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Naik N, Patel M, Sen R. Developmental Impacts of Epigenetics and Metabolism in COVID-19. J Dev Biol 2024; 12:9. [PMID: 38390960 PMCID: PMC10885083 DOI: 10.3390/jdb12010009] [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: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Developmental biology is intricately regulated by epigenetics and metabolism but the mechanisms are not completely understood. The situation becomes even more complicated during diseases where all three phenomena are dysregulated. A salient example is COVID-19, where the death toll exceeded 6.96 million in 4 years, while the virus continues to mutate into different variants and infect people. Early evidence during the pandemic showed that the host's immune and inflammatory responses to COVID-19 (like the cytokine storm) impacted the host's metabolism, causing damage to the host's organs and overall physiology. The involvement of angiotensin-converting enzyme 2 (ACE2), the pivotal host receptor for the SARS-CoV-2 virus, was identified and linked to epigenetic abnormalities along with other contributing factors. Recently, studies have revealed stronger connections between epigenetics and metabolism in COVID-19 that impact development and accelerate aging. Patients manifest systemic toxicity, immune dysfunction and multi-organ failure. Single-cell multiomics and other state-of-the-art high-throughput studies are only just beginning to demonstrate the extent of dysregulation and damage. As epigenetics and metabolism directly impact development, there is a crucial need for research implementing cutting-edge technology, next-generation sequencing, bioinformatics analysis, the identification of biomarkers and clinical trials to help with prevention and therapeutic interventions against similar threats in the future.
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Affiliation(s)
- Noopur Naik
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Mansi Patel
- Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Rwik Sen
- Active Motif, Inc., Carlsbad, CA 92008, USA
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Rosu LM, Prodan-Bărbulescu C, Maghiari AL, Bernad ES, Bernad RL, Iacob R, Stoicescu ER, Borozan F, Ghenciu LA. Current Trends in Diagnosis and Treatment Approach of Diabetic Retinopathy during Pregnancy: A Narrative Review. Diagnostics (Basel) 2024; 14:369. [PMID: 38396408 PMCID: PMC10887682 DOI: 10.3390/diagnostics14040369] [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: 01/11/2024] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Diabetes mellitus during pregnancy and gestational diabetes are major concerns worldwide. These conditions may lead to the development of severe diabetic retinopathy during pregnancy or worsen pre-existing cases. Gestational diabetes also increases the risk of diabetes for both the mother and the fetus in the future. Understanding the prevalence, evaluating risk factors contributing to pathogenesis, and identifying treatment challenges related to diabetic retinopathy in expectant mothers are all of utmost importance. Pregnancy-related physiological changes, including those in metabolism, blood flow, immunity, and hormones, can contribute to the development or worsening of diabetic retinopathy. If left untreated, this condition may eventually result in irreversible vision loss. Treatment options such as laser therapy, intravitreal anti-vascular endothelial growth factor drugs, and intravitreal steroids pose challenges in managing these patients without endangering the developing baby and mother. This narrative review describes the management of diabetic retinopathy during pregnancy, highlights its risk factors, pathophysiology, and diagnostic methods, and offers recommendations based on findings from previous literature.
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Affiliation(s)
- Luminioara M. Rosu
- Department of Anatomy and Embryology, Victor Babeș University of Medicine and Pharmacy, E. Murgu Square, No. 2, 300041 Timisoara, Romania; (L.M.R.); (A.L.M.); (R.I.); (F.B.)
| | - Cătălin Prodan-Bărbulescu
- Department of Anatomy and Embryology, Victor Babeș University of Medicine and Pharmacy, E. Murgu Square, No. 2, 300041 Timisoara, Romania; (L.M.R.); (A.L.M.); (R.I.); (F.B.)
| | - Anca Laura Maghiari
- Department of Anatomy and Embryology, Victor Babeș University of Medicine and Pharmacy, E. Murgu Square, No. 2, 300041 Timisoara, Romania; (L.M.R.); (A.L.M.); (R.I.); (F.B.)
| | - Elena S. Bernad
- Department of Obstetrics and Gynecology, Victor Babeș University of Medicine and Pharmacy, 300041 Timisoara, Romania;
- Clinic of Obstetrics and Gynecology, “Pius Brinzeu” County Clinical Emergency Hospital, 300723 Timisoara, Romania
- Center for Laparoscopy, Laparoscopic Surgery and In Vitro Fertilization, Victor Babeș University of Medicine and Pharmacy, 300041 Timisoara, Romania
- Department of Automatic Control and Applied Informatics, Politehnica University, 300223 Timisoara, Romania;
| | - Robert L. Bernad
- Department of Automatic Control and Applied Informatics, Politehnica University, 300223 Timisoara, Romania;
| | - Roxana Iacob
- Department of Anatomy and Embryology, Victor Babeș University of Medicine and Pharmacy, E. Murgu Square, No. 2, 300041 Timisoara, Romania; (L.M.R.); (A.L.M.); (R.I.); (F.B.)
- Discipline of Radiology and Medical Imaging, Victor Babeș University of Medicine and Pharmacy, E. Murgu Square, No. 2, 300041 Timisoara, Romania;
| | - Emil Robert Stoicescu
- Discipline of Radiology and Medical Imaging, Victor Babeș University of Medicine and Pharmacy, E. Murgu Square, No. 2, 300041 Timisoara, Romania;
- Research Center for Pharmaco-Toxicological Evaluations, Victor Babeș University of Medicine and Pharmacy, E. Murgu Square, No. 2, 300041 Timisoara, Romania
| | - Florina Borozan
- Department of Anatomy and Embryology, Victor Babeș University of Medicine and Pharmacy, E. Murgu Square, No. 2, 300041 Timisoara, Romania; (L.M.R.); (A.L.M.); (R.I.); (F.B.)
| | - Laura Andreea Ghenciu
- Department of Functional Sciences, Victor Babeș University of Medicine and Pharmacy, E. Murgu Square, No. 2, 300041 Timisoara, Romania;
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103
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Dreier MR, Walia J, de la Serna IL. Targeting SWI/SNF Complexes in Cancer: Pharmacological Approaches and Implications. Epigenomes 2024; 8:7. [PMID: 38390898 PMCID: PMC10885108 DOI: 10.3390/epigenomes8010007] [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: 12/29/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
SWI/SNF enzymes are heterogeneous multi-subunit complexes that utilize the energy from ATP hydrolysis to remodel chromatin structure, facilitating transcription, DNA replication, and repair. In mammalian cells, distinct sub-complexes, including cBAF, ncBAF, and PBAF exhibit varying subunit compositions and have different genomic functions. Alterations in the SWI/SNF complex and sub-complex functions are a prominent feature in cancer, making them attractive targets for therapeutic intervention. Current strategies in cancer therapeutics involve the use of pharmacological agents designed to bind and disrupt the activity of SWI/SNF complexes or specific sub-complexes. Inhibitors targeting the catalytic subunits, SMARCA4/2, and small molecules binding SWI/SNF bromodomains are the primary approaches for suppressing SWI/SNF function. Proteolysis-targeting chimeras (PROTACs) were generated by the covalent linkage of the bromodomain or ATPase-binding ligand to an E3 ligase-binding moiety. This engineered connection promotes the degradation of specific SWI/SNF subunits, enhancing and extending the impact of this pharmacological intervention in some cases. Extensive preclinical studies have underscored the therapeutic potential of these drugs across diverse cancer types. Encouragingly, some of these agents have progressed from preclinical research to clinical trials, indicating a promising stride toward the development of effective cancer therapeutics targeting SWI/SNF complex and sub-complex functions.
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Affiliation(s)
- Megan R Dreier
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
| | - Jasmine Walia
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
| | - Ivana L de la Serna
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
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Liu J, Ke M, Sun Y, Niu S, Zhang W, Li Y. Epigenetic regulation and epigenetic memory resetting during plant rejuvenation. J Exp Bot 2024; 75:733-745. [PMID: 37930766 DOI: 10.1093/jxb/erad435] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
Reversal of plant developmental status from the mature to the juvenile phase, thus leading to the restoration of the developmental potential, is referred to as plant rejuvenation. It involves multilayer regulation, including resetting gene expression patterns, chromatin remodeling, and histone modifications, eventually resulting in the restoration of juvenile characteristics. Although plants can be successfully rejuvenated using some forestry practices to restore juvenile morphology, physiology, and reproductive capabilities, studies on the epigenetic mechanisms underlying this process are in the nascent stage. This review provides an overview of the plant rejuvenation process and discusses the key epigenetic mechanisms involved in DNA methylation, histone modification, and chromatin remodeling in the process of rejuvenation, as well as the roles of small RNAs in this process. Additionally, we present new inquiries regarding the epigenetic regulation of plant rejuvenation, aiming to advance our understanding of rejuvenation in sexually and asexually propagated plants. Overall, we highlight the importance of epigenetic mechanisms in the regulation of plant rejuvenation, providing valuable insights into the complexity of this process.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Meng Ke
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Shihui Niu
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
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105
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Hartwig C, Müller J, Klett H, Kouhestani D, Mittelstädt A, Anthuber A, David P, Brunner M, Jacobsen A, Glanz K, Swierzy I, Roßdeutsch L, Klösch B, Grützmann R, Wittenberger T, Sohn K, Weber GF. Discrimination of pancreato-biliary cancer and pancreatitis patients by non-invasive liquid biopsy. Mol Cancer 2024; 23:28. [PMID: 38308296 PMCID: PMC10836044 DOI: 10.1186/s12943-024-01943-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Current diagnostics for the detection of pancreato-biliary cancers (PBCs) need to be optimized. We therefore propose that methylated cell-free DNA (cfDNA) derived from non-invasive liquid biopsies serves as a novel biomarker with the ability to discriminate pancreato-biliary cancers from non-cancer pancreatitis patients. METHODS Differentially methylated regions (DMRs) from plasma cfDNA between PBCs, pancreatitis and clinical control samples conditions were identified by next-generation sequencing after enrichment using methyl-binding domains and database searches to generate a discriminatory panel for a hybridization and capture assay with subsequent targeted high throughput sequencing. RESULTS The hybridization and capture panel, covering around 74 kb in total, was applied to sequence a cohort of 25 PBCs, 25 pancreatitis patients, 25 clinical controls, and seven cases of Intraductal Papillary Mucinous Neoplasia (IPMN). An unbiased machine learning approach identified the 50 most discriminatory methylation markers for the discrimination of PBC from pancreatitis and controls resulting in an AUROC of 0.85 and 0.88 for a training (n = 45) and a validation (n = 37) data set, respectively. The panel was also able to distinguish high grade from low grade IPMN samples. CONCLUSIONS We present a proof of concept for a methylation biomarker panel with better performance and improved discriminatory power than the current clinical marker CA19-9 for the discrimination of pancreato-biliary cancers from non-cancerous pancreatitis patients and clinical controls. This workflow might be used in future diagnostics for the detection of precancerous lesions, e.g. the identification of high grade IPMNs vs. low grade IPMNs.
