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Yang S, Xing J, Liu D, Song Y, Yu H, Xu S, Zuo Y. Review and new insights into the catalytic structural domains of the Fe(ll) and 2-Oxoglutarate families. Int J Biol Macromol 2024; 278:134798. [PMID: 39153678 DOI: 10.1016/j.ijbiomac.2024.134798] [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: 05/06/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Histone lysine demethylase (KDM), AlkB homolog (ALKBH), and Ten-Eleven Translocation (TET) proteins are members of the 2-Oxoglutarate (2OG) and ferrous iron-dependent oxygenases, each of which harbors a catalytic domain centered on a double-stranded β-helix whose topology restricts the regions directly involved in substrate binding. However, they have different catalytic functions, and the deeply structural biological reasons are not yet clear. In this review, the catalytic domain features of the three protein families are summarized from both sequence and structural perspectives. The construction of the phylogenetic tree and comparison of the structure show ten relatively conserved β-sheets and three key regions with substantial structural differences. We summarize the relationship between three key regions of remarkable differences and the substrate compatibility of the three protein families. This review facilitates research into substrate-selective inhibition and bioengineering by providing new insights into the catalytic domains of KDM, ALKBH, and TET proteins.
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Affiliation(s)
- Siqi Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Jixiang Xing
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Dongyang Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yancheng Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Haoyu Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Shuhua Xu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China; State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
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Du Y, He Z, Jin S, Jin G, Wang K, Yang F, Zhang J. Targeting histone methylation and demethylation for non-alcoholic fatty liver disease. Bioorg Chem 2024; 151:107698. [PMID: 39126869 DOI: 10.1016/j.bioorg.2024.107698] [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: 05/28/2024] [Revised: 07/16/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the leading chronic liver disease worldwide, facing increasing challenges in terms of prevention and treatment. The methylation of lysine and arginine residues on histone proteins is dynamically controlled by histone methyltransferases (HMTs) and histone demethylases (HDMs), regulating chromatin structure and gene transcription. Mutations, genetic translocations, and altered gene expression involving HMTs and HDMs are frequently observed in NAFLD. HMTs and HDMs are receiving increasing attention in regulating NALFD. Targeting specific HMTs and HDMs for drug development is becoming a new strategy for treating NAFLD. This review provides a comprehensive summary of the regulatory mechanism of histone methylation/demethylation in NAFLD. Additionally, we discuss the potential applications of HMTs and HDMs inhibitors in preventing NAFLD, which may provide a scientific basis for the treatment of NAFLD.
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Affiliation(s)
- Yuanbing Du
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Zhangxu He
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China.
| | - Sasa Jin
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Gang Jin
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Kaiyue Wang
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Feifei Yang
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China.
| | - Jingyu Zhang
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China.
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3
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Eawsakul K, Bunluepuech K. Exploring Synergistic Inhibition of Inflammatory and Antioxidant Potential: Integrated In Silico and In Vitro Analyses of Garcinia mangostana, Curcuma comosa, and Acanthus ebracteatus. Adv Pharmacol Pharm Sci 2024; 2024:8584015. [PMID: 39328582 PMCID: PMC11424873 DOI: 10.1155/2024/8584015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 09/04/2024] [Indexed: 09/28/2024] Open
Abstract
Compared with the use of a single herb alone, herb combinations can significantly increase their effectiveness in treating various diseases. The objective of this research was to determine the appropriate proportions of Garcinia mangostana (GM), Curcuma comosa (CC), and Acanthus ebracteatus (AE) to enhance their antioxidant and anti-inflammatory properties. The study employed computer modeling (in silico) and laboratory testing (in vitro). The optimal levels of phenolic and flavonoid compounds were achieved with a ratio of 15 parts GM, 5 parts CC, and 10 parts AE. In contrast, the 10 : 15 : 5 ratio resulted in the highest antioxidant activity, reducing DPPH radicals by 80.33% and ABTS radicals by 92.20%. The ratio had a synergistic effect and was within the safe range, ranging from 82.97 to 147.04 µg/mL. The ratio of 5 : 10 : 15 had the greatest anti-inflammatory effects, with an exceptional activity level of 98.86%. It effectively suppressed 23 genes or proteins, including the prominent NFE2L2 gene, and had a synergistic effect. This combination effectively inhibits inflammation (IC50: 12.05 µg/mL) and is safe for macrophages at concentrations up to 50 µg/mL. These findings emphasize the potential of these herbal mixtures for antioxidant and anti-inflammatory applications.
