1
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Nano M, Montell DJ. Apoptotic signaling: Beyond cell death. Semin Cell Dev Biol 2024; 156:22-34. [PMID: 37988794 DOI: 10.1016/j.semcdb.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023]
Abstract
Apoptosis is the best described form of regulated cell death, and was, until relatively recently, considered irreversible once particular biochemical points-of-no-return were activated. In this manuscript, we examine the mechanisms cells use to escape from a self-amplifying death signaling module. We discuss the role of feedback, dynamics, propagation, and noise in apoptotic signaling. We conclude with a revised model for the role of apoptosis in animal development, homeostasis, and disease.
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Affiliation(s)
- Maddalena Nano
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
| | - Denise J Montell
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
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2
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Di Tommaso E, Giunta S. Dynamic interplay between human alpha-satellite DNA structure and centromere functions. Semin Cell Dev Biol 2024; 156:130-140. [PMID: 37926668 DOI: 10.1016/j.semcdb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
Maintenance of genome stability relies on functional centromeres for correct chromosome segregation and faithful inheritance of the genetic information. The human centromere is the primary constriction within mitotic chromosomes made up of repetitive alpha-satellite DNA hierarchically organized in megabase-long arrays of near-identical higher order repeats (HORs). Centromeres are epigenetically specified by the presence of the centromere-specific histone H3 variant, CENP-A, which enables the assembly of the kinetochore for microtubule attachment. Notably, centromeric DNA is faithfully inherited as intact haplotypes from the parents to the offspring without intervening recombination, yet, outside of meiosis, centromeres are akin to common fragile sites (CFSs), manifesting crossing-overs and ongoing sequence instability. Consequences of DNA changes within the centromere are just starting to emerge, with unclear effects on intra- and inter-generational inheritance driven by centromere's essential role in kinetochore assembly. Here, we review evidence of meiotic selection operating to mitigate centromere drive, as well as recent reports on centromere damage, recombination and repair during the mitotic cell division. We propose an antagonistic pleiotropy interpretation to reconcile centromere DNA instability as both driver of aneuploidy that underlies degenerative diseases, while also potentially necessary for the maintenance of homogenized HORs for centromere function. We attempt to provide a framework for this conceptual leap taking into consideration the structural interface of centromere-kinetochore interaction and present case scenarios for its malfunctioning. Finally, we offer an integrated working model to connect DNA instability, chromatin, and structural changes with functional consequences on chromosome integrity.
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Affiliation(s)
- Elena Di Tommaso
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy.
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3
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Cumming T, Levayer R. Toward a predictive understanding of epithelial cell death. Semin Cell Dev Biol 2024; 156:44-57. [PMID: 37400292 DOI: 10.1016/j.semcdb.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
Epithelial cell death is highly prevalent during development and tissue homeostasis. While we have a rather good understanding of the molecular regulators of programmed cell death, especially for apoptosis, we still fail to predict when, where, how many and which specific cells will die in a tissue. This likely relies on the much more complex picture of apoptosis regulation in a tissular and epithelial context, which entails cell autonomous but also non-cell autonomous factors, diverse feedback and multiple layers of regulation of the commitment to apoptosis. In this review, we illustrate this complexity of epithelial apoptosis regulation by describing these different layers of control, all demonstrating that local cell death probability is a complex emerging feature. We first focus on non-cell autonomous factors that can locally modulate the rate of cell death, including cell competition, mechanical input and geometry as well as systemic effects. We then describe the multiple feedback mechanisms generated by cell death itself. We also outline the multiple layers of regulation of epithelial cell death, including the coordination of extrusion and regulation occurring downstream of effector caspases. Eventually, we propose a roadmap to reach a more predictive understanding of cell death regulation in an epithelial context.
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Affiliation(s)
- Tom Cumming
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr. Roux, 75015 Paris, France; Sorbonne Université, Collège Doctoral, F75005 Paris, France
| | - Romain Levayer
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr. Roux, 75015 Paris, France.