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Affiliation(s)
- Christina Hartwig
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
- Institute for Interfacial Engineering and Plasma Technology IGVP, University of Stuttgart, Stuttgart, Germany
| | - Jan Müller
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | | | - Dina Kouhestani
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Anke Mittelstädt
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Anna Anthuber
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Paul David
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Maximilian Brunner
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Anne Jacobsen
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Karolina Glanz
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Izabela Swierzy
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Lotta Roßdeutsch
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Bettina Klösch
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Robert Grützmann
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
- Comprehensive Cancer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), Erlangen, Germany
| | | | - Kai Sohn
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany.
| | - Georg F Weber
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany.
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany.
- Comprehensive Cancer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany.
- Bavarian Cancer Research Center (BZKF), Erlangen, Germany.
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106
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Rahman A, Sandeep Kumar Jain R, Meghana P, Nippu BN, Manjunatha KS, Rajaput PS, Kumaraswamy HM, Satyanarayan ND. Tetrahydrobenzothiophene derivatives ameliorate Mia PaCa-2 cell progression and induces apoptosis via inhibiting EGFR2 tyrosine kinase signal. Bioorg Chem 2024; 143:106968. [PMID: 38007893 DOI: 10.1016/j.bioorg.2023.106968] [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: 09/15/2023] [Revised: 10/28/2023] [Accepted: 11/12/2023] [Indexed: 11/28/2023]
Abstract
A series of new thiophene analogues with acarbonitrile-basedmoiety were designed and synthesized via structural optimization. The conjugates were assessed for their in-vitro cytotoxic activity against a human pancreatic cancer cell line (Mia PaCa-2) and among them compound 5b showed IC50 value of 13.37 ± 2.37 μM. The compounds 5b (20 µM & 25 µM) and 7c (30 & 35 µM) also showed reduced clonogenicity, enhanced ROS and decreased mitochondrial membrane potential in Mia PaCa-2 cells. Treatment with these compounds also increased apoptotic population as evident with the double staining assay. Among the evaluated series, compounds 5b, 5g, 7c, and 9a attained a greater inhibitory potency than first generation's reversible EGFR inhibitor, Gefitinib. EGFR2 enzyme inhibitory studies revealed that 5b efficiently and arbitrarily suppressed the development of EGFR2 dependent cells and inhibited the enzymatic activity with an IC50 value of 0.68 µM; interestingly, the most effective molecule 5b with N-methyl piperazine substitution, has 1.29-fold greater potency than well-known EGFR inhibitor Gefitinib and increased Gefitinib's anti-growth impact with 2.04 folds greater against Mia PaCa-2. The in-vitro studies were validated with in-silico docking studies wherein compounds 5b and 7c exhibited binding energies of -8.2 and -7.4 Kcal/mol respectively. The present study reveals that tetrahydrobenzothiophene based analogues could be a promising lead for the evolution of potent chemo preventives over pancreatic cancer.
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Affiliation(s)
- Abdul Rahman
- Department of Pharmaceutical Chemistry, Kuvempu University, Post Graduate Centre, Kadur, Chikkamagaluru, Karnataka 577548, India
| | - R Sandeep Kumar Jain
- Laboratory of Experimental Medicine, Department of Biotechnology, Kuvempu University, Shankargatta, Shimoga, Karnataka 577451, India
| | - P Meghana
- Laboratory of Experimental Medicine, Department of Biotechnology, Kuvempu University, Shankargatta, Shimoga, Karnataka 577451, India
| | - B N Nippu
- Department of Pharmaceutical Chemistry, Kuvempu University, Post Graduate Centre, Kadur, Chikkamagaluru, Karnataka 577548, India
| | - K S Manjunatha
- Department of Pharmaceutical Chemistry, Kuvempu University, Post Graduate Centre, Kadur, Chikkamagaluru, Karnataka 577548, India
| | - Pooja S Rajaput
- Laboratory of Experimental Medicine, Department of Biotechnology, Kuvempu University, Shankargatta, Shimoga, Karnataka 577451, India
| | - H M Kumaraswamy
- Laboratory of Experimental Medicine, Department of Biotechnology, Kuvempu University, Shankargatta, Shimoga, Karnataka 577451, India
| | - N D Satyanarayan
- Department of Pharmaceutical Chemistry, Kuvempu University, Post Graduate Centre, Kadur, Chikkamagaluru, Karnataka 577548, India.
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107
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Chen S, Liu S, Shi S, Yin H, Tang Y, Zhang J, Li W, Liu G, Qu K, Ding X, Wang Y, Liu J, Zhang S, Fang L, Yu Y. Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats. Mol Biol Evol 2024; 41:msae003. [PMID: 38266195 PMCID: PMC10834038 DOI: 10.1093/molbev/msae003] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Abstract
The cross-species characterization of evolutionary changes in the functional genome can facilitate the translation of genetic findings across species and the interpretation of the evolutionary basis underlying complex phenotypes. Yet, this has not been fully explored between cattle, sheep, goats, and other mammals. Here, we systematically characterized the evolutionary dynamics of DNA methylation and gene expression in 3 somatic tissues (i.e. brain, liver, and skeletal muscle) and sperm across 7 mammalian species, including 3 ruminant livestock species (cattle, sheep, and goats), humans, pigs, mice, and dogs, by generating and integrating 160 DNA methylation and transcriptomic data sets. We demonstrate dynamic changes of DNA hypomethylated regions and hypermethylated regions in tissue-type manner across cattle, sheep, and goats. Specifically, based on the phylo-epigenetic model of DNA methylome, we identified a total of 25,074 hypomethylated region extension events specific to cattle, which participated in rewiring tissue-specific regulatory network. Furthermore, by integrating genome-wide association studies of 50 cattle traits, we provided novel insights into the genetic and evolutionary basis of complex phenotypes in cattle. Overall, our study provides a valuable resource for exploring the evolutionary dynamics of the functional genome and highlights the importance of cross-species characterization of multiomics data sets for the evolutionary interpretation of complex phenotypes in cattle livestock.
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Affiliation(s)
- Siqian Chen
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuli Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Shaolei Shi
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hongwei Yin
- Agriculture Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yongjie Tang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jinning Zhang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenlong Li
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Liu
- National Animal Husbandry Service, Beijing 100125, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong 675000, China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianfeng Liu
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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108
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Zhang K, Fu R, Liu R, Su Z. Circulating cell-free DNA-based multi-cancer early detection. Trends Cancer 2024; 10:161-174. [PMID: 37709615 DOI: 10.1016/j.trecan.2023.08.010] [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: 07/03/2023] [Revised: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023]
Abstract
Patients benefit considerably from early detection of cancer. Existing single-cancer tests have various limitations, which could be effectively addressed by circulating cell-free DNA (cfDNA)-based multi-cancer early detection (MCED). With sensitive detection and accurate localization of multiple cancer types at a very low and fixed false-positive rate (FPR), MCED has great potential to revolutionize early cancer detection. Herein, we review state-of-the-art approaches for cfDNA-based MCED and their limitations and discuss both technical and clinical challenges in the development and application of MCED tests. Given the constant improvements in technology and understanding of cancer biology, we propose that a cfDNA-based targeted sequencing assay that integrates multimodal features should be optimized for MCED.
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Affiliation(s)
- Kai Zhang
- Department of Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, Chaoyang District, Beijing 100021, China
| | - Ruiqing Fu
- Singlera Genomics Ltd, Shanghai 201203, China
| | - Rui Liu
- Singlera Genomics Ltd, Shanghai 201203, China
| | - Zhixi Su
- Singlera Genomics Ltd, Shanghai 201203, China.
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109
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Singh VK, Ahmed S, Saini DK, Gahlaut V, Chauhan S, Khandare K, Kumar A, Sharma PK, Kumar J. Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities. Biochim Biophys Acta Gen Subj 2024; 1868:130544. [PMID: 38104668 DOI: 10.1016/j.bbagen.2023.130544] [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: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.
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Affiliation(s)
| | - Shoeb Ahmed
- Ch. Charan Singh University, Meerut 250004, India
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vijay Gahlaut
- University Centre for Research and Development, Chandigarh University, Mohali 140413, Punjab, India
| | | | - Kiran Khandare
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Ashutosh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Pradeep Kumar Sharma
- Ch. Charan Singh University, Meerut 250004, India; Maharaja Suhel Dev State University, Azamgarh 276404, U.P., India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali 140306, Punjab, India.
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110
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Abdullah AR, Gamal El-Din AM, El-Mahdy HA, Ismail Y, El-Husseiny AA. The crucial role of fascin-1 in the pathogenesis, metastasis, and chemotherapeutic resistance of breast cancer. Pathol Res Pract 2024; 254:155079. [PMID: 38219494 DOI: 10.1016/j.prp.2023.155079] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/27/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
Breast cancer (BC) is the most common type of cancer in women to be diagnosed, and it is also the second leading cause of cancer death in women globally. It is the disease that causes the most life years adjusted for disability lost among women, making it a serious worldwide health issue. Understanding and interpreting carcinogenesis and metastatic pathways is critical for curing malignancy. Fascin-1 was recognized as an actin-bundling protein with parallel, rigid bundles as a result of the cross-linking of F-actin microfilaments. Increasing levels of fascin-1 have been associated with bad prognostic profiles, aggressiveness of clinical courses, and poor survival outcomes in a variety of human malignancies. Cancer cells that overexpress fascin-1 have higher capabilities for proliferation, invasion, migration, and metastasis. Fascin-1 is being considered as a potential target for therapy as well as a potential biomarker for diagnostics in a variety of cancer types. This review aims to provide an overview of the FSCN1 gene and its protein structure, elucidate its physiological and pathological roles, and throw light on its involvement in the initiation, development, and chemotherapeutic resistance of BC.
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Affiliation(s)
- Ahmed R Abdullah
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
| | - Ayman M Gamal El-Din
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
| | - Yahia Ismail
- Medical Oncology Department, National Cancer Institute (NCI), Cairo University, Cairo 11796, Egypt
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt.
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111
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Guo Z, Duan D, Tang W, Zhu J, Bush WS, Zhang L, Zhu X, Jin F, Feng H. magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing. PLoS Comput Biol 2024; 20:e1011875. [PMID: 38346081 PMCID: PMC10890765 DOI: 10.1371/journal.pcbi.1011875] [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: 09/27/2023] [Revised: 02/23/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Recently, novel biotechnologies to quantify RNA modifications became an increasingly popular choice for researchers who study epitranscriptome. When studying RNA methylations such as N6-methyladenosine (m6A), researchers need to make several decisions in its experimental design, especially the sample size and a proper statistical power. Due to the complexity and high-throughput nature of m6A sequencing measurements, methods for power calculation and study design are still currently unavailable. In this work, we propose a statistical power assessment tool, magpie, for power calculation and experimental design for epitranscriptome studies using m6A sequencing data. Our simulation-based power assessment tool will borrow information from real pilot data, and inspect various influential factors including sample size, sequencing depth, effect size, and basal expression ranges. We integrate two modules in magpie: (i) a flexible and realistic simulator module to synthesize m6A sequencing data based on real data; and (ii) a power assessment module to examine a set of comprehensive evaluation metrics.