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Affiliation(s)
- Komgrit Eawsakul
- College of Graduate StudiesWalailak University, Nakhon Si Thammarat 80160, Thailand
- Applied Thai Traditional MedicineSchool of MedicineWalailak University, Nakhon Si Thammarat 80160, Thailand
- Research Excellence Center for Innovation and Health Products (RECIHP)Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Kingkan Bunluepuech
- Applied Thai Traditional MedicineSchool of MedicineWalailak University, Nakhon Si Thammarat 80160, Thailand
- Research Excellence Center for Innovation and Health Products (RECIHP)Walailak University, Nakhon Si Thammarat 80160, Thailand
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Ali A, Azmat U, Ji Z, Khatoon A, Murtaza B, Akbar K, Irshad U, Raza R, Su Z. Beyond Genes: Epiregulomes as Molecular Commanders in Innate Immunity. Int Immunopharmacol 2024; 142:113149. [PMID: 39278059 DOI: 10.1016/j.intimp.2024.113149] [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: 06/02/2024] [Revised: 08/09/2024] [Accepted: 09/08/2024] [Indexed: 09/17/2024]
Abstract
The natural fastest way to deal with pathogens or danger signals is the innate immune system. This system prevents too much inflammation and tissue damage and efficiently eliminates pathogens. The epiregulome is the chromatin structure influenced by epigenetic factors and linked to cis-regulatory elements (CREs). The epiregulome helps to end the inflammatory response and also assists innate immune cells to show specific action by making cell-specific gene expression patterns. This inspection unfolds two concepts: (1) how epiregulomes are shaped by switching the expression levels of genes, manoeuvre enzyme activity and earmark of chromatin modifiers on specific genes; during and after the infection, and (2) how the expression of specific genes (aids in prompt management of innate cell growth, or the reaction to aggravation and illness) command by epiregulomes that formed during the above process. In this review, the consequences of intrinsic immuno-metabolic remodelling on epiregulomes and potential difficulties in identifying the master epiregulome that regulates innate immunity and inflammation have been discussed.
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Affiliation(s)
- Ashiq Ali
- Department of Histology and Embryology, Shantou University Medical College, China.
| | - Urooj Azmat
- Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan
| | - Ziyi Ji
- Department of Histology and Embryology, Shantou University Medical College, China
| | - Aisha Khatoon
- Department of Pathology, University of Agriculture Faisalabad, Pakistan
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Science and Technology, Dalian, China
| | - Kaynaat Akbar
- Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan
| | - Urooj Irshad
- Department Biological Sciences, Faculty of Sciences, Superior University Lahore, Punjab, Pakistan
| | - Rameen Raza
- Department of Pathology, University of Agriculture Faisalabad, Pakistan
| | - Zhongjing Su
- Department of Histology and Embryology, Shantou University Medical College, China.