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4
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Sun G. Death and survival from executioner caspase activation. Semin Cell Dev Biol 2024; 156:66-73. [PMID: 37468421 DOI: 10.1016/j.semcdb.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Executioner caspases are evolutionarily conserved regulators of cell death under apoptotic stress. Activated executioner caspases drive apoptotic cell death through cleavage of diverse protein substrates or pyroptotic cell death in the presence of gasdermin E. On the other hand, activation of executioner caspases can also trigger pro-survival and pro-proliferation signals. In recent years, a growing body of studies have demonstrated that cells can survive from executioner caspase activation in response to stress and that the survivors undergo molecular and phenotypic alterations. This review focuses on death and survival from executioner caspase activation, summarizing the role of executioner caspases in apoptotic and pyroptotic cell death and discussing the potential mechanism and consequences of survival from stress-induced executioner caspase activation.
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Affiliation(s)
- Gongping Sun
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Histology and Embryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
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5
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Hudson EP. The Calvin Benson cycle in bacteria: New insights from systems biology. Semin Cell Dev Biol 2024; 155:71-83. [PMID: 37002131 DOI: 10.1016/j.semcdb.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
The Calvin Benson cycle in phototrophic and chemolithoautotrophic bacteria has ecological and biotechnological importance, which has motivated study of its regulation. I review recent advances in our understanding of how the Calvin Benson cycle is regulated in bacteria and the technologies used to elucidate regulation and modify it, and highlight differences between and photoautotrophic and chemolithoautotrophic models. Systems biology studies have shown that in oxygenic phototrophic bacteria, Calvin Benson cycle enzymes are extensively regulated at post-transcriptional and post-translational levels, with multiple enzyme activities connected to cellular redox status through thioredoxin. In chemolithoautotrophic bacteria, regulation is primarily at the transcriptional level, with effector metabolites transducing cell status, though new methods should now allow facile, proteome-wide exploration of biochemical regulation in these models. A biotechnological objective is to enhance CO2 fixation in the cycle and partition that carbon to a product of interest. Flux control of CO2 fixation is distributed over multiple enzymes, and attempts to modulate gene Calvin cycle gene expression show a robust homeostatic regulation of growth rate, though the synthesis rates of products can be significantly increased. Therefore, de-regulation of cycle enzymes through protein engineering may be necessary to increase fluxes. Non-canonical Calvin Benson cycles, if implemented with synthetic biology, could have reduced energy demand and enzyme loading, thus increasing the attractiveness of these bacteria for industrial applications.
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Affiliation(s)
- Elton P Hudson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
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6
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Zhu XG, Treves H, Zhao H. Mechanisms controlling metabolite concentrations of the Calvin Benson Cycle. Semin Cell Dev Biol 2024; 155:3-9. [PMID: 36858897 DOI: 10.1016/j.semcdb.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/28/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023]
Abstract
Maintaining proper metabolite levels in a complex metabolic network is crucial for maintaining a high flux through the network. In this paper, we discuss major regulatory mechanisms over the Calvin Benson Cycle (CBC) with regard to their roles in conferring homeostasis of metabolite levels in CBC. These include: 1) Redox regulation of enzymes in the CBC on one hand ensures that metabolite levels stay above certain lower bounds under low light while on the other hand increases the flux through the CBC under high light. 2) Metabolite regulations, especially allosteric regulations of major regulatory enzymes, ensure the rapid up-regulation of fluxes to ensure sufficient amount of triose phosphate is available for end product synthesis and concurrently avoid phosphate limitation. 3) A balanced activities of enzymes in the CBC help maintain balanced flux through CBC; some innate product feedback mechanisms, in particular the ADP feedback regulation of GAPDH and F6P feedback regulation of FBPase, exist in CBC to achieve such a balanced enzyme activities and hence flux distribution in the CBC for greater photosynthetic efficiency. Transcriptional regulation and natural variations of enzymes controlling CBC metabolite homeostasis should be further explored to maximize the potential of engineering CBC for greater efficiency.
