 10.1080/15592294.2024.2318517] [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: 10/27/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024] Open
Abstract
Supplementation of one-carbon (1C) metabolism micronutrients, which include B-vitamins and methionine, is essential for the healthy growth and development of Atlantic salmon (Salmo salar). However, the recent shift towards non-fish meal diets in salmon aquaculture has led to the need for reassessments of recommended micronutrient levels. Despite the importance of 1C metabolism in growth performance and various cellular regulations, the molecular mechanisms affected by these dietary alterations are less understood. To investigate the molecular effect of 1C nutrients, we analysed gene expression and DNA methylation using two types of omics data: RNA sequencing (RNA-seq) and reduced-representation bisulphite sequencing (RRBS). We collected liver samples at the end of a feeding trial that lasted 220 days through the smoltification stage, where fish were fed three different levels of four key 1C nutrients: methionine, vitamin B6, B9, and B12. Our results indicate that the dosage of 1C nutrients significantly impacts genetic and epigenetic regulations in the liver of Atlantic salmon, particularly in biological pathways related to protein synthesis. The interplay between DNA methylation and gene expression in these pathways may play an important role in the mechanisms underlying growth performance affected by 1C metabolism.
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Affiliation(s)
- Takaya Saito
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
| | - Marit Espe
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
| | - Vibeke Vikeså
- Skretting AI, Aquaculture Innovation, Stavanger, Norway
| | - Christoph Bock
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Anne-Catrin Adam
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
| | | | - Kaja H Skjaerven
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
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20
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Carmon T, Hill N, Sripathi VR, Gossett ZB, Fakas S. The PAH1-encoded phosphatidate phosphatase of Yarrowia lipolytica differentially affects gene expression and lipid biosynthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159544. [PMID: 39089641 PMCID: PMC11380575 DOI: 10.1016/j.bbalip.2024.159544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Yarrowia lipolytica is a model oleaginous yeast with a strong capacity for lipid accumulation, yet its lipid metabolic pathways and regulatory mechanisms remain largely unexplored. The PAH1-encoded phosphatidate (PA) phosphatase governs lipid biosynthesis by its enzymatic activity and regulating the transcription of genes involved in phospholipid biosynthesis. In this work, we examined the effect of the loss of Pah1 (i.e., pah1Δ) on cell metabolism in cells growing in low- and high-glucose media. Multi-omics analyses revealed the global effect of the pah1Δ mutation on lipid and central carbon metabolism. Lipidomics analyses showed that the pah1Δ mutation caused a massive decrease in the masses of triacylglycerol (TAG) and diacylglycerol (DAG), and these effects were independent of glucose concentration in the media. Conversely, phospholipid levels declined in low-glucose media but increased in high-glucose media. The loss of Pah1 affected the expression of genes involved in key pathways of glucose metabolism, such as glycolysis, citric acid cycle, oxidative phosphorylation, and the pentose phosphate pathway, and these effects were more pronounced in high-glucose media. In lipid biosynthesis, the genes catalyzing phosphatidylcholine (PC) synthesis from phosphatidylethanolamine (PE) were upregulated within the CDP-DAG pathway. In contrast, PC synthesis through the Kennedy pathway was downregulated. The ethanolamine branch of the Kennedy pathway that synthesizes PE was also upregulated in pah1Δ. Interestingly, we noted a massive increase in the levels of lysophospholipids, consistent with the upregulation of genes involved in lipid turnover. Overall, this work identified novel regulatory roles of Pah1 in lipid biosynthesis and gene expression.
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Affiliation(s)
- Taylor Carmon
- Department of Food and Animal Sciences, Alabama A&M University, Normal, AL 35762, USA
| | - Na'Taja Hill
- Department of Food and Animal Sciences, Alabama A&M University, Normal, AL 35762, USA
| | | | - Zachary B Gossett
- Department of Food and Animal Sciences, Alabama A&M University, Normal, AL 35762, USA
| | - Stylianos Fakas
- Department of Food and Animal Sciences, Alabama A&M University, Normal, AL 35762, USA.
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21
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Cheng X, Meng X, Chen R, Song Z, Li S, Wei S, Lv H, Zhang S, Tang H, Jiang Y, Zhang R. The molecular subtypes of autoimmune diseases. Comput Struct Biotechnol J 2024; 23:1348-1363. [PMID: 38596313 PMCID: PMC11001648 DOI: 10.1016/j.csbj.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Autoimmune diseases (ADs) are characterized by their complexity and a wide range of clinical differences. Despite patients presenting with similar symptoms and disease patterns, their reactions to treatments may vary. The current approach of personalized medicine, which relies on molecular data, is seen as an effective method to address the variability in these diseases. This review examined the pathologic classification of ADs, such as multiple sclerosis and lupus nephritis, over time. Acknowledging the limitations inherent in pathologic classification, the focus shifted to molecular classification to achieve a deeper insight into disease heterogeneity. The study outlined the established methods and findings from the molecular classification of ADs, categorizing systemic lupus erythematosus (SLE) into four subtypes, inflammatory bowel disease (IBD) into two, rheumatoid arthritis (RA) into three, and multiple sclerosis (MS) into a single subtype. It was observed that the high inflammation subtype of IBD, the RA inflammation subtype, and the MS "inflammation & EGF" subtype share similarities. These subtypes all display a consistent pattern of inflammation that is primarily driven by the activation of the JAK-STAT pathway, with the effective drugs being those that target this signaling pathway. Additionally, by identifying markers that are uniquely associated with the various subtypes within the same disease, the study was able to describe the differences between subtypes in detail. The findings are expected to contribute to the development of personalized treatment plans for patients and establish a strong basis for tailored approaches to treating autoimmune diseases.
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Affiliation(s)
| | | | | | - Zerun Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuai Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Siyu Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuhao Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hao Tang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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22
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Li X, Yang Y, Xu S, Gui Y, Chen J, Xu J. Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning. Neural Regen Res 2024; 19:2723-2734. [PMID: 38595290 PMCID: PMC11168503 DOI: 10.4103/1673-5374.391306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/15/2023] [Accepted: 11/06/2023] [Indexed: 04/11/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202412000-00028/figure1/v/2024-04-08T165401Z/r/image-tiff Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal cord injury. They can greatly affect nerve regeneration and functional recovery. However, there is still limited understanding of the peripheral immune inflammatory response in spinal cord injury. In this study, we obtained microRNA expression profiles from the peripheral blood of patients with spinal cord injury using high-throughput sequencing. We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus (GEO) database (GSE151371). We identified 54 differentially expressed microRNAs and 1656 differentially expressed genes using bioinformatics approaches. Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways, such as neutrophil extracellular trap formation pathway, T cell receptor signaling pathway, and nuclear factor-κB signal pathway, were abnormally activated or inhibited in spinal cord injury patient samples. We applied an integrated strategy that combines weighted gene co-expression network analysis, LASSO logistic regression, and SVM-RFE algorithm and identified three biomarkers associated with spinal cord injury: ANO10, BST1, and ZFP36L2. We verified the expression levels and diagnostic performance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve. Quantitative polymerase chain reaction results showed that ANO10 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients. We also constructed a small RNA-mRNA interaction network using Cytoscape. Additionally, we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal cord injury patients using the CIBERSORT tool. The proportions of naïve B cells, plasma cells, monocytes, and neutrophils were increased while the proportions of memory B cells, CD8+ T cells, resting natural killer cells, resting dendritic cells, and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects, and ANO10, BST1 and ZFP26L2 were closely related to the proportion of certain immune cell types. The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal cord injury and suggest that ANO10, BST1, and ZFP36L2 are potential biomarkers for spinal cord injury. The study was registered in the Chinese Clinical Trial Registry (registration No. ChiCTR2200066985, December 12, 2022).
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Affiliation(s)
- Xiaolu Li
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Ye Yang
- Department of Rehabilitation Medicine, Guilin People’s Hospital, Guilin, Guangxi Zhuang Autonomous Region, China
| | - Senming Xu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Yuchang Gui
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Jianmin Chen
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jianwen Xu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
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23
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Luo P, Guo H, Liu B, Zhang Z, Xie Y, Yao J, Li X, Bian J, Zhuang J, Ouyang B, Wu J. Transcriptome analyses reveal key features of mouse seminal vesicle during aging. Syst Biol Reprod Med 2024; 70:249-260. [PMID: 39167124 DOI: 10.1080/19396368.2024.2388121] [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: 11/03/2023] [Revised: 07/24/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024]
Abstract
Despite the significant morphological changes that occur in the seminal vesicles with aging, the transcriptomic characteristics remain largely unexplored. To address this, we performed bulk RNA sequencing on seminal vesicle samples from mice aged 3, 13, and 21 months to uncover transcriptomic alterations. Our findings reveal that aged seminal vesicles display cystic dilatation, epithelial hypoplasia, disordered muscle layers, fibrosis, and reduced proliferation capability. A comparison between 3-month-old and 21-month-old mice indicated that leukocyte-mediated immunity and leukocyte migration were the most significantly upregulated biological processes among differentially expressed genes (DEGs). Notably, several DEGs associated with "leukocyte migration," such as Vcam1, Cxcl13, and Ccl8, exhibited an increasing trend in transcriptomic and protein expression at three different time points in the seminal vesicles of mice. Additionally, we identified multiple aging-associated DEGs, including P21 and Tnfrsf1b. Two genes (Cd209f and Ccl8) were consistently upregulated across all six regions of the male reproductive glands (testis, epididymis, and seminal vesicle) in the comparison of bulk RNA datasets from 3-month-old and 21-month-old mice. These analyses highlight an enhanced state of immune and inflammatory response in aged seminal vesicles. This study represents the first exploration of the overall transcriptome landscape of seminal vesicles in a murine model of natural aging, offering new insights into the mechanisms underlying aging-related seminal vesicle dysfunction.