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Jawale D, Khandibharad S, Singh S. Innate Immune Response and Epigenetic Regulation: A Closely Intertwined Tale in Inflammation. Adv Biol (Weinh) 2024:e2400278. [PMID: 39267219 DOI: 10.1002/adbi.202400278] [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: 05/23/2024] [Revised: 07/08/2024] [Indexed: 09/17/2024]
Abstract
Maintenance of delicate homeostasis is very important in various diseases because it ensures appropriate immune surveillance against pathogens and prevents excessive inflammation. In a disturbed homeostatic condition, hyperactivation of immune cells takes place and interplay between these cells triggers a plethora of signaling pathways, releasing various pro-inflammatory cytokines such as Tumor necrosis factor alpha (TNFα), Interferon-gamma (IFNƴ), Interleukin-6 (IL-6), and Interleukin-1 beta (IL-1β), which marks cytokine storm formation. To be precise, dysregulated balance can impede or increase susceptibility to various pathogens. Pathogens have the ability to hijack the host immune system by interfering with the host's chromatin architecture for their survival and replication in the host cell. Cytokines, particularly IL-6, Interleukin-17 (IL-17), and Interleukin-23 (IL-23), play a key role in orchestrating innate immune responses and shaping adaptive immunity. Understanding the interplay between immune response and the role of epigenetic modification to maintain immune homeostasis and the structural aspects of IL-6, IL-17, and IL-23 can be illuminating for a novel therapeutic regimen to treat various infectious diseases. In this review, the light is shed on how the orchestration of epigenetic regulation facilitates immune homeostasis.
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Affiliation(s)
- Diksha Jawale
- Systems Medicine Laboratory, Biotechnology Research and Innovation Council-National Centre for Cell Science (BRIC-NCCS), NCCS Complex, SPPU Campus, Ganeshkhind, Pune, 411007, India
| | - Shweta Khandibharad
- Systems Medicine Laboratory, Biotechnology Research and Innovation Council-National Centre for Cell Science (BRIC-NCCS), NCCS Complex, SPPU Campus, Ganeshkhind, Pune, 411007, India
| | - Shailza Singh
- Systems Medicine Laboratory, Biotechnology Research and Innovation Council-National Centre for Cell Science (BRIC-NCCS), NCCS Complex, SPPU Campus, Ganeshkhind, Pune, 411007, India
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Zhao Z, Attanasio C, Zong C, Pedano MS, Cadenas de Llano-Pérula M. How does orthodontic tooth movement influence the dental pulp? RNA-sequencing on human premolars. Int Endod J 2024. [PMID: 39086033 DOI: 10.1111/iej.14131] [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: 04/24/2024] [Revised: 06/11/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024]
Abstract
OBJECTIVES The objective of this study is to analyse the gene expression profile of the dental pulp (DP) of human premolars subjected to 7 and 28 days of orthodontic force (OF) in vivo by using RNA sequencing. The maxillary and mandibular DP were additionally compared. METHODS Healthy patients requiring orthodontic premolar extractions were randomly assigned to one of the three groups: control (CG) where no OF was applied, 7 and 28 days, where premolars were extracted either 7 or 28 days after the application of a 50-100 g OF. Total RNA was extracted from the DP and analysed via RNA-seq. Differentially expressed genes (DEGs) were identified using a false discovery rate and fold change threshold of <0.05 and ≥1.5, respectively. Functional analysis was performed. RESULTS After 7 days of OF, pulp reaction indicates immune response, hypoxia, DNA damage and epigenetic regulation. After 28 days, cell adhesion, migration, organization and tissue repair are evident. The maxillary and mandibular pulp tissues react differently to OF. The maxilla exhibits minimal alterations, mostly related to immune response at 7 days and tissue repair at 28 days, whereas the mandible shows mostly DNA damage and epigenetic regulation at 7 days and return to the original state at 28 days. CONCLUSIONS This study demonstrates that the early reaction of the DP to OF is marked by immune response, hypoxia and DNA damage. In contrast, after 28 days, cell adhesion, migration, organization, tissue repair and dentine formation are observed. Maxillary and mandibular premolars react differently to OF: although the maxilla exhibits minimal alterations at both time points, the mandible mostly shows DNA damage, epigenetic regulation, and immune response at 7 days. These disparities could stem from different blood supplies or the lower maxillary bone density, potentially triggering faster biological changes. Our findings provide insights into the gene regulatory networks modulating DP response to OF.