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Affiliation(s)
- Zhenxing Guo
- School of Data Science, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen, Guangdong, China
| | - Daoyu Duan
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Wen Tang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Julia Zhu
- Hathaway Brown School, Shaker Heights, Ohio, United States of America
| | - William S. Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Liangliang Zhang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Fulai Jin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Hao Feng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
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112
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Kwon Y, Choi Y, Kim M, Jo H, Jeong MS, Jung HS, Jeoung D. HDAC6-MYCN-CXCL3 axis mediates allergic inflammation and is necessary for allergic inflammation-promoted cellular interactions. Mol Immunol 2024; 166:1-15. [PMID: 38176167 DOI: 10.1016/j.molimm.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/27/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Histone deacetylase 6 (HDAC6) has been shown to play an important role in allergic inflammation. This study hypothesized that novel downstream targets of HDAC6 would mediate allergic inflammation. Experiments employing HDAC6 knock out C57BL/6 mice showed that HDAC6 mediated passive cutaneous anaphylaxis (PCA) and passive systemic anaphylaxis (PSA). Antigen stimulation increased expression of N-myc (MYCN) and CXCL3 in an HDAC6-dependent manner in the bone marrow-derived mast cells. MYCN and CXCL3 were necessary for both PCA and PSA. The role of early growth response 3 (EGR3) in the regulation of HDAC6 expression has been reported. ChIP assays showed EGR3 as a direct regulator of MYCN. miR-34a-5p was predicted to be a negative regulator of MYCN. Luciferase activity assays showed miR-34a-5p as a direct regulator of MYCN. miR-34a-5p mimic negatively regulated PCA and PSA. MYCN decreased miR-34a-5p expression in antigen-stimulated rat basophilic leukemia cells (RBL2H3). MYCN was shown to bind to the promoter sequence of CXCL3. In an IgE-independent manner, recombinant CXCL3 protein increased expression of HDAC6, MYCN, and β-hexosaminidase activity in RBL2H3 cells. Mouse recombinant CXCL3 protein enhanced the angiogenic potential of the culture medium of RBL2H3. CXCL3 was necessary for the enhanced angiogenic potential of the culture medium of antigen-stimulated RBL2H3. The culture medium of RBL2H3 was able to induce M2 macrophage polarization in a CXCL3-dependent manner. Recombinant CXCL3 protein also increased the expression of markers of M2 macrophage. Thus, the identification of the novel role of HDAC6-MYCN-CXCL3 axis can help better understand the pathogenesis of anaphylaxis.
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Affiliation(s)
- Yoojung Kwon
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, South Korea
| | - Yunji Choi
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, South Korea
| | - Misun Kim
- KM Science Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, South Korea
| | - Hyein Jo
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, South Korea
| | - Myeong Seon Jeong
- Chuncheon Center, Korea Basic Science Institute, Chuncheon 24341, South Korea
| | - Hyun Suk Jung
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, South Korea
| | - Dooil Jeoung
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, South Korea.
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113
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Prabhu KS, Sadida HQ, Kuttikrishnan S, Junejo K, Bhat AA, Uddin S. Beyond genetics: Exploring the role of epigenetic alterations in breast cancer. Pathol Res Pract 2024; 254:155174. [PMID: 38306863 DOI: 10.1016/j.prp.2024.155174] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/04/2024]
Abstract
Breast cancer remains a major global health challenge. Its rising incidence is attributed to factors such as delayed diagnosis, the complexity of its subtypes, and increasing drug resistance, all contributing to less-than-ideal patient outcomes. Central to the progression of breast cancer are epigenetic aberrations, which significantly contribute to drug resistance and the emergence of cancer stem cell traits. These include alterations in DNA methylation, histone modifications, and the expression of non-coding RNAs. Understanding these epigenetic changes is crucial for developing advanced breast cancer management strategies despite their complexity. Investigating these epigenetic modifications offers the potential for novel diagnostic markers, more accurate prognostic indicators, and the identification of reliable predictors of treatment response. This could lead to the development of new targeted therapies. However, this requires sustained, focused research efforts to navigate the challenges of understanding breast cancer carcinogenesis and its epigenetic underpinnings. A deeper understanding of epigenetic mechanisms in breast cancer can revolutionize personalized medicine. This could lead to significant improvements in patient care, including early detection, precise disease stratification, and more effective treatment options.
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Affiliation(s)
- Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Hana Q Sadida
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer Research Program, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Shilpa Kuttikrishnan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Kulsoom Junejo
- General Surgery Department, Hamad General Hospital, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Ajaz A Bhat
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer Research Program, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Laboratory of Animal Research Center, Qatar University, Doha 2713, Qatar.
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114
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Joeres M, Maksimov P, Höper D, Calvelage S, Calero-Bernal R, Fernández-Escobar M, Koudela B, Blaga R, Vrhovec MG, Stollberg K, Bier N, Sotiraki S, Sroka J, Piotrowska W, Kodym P, Basso W, Conraths FJ, Mercier A, Galal L, Dardé ML, Balea A, Spano F, Schulze C, Peters M, Scuda N, Lundén A, Davidson RK, Terland R, Waap H, de Bruin E, Vatta P, Caccio S, Ortega-Mora LM, Jokelainen P, Schares G. Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method. Eur J Clin Microbiol Infect Dis 2024; 43:355-371. [PMID: 38099986 PMCID: PMC10822014 DOI: 10.1007/s10096-023-04721-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/16/2023] [Indexed: 01/28/2024]
Abstract
PURPOSE A new high-resolution next-generation sequencing (NGS)-based method was established to type closely related European type II Toxoplasma gondii strains. METHODS T. gondii field isolates were collected from different parts of Europe and assessed by whole genome sequencing (WGS). In comparison to ME49 (a type II reference strain), highly polymorphic regions (HPRs) were identified, showing a considerable number of single nucleotide polymorphisms (SNPs). After confirmation by Sanger sequencing, 18 HPRs were used to design a primer panel for multiplex PCR to establish a multilocus Ion AmpliSeq typing method. Toxoplasma gondii isolates and T. gondii present in clinical samples were typed with the new method. The sensitivity of the method was tested with serially diluted reference DNA samples. RESULTS Among type II specimens, the method could differentiate the same number of haplotypes as the reference standard, microsatellite (MS) typing. Passages of the same isolates and specimens originating from abortion outbreaks were identified as identical. In addition, seven different genotypes, two atypical and two recombinant specimens were clearly distinguished from each other by the method. Furthermore, almost all SNPs detected by the Ion AmpliSeq method corresponded to those expected based on WGS. By testing serially diluted DNA samples, the method exhibited a similar analytical sensitivity as MS typing. CONCLUSION The new method can distinguish different T. gondii genotypes and detect intra-genotype variability among European type II T. gondii strains. Furthermore, with WGS data additional target regions can be added to the method to potentially increase typing resolution.
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Affiliation(s)
- M Joeres
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald - Insel Riems, Germany
| | - P Maksimov
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald - Insel Riems, Germany
| | - D Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald - Insel Riems, Germany
| | - S Calvelage
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald - Insel Riems, Germany
| | - R Calero-Bernal
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - M Fernández-Escobar
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - B Koudela
- Central European Institute of Technology (CEITEC), University of Veterinary Sciences Brno, Brno, Czech Republic
- Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - R Blaga
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, Laboratoire de Santé Animale, BIPAR, Maisons-Alfort, France
- University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | | | - K Stollberg
- German Federal Institute for Risk Assessment, Department for Biological Safety, Berlin, Germany
| | - N Bier
- German Federal Institute for Risk Assessment, Department for Biological Safety, Berlin, Germany
| | - S Sotiraki
- Veterinary Research Institute, Hellenic Agricultural Organisation-DIMITRA, Thessaloniki, Greece
| | - J Sroka
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - W Piotrowska
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - P Kodym
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - W Basso
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - F J Conraths
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald - Insel Riems, Germany
| | - A Mercier
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidemiology of chronic diseases in tropical zone, Institute of Epidemiology and Tropical Neurology, OmegaHealth, Limoges, France
- Centre National de Référence (CNR) Toxoplasmose Centre Hospitalier-Universitaire Dupuytren, Limoges, France
| | - L Galal
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidemiology of chronic diseases in tropical zone, Institute of Epidemiology and Tropical Neurology, OmegaHealth, Limoges, France
| | - M L Dardé
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidemiology of chronic diseases in tropical zone, Institute of Epidemiology and Tropical Neurology, OmegaHealth, Limoges, France
- Centre National de Référence (CNR) Toxoplasmose Centre Hospitalier-Universitaire Dupuytren, Limoges, France
| | - A Balea
- University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Faculty of Veterinary Medicine, Department of Parasitology and Parasitic Diseases, Cluj-Napoca, Romania
| | - F Spano
- Italian National Institute of Health, Rome, Italy
| | - C Schulze
- Landeslabor Berlin-Brandenburg, Frankfurt (Oder), Germany
| | - M Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, Standort Arnsberg, Arnsberg, Germany
| | - N Scuda
- Bavarian Health and Food Safety Authority, Erlangen, Germany
| | - A Lundén
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - R K Davidson
- Department of Animal Health, Welfare and Food Safety, Norwegian Veterinary Institute, Tromsø, Norway
| | - R Terland
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
| | - H Waap
- Parasitology Laboratory, Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, Portugal
| | - E de Bruin
- Dutch Wildlife Health Centre, Pathology Division, Department of Pathobiology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
| | - P Vatta
- Italian National Institute of Health, Rome, Italy
| | - S Caccio
- Italian National Institute of Health, Rome, Italy
| | - L M Ortega-Mora
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - P Jokelainen
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - G Schares
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald - Insel Riems, Germany.
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115
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Bikk A, Chaudhari J, Navaran P, Johnson L, Pandit V. Methamphetamine spasm in the large caliber arteries-the severity is likely underestimated. J Vasc Surg Cases Innov Tech 2024; 10:101376. [PMID: 38130364 PMCID: PMC10731595 DOI: 10.1016/j.jvscit.2023.101376] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/06/2023] [Indexed: 12/23/2023] Open
Abstract
This report describes two cases of rarely reported, severe large arterial vascular spasms seen on computed tomography images after methamphetamine abuse. Although the effects of methamphetamine on the central nervous system and smaller arteries are relatively well known, its effects on large caliber arteries are rarely discussed. We present two cases of severe large arterial multisegmented vasospasm, captured on contrast-enhanced computed tomography, several hours after methamphetamine abuse. One of the patients was discharged without apparent tissue loss or organ failure. The other developed severe heart failure, liver failure, and toe gangrene. The publication of the de-identified images has been approved by the VA Central California Health Care System's Research and Development Committee and Privacy Officer. Vascular surgeons and, perhaps, acute care physicians, who are usually aware of small arterial vasospastic conditions, should also be aware of this methamphetamine-induced large arterial finding, which can be quite dramatic in appearance on imaging.