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Affiliation(s)
- Xin-Guang Zhu
- Center of Excellence for Molecular Plant Sciences, Chinese Academy of Science, Shanghai 200032, China.
| | - Haim Treves
- School of Plant Sciences and Food Security, Tel-Aviv University, 6997801, Israel
| | - Honglong Zhao
- Center of Excellence for Molecular Plant Sciences, Chinese Academy of Science, Shanghai 200032, China
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7
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Lin A, Ramaswamy Y, Misra A. Developmental heterogeneity of vascular cells: Insights into cellular plasticity in atherosclerosis? Semin Cell Dev Biol 2024; 155:3-15. [PMID: 37316416 DOI: 10.1016/j.semcdb.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023]
Abstract
Smooth muscle cells, endothelial cells and macrophages display remarkable heterogeneity within the healthy vasculature and under pathological conditions. During development, these cells arise from numerous embryological origins, which confound with different microenvironments to generate postnatal vascular cell diversity. In the atherosclerotic plaque milieu, all these cell types exhibit astonishing plasticity, generating a variety of plaque burdening or plaque stabilizing phenotypes. And yet how developmental origin influences intraplaque cell plasticity remains largely unexplored despite evidence suggesting this may be the case. Uncovering the diversity and plasticity of vascular cells is being revolutionized by unbiased single cell whole transcriptome analysis techniques that will likely continue to pave the way for therapeutic research. Cellular plasticity is only just emerging as a target for future therapeutics, and uncovering how intraplaque plasticity differs across vascular beds may provide key insights into why different plaques behave differently and may confer different risks of subsequent cardiovascular events.
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Affiliation(s)
- Alexander Lin
- Atherosclerosis and Vascular Remodeling Group, Heart Research Institute, Sydney, NSW, Australia; School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia
| | - Yogambha Ramaswamy
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia
| | - Ashish Misra
- Atherosclerosis and Vascular Remodeling Group, Heart Research Institute, Sydney, NSW, Australia; Heart Research Institute, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
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8
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Lee C, Maier W, Jiang YY, Nakano K, Lechtreck KF, Gaertig J. Global and local functions of the Fused kinase ortholog CdaH in intracellular patterning in Tetrahymena. J Cell Sci 2024; 137:jcs261256. [PMID: 37667859 PMCID: PMC10565251 DOI: 10.1242/jcs.261256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023] Open
Abstract
Ciliates assemble numerous microtubular structures into complex cortical patterns. During ciliate division, the pattern is duplicated by intracellular segmentation that produces a tandem of daughter cells. In Tetrahymena thermophila, the induction and positioning of the division boundary involves two mutually antagonistic factors: posterior CdaA (cyclin E) and anterior CdaI (Hippo kinase). Here, we characterized the related cdaH-1 allele, which confers a pleiotropic patterning phenotype including an absence of the division boundary and an anterior-posterior mispositioning of the new oral apparatus. CdaH is a Fused or Stk36 kinase ortholog that localizes to multiple sites that correlate with the effects of its loss, including the division boundary and the new oral apparatus. CdaH acts downstream of CdaA to induce the division boundary and drives asymmetric cytokinesis at the tip of the posterior daughter. CdaH both maintains the anterior-posterior position of the new oral apparatus and interacts with CdaI to pattern ciliary rows within the oral apparatus. Thus, CdaH acts at multiple scales, from induction and positioning of structures on the cell-wide polarity axis to local organelle-level patterning.
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Affiliation(s)
- Chinkyu Lee
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wolfgang Maier
- Bioinformatics, University of Freiburg, 79110 Freiburg, Germany
| | - Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Kentaro Nakano
- Degree Programs in Biology, Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Karl F. Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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9
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Kotagama K, McJunkin K. Recent advances in understanding microRNA function and regulation in C. elegans. Semin Cell Dev Biol 2024; 154:4-13. [PMID: 37055330 PMCID: PMC10564972 DOI: 10.1016/j.semcdb.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/15/2023]
Abstract
MicroRNAs (miRNAs) were first discovered in C. elegans as essential post-transcriptional regulators of gene expression. Since their initial discovery, miRNAs have been implicated in numerous areas of physiology and disease in all animals examined. In recent years, the C. elegans model continues to contribute important advances to all areas of miRNA research. Technological advances in tissue-specific miRNA profiling and genome editing have driven breakthroughs in understanding biological functions of miRNAs, mechanism of miRNA action, and regulation of miRNAs. In this review, we highlight these new C. elegans findings from the past five to seven years.
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Affiliation(s)
- Kasuen Kotagama
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20892, USA
| | - Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20892, USA.