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Affiliation(s)
- Zuodong Zhao
- Department of Oral Health Sciences-Orthodontics, KU Leuven and Dentistry, University Hospitals Leuven, Leuven, Belgium
| | - Catia Attanasio
- Laboratory of Gene Regulation and Disease, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Chen Zong
- Department of Oral Health Sciences-Orthodontics, KU Leuven and Dentistry, University Hospitals Leuven, Leuven, Belgium
| | - Mariano Simón Pedano
- Department of Oral Health Sciences-Endodontics and BIOMAT - Biomaterials Research Group, KU Leuven and Dentistry, University Hospitals Leuven, Leuven, Belgium
| | - María Cadenas de Llano-Pérula
- Department of Oral Health Sciences-Orthodontics, KU Leuven and Dentistry, University Hospitals Leuven, Leuven, Belgium
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Zhang Y, Zhang Y, Wang C, Heo Y, Tumenbayar BI, Lee SH, Bae Y, Chin Heo S. Epigenetic Dynamics in Meniscus Cell Migration and its Zonal Dependency in Response to Inflammatory Conditions: Implications for Regeneration Strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.22.604178. [PMID: 39091842 PMCID: PMC11291020 DOI: 10.1101/2024.07.22.604178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Meniscus injuries pose significant challenges in clinical settings, primarily due to the intrinsic heterogeneity of the tissue and the limited efficacy of current treatments. Endogenous cell migration is crucial for the healing process, yet the regulatory mechanisms of meniscus cell migration and its zonal dependency within the meniscus are not fully understood. Thus, this study investigates the role of epigenetic mechanisms in governing meniscus cell migration under inflammatory conditions, with a focus on their implications for injury healing and regeneration. Here, we discovered that a proinflammatory cytokine, TNF-α treatment significantly impedes the migration speed of inner meniscus cells, while outer meniscus cells are unaffected, underscoring a zonal-dependent response within the meniscus. Our analysis identified distinct histone modification patterns and chromatin dynamics between inner and outer meniscus cells during migration, highlighting the necessity to consider these zonal-dependent properties in devising repair strategies. Specifically, we found that TNF-α differentially influences histone modifications, particularly H3K27me3, between the two cell types. Transcriptome analysis further revealed that TNF-α treatment induces substantial gene expression changes, with inner meniscus cells exhibiting more pronounced alterations than outer cells. Gene cluster analysis pointed to distinct responses in chromatin remodeling, extracellular matrix assembly, and wound healing processes between the zonal cell populations. Moreover, we identified potential therapeutic targets by employing existing epigenetic drugs, GSKJ4 (a histone demethylase inhibitor) and C646 (a histone acetyltransferase inhibitor), to successfully restore the migration speed of inner meniscus cells under inflammatory conditions. This highlights their potential utility in treating meniscus tear injuries. Overall, our findings elucidate the intricate interplay between epigenetic mechanisms and meniscus cell migration, along with its meniscus zonal dependency. This study provides insights into potential targets for enhancing meniscus repair and regeneration, which may lead to improved clinical outcomes for patients with meniscus injuries and osteoarthritis.