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Affiliation(s)
- Peng Luo
- Reproductive Medicine Center, The Key Laboratory for Reproductive Medicine of Guangdong Province, The First Affiliated Hospital, SunYat-sen University, Guangzhou, China
| | - Haibin Guo
- Department of Reproductive Medicine, Henan Province People's Hospital, Zhengzhou, China
| | - Baoning Liu
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhiqiang Zhang
- Department of Andrology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yun Xie
- Department of Urology and Andrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiahui Yao
- Department of Urology and Andrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiangping Li
- Department of Urology and Andrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jun Bian
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jintao Zhuang
- Department of Urology, The Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bin Ouyang
- Center for Reproductive Medicine, Guangdong Women and Children Hospital, Guangzhou, China
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jinhua Wu
- Department of Andrology, Ganzhou People's Hospital of Jiangxi Province, Ganzhou, China
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24
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Wang X, Wang Q, Zhao J, Chen J, Wu R, Pan J, Li J, Wang Z, Chen Y, Guo W, Li Y. RCDdb: A manually curated database and analysis platform for regulated cell death. Comput Struct Biotechnol J 2024; 23:3211-3221. [PMID: 39257527 PMCID: PMC11384979 DOI: 10.1016/j.csbj.2024.08.012] [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: 06/30/2024] [Revised: 08/11/2024] [Accepted: 08/11/2024] [Indexed: 09/12/2024] Open
Abstract
Regulated cell death is a pivotal regulatory mechanism governing the development and homeostasis of multicellular organisms. A comprehensive understanding of RCD's regulatory mechanisms is crucial for developing novel therapeutic strategies against diseases associated with cell death, such as cancer and neurodegenerative diseases. However, existing data repositories support limited types of cell death data and lack comprehensive annotation and analytical functionalities. Thus, establishing an extensive cell death database is an urgent imperative. To address this gap, we developed the Regulated Cell Death Database (RCDdb, chenyclab.com/RCDdb), the first comprehensively manually annotated database designed to support annotations and analytical capabilities across all RCD types. We compiled 3090 marker gene annotations associated with 15 RCD types from 2180 relevant articles. The RCDdb includes annotation data on these marker genes concerning diseases, drugs, pathways, proteins, and gene expressions. Furthermore, it provides 49 diverse visualization methods to present this information. More importantly, the RCDdb features three online analysis tools for identifying and analyzing RCD-related features within user-submitted data. Furthermore, the RCDdb offers a user-friendly interface for querying, browsing, analysis, and visualization of detailed information associated with each RCD category. This resource promises to significantly aid researchers in better understanding the mechanisms of cell death, thereby accelerating progress in research and therapeutic strategies aimed at combating RCD-related diseases.
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Affiliation(s)
- Xiaopeng Wang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
- Southwest United Graduate School, Kunming 650092, China
| | - Qing Wang
- College of Bioengineering, Graduate School, Chongqing University, Chongqing 400044, China
| | - Jun Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jiaxin Chen
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruo Wu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
| | - Juanjuan Pan
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Jiaxin Li
- Graduate School of Zunyi Medical University, Zunyi 563000, China
| | - Zechang Wang
- Economics and Management School of Wuhan University, Wuhan 430060, China
| | - Yongchang Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
- Southwest United Graduate School, Kunming 650092, China
| | - Wenting Guo
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
| | - Yuanyuan Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
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25
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Liang S, Lu M, Yu D, Xing G, Ji Z, Guo Z, Zhang Q, Huang W, Xie M, Hou S. Effects of age on differential resistance to duck hepatitis A virus genotype 3 in Pekin ducks by 16 S and transcriptomics. Comput Struct Biotechnol J 2024; 23:771-782. [PMID: 38304549 PMCID: PMC10832293 DOI: 10.1016/j.csbj.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/09/2024] [Accepted: 01/14/2024] [Indexed: 02/03/2024] Open
Abstract
Duck hepatitis A virus genotype 3 (DHAV-3) is the major cause of viral hepatitis in ducks in Asia. Previous studies have shown that ducklings younger than 21 days are more susceptible to DHAV-3. To elucidate the mechanism by which age affects the differential susceptibility of Pekin ducks to DHAV-3, intestinal (n = 520), liver (n = 40) and blood (n = 260) samples were collected from control and DHAV-3-infected ducks at 7, 10, 14, and 21 days of age. Comparisons of plasma markers, mortality rates, and intestinal histopathological data showed that the resistance of Pekin ducks to DHAV-3 varied with age. 16 S sequencing revealed that the ileal microbial composition was influenced by age, and this correlation was greater than that recorded for caecal microbes. Candidatus Arthromitus, Bacteroides, Corynebacterium, Enterococcus, Romboutsia, and Streptococcus were the differntially abundant microbes in the ileum at the genus level after DHAV-3 infection and were significantly correlated with 7 differentially expressed genes (DEGs) in 7- and 21-day-old ducklings. 3 immunity-related pathways were significantly different between 7- and 21-day-old ducklings, especially for IFIH1-mediated induction of the interferon-alpha/beta pathway, which induces differential production of CD8(+) T cells and was influenced by a combination of differentially abundant microbiota and DEGs. We found that microbes in the ileum changed regularly with age. The intestinal microbiota was associated with the expression of genes in the liver through IFIH1-mediated induction of the interferon-alpha/beta pathway, which may partially explain why younger ducklings were more susceptible to DHAV-3 infection.
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Affiliation(s)
- Suyun Liang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Meixi Lu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Daxin Yu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guangnan Xing
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhanqing Ji
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhanbao Guo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qi Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wei Huang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ming Xie
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuisheng Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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26
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Koletti A, Skliros D, Kalloniati C, Marka S, Zografaki ME, Infante C, Mantecón L, Flemetakis E. Global omics study of Tetraselmis chuii reveals time-related metabolic adaptations upon oxidative stress. Appl Microbiol Biotechnol 2024; 108:138. [PMID: 38229403 DOI: 10.1007/s00253-023-12936-z] [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: 08/03/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 01/18/2024]
Abstract
Microalgae species encounter oxidative stress in their natural environments, prompting the development of species-specific adaptation mechanisms. Understanding these mechanisms can offer valuable insights for biotechnological applications in microalgal metabolic manipulation. In this study, we investigated the response of Tetraselmis chuii, an industrially important microalga, to H2O2-induced oxidative stress. Exposure to 0.5-mM H2O2 resulted in reduced cell viability, and higher concentrations led to a drastic decline. After 1 h of exposure to H2O2, photosynthetic capacity (Qy) was negatively impacted, and this reduction intensified after 6 h of continuous stress. Global multi-omics analysis revealed that T. chuii rapidly responded to H2O2-induced oxidative stress within the first hour, causing significant changes in both transcriptomic and metabolomic profiles. Among the cellular functions negatively affected were carbon and energy flow, with photosynthesis-related PSBQ having a 2.4-fold downregulation, pyruvate kinase decreased by 1.5-fold, and urea content reduced by threefold. Prolonged exposure to H2O2 incurred a high energy cost, leading to unsuccessful attempts to enhance carbon metabolism, as depicted, for example, by the upregulation of photosystems-related PETC and PETJ by more than twofold. These findings indicate that T. chuii quickly responds to oxidative stress, but extended exposure can have detrimental effects on its cellular functions. KEY POINTS: • 0.5-mM H2O2-induced oxidative stress strongly affects T. chuii • Distinct short- and long-term adaptation mechanisms are induced • Major metabolic adaptations occur within the first hour of exposure.