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Affiliation(s)
- Andras Bikk
- Department of Surgery, VA Central California Health Care System, Fresno, CA
| | - Jeffery Chaudhari
- Department of Surgery, VA Central California Health Care System, Fresno, CA
| | - Prashanth Navaran
- Department for Surgery, VA Pacific Islands Health Care, Honolulu, HI
| | - Lauren Johnson
- Department of Surgery, VA Central California Health Care System, Fresno, CA
| | - Viraj Pandit
- Department of Surgery, VA Central California Health Care System, Fresno, CA
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116
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El-Kadi RA, AbdelKader NF, Zaki HF, Kamel AS. Influence of β-catenin signaling on neurogenesis in neuropsychiatric disorders: Anxiety and depression. Drug Dev Res 2024; 85:e22157. [PMID: 38349261 DOI: 10.1002/ddr.22157] [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: 11/02/2023] [Revised: 12/28/2023] [Accepted: 01/21/2024] [Indexed: 02/15/2024]
Abstract
It has been proven that stress, mainly in the early years of life, can lead to anxiety and mood problems. Current treatments for psychiatric disorders are not enough, and some of them show intolerable side effects, emphasizing the urgent need for new treatment targets. Hence, a better understanding of the different brain networks, which are involved in the response to anxiety and depression, may evoke treatments with more specific targets. One of these targets is β-catenin that regulates brain circuits. β-Catenin has a dual response toward stress, which may influence coping or vulnerability to stress response. Indeed, β-catenin signaling involves several processes such as inflammation-directed brain repair, inflammation-induced brain damage, and neurogenesis. Interestingly, β-catenin reduction is accompanied by low neurogenesis, which leads to anxiety and depression. However, in another state, this reduction activates a compensatory mechanism that enhances neurogenesis to protect against depression but may precipitate anxiety. Thus, understanding the molecular mechanism of β-catenin could enhance our knowledge about anxiety and depression's pathophysiology, potentially improving clinical results by targeting it. Herein, the different states of β-catenin were discussed, shedding light on possible drugs that showed action on psychiatric disorders through β-catenin.
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Affiliation(s)
| | - Noha F AbdelKader
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Hala F Zaki
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ahmed S Kamel
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Vivek Hari Sundar G, Madhu A, Archana A, Shivaprasad PV. Plant histone variants at the nexus of chromatin readouts, stress and development. Biochim Biophys Acta Gen Subj 2024; 1868:130539. [PMID: 38072208 DOI: 10.1016/j.bbagen.2023.130539] [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: 06/02/2023] [Revised: 11/21/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
Histones are crucial proteins that are involved in packaging the DNA as condensed chromatin inside the eukaryotic cell nucleus. Rather than being static packaging units, these molecules undergo drastic variations spatially and temporally to facilitate accessibility of DNA to replication, transcription as well as wide range of gene regulatory machineries. In addition, incorporation of paralogous variants of canonical histones in the chromatin is ascribed to specific functions. Given the peculiar requirement of plants to rapidly modulate gene expression levels on account of their sessile nature, histones and their variants serve as additional layers of gene regulation. This review summarizes the mechanisms and implications of distribution, modifications and differential incorporation of histones and their variants across plant genomes, and outlines emerging themes.
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Affiliation(s)
- G Vivek Hari Sundar
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India
| | - Aravind Madhu
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India; SASTRA University, Thirumalaisamudram, Thanjavur 613 401, India
| | - A Archana
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India; SASTRA University, Thirumalaisamudram, Thanjavur 613 401, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India.
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118
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Gohari G, Jiang M, Manganaris GA, Zhou J, Fotopoulos V. Next generation chemical priming: with a little help from our nanocarrier friends. Trends Plant Sci 2024; 29:150-166. [PMID: 38233253 DOI: 10.1016/j.tplants.2023.11.024] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/19/2024]
Abstract
Plants are exposed to multiple threats linked to climate change which can cause critical yield losses. Therefore, designing novel crop management tools is crucial. Chemical priming has recently emerged as an effective technology for improving tolerance to stress factors. Several compounds such as phytohormones, reactive species, and synthetic chimeras have been identified as promising priming agents. Following remarkable developments in nanotechnology, several unique nanocarriers (NCs) have been engineered that can act as smart delivery systems. These provide an eco-friendly, next-generation method for chemical priming, leading to increased efficiency and reduced overall chemical usage. We review novel engineered NCs (NENCs) as vehicles for chemical agents in advanced priming strategies, and address challenges and opportunities to be met towards achieving sustainable agriculture.
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Affiliation(s)
- Gholamreza Gohari
- Department of Agricultural Sciences Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus; Department of Horticulture, Faculty of Horticulture, University of Maragheh, Maragheh, Iran
| | - Meng Jiang
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, PR China
| | - George A Manganaris
- Department of Agricultural Sciences Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Jie Zhou
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, PR China; Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, PR China
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus.
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119
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Xu G, Law JA. Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation. Curr Opin Genet Dev 2024; 84:102147. [PMID: 38176333 PMCID: PMC10922829 DOI: 10.1016/j.gde.2023.102147] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
DNA methylation is a conserved epigenetic modification associated with transposon silencing and gene regulation. The stability of this modification relies on intimate connections between DNA and histone modifications that generate self-reinforcing loops wherein the presence of one mark promotes the other. However, it is becoming increasingly clear that the efficiency of these loops is affected by cross-talk between pathways and by chromatin accessibility, which is heavily influenced by histone variants. Focusing primarily on plants, this review provides an update on the aforementioned self-reinforcing loops, highlights recent advances in understanding how DNA methylation pathways are restricted to prevent encroachment on genes, and discusses the roles of histone variants in compartmentalizing epigenetic pathways within the genome. This multilayered approach facilitates two essential, yet opposing functions, the ability to maintain heritable DNA methylation patterns while retaining the flexibility to modify these patterns during development.
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Affiliation(s)
- Guanghui Xu
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA. https://twitter.com/@GuanghuiXu1
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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Yi Y, Wang Y, Wu Y, Liu Y. Targeting SIRT4/TET2 Signaling Alleviates Human Keratinocyte Senescence by Reducing 5-hydroxymethylcytosine Loss. J Transl Med 2024; 104:100268. [PMID: 37898292 DOI: 10.1016/j.labinv.2023.100268] [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: 04/06/2023] [Revised: 10/07/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023] Open
Abstract
Skin aging is characterized by wrinkle formation and increased frailty and laxity, leading to the risk of age-related skin diseases. Keratinocyte is an important component of the epidermis in skin structure, and keratinocyte senescence has been identified as a pivotal factor in skin aging development. Because epigenetic pathways play a vital role in the regulation of skin aging, we evaluated human skin samples for DNA hydroxymethylation (5-hydroxymethylcytosine; 5-hmC) and SIRT4 expressions. Results found that both 5-hmC and SIRT4 showed a significant decrease in aged human skin samples. To test the results in vitro, human keratinocytes were cultured in H2O2, which modulates skin aging in vivo. However, H2O2-induced keratinocytes showed senescence-associated protein expression and significant downregulation of 5-hmC and SIRT4 expressions. Moreover, 5-hmC-converting enzymes ten eleven translocation 2 (TET2) showed a decrease and enhanced TET2 acetylation level in H2O2-induced keratinocytes. However, the overexpression of SIRT4 in keratinocytes alleviates the senescence phenotype, such as senescence-associated protein expression, decreases the TET2 acetylation, but increases TET2 and 5-hmC expressions. Our results provide a novel relevant mechanism whereby the epigenetic regulation of keratinocytes in skin aging may be correlated with SIRT4 expression and TET2 acetylation in 5-hmC alteration. Our study may provide a potential strategy for antiskin aging, which targets the SIRT4/TET2 axis involving epigenetic modification in keratinocyte senescence.
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Affiliation(s)
- Yi Yi
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Yuchang Wang
- Trauma Center/Department of Emergency and Traumatic Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yiping Wu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Yukun Liu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China.
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121
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Fadl J, Aljuhani RA, Albog YH, Khraisat AF, Alsubaie KA. Role of microRNA in Sex Steroid Hormones Signaling and Its Effect in Regulation of Endometrial, Ovarian, and Cervical Cancer: A Literature Review. Cureus 2024; 16:e54773. [PMID: 38523927 PMCID: PMC10961145 DOI: 10.7759/cureus.54773] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 03/26/2024] Open
Abstract
Worldwide, in 2020, an estimated 417,367 people were diagnosed with uterine cancer. Endometrial cancer accounts for more than 90% of all uterine cancers. The 15th most frequent cancer overall and the sixth most frequent cancer in women is endometrial cancer. Global ovarian cancer Incidence was diagnosed estimated at 313,959 new cases worldwide in 2020. Cervical cancer is the fourth most common malignancy in women worldwide. It has been demonstrated that sex steroid hormones (SSHs) have an essential role in regulating the susceptibility of cancer to cytotoxic therapy. Dysregulation of DNA repair contributes to genomic instability, aberrant cell survival, and cancer development as well as therapy resistance. Several crucial DNA repair components have been discovered to interact with the three main SSHs: androgen, estrogen, and progesterone. MicroRNA (miRNA) dysregulation has been associated with aberrant sex steroid hormone signaling as well as an increased risk of endometrial, cervical, and ovarian cancer. The expression of estrogen and progesterone receptors is modulated by a number of miRNAs, and it has been demonstrated that the miRNA expression profile may predict the way a patient would respond to hormone therapy. Additionally, particular miRNAs have been linked to the control of genes involved in signaling pathways connected to hormones. Recent research has shown that miRNAs can modify hormone signaling pathways and affect the expression of sex steroid hormone receptors. Our goal in this literature review is to present an overview of current knowledge regarding the role of miRNAs in cancers regulated by sex steroid hormone pathways, as well as to identify particular miRNA targets for hormonal therapy.
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Affiliation(s)
- Jina Fadl
- Obstetrics and Gynaecology, Batterjee Medical College, Jeddah, SAU
| | | | - Yusef H Albog
- Obstetrics and Gynaecology, Batterjee Medical College, Jeddah, SAU
| | - Ayda F Khraisat
- Obstetrics and Gynaecology, Batterjee Medical College, Jeddah, SAU
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122
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Bharti H, Han S, Chang HW, Reinberg D. Polycomb repressive complex 2 accessory factors: rheostats for cell fate decision? Curr Opin Genet Dev 2024; 84:102137. [PMID: 38091876 DOI: 10.1016/j.gde.2023.102137] [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: 10/04/2023] [Accepted: 11/15/2023] [Indexed: 02/12/2024]
Abstract
Epigenetic reprogramming during development is key to cell identity and the activities of the Polycomb repressive complexes are vital for this process. We focus on polycomb repressive complex 2 (PRC2), which catalyzes H3K27me1/2/3 and safeguards cellular integrity by ensuring proper gene repression. Notably, various accessory factors associate with PRC2, strongly influencing cell fate decisions, and their deregulation contributes to various illnesses. Yet, the exact role of these factors during development and carcinogenesis is not fully understood. Here, we present recent progress toward addressing these points and an analysis of the expression levels of PRC2 accessory factors in various tissues and developmental stages to highlight their abundance and roles. Last, we evaluate their contribution to cancer-specific phenotypes, providing insight into novel anticancer therapies.
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Affiliation(s)
- Hina Bharti
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Sungwook Han
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Han-Wen Chang
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA.