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Affiliation(s)
- Yize Zhang
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Yujia Zhang
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine Wang
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuna Heo
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Bat-Ider Tumenbayar
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Se-Hwan Lee
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yongho Bae
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biomedical Engineering, School of Engineering and Applied Sciences, University at Buffalo, Buffalo, NY, USA
| | - Su Chin Heo
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
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8
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Ma J, Liangpunsakul S. Solving the puzzle of fibrosis resolution in alcohol-associated liver disease: An insight from KDM5 demethylases and LXR activation. Hepatology 2024; 80:14-17. [PMID: 38449427 DOI: 10.1097/hep.0000000000000781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 03/08/2024]
Affiliation(s)
- Jing Ma
- Department of Medicine, Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Suthat Liangpunsakul
- Department of Medicine, Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Roudebush Veterans Administration Medical Center, Medicine Service, Indianapolis, Indiana, USA
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Britto LS, Balasubramani D, Desai S, Phillips P, Trehan N, Cesarman E, Koff JL, Singh A. T Cells Spatially Regulate B Cell Receptor Signaling in Lymphomas through H3K9me3 Modifications. Adv Healthc Mater 2024:e2401192. [PMID: 38837879 DOI: 10.1002/adhm.202401192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/27/2024] [Indexed: 06/07/2024]
Abstract
Activated B cell-like diffuse large B-cell lymphoma (ABC-DLBCL) is a subtype associated with poor survival outcomes. Despite identifying therapeutic targets through molecular characterization, targeted therapies have limited success. New strategies using immune-competent tissue models are needed to understand how DLBCL cells evade treatment. Here, synthetic hydrogel-based lymphoma organoids are used to demonstrate how signals in the lymphoid tumor microenvironment (Ly-TME) can alter B cell receptor (BCR) signaling and specific histone modifications, tri-methylation of histone 3 at lysine 9 (H3K9me3), dampening the effects of BCR pathway inhibition. Using imaging modalities, T cells increase DNA methyltransferase 3A expression and cytoskeleton formation in proximal ABC-DLBCL cells, regulated by H3K9me3. Expansion microscopy on lymphoma organoids reveals T cells increase the size and quantity of segregated H3K9me3 clusters in ABC-DLBCL cells. Findings suggest the re-organization of higher-order chromatin structures that may contribute to evasion or resistance to therapy via the emergence of novel transcriptional states. Treating ABC-DLBCL cells with a G9α histone methyltransferase inhibitor reverses T cell-mediated modulation of H3K9me3 and overcomes T cell-mediated attenuation of treatment response to BCR pathway inhibition. This study emphasizes the Ly-TME's role in altering DLBCL fate and suggests targeting aberrant signaling and microenvironmental cross-talk that can benefit high-risk patients.
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Affiliation(s)
- Lucy S Britto
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Deepali Balasubramani
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Sona Desai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Phunterion Phillips
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Neev Trehan
- St Richards Hospital, University Hospitals Sussex NHS Foundation Trust, Chichester, West Sussex, PO19 6SE, UK
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jean L Koff
- Winship Cancer Center, Emory University School of Medicine, Atlanta, GA, 30307, USA
| | - Ankur Singh
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30318, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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Khan H, Rafi Z, Khan MY, Maarfi F, Rehman S, Kaur K, Ahmad MK, Shahab U, Ahmad N, Ahmad S. Epigenetic contributions to cancer: Exploring the role of glycation reactions. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 387:143-193. [PMID: 39179346 DOI: 10.1016/bs.ircmb.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
Advanced Glycation End-products (AGEs), with their prolonged half-life in the human body, are emerging as potent diagnostic indicators. Early intervention studies, focusing on AGE cross-link breakers, have shown encouraging results in heart failure patients, paving the way for disease progression monitoring and therapy effectiveness evaluation. AGEs are the byproducts of a non-enzymatic reaction where sugars interact with proteins, lipids, and nucleic acids. These compounds possess the power to alter numerous biological processes, ranging from disrupting molecular conformation and promoting cross-linking to modifying enzyme activity, reducing clearance, and impairing receptor recognition. The damage inflicted by AGEs through the stimulation of intracellular signaling pathways is associated with the onset of chronic diseases across various organ systems. This review consolidates the characteristics of AGEs and the challenges posed by their expression in diverse physiological and pathological states. Furthermore, it highlights the clinical relevance of AGEs and the latest research breakthroughs aimed at reducing AGE accumulation.
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Affiliation(s)
- Hamda Khan
- Department of Biochemistry, Faculty of Medicine, Jawahar Lal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Zeeshan Rafi
- Department of Bioengineering, Integral University, Lucknow, India
| | - Mohd Yasir Khan
- School of Applied & Life Sciences, Uttaranchal University, Dehradun, India
| | - Farah Maarfi
- School of Applied & Life Sciences, Uttaranchal University, Dehradun, India
| | | | - Kirtanjot Kaur
- University Centre for Research and Development, Chandigarh University, Mohali, India
| | | | - Uzma Shahab
- Department of Biochemistry, King George Medical University, Lucknow, India
| | - Naved Ahmad
- Department of Computer Science and Information System, College of Applied Sciences, AlMaarefa University, Riyadh, Saudi Arabia
| | - Saheem Ahmad
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Saudi Arabia.