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Affiliation(s)
- Aikaterini Koletti
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Dimitrios Skliros
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Chrysanthi Kalloniati
- Department of Marine Sciences, University of the Aegean, University Hill 81100, Mytilene, Greece
| | - Sofia Marka
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Maria-Eleftheria Zografaki
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Carlos Infante
- Fitoplancton Marino, S.L., Dársena Comercial S/N (Muelle Pesquero), 11500, El Puerto de Santa María (Cádiz), Spain
| | - Lalia Mantecón
- Fitoplancton Marino, S.L., Dársena Comercial S/N (Muelle Pesquero), 11500, El Puerto de Santa María (Cádiz), Spain
| | - Emmanouil Flemetakis
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece.
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Sapozhnikov DM, Szyf M. Genetic confounds of transgenerational epigenetic inheritance in mice. Epigenetics 2024; 19:2318519. [PMID: 38369744 PMCID: PMC10878023 DOI: 10.1080/15592294.2024.2318519] [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: 10/15/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024] Open
Abstract
Transgenerational epigenetic inheritance in mammals remains a controversial phenomenon. A recent study by Takahashi et al. provides evidence for this mode of inheritance in mice by using a CRISPR/Cas9-based epigenetic editing technique to modify DNA methylation levels at specific promoters and then demonstrating the inheritance of the gain in methylation in offspring. In this technical commentary, we argue that the method used in the original study inherently amplifies the likelihood of genetic changes that thereafter lead to the heritability of epigenetic changes. We provide evidence that genetic changes from multiple sources do indeed occur in these experiments and explore several avenues by which these changes could be causal to the apparent inheritance of epigenetic changes. We conclude a genetic basis of inheritance cannot be ruled out and thus transgenerational epigenetic inheritance has not been adequately established by the original study.
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Affiliation(s)
- Daniel M. Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
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Yang X, Zeng J, Wang D, Zhou Q, Yu X, Wang Z, Bai T, Luan G, Xu Y. NagZ modulates the virulence of E. cloacae by acting through the gene of unknown function, ECL_03795. Virulence 2024; 15:2367652. [PMID: 38912723 PMCID: PMC11197897 DOI: 10.1080/21505594.2024.2367652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/09/2024] [Indexed: 06/25/2024] Open
Abstract
β-N-acetylglucosaminidase (NagZ), a cytosolic glucosaminidase, plays a pivotal role in peptidoglycan recycling. Previous research demonstrated that NagZ knockout significantly eradicated AmpC-dependent β-lactam resistance in Enterobacter cloacae. However, NagZ's role in the virulence of E. cloacae remains unclear. Our study, incorporating data on mouse and Galleria mellonella larval mortality rates, inflammation markers, and histopathological examinations, revealed a substantial reduction in the virulence of E. cloacae following NagZ knockout. Transcriptome sequencing uncovered differential gene expression between NagZ knockout and wild-type strains, particularly in nucleotide metabolism pathways. Further investigation demonstrated that NagZ deletion led to a significant increase in cyclic diguanosine monophosphate (c-di-GMP) levels. Additionally, transcriptome sequencing and RT-qPCR confirmed significant differences in the expression of ECL_03795, a gene with an unknown function but speculated to be involved in c-di-GMP metabolism due to its EAL domain known for phosphodiesterase activity. Interestingly, in ECL_03795 knockout strains, a notable reduction in the virulence was observed, and virulence was rescued upon complementation with ECL_03795. Consequently, our study suggests that NagZ's function on virulence is partially mediated through the ECL_03795→c-di-GMP pathway, providing insight into the development of novel therapies and strongly supporting the interest in creating highly efficient NagZ inhibitors.
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Affiliation(s)
- Xianggui Yang
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Zeng
- Division of Pulmonary and Critical Care Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Dan Wang
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Qin Zhou
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Xuejing Yu
- Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhenguo Wang
- Department of Stomatology, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Tingting Bai
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Guangxin Luan
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Ying Xu
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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29
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Sacramento CM, Saito MT, Casati MZ, Sallum EA, Casarin RCV, Silvério KG. CCKR signaling map, G-Protein bindings, hormonal regulation, and neural mechanisms may influence the osteogenic/cementogenic differentiation potential of hPDLSCs. Arch Oral Biol 2024; 168:106069. [PMID: 39208712 DOI: 10.1016/j.archoralbio.2024.106069] [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: 03/08/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVE Periodontal regeneration poses challenges due to the periodontium's complexity, relying on mesenchymal cells from the periodontal ligament (hPDLSCs) to regenerate hard tissues like bone and cementum. While some hPDLSCs have high regeneration potential (HOP-hPDLSCs), most are low potential (LOP-hPDLSCs). This study analyzed hPDLSCs from a single donor to minimize inter-individual variability and focus on key differences in differentiation potentials. DESIGN This study used RNA-seq, genomic databases, and bioinformatics tools to explore signaling pathways (SPs), biological processes (BPs), and molecular functions (MFs) guiding HOP cells to mineralized matrix production. It also investigated limitations of LOP cells and strategies for enhancing their osteo/cementogenesis. RESULTS In basal conditions, HOP exhibited a multifunctional gene network with higher expression of genes related to osteo/cementogenesis, cell differentiation, immune modulation, stress response, and hormonal regulation. In contrast, LOP focused on steroid hormone biosynthesis and nucleic acid maintenance. During osteo/cementogenic induction, HOP showed strong modulation of genes related to angiogenesis, cell division, mesenchymal differentiation, and extracellular matrix production. LOP demonstrated neural synaptic-related processes and preserved cellular cytoskeleton integrity. CCKR map signaling and G-protein receptor bindings gained significance during osteo/cementogenesis in HOP-hPDLSCs. Both HOP and LOP shared common BPs related to gastrointestinal and reproductive system development. CONCLUSION The osteo/cementogenic differentiation of HOP cells may be regulated by CCKR signaling, G-protein bindings, and specific hormonal regulation. LOP cells seem committed to neural mechanisms. This study sheds light on hPDLSCs' complex characteristics, offering a deeper understanding of their differentiation potential for future periodontal regeneration research and therapies.
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Affiliation(s)
- Catharina Marques Sacramento
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil
| | - Miki Taketomi Saito
- Faculdade de Odontologia, Universidade Federal do Pará - UFPA, Departamento de Saúde Coletiva, Belém 66075-110, Brazil.
| | - Márcio Zaffalon Casati
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
| | - Enilson Antonio Sallum
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
| | - Renato Correa Viana Casarin
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
| | - Karina Gonzales Silvério
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
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Wang Y, Wang J, Yang S, Liang Q, Gu Z, Wang Y, Mou H, Sun H. Selecting a preculture strategy for improving biomass and astaxanthin productivity of Chromochloris zofingiensis. Appl Microbiol Biotechnol 2024; 108:117. [PMID: 38204137 PMCID: PMC10781847 DOI: 10.1007/s00253-023-12873-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 01/12/2024]
Abstract
Chromochloris zofingiensis is a potential source of natural astaxanthin; however, its rapid growth and astaxanthin enrichment cannot be achieved simultaneously. This study established autotrophic, mixotrophic, and heterotrophic preculture patterns to assess their ameliorative effect on the C. zofingiensis heterotrophic growth state. In comparison, mixotrophic preculture (MP) exhibited the best improving effect on heterotrophic biomass concentration of C. zofingiensis (up to 121.5 g L-1) in a 20 L fermenter, reaching the global leading level. The astaxanthin productivity achieved 111 mg L-1 day-1, 7.4-fold higher than the best record. The transcriptome and 13C tracer-based metabolic flux analysis were used for mechanism inquiry. The results revealed that MP promoted carotenoid and lipid synthesis, and supported synthesis preference of low unsaturated fatty acids represented by C18:1 and C16:0. The MP group maintained the best astaxanthin productivity via mastering the balance between increasing glucose metabolism and inhibition of carotenoid synthesis. The MP strategy optimized the physiological state of C. zofingiensis and realized its heterotrophic high-density growth for an excellent astaxanthin yield on a pilot scale. This strategy exhibits great application potential in the microalgae-related industry. KEY POINTS: • Preculture strategies changed carbon flux and gene expression in C. zofingiensis • C. zofingiensis realized a high-density culture with MP and fed-batch culture (FBC) • Astaxanthin productivity achieved 0.111 g L-1 day-1 with MP and FBC.