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123
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Nylund P, Garrido-Zabala B, Párraga AA, Vasquez L, Pyl PT, Harinck GM, Ma A, Jin J, Öberg F, Kalushkova A, Wiklund HJ. PVT1 interacts with polycomb repressive complex 2 to suppress genomic regions with pro-apoptotic and tumour suppressor functions in multiple myeloma. Haematologica 2024; 109:567-577. [PMID: 37496441 PMCID: PMC10828784 DOI: 10.3324/haematol.2023.282965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/01/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Multiple myeloma is a heterogeneous hematological disease that originates from the bone marrow and is characterized by the monoclonal expansion of malignant plasma cells. Despite novel therapies, multiple myeloma remains clinically challenging. A common feature among patients with poor prognosis is the increased activity of the epigenetic silencer EZH2, which is the catalytic subunit of the PRC2. Interestingly, the recruitment of PRC2 lacks sequence specificity and, to date, the molecular mechanisms that define which genomic locations are destined for PRC2-mediated silencing remain unknown. The presence of a long non-coding RNA (lncRNA)-binding pocket on EZH2 suggests that lncRNA could potentially mediate PRC2 recruitment to specific genomic regions. Here, we coupled RNA immunoprecipitation sequencing, RNA-sequencing and chromatin immunoprecipitation-sequencing analysis of human multiple myeloma primary cells and cell lines to identify potential lncRNA partners to EZH2. We found that the lncRNA plasmacytoma variant translocation 1 (PVT1) directly interacts with EZH2 and is overexpressed in patients with a poor prognosis. Moreover, genes predicted to be targets of PVT1 exhibited H3K27me3 enrichment and were associated with pro-apoptotic and tumor suppressor functions. In fact, PVT1 inhibition independently promotes the expression of the PRC2 target genes ZBTB7C, RNF144A and CCDC136. Altogether, our work suggests that PVT1 is an interacting partner in PRC2-mediated silencing of tumor suppressor and pro-apoptotic genes in multiple myeloma, making it a highly interesting potential therapeutic target.
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Affiliation(s)
- Patrick Nylund
- Science for Life Laboratory, Department of Immunology, Genetic and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala.
| | - Berta Garrido-Zabala
- Science for Life Laboratory, Department of Immunology, Genetic and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala
| | - Alba Atienza Párraga
- Science for Life Laboratory, Department of Immunology, Genetic and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala
| | - Louella Vasquez
- Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund
| | - Paul Theodor Pyl
- Department of Clinical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory Lund University, Lund
| | - George Mickhael Harinck
- Science for Life Laboratory, Department of Immunology, Genetic and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala
| | - Anqi Ma
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Fredrik Öberg
- Science for Life Laboratory, Department of Immunology, Genetic and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala
| | - Antonia Kalushkova
- Science for Life Laboratory, Department of Immunology, Genetic and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala
| | - Helena Jernberg Wiklund
- Science for Life Laboratory, Department of Immunology, Genetic and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala.
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Hargreave M, Jezek AH, Hemmingsen CH, Andersen EA, Pagsberg AK, Holmberg T, Mørch LS, Kjaer SK. Maternal use of hormonal contraception and risk of childhood autism spectrum disorders: A Parental Exposures and Child Health (PECH) cohort study. Psychiatry Res 2024; 332:115695. [PMID: 38157710 DOI: 10.1016/j.psychres.2023.115695] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
A recent hypothesis suggests that maternal hormonal contraception use has contributed to the increasing incidence of autism spectrum disorders (ASD). We used a nationwide population-based cohort (the PECH cohort) including 1,056,149 Danish children born in the period January 1, 1998, to December 31, 2014, to assess associations between maternal hormonal contraception use and childhood ASD (end of follow-up: December 31, 2017). Maternal hormonal contraception use was grouped as "recent use" (≤ 3 months before pregnancy start or during pregnancy), "previous use" (>3 months before pregnancy start) and "never use", except for few products. Incidence rate ratios (IRRs) were estimated using Poisson regression. During follow-up of nearly 12 million person-years, 19,996 children were diagnosed with ASD. A slightly higher IRR was observed for maternal recent use of any hormonal contraception, compared to previous use. This association was largely driven by the non-oral progestin-only products, and associations were especially seen for infantile autism and other/unspecified ASD. An increased IRR of infantile autism was also observed for recent use of the oral progestin-only products, compared to previous use. Our results suggest that maternal use of hormonal contraception may be associated with ASD risk in children, especially for the progestin-only products.
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Affiliation(s)
- Marie Hargreave
- Virus, Lifestyle and Genes, Danish Cancer Institute, Copenhagen DK-2100, Denmark.
| | - Andrea H Jezek
- Virus, Lifestyle and Genes, Danish Cancer Institute, Copenhagen DK-2100, Denmark
| | | | | | - Anne K Pagsberg
- Child and Adolescent Mental Health Center, Mental Health Services, Capital Region of Denmark, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Lina S Mørch
- Cancer Surveillance and Pharmacoepidemiology, Danish Cancer Institute, Copenhagen, Denmark
| | - Susanne K Kjaer
- Virus, Lifestyle and Genes, Danish Cancer Institute, Copenhagen DK-2100, Denmark; Department of Gynecology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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125
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Luchsinger-Morcelle SJ, Gribnau J, Mira-Bontenbal H. Orchestrating Asymmetric Expression: Mechanisms behind Xist Regulation. Epigenomes 2024; 8:6. [PMID: 38390897 PMCID: PMC10885031 DOI: 10.3390/epigenomes8010006] [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: 12/20/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Compensation for the gene dosage disequilibrium between sex chromosomes in mammals is achieved in female cells by repressing one of its X chromosomes through a process called X chromosome inactivation (XCI), exemplifying the control of gene expression by epigenetic mechanisms. A critical player in this mechanism is Xist, a long, non-coding RNA upregulated from a single X chromosome during early embryonic development in female cells. Over the past few decades, many factors involved at different levels in the regulation of Xist have been discovered. In this review, we hierarchically describe and analyze the different layers of Xist regulation operating concurrently and intricately interacting with each other to achieve asymmetric and monoallelic upregulation of Xist in murine female cells. We categorize these into five different classes: DNA elements, transcription factors, other regulatory proteins, long non-coding RNAs, and the chromatin and topological landscape surrounding Xist.
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Affiliation(s)
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Hegias Mira-Bontenbal
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
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126
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Augustyniak M, Ajay AK, Kędziorski A, Tarnawska M, Rost-Roszkowska M, Flasz B, Babczyńska A, Mazur B, Rozpędek K, Alian RS, Skowronek M, Świerczek E, Wiśniewska K, Ziętara P. Survival, growth and digestive functions after exposure to nanodiamonds - Transgenerational effects beyond contact time in house cricket strains. Chemosphere 2024; 349:140809. [PMID: 38036229 DOI: 10.1016/j.chemosphere.2023.140809] [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: 09/09/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/02/2023]
Abstract
The long-term exposure effects of nanodiamonds (NDs), spanning an organism's entire lifespan and continuing for subsequent generation, remain understudied. Most research has focused on evaluating their biological impacts on cell lines and selected organisms, typically over short exposure durations lasting hours or days. The study aimed to assess growth, mortality, and digestive functions in wild (H) and long-lived (D) strains of Acheta domesticus (Insecta: Orthoptera) after two-generational exposure to NDs in concentrations of 0.2 or 2 mg kg-1 of food, followed by their elimination in the third generation. NDs induced subtle stimulating effect that depended on the strain and generation. In the first generation, more such responses occurred in the H than in the D strain. In the first generation of H strain insects, contact with NDs increased survival, stimulated the growth of young larvae, and the activity of most digestive enzymes in mature adults. The same doses and exposure time did not cause similar effects in the D strain. In the first generation of D strain insects, survival and growth were unaffected by NDs, whereas, in the second generation, significant stimulation of those parameters was visible. Selection towards longevity appears to support higher resistance of the insects to exposure to additional stressor, at least in the first generation. The cessation of ND exposure in the third generation caused potentially harmful changes, which included, e.g., decreased survival probability in H strain insects, slowed growth of both strains, as well as changes in heterochromatin density and distribution in nuclei of the gut cells in both strains. Such a reaction may suggest the involvement of epigenetic inheritance mechanisms, which may become inadequate after the stress factor is removed.
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Affiliation(s)
- Maria Augustyniak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland.
| | - Amrendra K Ajay
- Department of Medicine, Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrzej Kędziorski
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Monika Tarnawska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Magdalena Rost-Roszkowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Barbara Flasz
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Agnieszka Babczyńska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Beata Mazur
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Katarzyna Rozpędek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Reyhaneh Seyed Alian
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Magdalena Skowronek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Ewa Świerczek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Klaudia Wiśniewska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Patrycja Ziętara
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
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127
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Mathes A, Duman MB, Neumann A, Dobreva G, Schmidt T. S-adenosylmethionine treatment affects histone methylation in prostate cancer cells. Gene 2024; 893:147915. [PMID: 37866662 DOI: 10.1016/j.gene.2023.147915] [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: 08/03/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
S-adenosylmethionine (SAM) represents a potent inhibitor of cancer cell proliferation, migration, and invasionin vitro.The underlying mechanisms remain elusive. Here, we examined, if treatment with SAM may cause alterations in the methylation of the histone marks H3K4me3 and H3K27me3, which are both known to play important roles in the initiation and progression of prostate cancer. We treated PC-3 cells with 200 µmol SAM, a concentration known to cause anticancerogenic effects, followed by ChIP-sequencing for H3K4me3 and H3K27me3. We detected 236 differentially methylated regions for H3K27me3 and 560 differentially methylated regions for H3K4me3. GO Term enrichment showed upregulation of anticancerogenic, as well as downregulation of cancerogenic related biological processes, molecular functions, and pathways. Furthermore, we compared specific methylation profiles of SAM treated samples to gene expression changes (RNA-Seq). 35 upregulated and 56 downregulated genes (total: 604 differentially expressed genes) could be related to hypomethylated and hypermethylated regions. 17 upregulated genes could be identified as tumor suppressor genes, 45 downregulated genes in contrast are considered as oncogenes. As a conclusion it can be stated that SAM treatment of prostate cancer cells resulted in alterations of H3K4me3 and H3K27me3 methylation profiles. Gene to peak annotation, alignment with results of a transcriptome study as well as GO-term analysis underpinned the biological relevance of methylation changes.