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10
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Mao Y, Qian SB. Making sense of mRNA translational "noise". Semin Cell Dev Biol 2024; 154:114-122. [PMID: 36925447 PMCID: PMC10500040 DOI: 10.1016/j.semcdb.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023]
Abstract
The importance of translation fidelity has been apparent since the discovery of genetic code. It is commonly believed that translation deviating from the main coding region is to be avoided at all times inside cells. However, ribosome profiling and mass spectrometry have revealed pervasive noncanonical translation. Both the scope and origin of translational "noise" are just beginning to be appreciated. Although largely overlooked, those translational "noises" are associated with a wide range of cellular functions, such as producing unannotated protein products. Furthermore, the dynamic nature of translational "noise" is responsive to stress conditions, highlighting the beneficial effect of translational "noise" in stress adaptation. Mechanistic investigation of translational "noise" will provide better insight into the mechanisms of translational regulation. Ultimately, they are not "noise" at all but represent a signature of cellular activities under pathophysiological conditions. Deciphering translational "noise" holds the therapeutic and diagnostic potential in a wide spectrum of human diseases.
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Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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11
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Smith TJ, Giles RN, Koutmou KS. Anticodon stem-loop tRNA modifications influence codon decoding and frame maintenance during translation. Semin Cell Dev Biol 2024; 154:105-113. [PMID: 37385829 DOI: 10.1016/j.semcdb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023]
Abstract
RNAs are central to protein synthesis, with ribosomal RNA, transfer RNAs and messenger RNAs comprising the core components of the translation machinery. In addition to the four canonical bases (uracil, cytosine, adenine, and guanine) these RNAs contain an array of enzymatically incorporated chemical modifications. Transfer RNAs (tRNAs) are responsible for ferrying amino acids to the ribosome, and are among the most abundant and highly modified RNAs in the cell across all domains of life. On average, tRNA molecules contain 13 post-transcriptionally modified nucleosides that stabilize their structure and enhance function. There is an extensive chemical diversity of tRNA modifications, with over 90 distinct varieties of modifications reported within tRNA sequences. Some modifications are crucial for tRNAs to adopt their L-shaped tertiary structure, while others promote tRNA interactions with components of the protein synthesis machinery. In particular, modifications in the anticodon stem-loop (ASL), located near the site of tRNA:mRNA interaction, can play key roles in ensuring protein homeostasis and accurate translation. There is an abundance of evidence indicating the importance of ASL modifications for cellular health, and in vitro biochemical and biophysical studies suggest that individual ASL modifications can differentially influence discrete steps in the translation pathway. This review examines the molecular level consequences of tRNA ASL modifications in mRNA codon recognition and reading frame maintenance to ensure the rapid and accurate translation of proteins.
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Affiliation(s)
- Tyler J Smith
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA
| | - Rachel N Giles
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA
| | - Kristin S Koutmou
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA.
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12
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Liu S, Loo YT, Zhang Y, Ng K. Electrospray alginate microgels co-encapsulating degraded Konjac glucomannan and quercetin modulate human gut microbiota in vitro. Food Chem 2024; 434:137508. [PMID: 37738812 DOI: 10.1016/j.foodchem.2023.137508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023]
Abstract
Alginate microgels co-encapsulating degraded Konjac glucomannan (KGM60) underwent in vitro fecal fermentation and their effects on human microbiota and metabolites were investigated. KGM60 delayed quercetin release and enhanced phenolic metabolites production. Microgels co-encapsulating KGM60 and quercetin increased linear short chain fatty acid but decreased branched chain fatty acid production. Microgels encapsulated with quercetin with or without KGM60 decreased Firmicutes while increased Bacteroidetes over 24 h of fermentation, at genus level promoted Bacteroides growth at 24 h and decreased the abundance of Negativibacillus, Ruminococcus_NK4A214, and Christensenellaceae R_7. Faecalibacterium and Collinsella levels were exclusively promoted by microgels encapsulating KGM60 with or without quercetin, highlighting prebiotic effect of KGM60. Only microgels co-encapsulating both KGM60 and quercetin enhanced Dialister while inhibited Lachnoclostridium, indicating synergism between KGM60 and quercetin. Our study indicates that co-encapsulating KGM60 and quercetin in alginate microgel is effective in modulating human gut microbiota and metabolites production potentially beneficial to gut health.
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Affiliation(s)
- Siyao Liu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Yit Tao Loo
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Yianna Zhang
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ken Ng
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia.