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Affiliation(s)
- Yuxin Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Jia Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Shufang Yang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Qingping Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Ziqiang Gu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Ying Wang
- Marine Science research Institute of Shandong Province, Qingdao, 266003, China.
| | - Haijin Mou
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
| | - Han Sun
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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31
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Drozdova P, Gurkov A, Saranchina A, Vlasevskaya A, Zolotovskaya E, Indosova E, Timofeyev M, Borvinskaya E. Transcriptional response of Saccharomyces cerevisiae to lactic acid enantiomers. Appl Microbiol Biotechnol 2024; 108:121. [PMID: 38229303 DOI: 10.1007/s00253-023-12863-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/16/2023] [Accepted: 10/24/2023] [Indexed: 01/18/2024]
Abstract
The model yeast, Saccharomyces cerevisiae, is a popular object for both fundamental and applied research, including the development of biosensors and industrial production of pharmaceutical compounds. However, despite multiple studies exploring S. cerevisiae transcriptional response to various substances, this response is unknown for some substances produced in yeast, such as D-lactic acid (DLA). Here, we explore the transcriptional response of the BY4742 strain to a wide range of DLA concentrations (from 0.05 to 45 mM), and compare it to the response to 45 mM L-lactic acid (LLA). We recorded a response to 5 and 45 mM DLA (125 and 113 differentially expressed genes (DEGs), respectively; > 50% shared) and a less pronounced response to 45 mM LLA (63 DEGs; > 30% shared with at least one DLA treatment). Our data did not reveal natural yeast promoters quantitatively sensing DLA but provide the first description of the transcriptome-wide response to DLA and enrich our understanding of the LLA response. Some DLA-activated genes were indeed related to lactate metabolism, as well as iron uptake and cell wall structure. Additional analyses showed that at least some of these genes were activated only by acidic form of DLA but not its salt, revealing the role of pH. The list of LLA-responsive genes was similar to those published previously and also included iron uptake and cell wall genes, as well as genes responding to other weak acids. These data might be instrumental for optimization of lactate production in yeast and yeast co-cultivation with lactic acid bacteria. KEY POINTS: • We present the first dataset on yeast transcriptional response to DLA. • Differential gene expression was correlated with yeast growth inhibition. • The transcriptome response to DLA was richer in comparison to LLA.
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Affiliation(s)
- Polina Drozdova
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation.
- Baikal Research Centre, Rabochaya Str. 5V, Irkutsk, 664011, Russian Federation.
| | - Anton Gurkov
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
- Baikal Research Centre, Rabochaya Str. 5V, Irkutsk, 664011, Russian Federation
| | | | | | - Elena Zolotovskaya
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
| | - Elizaveta Indosova
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
| | - Maxim Timofeyev
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
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Wang X, Zhao S, Guo Y, Wang C, Han S, Wang X. CST2 promotes cell proliferation and regulates cell cycle by activating Wnt-β-catenin signalling pathway in serous ovarian cancer. J OBSTET GYNAECOL 2024; 44:2363515. [PMID: 38864487 DOI: 10.1080/01443615.2024.2363515] [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: 12/16/2023] [Accepted: 05/29/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND Cystatin SA (CST2) plays multiple roles in different types of malignant tumours; however, its role in serous ovarian cancer (SOC) remains unclear. Therefore, we aimed to investigate the expression levels, survival outcomes, immune cell infiltration, proliferation, cell cycle, and underlying molecular mechanisms associated with the CST2 signature in SOC. METHODS The Cancer Genome Atlas database was used to acquire clinical information and CST2 expression profiles from patients with SOC. Wilcoxon rank-sum tests were used to compare CST2 expression levels between SOC and normal ovarian tissues. A prognostic assessment of CST2 was conducted using Cox regression analysis and the Kaplan-Meier method. Differentially expressed genes were identified using functional enrichment analysis. Immune cell infiltration was examined using a single-sample gene set enrichment analysis. Cell cycle characteristics and proliferation were assessed using a colony formation assay, flow cytometry, and a cell counting kit-8 assay. Western blots and quantitative reverse transcription PCR analyses were employed to examine CST2 expressions and related genes involved in the cell cycle and the Wnt-β-catenin signalling pathway. RESULTS Our findings revealed significant upregulation of CST2 in SOC, and elevated CST2 expression was correlated with advanced clinicopathological characteristics and unfavourable prognoses. Pathway enrichment analysis highlighted the association between the cell cycle and the Wnt signalling pathway. Moreover, increased CST2 levels were positively correlated with immune cell infiltration. Functionally, CST2 played vital roles in promoting cell proliferation, orchestrating the G1-to-S phase transition, and driving malignant SOC progression through activating the Wnt-β-catenin signalling pathway. CONCLUSIONS The elevated expression of CST2 may be related to the occurrence and progression of SOC by activating the Wnt-β-catenin pathway. Additionally, our findings suggest that CST2 is a promising novel biomarker with potential applications in therapeutic, prognostic, and diagnostic strategies for SOC.
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Affiliation(s)
- Xiaohua Wang
- Department of Gynecology and Obstetrics, The Second Hospital of HeiBei Medical University, Shijiazhuang, China
- Department of Gynecology, Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Sufen Zhao
- Department of Gynecology and Obstetrics, The Second Hospital of HeiBei Medical University, Shijiazhuang, China
| | - Yanwei Guo
- Department of Obstetrics, Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Chunhui Wang
- Department of Gynecology, Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Shuyu Han
- Department of Gynecology, Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Xingcha Wang
- Department of Gynecology, Affiliated Hospital of Chengde Medical University, Chengde, China
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Werry N, Russell SJ, Sivakumar R, Miller S, Hickey K, Larmer S, Lohuis M, Librach C, LaMarre J. piRNA expression patterns in high vs. low fertility bovine sperm. Syst Biol Reprod Med 2024; 70:183-194. [PMID: 38924761 DOI: 10.1080/19396368.2024.2364742] [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: 11/06/2023] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
PIWI-interacting RNAs (piRNAs) are 24-32 nucleotide RNA sequences primarily expressed in germ cells and developing embryos that suppress transposable element expression to protect genomic integrity during epigenetic reprogramming events. We characterized the expression of piRNA sequences and their encoding clusters in sperm samples from an idiopathic fertility model of Holstein bulls with high and low Sire Conception Rates. The piRNA populations were determined to be mostly similar between fertility conditions when investigated by principal component and differential expression analysis, suggesting that a high degree of conservation in the piRNA system is likely necessary for the production of viable sperm. Both fertility conditions demonstrated evidence of 'ping-pong' activity - a secondary biogenesis pathway associated with active transposable element targeting and suppression. Most sperm-borne piRNAs were between 29-30 nucleotides in length and originated from 226 clusters across the genome, with the exception of chromosome 20. Mapping analysis revealed abundant targeting of several transposable element families, suggesting a suppressive function of sperm piRNAs consistent with their established roles. Expression of genes targeted by sperm-borne piRNAs is significantly reduced throughout early embryogenesis compared to the mRNA population. Limited transposable element expression is known to be essential for spermatogenesis, thus epigenetic regulation of this pathway is likely to influence sperm quality and fertilizing capacity.
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Affiliation(s)
- Nicholas Werry
- Department of Biomedical Sciences, The University of Guelph, Guelph, Ontario, Canada
| | | | - Raamkumaar Sivakumar
- Department of Biomedical Sciences, The University of Guelph, Guelph, Ontario, Canada
| | | | | | | | | | - Clifford Librach
- CReATe Fertility Centre, Toronto, Ontario, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan LaMarre
- Department of Biomedical Sciences, The University of Guelph, Guelph, Ontario, Canada
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Papagiannopoulos OD, Pezoulas VC, Papaloukas C, Fotiadis DI. 3D clustering of gene expression data from systemic autoinflammatory diseases using self-organizing maps (Clust3D). Comput Struct Biotechnol J 2024; 23:2152-2162. [PMID: 38827234 PMCID: PMC11141280 DOI: 10.1016/j.csbj.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 06/04/2024] Open
Abstract
Background and objective Systemic autoinflammatory diseases (SAIDs) are characterized by widespread inflammation, but for most of them there is a lack of specific biomarkers for accurate diagnosis. Although a number of machine learning algorithms have been used to analyze SAID datasets, aiding in the discovery of novel biomarkers, there is a growing recognition of the importance of SAID timeseries clustering, as it can capture the temporal dynamics of gene expression patterns. Methodology This paper proposes a novel clustering methodology to efficiently associate three-dimensional data. The algorithm utilizes competitive learning to create a self-organizing neural network and adjust neuron positions in time-dependent and high dimensional feature space in order to assign them as clustering centers. The quantitative evaluation of the clustering was based on well-known clustering indices. Furthermore, a differential expression analysis and classification pipeline was employed to assess the capability of the proposed methodology to extract more accurate pathway-specific genes from its clusters. For that, a comparative analysis was also conducted against a heuristic timeseries clustering method. Results The proposed methodology achieved better overall clustering indices scores and classification metrics using genes derived from its clusters. Notable cases include a threefold increase in the Calinski-Harabasz clustering index, a twofold improvement in the Davies-Bouldin clustering index and a ∼ 60 % increase in the classification specificity score. Conclusion A novel clustering methodology was developed and applied on several gene expression timeseries datasets from systemic autoinflammatory diseases, and its ability to efficiently produce well separated clusters compared to existing heuristic methods was demonstrated.