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Affiliation(s)
- Arthur Mathes
- Cardiovascular Genomics and Epigenomics, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | | | - Gergana Dobreva
- Cardiovascular Genomics and Epigenomics, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Schmidt
- Anatomy and Developmental Biology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
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Dai XJ, Ji SK, Fu MJ, Liu GZ, Liu HM, Wang SP, Shen L, Wang N, Herdewijn P, Zheng YC, Wang SQ, Chen XB. Degraders in epigenetic therapy: PROTACs and beyond. Theranostics 2024; 14:1464-1499. [PMID: 38389844 PMCID: PMC10879860 DOI: 10.7150/thno.92526] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/21/2024] [Indexed: 02/24/2024] Open
Abstract
Epigenetics refers to the reversible process through which changes in gene expression occur without changing the nucleotide sequence of DNA. The process is currently gaining prominence as a pivotal objective in the treatment of cancers and other ailments. Numerous drugs that target epigenetic mechanisms have obtained approval from the Food and Drug Administration (FDA) for the therapeutic intervention of diverse diseases; many have drawbacks, such as limited applicability, toxicity, and resistance. Since the discovery of the first proteolysis-targeting chimeras (PROTACs) in 2001, studies on targeted protein degradation (TPD)-encompassing PROTACs, molecular glue (MG), hydrophobic tagging (HyT), degradation TAG (dTAG), Trim-Away, a specific and non-genetic inhibitor of apoptosis protein (IAP)-dependent protein eraser (SNIPER), antibody-PROTACs (Ab-PROTACs), and other lysosome-based strategies-have achieved remarkable progress. In this review, we comprehensively highlight the small-molecule degraders beyond PROTACs that could achieve the degradation of epigenetic proteins (including bromodomain-containing protein-related targets, histone acetylation/deacetylation-related targets, histone methylation/demethylation related targets, and other epigenetic targets) via proteasomal or lysosomal pathways. The present difficulties and forthcoming prospects in this domain are also deliberated upon, which may be valuable for medicinal chemists when developing more potent, selective, and drug-like epigenetic drugs for clinical applications.
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Affiliation(s)
- Xing-Jie Dai
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shi-Kun Ji
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Meng-Jie Fu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Gao-Zhi Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hui-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shao-Peng Wang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Liang Shen
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ning Wang
- The School of Chinese Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Piet Herdewijn
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000 Leuven, Belgium
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Sai-Qi Wang
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, China
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer & Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
| | - Xiao-Bing Chen
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, China
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer & Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
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129
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Ehrlich M, Ehrlich KC, Lacey M, Baribault C, Sen S, Estève PO, Pradhan S. Epigenetics of Genes Preferentially Expressed in Dissimilar Cell Populations: Myoblasts and Cerebellum. Epigenomes 2024; 8:4. [PMID: 38390894 PMCID: PMC10885033 DOI: 10.3390/epigenomes8010004] [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: 12/12/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
While studying myoblast methylomes and transcriptomes, we found that CDH15 had a remarkable preference for expression in both myoblasts and cerebellum. To understand how widespread such a relationship was and its epigenetic and biological correlates, we systematically looked for genes with similar transcription profiles and analyzed their DNA methylation and chromatin state and accessibility profiles in many different cell populations. Twenty genes were expressed preferentially in myoblasts and cerebellum (Myob/Cbl genes). Some shared DNA hypo- or hypermethylated regions in myoblasts and cerebellum. Particularly striking was ZNF556, whose promoter is hypomethylated in expressing cells but highly methylated in the many cell populations that do not express the gene. In reporter gene assays, we demonstrated that its promoter's activity is methylation sensitive. The atypical epigenetics of ZNF556 may have originated from its promoter's hypomethylation and selective activation in sperm progenitors and oocytes. Five of the Myob/Cbl genes (KCNJ12, ST8SIA5, ZIC1, VAX2, and EN2) have much higher RNA levels in cerebellum than in myoblasts and displayed myoblast-specific hypermethylation upstream and/or downstream of their promoters that may downmodulate expression. Differential DNA methylation was associated with alternative promoter usage for Myob/Cbl genes MCF2L, DOK7, CNPY1, and ANK1. Myob/Cbl genes PAX3, LBX1, ZNF556, ZIC1, EN2, and VAX2 encode sequence-specific transcription factors, which likely help drive the myoblast and cerebellum specificity of other Myob/Cbl genes. This study extends our understanding of epigenetic/transcription associations related to differentiation and may help elucidate relationships between epigenetic signatures and muscular dystrophies or cerebellar-linked neuropathologies.
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Hayward Human Genetics Center, Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Kenneth C Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
| | - Carl Baribault
- Information Technology, Tulane University, New Orleans, LA 70118, USA
| | - Sagnik Sen
- Genome Biology Division, New England Biolabs, Ipswich, MA 01938, USA
| | | | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Ipswich, MA 01938, USA
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Stark MS, Sturm RA, Pan Y, Smit DJ, Kommajosyula V, Lee KJ, Jagirdar K, McLean C, Duffy DL, Soyer HP, Mar VJ. Assessing the genetic risk of nodular melanoma using a candidate gene approach. Br J Dermatol 2024; 190:199-206. [PMID: 37766469 DOI: 10.1093/bjd/ljad365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/16/2023] [Revised: 08/28/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
BACKGROUND Nodular melanoma (NM) is a challenge to diagnose early due to its rapid growth and more atypical clinical presentation, making it the largest contributor to melanoma mortality. OBJECTIVES Our study aim was to perform a rare-variant allele (RVA) analysis of whole-exome sequencing of patients with NM and non-NM (minor allele frequency ≤ 1% non-Finnish European) for a set of 500 candidate genes potentially implicated in melanoma. METHODS This study recruited 131 participants with NM and 194 with non-NM from South-east Queensland and patients with NM from Victoria to perform a comparative analysis of possible genetic differences or similarities between the two melanoma cohorts. RESULTS Phenotypic analysis revealed that a majority of patients diagnosed with NM were older males with a higher frequency of fair skin and red hair than is seen in the general population. The distribution of common melanoma polygenic risk scores was similar in patients with NM and non-NM, with over 28% in the highest quantile of scores. There was also a similar frequency of carriage of familial/high-penetrant melanoma gene and loss-of-function variants. We identified 39 genes by filtering 500 candidate genes based on the greatest frequency in NM compared with non-NM cases. The genes with RVAs of greatest frequency in NM included PTCH1, ARID2 and GHR. Rare variants in the SMO gene, which interacts with PTCH1 as ligand and receptor, were also identified, providing evidence that the Hedgehog pathway may contribute to NM risk. There was a cumulative effect in carrying multiple rare variants in the NM-associated genes. A 14.8-fold increased ratio for NM compared with non-NM was seen when two RVAs of the 39 genes were carried by a patient. CONCLUSIONS This study highlights the importance of considering frequency of RVA to identify those at risk of NM in addition to known high penetrance genes.
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Affiliation(s)
- Mitchell S Stark
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Richard A Sturm
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Yan Pan
- Victorian Melanoma Service, The Alfred Hospital, Melbourne, Vic, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences
| | - Darren J Smit
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Varsha Kommajosyula
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Katie J Lee
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Kasturee Jagirdar
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Catriona McLean
- Victorian Melanoma Service, The Alfred Hospital, Melbourne, Vic, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences
| | - David L Duffy
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - H Peter Soyer
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
| | - Victoria J Mar
- Victorian Melanoma Service, The Alfred Hospital, Melbourne, Vic, Australia
- School of Public Health and Preventive Medicine; Monash University, Melbourne, Vic, Australia
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131
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Godwin J, Govindasamy M, Nedounsejian K, March E, Halton R, Bourbousse C, Wolff L, Fort A, Krzyszton M, López Corrales J, Swiezewski S, Barneche F, Schubert D, Farrona S. The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development. Nat Commun 2024; 15:667. [PMID: 38253560 PMCID: PMC10803359 DOI: 10.1038/s41467-023-44546-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. In recent years, there is increasing evidence of the complexity of PRCs' interaction networks and the interplay of these interactors with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a chromatin player able to counteract the deposition of the two PRCs' epigenetic hallmarks in Arabidopsis thaliana. We demonstrated that UBP5 is a plant developmental regulator based on functional analyses of ubp5-CRISPR Cas9 mutant plants. UBP5 promotes H2A monoubiquitination erasure, leading to transcriptional de-repression. Furthermore, preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining in ubp5 mutant plants suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, acting as an antagonist of the pivotal epigenetic repressive marks H2Aub and H3K27me3, UBP5 provides novel insights to disentangle the complex regulation of PRCs' activities.
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Affiliation(s)
- James Godwin
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Mohan Govindasamy
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Kiruba Nedounsejian
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Eduardo March
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Ronan Halton
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Clara Bourbousse
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léa Wolff
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Antoine Fort
- Dept. of Veterinary and Microbial Sciences, Technological University of The Shannon: Midlands, Athlone, Co., Roscommon, Ireland
| | - Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw, 02-106, Poland
| | - Jesús López Corrales
- Molecular Parasitology Laboratory (MPL), Centre for One Health and Ryan Institute, School of Natural Sciences, University of Galway, Galway, H91 DK59, Ireland
| | - Szymon Swiezewski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw, 02-106, Poland
| | - Fredy Barneche
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Daniel Schubert
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Sara Farrona
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland.
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Seif E, Francis NJ. A Two-Step Mechanism for Creating Stable, Condensed Chromatin with the Polycomb Complex PRC1. Molecules 2024; 29:323. [PMID: 38257239 PMCID: PMC10821450 DOI: 10.3390/molecules29020323] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
The Drosophila PRC1 complex regulates gene expression by modifying histone proteins and chromatin architecture. Two PRC1 subunits, PSC and Ph, are most implicated in chromatin architecture. In vitro, PRC1 compacts chromatin and inhibits transcription and nucleosome remodeling. The long disordered C-terminal region of PSC (PSC-CTR) is important for these activities, while Ph has little effect. In cells, Ph is important for condensate formation, long-range chromatin interactions, and gene regulation, and its polymerizing sterile alpha motif (SAM) is implicated in these activities. In vitro, truncated Ph containing the SAM and two other conserved domains (mini-Ph) undergoes phase separation with chromatin, suggesting a mechanism for SAM-dependent condensate formation in vivo. How the distinct activities of PSC and Ph on chromatin function together in PRC1 is not known. To address this question, we analyzed structures formed with large chromatin templates and PRC1 in vitro. PRC1 bridges chromatin into extensive fibrillar networks. Ph, its SAM, and SAM polymerization activity have little effect on these structures. Instead, the PSC-CTR controls their growth, and is sufficient for their formation. To understand how phase separation driven by Ph SAM intersects with the chromatin bridging activity of the PSC-CTR, we used mini-Ph to form condensates with chromatin and then challenged them with PRC1 lacking Ph (PRC1ΔPh). PRC1ΔPh converts mini-Ph chromatin condensates into clusters of small non-fusing condensates and bridged fibers. These condensates retain a high level of chromatin compaction and do not intermix. Thus, phase separation of chromatin by mini-Ph, followed by the action of the PSC-CTR, creates a unique chromatin organization with regions of high nucleosome density and extraordinary stability. We discuss how this coordinated sequential activity of two proteins found in the same complex may occur and the possible implications of stable chromatin architectures in maintaining transcription states.
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Affiliation(s)
- Elias Seif
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada;
| | - Nicole J. Francis
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada;
- Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montréal, QC H4A 3J1, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada
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Manan S, Bilal S. Editorial: Molecular regulation of seed development and storage reserve metabolism in crops. Front Plant Sci 2024; 14:1348252. [PMID: 38269135 PMCID: PMC10807039 DOI: 10.3389/fpls.2023.1348252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/29/2023] [Indexed: 01/26/2024]
Affiliation(s)
- Sehrish Manan
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Saqib Bilal
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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134
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Maleszka R. Reminiscences on the honeybee genome project and the rise of epigenetic concepts in insect science. Insect Mol Biol 2024. [PMID: 38196200 DOI: 10.1111/imb.12888] [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: 06/13/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
The sequencing of the honeybee genome in 2006 was an important technological and logistic achievement experience. But what benefits have flown from the honeybee genome project? What does the annotated genomic assembly mean for the study of behavioural complexity and organismal function in honeybees? Here, I discuss several lines of research that have arisen from this project and highlight the rapidly expanding studies on insect epigenomics, emergent properties of royal jelly, the mechanism of nutritional control of development and the contribution of epigenomic regulation to the evolution of sociality. I also argue that the term 'insect epigenetics' needs to be carefully redefined to reflect the diversity of epigenomic toolkits in insects and the impact of lineage-specific innovations on organismal outcomes. The honeybee genome project helped pioneer advances in social insect molecular biology, and fuelled breakthrough research into the role of flexible epigenomic control systems in linking genotype to phenotype.