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13
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Yang M, Du D, Zhu F, Qin H. Metabolic network and proteomic expression perturbed by cyclosporine A to model microbe Escherichia coli. J Hazard Mater 2024; 464:132975. [PMID: 38044020 DOI: 10.1016/j.jhazmat.2023.132975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023]
Abstract
Cyclosporine A (CsA) is a model drug that has caused great concern due to its widespread use and abuse in the environment. However, the potential harm of CsA to organisms also remains largely unknown, and this issue is exceptionally important for the health risk assessment of antibiotics. To address this concern, the crosstalk between CsA stress and cellular metabolism at the proteomic level in Escherichia coli was investigated and dissected in this study. The results showed that CsA inhibited E. coli growth in a time-dependent manner. CsA induced reactive oxygen species (ROS) overproduction in a dose- and time-dependent manner, leading to membrane depolarization followed by cell apoptosis. In addition, translation, the citric acid cycle, amino acid biosynthesis, glycolysis and responses to oxidative stress and heat were the central metabolic pathways induced by CsA stress. The upregulated proteins, including PotD, PotF and PotG, controlled cell growth. The downregulated proteins, including SspA, SspB, CstA and DpS, were regulators of self-feedback during the starvation process. And the up- and downregulated proteins, including AtpD, Adk, GroS, GroL and DnaK, controlled energy production. These results provide an important reference for the environmental health risk assessment of CsA.
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Affiliation(s)
- Meng Yang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Daolin Du
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Fang Zhu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Huaming Qin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
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14
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Lee SH, Jung EM. Adverse effects of early-life stress: focus on the rodent neuroendocrine system. Neural Regen Res 2024; 19:336-341. [PMID: 37488887 PMCID: PMC10503627 DOI: 10.4103/1673-5374.377587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/28/2023] [Accepted: 04/24/2023] [Indexed: 07/26/2023] Open
Abstract
Early-life stress is associated with a high prevalence of mental illnesses such as post-traumatic stress disorders, attention-deficit/hyperactivity disorder, schizophrenia, and anxiety or depressive behavior, which constitute major public health problems. In the early stages of brain development after birth, events such as synaptogenesis, neuron maturation, and glial differentiation occur in a highly orchestrated manner, and external stress can cause adverse long-term effects throughout life. Our body utilizes multifaceted mechanisms, including neuroendocrine and neurotransmitter signaling pathways, to appropriately process external stress. Newborn individuals first exposed to early-life stress deploy neurogenesis as a stress-defense mechanism; however, in adulthood, early-life stress induces apoptosis of mature neurons, activation of immune responses, and reduction of neurotrophic factors, leading to anxiety, depression, and cognitive and memory dysfunction. This process involves the hypothalamus-pituitary-adrenal axis and neurotransmitters secreted by the central nervous system, including norepinephrine, dopamine, and serotonin. The rodent early-life stress model is generally used to experimentally assess the effects of stress during neurodevelopment. This paper reviews the use of the early-life stress model and stress response mechanisms of the body and discusses the experimental results regarding how early-life stress mediates stress-related pathways at a high vulnerability of psychiatric disorder in adulthood.
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Affiliation(s)
- Seung Hyun Lee
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Eui-Man Jung
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
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15
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Gavriil M, Proietto M, Paczia N, Ginolhac A, Halder R, Valceschini E, Sauter T, Linster CL, Sinkkonen L. 2-Hydroxyglutarate modulates histone methylation at specific loci and alters gene expression via Rph1 inhibition. Life Sci Alliance 2024; 7:e202302333. [PMID: 38011998 PMCID: PMC10681907 DOI: 10.26508/lsa.202302333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023] Open
Abstract
2-Hydroxyglutarate (2-HG) is an oncometabolite that accumulates in certain cancers. Gain-of-function mutations in isocitrate dehydrogenase lead to 2-HG accumulation at the expense of alpha-ketoglutarate. Elevated 2-HG levels inhibit histone and DNA demethylases, causing chromatin structure and gene regulation changes with tumorigenic consequences. We investigated the effects of elevated 2-HG levels in Saccharomyces cerevisiae, a yeast devoid of DNA methylation and heterochromatin-associated histone methylation. Our results demonstrate genetic background-dependent gene expression changes and altered H3K4 and H3K36 methylation at specific loci. Analysis of histone demethylase deletion strains indicated that 2-HG inhibits Rph1 sufficiently to induce extensive gene expression changes. Rph1 is the yeast homolog of human KDM4 demethylases and, among the yeast histone demethylases, was the most sensitive to the inhibitory effect of 2-HG in vitro. Interestingly, Rph1 deficiency favors gene repression and leads to further down-regulation of already silenced genes marked by low H3K4 and H3K36 trimethylation, but abundant in H3K36 dimethylation. Our results provide novel insights into the genome-wide effects of 2-HG and highlight Rph1 as its preferential demethylase target.