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Affiliation(s)
- Orestis D. Papagiannopoulos
- Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina GR45110, Greece
| | - Vasileios C. Pezoulas
- Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina GR45110, Greece
| | - Costas Papaloukas
- Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina GR45110, Greece
- Dept. of Biological Applications and Technology, University of Ioannina, Ioannina GR45110, Greece
- Institute of Biomedical Research, FORTH (Foundation for Research & Technology), Ioannina GR45110, Greece
| | - Dimitrios I. Fotiadis
- Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina GR45110, Greece
- Institute of Biomedical Research, FORTH (Foundation for Research & Technology), Ioannina GR45110, Greece
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Duncan JD, Devillers H, Camarasa C, Setati ME, Divol B. Oxygen alters redox cofactor dynamics and induces metabolic shifts in Saccharomyces cerevisiae during alcoholic fermentation. Food Microbiol 2024; 124:104624. [PMID: 39244375 DOI: 10.1016/j.fm.2024.104624] [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: 06/27/2024] [Revised: 08/08/2024] [Accepted: 08/25/2024] [Indexed: 09/09/2024]
Abstract
Environmental conditions significantly impact the metabolism of Saccharomyces cerevisiae, a Crabtree-positive yeast that maintains a fermentative metabolism in high-sugar environments even in the presence of oxygen. Although the introduction of oxygen has been reported to induce alterations in yeast metabolism, knowledge of the mechanisms behind these metabolic adaptations in relation to redox cofactor metabolism and their implications in the context of wine fermentation remains limited. This study aimed to compare the intracellular redox cofactor levels, the cofactor ratios, and primary metabolite production in S. cerevisiae under aerobic and anaerobic conditions in synthetic grape juice. The molecular mechanisms underlying these metabolic differences were explored using a transcriptomic approach. Aerobic conditions resulted in an enhanced fermentation rate and biomass yield. Total NADP(H) levels were threefold higher during aerobiosis, while a decline in the total levels of NAD(H) was observed. However, there were stark differences in the ratio of NAD+/NADH between the treatments. Despite few changes in the differential expression of genes involved in redox cofactor metabolism, anaerobiosis resulted in an increased expression of genes involved in lipid biosynthesis pathways, while the presence of oxygen increased the expression of genes associated with thiamine, methionine, and sulfur metabolism. The production of fermentation by-products was linked with differences in the redox metabolism in each treatment. This study provides valuable insights that may help steer the production of metabolites of industrial interest during alcoholic fermentation (including winemaking) by using oxygen as a lever of redox metabolism.
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Affiliation(s)
- James D Duncan
- South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Hugo Devillers
- UMR SPO, INRAE, Institut Agro, Université de Montpellier, Montpellier, France
| | - Carole Camarasa
- South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa; UMR SPO, INRAE, Institut Agro, Université de Montpellier, Montpellier, France
| | - Mathabatha E Setati
- South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Benoit Divol
- South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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Matarredona L, Zafrilla B, Rubio-Portillo E, Bonete MJ, Esclapez J. Deepening the knowledge of universal stress proteins in Haloferax mediterranei. Appl Microbiol Biotechnol 2024; 108:124. [PMID: 38229402 DOI: 10.1007/s00253-023-12899-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 01/18/2024]
Abstract
Haloarchaea, like many other microorganisms, have developed defense mechanisms such as universal stress proteins (USPs) to cope with environmental stresses affecting microbial growth. Despite the wide distribution of these proteins in Archaea, their biochemical characteristics still need to be discovered, and there needs to be more knowledge about them focusing on halophilic Archaea. Therefore, elucidating the role of USPs would provide valuable information to improve future biotechnological applications. Accordingly, transcriptional expression of the 37 annotated USPs in the Haloferax mediterranei genome has been examined under different stress conditions. From a global perspective, finding a clear tendency between particular USPs and specific stress conditions was not possible. Contrary, data analysis indicates that there is a recruitment mechanism of proteins with a similar sequence able to modulate the H. mediterranei growth, accelerating or slowing it, depending on their number. In fact, only three of these USPs were expressed in all the tested conditions, pointing to the cell needing a set of USPs to cope with stress conditions. After analysis of the RNA-Seq data, three differentially expressed USPs were selected and homologously overexpressed. According to the growth data, the overexpression of USPs induces a gain of tolerance in response to stress, as a rule. Therefore, this is the only work that studies all the USPs in an archaeon. It represents a significant first base to continue advancing, not only in this important family of stress proteins but also in the field of biotechnology and, at an industrial level, to improve applications such as designing microorganisms resistant to stress situations. KEY POINTS: • Expression of Haloferax mediterranei USPs has been analyzed in stress conditions. • RNA-seq analysis reveals that most of the USPs in H. mediterranei are downregulated. • Homologous overexpression of USPs results in more stress-tolerant strains.
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Affiliation(s)
- Laura Matarredona
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - Basilio Zafrilla
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - Julia Esclapez
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
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Li J, Tian J, Liu Y, Liu Z, Tong M. Personalized analysis of human cancer multi-omics for precision oncology. Comput Struct Biotechnol J 2024; 23:2049-2056. [PMID: 38783900 PMCID: PMC11112262 DOI: 10.1016/j.csbj.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Multi-omics technologies, encompassing genomics, proteomics, and transcriptomics, provide profound insights into cancer biology. A fundamental computational approach for analyzing multi-omics data is differential analysis, which identifies molecular distinctions between cancerous and normal tissues. Traditional methods, however, often fail to address the distinct heterogeneity of individual tumors, thereby neglecting crucial patient-specific molecular traits. This shortcoming underscores the necessity for tailored differential analysis algorithms, which focus on particular patient variations. Such approaches offer a more nuanced understanding of cancer biology and are instrumental in pinpointing personalized therapeutic strategies. In this review, we summarize the principles of current individualized techniques. We also review their efficacy in analyzing cancer multi-omics data and discuss their potential applications in clinical practice.
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Affiliation(s)
- Jiaao Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
- School of Informatics, Xiamen University, Xiamen 316000, China
| | - Jingyi Tian
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
- School of Informatics, Xiamen University, Xiamen 316000, China
| | - Yachen Liu
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
- School of Informatics, Xiamen University, Xiamen 316000, China
| | - Zan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
- School of Informatics, Xiamen University, Xiamen 316000, China
| | - Mengsha Tong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
- School of Informatics, Xiamen University, Xiamen 316000, China
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38
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Collinson RJ, Wilson L, Boey D, Ng ZY, Mirzai B, Chuah HS, Howman R, Grove CS, Malherbe JAJ, Leahy MF, Linden MD, Fuller KA, Erber WN, Guo BB. Transcription factor 3 is dysregulated in megakaryocytes in myelofibrosis. Platelets 2024; 35:2304173. [PMID: 38303515 DOI: 10.1080/09537104.2024.2304173] [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: 11/15/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024]
Abstract
Transcription factor 3 (TCF3) is a DNA transcription factor that modulates megakaryocyte development. Although abnormal TCF3 expression has been identified in a range of hematological malignancies, to date, it has not been investigated in myelofibrosis (MF). MF is a Philadelphia-negative myeloproliferative neoplasm (MPN) that can arise de novo or progress from essential thrombocythemia [ET] and polycythemia vera [PV] and where dysfunctional megakaryocytes have a role in driving the fibrotic progression. We aimed to examine whether TCF3 is dysregulated in megakaryocytes in MPN, and specifically in MF. We first assessed TCF3 protein expression in megakaryocytes using an immunohistochemical approach analyses and showed that TCF3 was reduced in MF compared with ET and PV. Further, the TCF3-negative megakaryocytes were primarily located near trabecular bone and had the typical "MF-like" morphology as described by the WHO. Genomic analysis of isolated megakaryocytes showed three mutations, all predicted to result in a loss of function, in patients with MF; none were seen in megakaryocytes isolated from ET or PV marrow samples. We then progressed to transcriptomic sequencing of platelets which showed loss of TCF3 in MF. These proteomic, genomic and transcriptomic analyses appear to indicate that TCF3 is downregulated in megakaryocytes in MF. This infers aberrations in megakaryopoiesis occur in this progressive phase of MPN. Further exploration of this pathway could provide insights into TCF3 and the evolution of fibrosis and potentially lead to new preventative therapeutic targets.