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Affiliation(s)
- Ryszard Maleszka
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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135
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Calabrò L, Bronte G, Grosso F, Cerbone L, Delmonte A, Nicolini F, Mazza M, Di Giacomo AM, Covre A, Lofiego MF, Crinò L, Maio M. Immunotherapy of mesothelioma: the evolving change of a long-standing therapeutic dream. Front Immunol 2024; 14:1333661. [PMID: 38259475 PMCID: PMC10800748 DOI: 10.3389/fimmu.2023.1333661] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Pleural mesothelioma (PM) is an aggressive and rare disease, characterized by a very poor prognosis. For almost two decades, the world standard treatment regimen for unresectable PM has consisted of a platinum-based drug plus pemetrexed, leading to an overall survival of approximately 12 months. The dramatic therapeutic scenario of PM has recently changed with the entry into the clinic of immune checkpoint inhibition, which has proven to be an effective approach to improve the survival of PM patients. The aim of the present review is to provide a comprehensive overview of the most promising immunotherapeutic-based strategies currently under investigation for advanced PM.
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Affiliation(s)
- Luana Calabrò
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Oncology, University Hospital of Ferrara, Ferrara, Italy
| | - Giuseppe Bronte
- Department of Clinical and Molecular Sciences (DISCLIMO), Università Politecnica Delle Marche, Ancona, Italy
- Clinic of Laboratory and Precision Medicine, National Institute of Health and Sciences On Ageing (IRCCS INRCA), Ancona, Italy
| | - Federica Grosso
- Mesothelioma, Melanoma and Sarcoma Unit, Azienda Ospedaliera SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Luigi Cerbone
- Mesothelioma, Melanoma and Sarcoma Unit, Azienda Ospedaliera SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Angelo Delmonte
- Department of Medical Oncology, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Fabio Nicolini
- IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Massimiliano Mazza
- IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Anna Maria Di Giacomo
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, Department of Oncology, University Hospital of Siena, Siena, Italy
- Center for Immuno-Oncology, University of Siena, Siena, Italy
| | - Alessia Covre
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, Department of Oncology, University Hospital of Siena, Siena, Italy
- Center for Immuno-Oncology, University of Siena, Siena, Italy
- EPigenetic Immune-Oncology Consortium Airc (EPICA), Siena, Italy
| | - Maria Fortunata Lofiego
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, Department of Oncology, University Hospital of Siena, Siena, Italy
- Center for Immuno-Oncology, University of Siena, Siena, Italy
- EPigenetic Immune-Oncology Consortium Airc (EPICA), Siena, Italy
| | - Lucio Crinò
- Department of Medical Oncology, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Michele Maio
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, Department of Oncology, University Hospital of Siena, Siena, Italy
- Center for Immuno-Oncology, University of Siena, Siena, Italy
- EPigenetic Immune-Oncology Consortium Airc (EPICA), Siena, Italy
- Fondazione Network Italiano per la Bioterapia dei Tumori (NIBIT) Onlus, Siena, Italy
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Abdulraheem MI, Xiong Y, Moshood AY, Cadenas-Pliego G, Zhang H, Hu J. Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. Plants (Basel) 2024; 13:163. [PMID: 38256717 PMCID: PMC10820249 DOI: 10.3390/plants13020163] [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: 12/15/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.
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Affiliation(s)
- Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Yani Xiong
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Abiodun Yusuff Moshood
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Gregorio Cadenas-Pliego
- Centro de Investigación en Química Aplicada, Blvd. Enrique Reyna 140, Saltillo 25294, Mexico;
| | - Hao Zhang
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
| | - Jiandong Hu
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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137
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Grison S, Braga-Tanaka II, Baatout S, Klokov D. In utero exposure to ionizing radiation and metabolic regulation: perspectives for future multi- and trans-generation effects studies. Int J Radiat Biol 2024:1-14. [PMID: 38180060 DOI: 10.1080/09553002.2023.2295293] [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: 05/30/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024]
Abstract
PURPOSE The radiation protection community has been particularly attentive to the risks of delayed effects on offspring from low dose or low dose-rate exposures to ionizing radiation. Despite this, the current epidemiologic studies and scientific data are still insufficient to provide the necessary evidence for improving risk assessment guidelines. This literature review aims to inform future studies on multigenerational and transgenerational effects. It primarily focuses on animal studies involving in utero exposure and discusses crucial elements for interpreting the results. These elements include in utero exposure scenarios relative to the developmental stages of the embryo/fetus, and the primary biological mechanisms responsible for transmitting heritable or hereditary effects to future generations. The review addresses several issues within the contexts of both multigenerational and transgenerational effects, with a focus on hereditary perspectives. CONCLUSIONS Knowledge consolidation in the field of Developmental Origins of Health and Disease (DOHaD) has led us to propose a new study strategy. This strategy aims to address the transgenerational effects of in utero exposure to low dose and low dose-rate radiation. Within this concept, there is a possibility that disruption of epigenetic programming in embryonic and fetal cells may occur. This disruption could lead to metabolic dysfunction, which in turn may cause abnormal responses to future environmental challenges, consequently increasing disease risk. Lastly, we discuss methodological limitations in our studies. These limitations are related to cohort size, follow-up time, model radiosensitivity, and analytical techniques. We propose scientific and analytical strategies for future research in this field.
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Affiliation(s)
- Stéphane Grison
- PSE-SANTE, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay-aux-Roses, France
| | - Ignacia Iii Braga-Tanaka
- Department of Radiobiology, Institute for Environmental Sciences (IES), Rokkasho Kamikita, Aomori, Japan
| | - Sarah Baatout
- Belgian Nuclear Research Centre, SCK CEN, Institute of Nuclear Medical Applications, Mol, Belgium
- Department of Molecular Biotechnology (BW25) and Department of Human Structure and Repair (GE38), Ghent University, Ghent, Belgium
| | - Dmitry Klokov
- PSE-SANTE, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay-aux-Roses, France
- Department of Microbiology, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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Chow CN, Yang CW, Wu NY, Wang HT, Tseng KC, Chiu YH, Lee TY, Chang WC. PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters. Nucleic Acids Res 2024; 52:D1569-D1578. [PMID: 37897338 PMCID: PMC10767843 DOI: 10.1093/nar/gkad945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/14/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 species. PlantPAN 4.0 can help users characterize the evolutionary differences and similarities among cis-regulatory elements; furthermore, this system can now help in identification of conserved non-coding sequences among homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices for 18305 transcription factors; this expansion helps in exploration of combinational and nucleotide variants of cis-regulatory elements in conserved non-coding sequences. Additionally, the genomic landscapes of regulatory factors were manually updated, and ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) were added. Furthermore, the statistical review and graphical analysis components were improved to offer intelligible information through ChIP-seq data analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces for the identification of promoter regions' binding preferences by considering experimental condition clusters and peak visualization for all regulatory factors, and the 20 most significantly enriched gene ontology functions for regulatory factors. Thus, PlantPAN 4.0 can effectively reconstruct gene regulatory networks and help compare genomic cis-regulatory elements across plant species and experiments.
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Affiliation(s)
- Chi-Nga Chow
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
- School of Molecular Sciences, Arizona State University, Tempe 85281, USA
| | - Chien-Wen Yang
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Nai-Yun Wu
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Hung-Teng Wang
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Kuan-Chieh Tseng
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yu-Hsuan Chiu
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan 701, Taiwan
| | - Tzong-Yi Lee
- Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Wen-Chi Chang
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan 701, Taiwan
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Wu Z, Qu J, Zhang W, Liu GH. Stress, epigenetics, and aging: Unraveling the intricate crosstalk. Mol Cell 2024; 84:34-54. [PMID: 37963471 DOI: 10.1016/j.molcel.2023.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/22/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023]
Abstract
Aging, as a complex process involving multiple cellular and molecular pathways, is known to be exacerbated by various stresses. Because responses to these stresses, such as oxidative stress and genotoxic stress, are known to interplay with the epigenome and thereby contribute to the development of age-related diseases, investigations into how such epigenetic mechanisms alter gene expression and maintenance of cellular homeostasis is an active research area. In this review, we highlight recent studies investigating the intricate relationship between stress and aging, including its underlying epigenetic basis; describe different types of stresses that originate from both internal and external stimuli; and discuss potential interventions aimed at alleviating stress and restoring epigenetic patterns to combat aging or age-related diseases. Additionally, we address the challenges currently limiting advancement in this burgeoning field.
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Affiliation(s)
- Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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140
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LeeVan E, Pinsky P. Predictive Performance of Cell-Free Nucleic Acid-Based Multi-Cancer Early Detection Tests: A Systematic Review. Clin Chem 2024; 70:90-101. [PMID: 37791504 DOI: 10.1093/clinchem/hvad134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 06/02/2023] [Accepted: 07/24/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Cancer-screening tests that can detect multiple cancer types, or multi-cancer early detection (MCED) tests, have emerged recently as a potential new tool in decreasing cancer morbidity and mortality. Most MCED assays are based on detecting cell-free tumor DNA (CF-DNA) in the blood. MCEDs offer the potential for screening for cancer organ sites with high mortality, both with and without recommended screening. However, their clinical utility has not been established. Before clinical utility can be established, the clinical validity of MCEDs, i.e., their ability to predict cancer status, must be demonstrated. In this study we performed a systematic review of the predictive ability for cancer of cell-free-nucleic acid-based MCED tests. CONTENT We searched PubMed for relevant publications from January 2017 to February 2023, using MeSH terms related to multi-cancer detection, circulating DNA, and related concepts. Of 1811 publications assessed, 61 were reviewed in depth and 20 are included in this review. For almost all studies, the cancer cases were assessed at time of diagnosis. Most studies reported specificity (generally 95% or higher) and overall sensitivity (73% median). The median number of cancer types assessed per assay was 5. Many studies also reported sensitivity by stage and/or cancer type. Sensitivity generally increased with stage. SUMMARY To date, relatively few published studies have assessed the clinical validity of MCED tests. Most used cancer cases assessed at diagnosis, with generally high specificity and variable sensitivity depending on cancer type and stage. The next steps should be testing in the intended-use population, i.e., asymptomatic persons.