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11
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Ye W, Zhang C, Fan Z. MiR-26b-5p/TET3 regulates the osteogenic differentiation of human bone mesenchymal stem cells and bone reconstruction in female rats with calvarial defects. Mol Biol Rep 2024; 51:632. [PMID: 38724827 DOI: 10.1007/s11033-024-09577-4] [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: 03/05/2024] [Accepted: 04/22/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND MicroRNAs (miRNAs) play critical roles in the osteogenic differentiation of human bone mesenchymal stem cells (hBMSCs), but the mechanism by which miRNAs indirectly modulate osteogenesis remains unclear. Here, we explored the mechanism by which miRNAs indirectly modulate gene expression through histone demethylases to promote bone regeneration. METHODS AND RESULTS Bioinformatics analysis was performed on hBMSCs after 7 days of osteogenic induction. The differentially expressed miRNAs were screened, and potential target mRNAs were identified. To determine the bioactivity and stemness of hBMSCs and their potential for bone repair, we performed wound healing, Cell Counting Kit-8 (CCK-8), real-time reverse transcription quantitative polymerase chain reaction (RT‒qPCR), alkaline phosphatase activity, alizarin red S (ARS) staining and radiological and histological analyses on SD rats with calvarial bone defects. Additionally, a dual-luciferase reporter assay was utilized to investigate the interaction between miR-26b-5p and ten-eleven translocation 3 (TET3) in human embryonic kidney 293T cells. The in vitro and in vivo results suggested that miR-26b-5p effectively promoted the migration, proliferation and osteogenic differentiation of hBMSCs, as well as the bone reconstruction of calvarial defects in SD rats. Mechanistically, miR-26b-5p bound to the 3' untranslated region of TET3 mRNA to mediate gene silencing. CONCLUSIONS MiR-26b-5p downregulated the expression of TET3 to increase the osteogenic differentiation of hBMSCs and bone repair in rat calvarial defects. MiR-26b-5p/TET3 crosstalk might be useful in large-scale critical bone defects.
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Affiliation(s)
- Weilong Ye
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, 100050, China
| | - Chen Zhang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, 100050, China.
- Department of Dental Emergency, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, 100050, China.
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, 100050, China.
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing, 100050, China.
- Research Unit of Tooth Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Alkhatabi HA. Deciphering aging-associated molecular mechanisms in bone marrow derived hematopoietic stem cells in the elderly using NGS data. Bioinformation 2024; 20:180-189. [PMID: 38497076 PMCID: PMC10941783 DOI: 10.6026/973206300200180] [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: 02/01/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
Aging is a complex process that is not yet fully understood. Despite advancements in research, a deeper understanding of the underlying biological mechanisms is necessary to develop interventions that promote healthy longevity. The aim of this study was to elucidate the complex mechanisms associated with healthy aging and longevity in healthy elderly individuals. The RNA sequencing (RNA-seq) data used in this study was obtained from the Gene Expression Omnibus (GEO) database (accession number GSE104406), which was collected from Fluorescent Activated Cell Sorting (FACS) of human bone marrow derived human hematopoietic stem cells (BM-HSCs) (Lineage-, CD34+, CD38-) young (18-30 years old) and aged (65-75 years old) donors who had no known hematological malignancy, with 10 biological replicates per group. The GEO RNA-seq Experiments Interactive Navigator (GREIN) software was used to obtain raw gene-level counts and filtered metadata for this dataset. Next generation knowledge discovery (NGKD) tools provided by BioJupies were used to obtain differentially regulated pathways, gene ontologies (GO), and gene signatures in the BM-HSCs. Finally, the L1000 Characteristic Direction Signature Search Engine (L1000CDS2) tool was used to identify specific drugs that reverse aging-associated gene signatures in old but healthy individuals. The down-regulation of signaling pathways such as longevity regulation, proteasome, Notch, apoptosis, nuclear factor kappa B (NFkB), and peroxisome proliferator-activated receptors (PPAR) signaling pathways in the BM-HSCs of healthy elderly. GO functions related to negative regulation of bone morphogenetic protein (BMP), telomeric DNA binding, nucleoside binding, calcium -dependent protein binding, chromatin-DNA binding, SMAD binding, and demethylase activity were significantly downregulated in the BM-HSCs of the elderly compared to the healthy young group. Importantly, potential drugs such as salermide, celestrol, cercosporin, dorsomorphin dihydrochloride, and LDN-193189 monohydrochloride that can reverse the aging-associated signatures in HSCs from healthy elderly were identified. The analysis of RNA-seq data based on NGKD techniques revealed a plethora of differentially regulated pathways, gene ontologies, and drugs with anti-aging potential to promote healthspan in the elderly.