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Affiliation(s)
- Ryan J Collinson
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Lynne Wilson
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Darren Boey
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Zi Yun Ng
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
| | - Bob Mirzai
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Hun S Chuah
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
- Department of Haematology, Rockingham General Hospital, Rockingham, WA, Australia
| | - Rebecca Howman
- Department of Haematology, Sir Charles Gairdner Hospital Nedlands Australia
| | - Carolyn S Grove
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- Department of Haematology, Sir Charles Gairdner Hospital Nedlands Australia
| | | | - Michael F Leahy
- Department of Haematology, Royal Perth Hospital, Perth, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Matthew D Linden
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Kathryn A Fuller
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Wendy N Erber
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Belinda B Guo
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
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Shimizu T, Suzuki K, Inui M. A mycofactocin-associated dehydrogenase is essential for ethylene glycol metabolism by Rhodococcus jostii RHA1. Appl Microbiol Biotechnol 2024; 108:58. [PMID: 38175243 DOI: 10.1007/s00253-023-12966-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
Ethylene glycol is an industrially important diol in many manufacturing processes and a building block of polymers, such as poly(ethylene terephthalate). In this study, we found that a mycolic acid-containing bacterium Rhodococcus jostii RHA1 can grow with ethylene glycol as a sole source of carbon and energy. Deletion of a putative glycolate dehydrogenase gene (RHA1_ro03227) abolished growth with ethylene glycol, indicating that ethylene glycol is assimilated via glycolate in R. jostii RHA1. Transcriptome sequencing and gene deletion analyses revealed that a gene homologous to mycofactocin (MFT)-associated dehydrogenase (RHA1_ro06057), hereafter referred to as EgaA, is essential for ethylene glycol assimilation. Furthermore, egaA deletion also negatively affected the utilization of ethanol, 1-propanol, propylene glycol, and 1-butanol, suggesting that EgaA is involved in the utilization of various alcohols in R. jostii RHA1. Deletion of MFT biosynthetic genes abolished growth with ethylene glycol, indicating that MFT is the physiological electron acceptor of EgaA. Further genetic studies revealed that a putative aldehyde dehydrogenase (RHA1_ro06081) is a major aldehyde dehydrogenase in ethylene glycol metabolism by R. jostii RHA1. KEY POINTS: • Rhodococcus jostii RHA1 can assimilate ethylene glycol via glycolate • A mycofactocin-associated dehydrogenase is involved in the oxidation of ethylene glycol • An aldehyde dehydrogenase gene is important for the ethylene glycol assimilation.
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Affiliation(s)
- Tetsu Shimizu
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa-Shi, Kyoto, 619-0292, Japan
| | - Kai Suzuki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, 630-0192, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa-Shi, Kyoto, 619-0292, Japan.
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, 630-0192, Japan.
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40
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Katirtzoglou A, Hansen SB, Sveier H, Martin MD, Brealey JC, Limborg MT. Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon ( Salmo salar). Epigenetics 2024; 19:2392049. [PMID: 39151124 PMCID: PMC11332636 DOI: 10.1080/15592294.2024.2392049] [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: 03/08/2024] [Revised: 07/23/2024] [Accepted: 08/06/2024] [Indexed: 08/18/2024] Open
Abstract
The canonical view of DNA methylation, a pivotal epigenetic regulation mechanism in eukaryotes, dictates its role as a suppressor of gene activity, particularly within promoter regions. However, this view is being challenged as it is becoming increasingly evident that the connection between DNA methylation and gene expression varies depending on the genomic location and is therefore more complex than initially thought. We examined DNA methylation levels in the gut epithelium of Atlantic salmon (Salmo salar) using whole-genome bisulfite sequencing, which we correlated with gene expression data from RNA sequencing of the same gut tissue sample (RNA-seq). Assuming epigenetic signals might be pronounced between distinctive phenotypes, we compared large and small fish, finding 22 significant associations between 22 differentially methylated regions and 21 genes. We did not detect significant methylation differences between large and small fish. However, we observed a consistent signal of methylation levels around the transcription start sites (TSS), being negatively correlated with the expression levels of those genes. We found both negative and positive associations of methylation levels with gene expression further upstream or downstream of the TSS, revealing a more unpredictable pattern. The 21 genes showing significant methylation-expression correlations were involved in biological processes related to salmon health, such as growth and immune responses. Deciphering how DNA methylation affects the expression of such genes holds great potential for future applications. For instance, our results suggest the importance of genomic context in targeting epigenetic modifications to improve the welfare of aquaculture species like Atlantic salmon.
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Affiliation(s)
- Aikaterini Katirtzoglou
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren B. Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Terrestrial Biodiversity, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Morten T. Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Barchi A, Massimino L, Mandarino FV, Vespa E, Sinagra E, Almolla O, Passaretti S, Fasulo E, Parigi TL, Cagliani S, Spanò S, Ungaro F, Danese S. Microbiota profiling in esophageal diseases: Novel insights into molecular staining and clinical outcomes. Comput Struct Biotechnol J 2024; 23:626-637. [PMID: 38274997 PMCID: PMC10808859 DOI: 10.1016/j.csbj.2023.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024] Open
Abstract
Gut microbiota is recognized nowadays as one of the key players in the development of several gastro-intestinal diseases. The first studies focused mainly on healthy subjects with staining of main bacterial species via culture-based techniques. Subsequently, lots of studies tried to focus on principal esophageal disease enlarged the knowledge on esophageal microbial environment and its role in pathogenesis. Gastro Esophageal Reflux Disease (GERD), the most widespread esophageal condition, seems related to a certain degree of mucosal inflammation, via interleukin (IL) 8 potentially enhanced by bacterial components, lipopolysaccharide (LPS) above all. Gram- bacteria, producing LPS), such as Campylobacter genus, have been found associated with GERD. Barrett esophagus (BE) seems characterized by a Gram- and microaerophils-shaped microbiota. Esophageal cancer (EC) development leads to an overturn in the esophageal environment with the shift from an oral-like microbiome to a prevalently low-abundant and low-diverse Gram--shaped microbiome. Although underinvestigated, also changes in the esophageal microbiome are associated with rare chronic inflammatory or neuropathic disease pathogenesis. The paucity of knowledge about the microbiota-driven mechanisms in esophageal disease pathogenesis is mainly due to the scarce sensitivity of sequencing technology and culture methods applied so far to study commensals in the esophagus. However, the recent advances in molecular techniques, especially with the advent of non-culture-based genomic sequencing tools and the implementation of multi-omics approaches, have revolutionized the microbiome field, with promises of implementing the current knowledge, discovering more mechanisms underneath, and giving insights into the development of novel therapies aimed to re-establish the microbial equilibrium for ameliorating esophageal diseases..
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Affiliation(s)
- Alberto Barchi
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Luca Massimino
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Edoardo Vespa
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Emanuele Sinagra
- Gastroenterology & Endoscopy Unit, Fondazione Istituto G. Giglio, Cefalù, Italy
| | - Omar Almolla
- Università Vita-Salute San Raffaele, Faculty of Medicine, Milan, Italy
| | - Sandro Passaretti
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ernesto Fasulo
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Tommaso Lorenzo Parigi
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Faculty of Medicine, Milan, Italy
| | - Stefania Cagliani
- Università Vita-Salute San Raffaele, Faculty of Medicine, Milan, Italy
| | - Salvatore Spanò
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Federica Ungaro
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Silvio Danese
- Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Faculty of Medicine, Milan, Italy
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42
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Yi L, Guo X, Liu Y, Jirimutu, Wang Z. Single-cell 5' RNA sequencing of camelid peripheral B cells provides insights into cellular basis of heavy-chain antibody production. Comput Struct Biotechnol J 2024; 23:1705-1714. [PMID: 38689719 PMCID: PMC11059136 DOI: 10.1016/j.csbj.2024.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Camelids produce both conventional tetrameric antibodies (Abs) and dimeric heavy-chain antibodies (HCAbs). Although B cells that generate these two types of Abs exhibit distinct B cell receptors (BCRs), whether these two B cell populations differ in their phenotypes and developmental processes remains unclear. Here, we performed single-cell 5' RNA profiling of peripheral blood mononuclear cell samples from Bactrian camels before and after immunization. We characterized the functional subtypes and differentiation trajectories of circulating B cells in camels, and reconstructed single-cell BCR sequences. We found that in contrast to humans, the proportion of T-bet+ B cells was high among camelid peripheral B cells. Several marker genes of human B cell subtypes, including CD27 and IGHD, were expressed at low levels in the corresponding camel B cell subtypes. Camelid B cells expressing variable genes of HACbs (VHH) were widely present in various functional subtypes and showed highly overlapping differentiation trajectories with B cells expressing variable genes of conventional Abs (VH). After immunization, the transcriptional changes in VHH+ and VH+ B cells were largely consistent. Through structure modeling, we identified a variety of scaffold types among the reconstructed VHH sequences. Our study provides insights into the cellular context of HCAb production in camels and lays the foundation for developing single-B cell-based camelid single-domain Ab screening.