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Affiliation(s)
- Marios Gavriil
- https://ror.org/036x5ad56 Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Marco Proietto
- https://ror.org/036x5ad56 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Nicole Paczia
- https://ror.org/036x5ad56 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Aurelien Ginolhac
- https://ror.org/036x5ad56 Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Rashi Halder
- https://ror.org/036x5ad56 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Elena Valceschini
- https://ror.org/036x5ad56 Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Thomas Sauter
- https://ror.org/036x5ad56 Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carole L Linster
- https://ror.org/036x5ad56 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Lasse Sinkkonen
- https://ror.org/036x5ad56 Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
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Fang Z, Huang T, Chai X, Zhan J, Zhu Q, Sun P, Zeng D, Liu C, Jiang B, He L, Zhou X, Liu M, Zhang X. Protein methylation characterization using NMR without isotopic labeling. Talanta 2024; 268:125289. [PMID: 37862753 DOI: 10.1016/j.talanta.2023.125289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/15/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023]
Abstract
Protein methylation is crucial in epigenetics, and targeting the involved methyltransferases shows great potential for therapeutic intervention with several inhibitors in clinical trials for oncology indications. Therefore, characterization of protein methylation is essential for understanding the methyltransferase function and discovering chemical inhibitors and antagonists. While NMR has been used to measure methylation rates, isotopic labeling of protein or methyl donors can be costly and cannot characterize demethylation of proteins extracted from natural sources. Our method employs a four-quantum filter 1H-13C experiment that selectively detects methyl groups, providing a simple way to characterize methylation and demethylation features of methyltransferases and demethylases, respectively, without requiring isotopic labeling. In our experiments, we successfully observed the methylation of H3 under lysate from various cells and tissues of mice with cancerous growth. The results revealed that H3 undergoes both mono- and dimethylation in all the tested lysates, but at varying rates and degrees. Significantly lower H3 methylation rates and levels were observed in both cervical tumor and breast tumor lysates compared with the corresponding cancerous cells and healthy cells lysates. These findings highlight the variability of histone H3 methylation patterns among healthy cells, cancerous cells, tumor tissues, and different tumor types, and suggest that this method has great potential in facilitating the development of effective interventions against these diseases. By characterizing the methylation features of suspected tumors or areas of concern, it provides valuable insights into the underlying mechanisms of cancer development and aids in identifying potential targets for therapeutic interventions.
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Affiliation(s)
- Zhongpei Fang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Huang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xin Chai
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhua Zhan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Qinjun Zhu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Peng Sun
- Philips Healthcare, Wuhan, 430071, China
| | - Danyun Zeng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caixiang Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; Optics Valley Laboratory, Wuhan, 430074, China
| | - Lichun He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; Optics Valley Laboratory, Wuhan, 430074, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; Optics Valley Laboratory, Wuhan, 430074, China.
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; Optics Valley Laboratory, Wuhan, 430074, China.