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Affiliation(s)
- Hind A Alkhatabi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
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Mecca M, Picerno S, Cortellino S. The Killer's Web: Interconnection between Inflammation, Epigenetics and Nutrition in Cancer. Int J Mol Sci 2024; 25:2750. [PMID: 38473997 DOI: 10.3390/ijms25052750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Inflammation is a key contributor to both the initiation and progression of tumors, and it can be triggered by genetic instability within tumors, as well as by lifestyle and dietary factors. The inflammatory response plays a critical role in the genetic and epigenetic reprogramming of tumor cells, as well as in the cells that comprise the tumor microenvironment. Cells in the microenvironment acquire a phenotype that promotes immune evasion, progression, and metastasis. We will review the mechanisms and pathways involved in the interaction between tumors, inflammation, and nutrition, the limitations of current therapies, and discuss potential future therapeutic approaches.
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Affiliation(s)
- Marisabel Mecca
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), 85028 Rionero in Vulture, PZ, Italy
| | - Simona Picerno
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), 85028 Rionero in Vulture, PZ, Italy
| | - Salvatore Cortellino
- Laboratory of Preclinical and Translational Research, Responsible Research Hospital, 86100 Campobasso, CB, Italy
- Scuola Superiore Meridionale (SSM), Clinical and Translational Oncology, 80138 Naples, NA, Italy
- S.H.R.O. Italia Foundation ETS, 10060 Candiolo, TO, Italy
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Ajithkumar P, Vasantharajan SS, Pattison S, McCall JL, Rodger EJ, Chatterjee A. Exploring Potential Epigenetic Biomarkers for Colorectal Cancer Metastasis. Int J Mol Sci 2024; 25:874. [PMID: 38255946 PMCID: PMC10815915 DOI: 10.3390/ijms25020874] [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: 11/30/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Metastatic progression is a complex, multistep process and the leading cause of cancer mortality. There is growing evidence that emphasises the significance of epigenetic modification, specifically DNA methylation and histone modifications, in influencing colorectal (CRC) metastasis. Epigenetic modifications influence the expression of genes involved in various cellular processes, including the pathways associated with metastasis. These modifications could contribute to metastatic progression by enhancing oncogenes and silencing tumour suppressor genes. Moreover, specific epigenetic alterations enable cancer cells to acquire invasive and metastatic characteristics by altering cell adhesion, migration, and invasion-related pathways. Exploring the involvement of DNA methylation and histone modification is crucial for identifying biomarkers that impact cancer prediction for metastasis in CRC. This review provides a summary of the potential epigenetic biomarkers associated with metastasis in CRC, particularly DNA methylation and histone modifications, and examines the pathways associated with these biomarkers.
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Affiliation(s)
- Priyadarshana Ajithkumar
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Sai Shyam Vasantharajan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Sharon Pattison
- Department of Medicine, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - John L. McCall
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
- School of Health Sciences and Technology, UPES University, Dehradun 248007, India
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