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Affiliation(s)
- Li Yi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Xin Guo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuexing Liu
- Guangzhou Laboratory, Guangzhou 510005, China
| | - Jirimutu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
- Inner Mongolia China-Kazakhstan Camel Research Institute, Alxa 750306, China
| | - Zhen Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Liu X, Li J, Zhu L, Huang J, Zhang Q, Wang J, Xie J, Dong Q, Zou Z, Huang G, Gu Q, Wang J, Li J. Mechanistic insights into zinc oxide nanoparticles induced embryotoxicity via H3K9me3 modulation. Biomaterials 2024; 311:122679. [PMID: 38943823 DOI: 10.1016/j.biomaterials.2024.122679] [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: 02/08/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
The widespread application of nanoparticles (NPs) in various fields has raised health concerns, especially in reproductive health. Our research has shown zinc oxide nanoparticles (ZnONPs) exhibit the most significant toxicity to pre-implantation embryos in mice compared to other common NPs. In patients undergoing assisted reproduction technology (ART), a significant negative correlation was observed between Zn concentration and clinical outcomes. Therefore, this study explores the impact of ZnONPs exposure on pre-implantation embryonic development and its underlying mechanisms. We revealed that both in vivo and in vitro exposure to ZnONPs impairs pre-implantation embryonic development. Moreover, ZnONPs were found to reduce the pluripotency of mouse embryonic stem cells (mESCs), as evidenced by teratoma and diploid chimera assays. Employing multi-omics approaches, including RNA-Seq, CUT&Tag, and ATAC-seq, the embryotoxicity mechanisms of ZnONPs were elucidated. The findings indicate that ZnONPs elevate H3K9me3 levels, leading to increased heterochromatin and consequent inhibition of gene expression related to development and pluripotency. Notably, Chaetocin, a H3K9me3 inhibitor, sucessfully reversed the embryotoxicity effects induced by ZnONPs. Additionally, the direct interaction between ZnONPs and H3K9me3 was verified through pull-down and immunoprecipitation assays. Collectively, these findings offer new insights into the epigenetic mechanisms of ZnONPs toxicity, enhancing our understanding of their impact on human reproductive health.
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Affiliation(s)
- Xuemei Liu
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jie Li
- Molecular Biology Laboratory of Respiratory Disease, Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Ling Zhu
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jiayu Huang
- Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qi Zhang
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jianwu Wang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Juan Xie
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Qiang Dong
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Zhen Zou
- Molecular Biology Laboratory of Respiratory Disease, Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Guoning Huang
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China.
| | - Qi Gu
- State Key Laboratory of Membrane Biology and the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Jianyu Wang
- Molecular Biology Laboratory of Respiratory Disease, Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China.
| | - Jingyu Li
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China.
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Migliaccio G, Morikka J, Del Giudice G, Vaani M, Möbus L, Serra A, Federico A, Greco D. Methylation and transcriptomic profiling reveals short term and long term regulatory responses in polarized macrophages. Comput Struct Biotechnol J 2024; 25:143-152. [PMID: 39257962 PMCID: PMC11385784 DOI: 10.1016/j.csbj.2024.08.018] [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: 06/20/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 09/12/2024] Open
Abstract
Macrophage plasticity allows the adoption of distinct functional states in response to environmental cues. While unique transcriptomic profiles define these states, focusing solely on transcription neglects potential long-term effects. The investigation of epigenetic changes can be used to understand how temporary stimuli can result in lasting effects. Epigenetic alterations play an important role in the pathophysiology of macrophages, including their trained innate immunity, enabling faster and more efficient inflammatory responses upon subsequent encounters to the same pathogen or insult. In this study, we used a multi-omics approach to elucidate the interplay between gene expression and DNA-methylation, to explore the potential long-term effects of diverse polarizing environments on macrophage activity. We identified a common core set of genes that are differentially methylated regardless of exposure type, indicating a potential common fundamental mechanism for adaptation to various stimuli. Functional analysis revealed that processes requiring rapid responses displayed transcriptomic regulation, whereas functions critical for long-term adaptations exhibited co-regulation at both transcriptomic and epigenetic levels. Our study uncovers a novel set of genes linked to the long-term effects of macrophage polarization. This discovery underscores the potential of epigenetics in elucidating how macrophages establish long-term memory and influence health outcomes.
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Affiliation(s)
- Giorgia Migliaccio
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jack Morikka
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
| | - Giusy Del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Maaret Vaani
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lena Möbus
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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Jureckova K, Nykrynova M, Slaninova E, Fleuriot-Blitman H, Amstutz V, Hermankova K, Bezdicek M, Mrazova K, Hrubanova K, Zinn M, Obruca S, Sedlar K. Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum. Comput Struct Biotechnol J 2024; 23:2681-2694. [PMID: 39035834 PMCID: PMC11259993 DOI: 10.1016/j.csbj.2024.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/11/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024] Open
Abstract
Purple photosynthetic bacteria (PPB) are versatile microorganisms capable of producing various value-added chemicals, e.g., biopolymers and biofuels. They employ diverse metabolic pathways, allowing them to adapt to various growth conditions and even extreme environments. Thus, they are ideal organisms for the Next Generation Industrial Biotechnology concept of reducing the risk of contamination by using naturally robust extremophiles. Unfortunately, the potential of PPB for use in biotechnology is hampered by missing knowledge on regulations of their metabolism. Although Rhodospirillum rubrum represents a model purple bacterium studied for polyhydroxyalkanoate and hydrogen production, light/chemical energy conversion, and nitrogen fixation, little is known regarding the regulation of its metabolism at the transcriptomic level. Using RNA sequencing, we compared gene expression during the cultivation utilizing fructose and acetate as substrates in case of the wild-type strain R. rubrum DSM 467T and its knock-out mutant strain that is missing two polyhydroxyalkanoate synthases PhaC1 and PhaC2. During this first genome-wide expression study of R. rubrum, we were able to characterize cultivation-driven transcriptomic changes and to annotate non-coding elements as small RNAs.
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Affiliation(s)
- Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Marketa Nykrynova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Eva Slaninova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Hugo Fleuriot-Blitman
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland Valais-Wallis (HES-SO Valais-Wallis), Sion, Switzerland
| | - Véronique Amstutz
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland Valais-Wallis (HES-SO Valais-Wallis), Sion, Switzerland
| | - Kristyna Hermankova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Matej Bezdicek
- Department of Internal Medicine – Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine – Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Katerina Mrazova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Kamila Hrubanova
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Manfred Zinn
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland Valais-Wallis (HES-SO Valais-Wallis), Sion, Switzerland
| | - Stanislav Obruca
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
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Niu L, Wu X, Liu H, Hu X, Wang W. Leaf starch degradation by β-amylase ZmBAM8 influences drought tolerance in maize. Carbohydr Polym 2024; 345:122555. [PMID: 39227118 DOI: 10.1016/j.carbpol.2024.122555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/20/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024]
Abstract
As a typical C4 plant and important crop worldwide, maize is susceptible to drought. In maize, transitory starch (TS) turnover occurs in the vascular bundle sheath of leaves, differing from that in Arabidopsis (a C3 plant). This process, particularly its role in drought tolerance and the key starch-hydrolyzing enzymes involved, is not fully understood. We discovered that the expression of the β-amylase (BAM) gene ZmBAM8 is highly upregulated in the drought-tolerant inbred line Chang7-2t. Inspired by this finding, we systematically investigated TS degradation in maize lines, including Chang7-2t, Chang7-2, B104, and ZmBAM8 overexpression (OE) and knockout (KO) lines. We found that ZmBAM8 was significantly induced in the vascular bundle sheath by drought, osmotic stress, and abscisic acid. The stress-induced gene expression and chloroplast localization of ZmBAM8 align with the tissue and subcellular sites where TS turnover occurs. The recombinant ZmBAM8 was capable of effectively hydrolyzing leaf starch. Under drought conditions, the leaf starch in ZmBAM8-OE plants substantially decreased under light, while that in ZmBAM8-KO plants did not decrease. Compared with ZmBAM8-KO plants, ZmBAM8-OE plants exhibited increased drought tolerance. Our study provides insights into the significance of leaf starch degradation in C4 crops and contributes to the development of drought-resistant maize.
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Affiliation(s)
- Liangjie Niu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaolin Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Hui Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China.
| | - Xiuli Hu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Wei Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China.