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Kocanova S, Raynal F, Goiffon I, Oksuz BA, Baú D, Kamgoué A, Cantaloube S, Zhan Y, Lajoie B, Marti-Renom MA, Dekker J, Bystricky K. Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells. Life Sci Alliance 2024; 7:e202302154. [PMID: 37989525 PMCID: PMC10663337 DOI: 10.26508/lsa.202302154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023] Open
Abstract
The genome is organized in functional compartments and structural domains at the sub-megabase scale. How within these domains interactions between numerous cis-acting enhancers and promoters regulate transcription remains an open question. Here, we determined chromatin folding and composition over several hundred kb around estrogen-responsive genes in human breast cancer cell lines after hormone stimulation. Modeling of 5C data at 1.8 kb resolution was combined with quantitative 3D analysis of multicolor FISH measurements at 100 nm resolution and integrated with ChIP-seq data on transcription factor binding and histone modifications. We found that rapid estradiol induction of the progesterone gene expression occurs in the context of preexisting, cell type-specific chromosomal architectures encompassing the 90 kb progesterone gene coding region and an enhancer-spiked 5' 300 kb upstream genomic region. In response to estradiol, interactions between estrogen receptor α (ERα) bound regulatory elements are reinforced. Whereas initial enhancer-gene contacts coincide with RNA Pol 2 binding and transcription initiation, sustained hormone stimulation promotes ERα accumulation creating a regulatory hub stimulating transcript synthesis. In addition to implications for estrogen receptor signaling, we uncover that preestablished chromatin architectures efficiently regulate gene expression upon stimulation without the need for de novo extensive rewiring of long-range chromatin interactions.
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Affiliation(s)
- Silvia Kocanova
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Flavien Raynal
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Isabelle Goiffon
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Betul Akgol Oksuz
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Davide Baú
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Alain Kamgoué
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Sylvain Cantaloube
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Ye Zhan
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Bryan Lajoie
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marc A Marti-Renom
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
- Genome Biology Program, Centre de Regulació Genòmica (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Job Dekker
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Kerstin Bystricky
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
- Institut Universitaire de France (IUF), Paris, France
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Bamgbose G, Tulin A. PARP-1 is a transcriptional rheostat of metabolic and bivalent genes during development. Life Sci Alliance 2024; 7:e202302369. [PMID: 38012002 PMCID: PMC10682175 DOI: 10.26508/lsa.202302369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
PARP-1 participates in various cellular processes, including gene regulation. In Drosophila, PARP-1 mutants undergo developmental arrest during larval-to-pupal transition. In this study, we investigated PARP-1 binding and its transcriptional regulatory role at this stage. Our findings revealed that PARP-1 binds and represses active metabolic genes, including glycolytic genes, whereas activating low-expression developmental genes, including a subset of "bivalent" genes in third-instar larvae. These bivalent promoters, characterized by dual enrichment of low H3K4me3 and high H3K27me3, a unimodal H3K4me1 enrichment at the transcription start site (conserved in C. elegans and zebrafish), H2Av depletion, and high accessibility, may persist throughout development. In PARP-1 mutant third-instar larvae, metabolic genes typically down-regulated during the larval-to-pupal transition in response to reduced energy needs were repressed by PARP-1. Simultaneously, developmental and bivalent genes typically active at this stage were activated by PARP-1. In addition, glucose and ATP levels were significantly reduced in PARP-1 mutants, suggesting an imbalance in metabolic regulation. We propose that PARP-1 is essential for maintaining the delicate balance between metabolic and developmental gene expression programs to ensure proper developmental progression.
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Affiliation(s)
- Gbolahan Bamgbose
- https://ror.org/04a5szx83 Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Alexei Tulin
- https://ror.org/04a5szx83 Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
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Xiao T, Cheng X, Zhi Y, Tian F, Wu A, Huang F, Tao L, Guo Z, Shen X. Ameliorative effect of Alangium chinense (Lour.) Harms on rheumatoid arthritis by reducing autophagy with targeting regulate JAK3-STAT3 and COX-2 pathways. J Ethnopharmacol 2024; 319:117133. [PMID: 37690476 DOI: 10.1016/j.jep.2023.117133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Alangium chinense has been used as traditional folk medicine for centuries to treat rheumatoid arthritis (RA) by Guizhou Miao nationality with remarkable clinical effect. But the mechanism of its anti-RA is not fully clarified. AIM OF THE STUDY To explore the effect and underlying mechanism of A. chinense against RA. MATERIAL AND METHODS RA rats were induced by CII/IFA, and oral administrated with or without ethyl acetate extracts of Alangium chinense (ACEE) and tripterygium glycosides (GTW). Then arthritis scores, inflammatory factors in serum and histological evaluation were evaluated to assess the degree of joints disease. Proteomics were conducted via LC-MS/MS to clarify the mechanism of ACEE preliminarily, and further examined by immunohistochemistry, immunofluorescence, western botting, and molecular docking. RESULTS ACEE decreased joints swelling, cell abscission and necrosis of joint tissues arthropathy of RA rats, and attenuated expression of TNF-α, IL-1β, IL-6, PGE2, TGF-β. Meanwhile, differentially expressed proteins in the ACEE treated groups were observed, which were involved in RA, spliceosome, cell adhesion molecules, phagosome and lysosome signaling pathways. Moreover, ACEE significantly ameliorated arthropathy, suppressed JAK-STAT pathway (JAK3, p-JAK3, STAT3, iNOS, RANKL), COX-2 pathway (COX-2, TNF-α, IL-6I, L-1β, 5-LOX), and autophagic signaling pathway (LC3-Ⅰ, LC3-Ⅱ, p62, mTOR). But it showed little effect on the expression of COX-1, JAK1, JAK2, TyK2. CONCLUSION It is the first evidence that A. chinense significantly ameliorates RA, and the underlying immune mechanism involves reducing autophagy with targeting regulate JAK3-STAT3 and COX-2 pathways.
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Affiliation(s)
- Ting Xiao
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550025, China; The Department of Pharmacology of Materia Medica (The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources (The Union Key Laboratory of Guiyang City-Guizhou Medical University), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China.
| | - Xingyan Cheng
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550025, China; The Department of Pharmacology of Materia Medica (The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources (The Union Key Laboratory of Guiyang City-Guizhou Medical University), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China.
| | - Yuan Zhi
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550025, China; The Department of Pharmacology of Materia Medica (The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources (The Union Key Laboratory of Guiyang City-Guizhou Medical University), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China.
| | - Fangfang Tian
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550025, China; The Department of Pharmacology of Materia Medica (The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources (The Union Key Laboratory of Guiyang City-Guizhou Medical University), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China.
| | - Ai Wu
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550025, China; The Department of Pharmacology of Materia Medica (The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources (The Union Key Laboratory of Guiyang City-Guizhou Medical University), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China.
| | - Feilong Huang
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550025, China; The Department of Pharmacology of Materia Medica (The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources (The Union Key Laboratory of Guiyang City-Guizhou Medical University), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China.
| | - Ling Tao
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550025, China; The Department of Pharmacology of Materia Medica (The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources (The Union Key Laboratory of Guiyang City-Guizhou Medical University), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China.
| | - Zhenghong Guo
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China.
| | - Xiangchun Shen
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550025, China; The Department of Pharmacology of Materia Medica (The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China; The Key Laboratory of Optimal Utilization of Natural Medicine Resources (The Union Key Laboratory of Guiyang City-Guizhou Medical University), School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550031, China.
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Beirute-Herrera J, López-Amo Calvo B, Edenhofer F, Esk C. The promise of genetic screens in human in vitro brain models. Biol Chem 2024; 405:13-24. [PMID: 37697643 DOI: 10.1515/hsz-2023-0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/21/2023] [Indexed: 09/13/2023]
Abstract
Advances of in vitro culture models have allowed unprecedented insights into human neurobiology. At the same time genetic screening has matured into a robust and accessible experimental strategy allowing for the simultaneous study of many genes in parallel. The combination of both technologies is a newly emerging tool for neuroscientists, opening the door to identifying causal cell- and tissue-specific developmental and disease mechanisms. However, with complex experimental genetic screening set-ups new challenges in data interpretation and experimental scope arise that require a deep understanding of the benefits and challenges of individual approaches. In this review, we summarize the literature that applies genetic screening to in vitro brain models, compare experimental strengths and weaknesses and point towards future directions of these promising approaches.
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Affiliation(s)
- Julianne Beirute-Herrera
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Beatriz López-Amo Calvo
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Frank Edenhofer
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Christopher Esk
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
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Li T, Xu B, Chen H, Shi Y, Li J, Yu M, Xia S, Wu S. Gut toxicity of polystyrene microplastics and polychlorinated biphenyls to Eisenia fetida: Single and co-exposure effects with a focus on links between gut bacteria and bacterial translocation stemming from gut barrier damage. Sci Total Environ 2024; 908:168254. [PMID: 37923278 DOI: 10.1016/j.scitotenv.2023.168254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] |