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Zhao J, Pu D, Li Z, Zhang Y, Liu X, Zhuo X, Lu B, Cao B. Loss and gain of ceftazidime-avibactam susceptibility in a non-carbapenemase-producing K1-ST23 hypervirulent Klebsiella pneumoniae. Virulence 2024; 15:2348251. [PMID: 38697754 PMCID: PMC11067985 DOI: 10.1080/21505594.2024.2348251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
OBJECTIVES This study aimed at revealing the underlying mechanisms of the loss and gain of ceftazidime-avibactam susceptibility in a non-carbapenemase-producing hypervirulent Klebsiella pneumoniae (hvKp). METHODS Here we longitudinally recovered 3 non-carbapenemase-producing K1-ST23 hvKp strains at a one-month interval (KP29105, KP29499 and KP30086) from an elderly male. Antimicrobial susceptibility testing, whole genome sequencing, transcriptomic sequencing, gene cloning, plasmid conjugation, quantitative real-time PCR (qRT-PCR), and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) were conducted. RESULTS Among the 3 hvKp strains, KP29105 was resistant to the third- and fourth-generation cephalosporins, KP29499 acquired resistance to both ceftazidime-avibactam and carbapenems, while KP30086 restored its susceptibility to ceftazidime-avibactam, imipenem and meropenem but retained low-level resistance to ertapenem. KP29105 and KP29499 carried plasmid-encoded genes blaCTX-M-15 and blaCTX-M-71, respectively, but KP30086 lost both. Cloning of gene blaCTX-M-71 and conjugation experiment of blaCTX-M-71-carrying plasmid showed that the transformant and transconjugant were susceptible to ceftazidime-avibactam but had a more than 8-fold increase in MICs. Supplementation with an outer membrane permeabilizer could reduce the MIC of ceftazidime-avibactam by 32 folds, indicating that porins play a key role in ceftazidime-avibactam resistance. The OmpK35 of the 3 isolates was not expressed, and the OmpK36 of KP29499 and KP30086 had a novel amino acid substitution (L359R). SDS-PAGE and qRT-PCR showed that the expression of porin OmpK36 of KP29499 and KP30086 was significantly down-regulated compared with KP29105. CONCLUSIONS In summary, we reported the rare ceftazidime-avibactam resistance in a non-carbapenemase-producing hvKp strain. Resistance plasmid carrying blaCTX-M-71 and mutated OmpK36 had a synergetic effect on the resistance.
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Affiliation(s)
- Jiankang Zhao
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Danni Pu
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ziyao Li
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Yulin Zhang
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xinmeng Liu
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xianxia Zhuo
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Department of Respiratory Medicine, Capital Medical University, Beijing, China
| | - Binghuai Lu
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Cao
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Department of Respiratory Medicine, Capital Medical University, Beijing, China
- Tsinghua University-Peaking University Joint Center for Life Sciences, Beijing, China
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48
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Fang X, Shen J, Zhang L, Zou X, Jin L. Metabolomic and transcriptomic integration reveals the mechanism of aroma formation as strawberries naturally turn colors while ripening. Food Chem 2024; 460:140765. [PMID: 39121779 DOI: 10.1016/j.foodchem.2024.140765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/30/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
Aroma is an important indicator of fruit flavor, but mechanisms of aroma formation in strawberries (Fragaria spp.) during natural ripening are still not clear. In this study, aroma compounds in strawberry cultivars were analyzed using gas chromatography-mass spectrometry (GC-MS). Richly creamy strawberry cultivars in particular expressed high levels of vanillin acetate and coumarin (up-regulated by 12.6- and 9.8-fold, respectively), while the aroma-free cultivars were dominated by differential changes in terpenes and alcohols. Further research using liquid chromatography-mass spectrometry (LC-MS) and RNA-Seq indicated that the activation of the phenylpropanoid biosynthesis and alpha-linolenic acid metabolic pathways constituted the key to formation of aroma compounds in creamy strawberry cultivars. The results of this study not only provide a well-defined database to detect aroma compounds in different strawberry cultivars but also explore the underlying mechanisms of creamy aroma formation in strawberries.
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Affiliation(s)
- Xianping Fang
- Institute of Forestry and Pomology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Jiansheng Shen
- Jinhua Academy of Agricultural Sciences, Jinhua, 321017, China
| | - Liqing Zhang
- Institute of Forestry and Pomology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xiaohua Zou
- Institute of Forestry and Pomology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Liang Jin
- Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China.
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Krappinger JC, Aguilar Gomez CM, Hoenikl A, Schusterbauer V, Hatzl AM, Feichtinger J, Glieder A. dMAD7 is a promising tool for targeted gene regulation in the methylotrophic yeast Komagataella phaffii. N Biotechnol 2024; 83:110-120. [PMID: 38960022 DOI: 10.1016/j.nbt.2024.06.008] [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: 03/27/2024] [Revised: 06/07/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
The methylotrophic yeast Komagataella phaffii is a popular host system for the pharmaceutical and biotechnological production of recombinant proteins. CRISPR-Cas9 and its derivative CRISPR interference (CRISPRi) offer a promising avenue to further enhance and exploit the full capabilities of this host. MAD7 and its catalytically inactive variant "dead" MAD7 (dMAD7) represent an interesting alternative to established CRISPR-Cas9 systems and are free to use for industrial and academic research. CRISPRi utilizing dMAD7 does not introduce double-strand breaks but only binds to the DNA to regulate gene expression. Here, we report the first use of dMAD7 in K. phaffii to regulate the expression of the enhanced green fluorescent protein (eGFP). A reduction of eGFP fluorescence level (up to 88 %) was achieved in random integration experiments using dMAD7 plasmids. Integration loci/events of investigated strains were assessed through whole genome sequencing. Additionally, RNA-sequencing experiments corroborated the whole genome sequencing results and showed a significantly reduced expression of eGFP in strains containing a dMAD7 plasmid, among others. Our findings conclusively demonstrate the utility of dMAD7 in K. phaffii through successfully regulating eGFP expression.
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Affiliation(s)
- Julian C Krappinger
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Carla M Aguilar Gomez
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Andrea Hoenikl
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Anna-Maria Hatzl
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Julia Feichtinger
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria.
| | - Anton Glieder
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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50
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Han L, Yan J, Li T, Shen P, Ba X, Lin W, Zhang R, Yang Y, Li Y, Li C, Huang Y, Qin K, Liu Y, Huang H, Zou L, Wang Y, Chen Z, Huang Y, Tu S. Wutou decoction alleviates arthritis inflammation in CIA mice by regulating Treg cell stability and Treg/Th17 balance via the JAK2/STAT3 pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 334:118463. [PMID: 38908493 DOI: 10.1016/j.jep.2024.118463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/04/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Wutou Decoction (WTD) is a classic traditional Chinese medicine formula, which has shown clinical efficacy in treating rheumatoid arthritis (RA). The Treg stability and Th17/Treg imbalance is an important immunological mechanism in RA progression. Whether WTD regulates CD4+ T cell subsets has not been thoroughly investigated yet. AIM OF THE STUDY This study aimed to explore the potential role and mechanisms of WTD in regulating the diminished stability of Treg cells and the imbalance of CD4+ T cell subsets via in vivo and in vitro experiments. MATERIALS AND METHODS Firstly, the therapeutic effects of WTD on the collagen-induced arthritis (CIA) mouse and its potential regulatory function on CD4+ T cell subsets were evaluated in vivo. Animal specimens were collected after 31 days of treatment with WTD. The anti-arthritic and anti-inflammatory effects of WTD were assessed through arthritis scoring, body weight, spleen index, serum IL-6 levels, and micro-PET/CT imaging. Gene enrichment analysis was performed to evaluate the activation T cell-related signaling pathway. Flow cytometry was used to determine the proportions of CD4+ T cell subsets in vitro and in vitro. Additionally, ELISA was used to assess the secretion of IL-10 and TGF-β by Treg cells under inflammatory conditions. The suppressive function of Treg cells on cell proliferation under inflammatory conditions was examined using CFSE labeling. Immunofluorescence staining was performed to detect the phosphorylation levels of STAT3 in CD4+ T cells from mouse spleen tissues. Western blotting was used to evaluate the phosphorylation levels of JAK2/STAT3 in Treg cells. RESULTS WTD significantly alleviated joint inflammation in CIA mice. WTD reduced serum IL-6 levels in CIA mice, improved their body weight and spleen index. WTD treatment inhibited the activation of CD4+ T cell subgroup-related signaling in the joint tissues of CIA mice. In vitro and in vitro experiments showed that WTD increased the proportion of Treg cells and decreased the proportion of Th17 cells in CIA mice spleen. Furthermore, WTD promoted the secretion of IL-10 and TGF-β by Treg cells and enhanced the inhibitory capacity of Treg cells on cell proliferation under inflammatory conditions. Immunofluorescence detected decreased STAT3 phosphorylation levels in CD4+ T cells from CIA mice spleen, while western blotting revealed a decrease in JAK2/STAT3 phosphorylation levels in Treg cells in vitro. CONCLUSIONS Inhibiting JAK2/STAT3 phosphorylation is a potential mechanism through which WTD improves Treg cell stability, balances CD4+ T cell subsets, and attenuates RA joint inflammation.
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Affiliation(s)
- Liang Han
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahui Yan
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Li
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pan Shen
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Ba
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weiji Lin
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruiyuan Zhang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuyao Yang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yifei Li
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chennan Li
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Huang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Qin
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yafei Liu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hua Huang
- Department of Rheumatology, Jingmen People's Hospital, Jingmen, Hubei, China
| | - Liang Zou
- Department of Rheumatology, Jingmen People's Hospital, Jingmen, Hubei, China
| | - Yu Wang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhe Chen
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yao Huang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Shenghao Tu
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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