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Affiliation(s)
- Elyse LeeVan
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, United States
| | - Paul Pinsky
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, United States
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141
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Yan X, Xia Y, Li B, Ye Z, Li L, Yuan T, Song B, Yu W, Rao T, Ning J, Lin F, Mei S, Mao Z, Zhou X, Li W, Cheng F. The SOX4/EZH2/SLC7A11 signaling axis mediates ferroptosis in calcium oxalate crystal deposition-induced kidney injury. J Transl Med 2024; 22:9. [PMID: 38169402 PMCID: PMC10763321 DOI: 10.1186/s12967-023-04793-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/09/2023] [Indexed: 01/05/2024] Open
Abstract
Epigenetic regulation is reported to play a significant role in the pathogenesis of various kidney diseases, including renal cell carcinoma, acute kidney injury, renal fibrosis, diabetic nephropathy, and lupus nephritis. However, the role of epigenetic regulation in calcium oxalate (CaOx) crystal deposition-induced kidney injury remains unclear. Our study demonstrated that the upregulation of enhancer of zeste homolog 2 (EZH2)-mediated ferroptosis facilitates CaOx-induced kidney injury. CaOx crystal deposition promoted ferroptosis in vivo and in vitro. Usage of liproxstatin-1 (Lip-1), a ferroptosis inhibitor, mitigated CaOx-induced kidney damage. Single-nucleus RNA-sequencing, RNA-sequencing, immunohistochemical and western blotting analyses revealed that EZH2 was upregulated in kidney stone patients, kidney stone mice, and oxalate-stimulated HK-2 cells. Experiments involving in vivo EZH2 knockout, in vitro EZH2 knockdown, and in vivo GSK-126 (an EZH2 inhibitor) treatment confirmed the protective effects of EZH2 inhibition on kidney injury and ferroptosis. Mechanistically, the results of RNA-sequencing and chromatin immunoprecipitation assays demonstrated that EZH2 regulates ferroptosis by suppressing solute carrier family 7, member 11 (SLC7A11) expression through trimethylation of histone H3 lysine 27 (H3K27me3) modification. Additionally, SOX4 regulated ferroptosis by directly modulating EZH2 expression. Thus, this study demonstrated that SOX4 facilitates ferroptosis in CaOx-induced kidney injury through EZH2/H3K27me3-mediated suppression of SLC7A11.
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Affiliation(s)
- Xinzhou Yan
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Yuqi Xia
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Bojun Li
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Zehua Ye
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Lei Li
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Tianhui Yuan
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Baofeng Song
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Weimin Yu
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Ting Rao
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Jinzhuo Ning
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Fangyou Lin
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Shuqin Mei
- Department of Nephrology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, People's Republic of China
| | - Zhiguo Mao
- Department of Nephrology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, People's Republic of China
| | - Xiangjun Zhou
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China.
| | - Wei Li
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China.
| | - Fan Cheng
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China.
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Shan Y, Chen W, Li Y. The role of m 6A RNA methylation in autoimmune diseases: Novel therapeutic opportunities. Genes Dis 2024; 11:252-267. [PMID: 37588214 PMCID: PMC10425809 DOI: 10.1016/j.gendis.2023.02.013] [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: 06/07/2022] [Revised: 08/02/2022] [Accepted: 02/08/2023] [Indexed: 03/29/2023] Open
Abstract
N6-methyladenosine (m6A) modifications, as one of the most common forms of internal RNA chemical modifications in eukaryotic cells, have gained increasing attention in recent years. The m6A RNA modifications exert various crucial roles in various biological processes, such as embryonic development, neurogenesis, circadian rhythms, and tumorigenesis. Recent advances have highlighted that m6A RNA modification plays an important role in immune response, especially in the initiation and progression of autoimmune diseases. In this review, we summarized the regulatory mechanisms of m6A methylation and its biological functions in the immune system and mainly focused on recent progress in research on the potential role of m6A RNA methylation in the pathogenesis of autoimmune diseases, thus providing possible biomarkers and potential targets for the prevention and treatment of autoimmune diseases.
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Affiliation(s)
- Yunan Shan
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, China
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Neuroimmunology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong 250013, China
| | - Wei Chen
- Department of Gastroenterology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Yanbin Li
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Neuroimmunology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong 250013, China
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143
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Lismer A, Shao X, Dumargne MC, Lafleur C, Lambrot R, Chan D, Toft G, Bonde JP, MacFarlane AJ, Bornman R, Aneck-Hahn N, Patrick S, Bailey JM, de Jager C, Dumeaux V, Trasler JM, Kimmins S. The Association between Long-Term DDT or DDE Exposures and an Altered Sperm Epigenome-a Cross-Sectional Study of Greenlandic Inuit and South African VhaVenda Men. Environ Health Perspect 2024; 132:17008. [PMID: 38294233 PMCID: PMC10829569 DOI: 10.1289/ehp12013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/26/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND The organochlorine dichlorodiphenyltrichloroethane (DDT) is banned worldwide owing to its negative health effects. It is exceptionally used as an insecticide for malaria control. Exposure occurs in regions where DDT is applied, as well as in the Arctic, where its endocrine disrupting metabolite, p , p ' -dichlorodiphenyldichloroethylene (p , p ' -DDE) accumulates in marine mammals and fish. DDT and p , p ' -DDE exposures are linked to birth defects, infertility, cancer, and neurodevelopmental delays. Of particular concern is the potential of DDT use to impact the health of generations to come via the heritable sperm epigenome. OBJECTIVES The objective of this study was to assess the sperm epigenome in relation to p , p ' -DDE serum levels between geographically diverse populations. METHODS In the Limpopo Province of South Africa, we recruited 247 VhaVenda South African men and selected 50 paired blood serum and semen samples, and 47 Greenlandic Inuit blood and semen paired samples were selected from a total of 193 samples from the biobank of the INUENDO cohort, an EU Fifth Framework Programme Research and Development project. Sample selection was based on obtaining a range of p , p ' -DDE serum levels (mean = 870.734 ± 134.030 ng / mL ). We assessed the sperm epigenome in relation to serum p , p ' -DDE levels using MethylC-Capture-sequencing (MCC-seq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq). We identified genomic regions with altered DNA methylation (DNAme) and differential enrichment of histone H3 lysine 4 trimethylation (H3K4me3) in sperm. RESULTS Differences in DNAme and H3K4me3 enrichment were identified at transposable elements and regulatory regions involved in fertility, disease, development, and neurofunction. A subset of regions with sperm DNAme and H3K4me3 that differed between exposure groups was predicted to persist in the preimplantation embryo and to be associated with embryonic gene expression. DISCUSSION These findings suggest that DDT and p , p ' -DDE exposure impacts the sperm epigenome in a dose-response-like manner and may negatively impact the health of future generations through epigenetic mechanisms. Confounding factors, such as other environmental exposures, genetic diversity, and selection bias, cannot be ruled out. https://doi.org/10.1289/EHP12013.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marie-Charlotte Dumargne
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Christine Lafleur
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
| | - Romain Lambrot
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
| | - Donovan Chan
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Gunnar Toft
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Peter Bonde
- Department of Occupational and Environmental Medicine, Bispebjerg University Hospital, Copenhagen, Denmark
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Amanda J. MacFarlane
- Agriculture Food and Nutrition Evidence Center, Texas A&M University, Fort Worth, Texas, USA
| | - Riana Bornman
- Environmental Chemical Pollution and Health Research Unit, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Natalie Aneck-Hahn
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Sean Patrick
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Janice M. Bailey
- Research Centre on Reproduction and Intergenerational Health, Department of Animal Sciences, Université Laval, Quebec, Quebec, Canada
| | - Christiaan de Jager
- Environmental Chemical Pollution and Health Research Unit, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Vanessa Dumeaux
- Department of Anatomy and Cell Biology, Western University, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Jacquetta M. Trasler
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, University of Montreal, Quebec, Canada
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144
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Wang Y, Chen C, Yan W, Fu Y. Epigenetic modification of m 6A methylation: Regulatory factors, functions and mechanism in inflammatory bowel disease. Int J Biochem Cell Biol 2024; 166:106502. [PMID: 38030117 DOI: 10.1016/j.biocel.2023.106502] [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: 08/31/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
Although the exact cause of inflammatory bowel disease (IBD) is still unknown, there is a lot of evidence to support the notion that it results from a combination of environmental factors, immune system issues, gut microbial changes, and genetic susceptibility. In recent years, the role of epigenetics in the pathogenesis of IBD has drawn increasing attention. The regulation of IBD-related immunity, the preservation of the intestinal epithelial barrier, and autophagy are all significantly influenced by epigenetic factors. The most extensive epigenetic methylation modification of mammalian mRNA among them is N6-methyladenosine (m6A). It summarizes the general structure and function of the m6A regulating factors, as well as their complex effects on IBD by regulating the intestinal mucous barrier, intestine mucosal immunity, epidermal cell death, and intestinal microorganisms.This paper provides key insights for the future identification of potential new targets for the diagnosis and treatment of IBD.
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Affiliation(s)
- Yanping Wang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaoyue Chen
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yan
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yu Fu
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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145
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Grafft N, Lo B, Easton SD, Pineros-Leano M, Davison KK. Maternal and Paternal Adverse Childhood Experiences (ACEs) and Offspring Health and Wellbeing: A Scoping Review. Matern Child Health J 2024; 28:52-66. [PMID: 37914980 DOI: 10.1007/s10995-023-03825-y] [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] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Adverse childhood experiences (ACEs) are common, often co-occur, and are associated with poor health outcomes across the life course. Emerging research has emphasized the lasting consequences of ACEs across generations, suggesting parental ACEs are associated with poor physical and mental health outcomes in children. However, the individual effects of fathers' ACEs and pathways of transmission remain unclear. A scoping review was conducted to summarize the current knowledgebase of the intergenerational consequences of parental ACEs on offspring health, clarify pathways of transmission, understand how ACEs are operationalized in the intergenerational literature, and identify gaps in knowledge. METHODS Six electronic databases were searched for articles published in English from 1995 to 2022 relating to the long-term consequences of parental ACEs on offspring physical and mental health. Articles underwent title, abstract, and full-text review by two investigators. Content analysis was performed to integrate findings across the included studies. RESULTS The search yielded 14,542 unique articles; 49 met the inclusion criteria. Thirty-six articles focused exclusively on mothers, one solely on fathers, and 12 included both mothers and fathers in their analyses. Six studies used an expanded definition of ACEs. Both direct and indirect associations between parental ACEs and poor offspring outcomes were identified, primarily through biological and psychosocial pathways. CONCLUSIONS Findings underscore the importance and oversight of fathers and the need to solidify a unified definition and measure of ACEs. This review identified modifiable protective factors (social support, father involvement) and pathways of transmission (parental mental health, parenting); both having important implications for intervention development.
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Affiliation(s)
- Natalie Grafft
- Boston College School of Social Work, 140 Commonwealth Ave, Chestnut Hill, MA, 20467, USA.
| | - Brian Lo
- Boston College School of Social Work, 140 Commonwealth Ave, Chestnut Hill, MA, 20467, USA
| | - Scott D Easton
- Boston College School of Social Work, 140 Commonwealth Ave, Chestnut Hill, MA, 20467, USA
| | - Maria Pineros-Leano
- Boston College School of Social Work, 140 Commonwealth Ave, Chestnut Hill, MA, 20467, USA
| | - Kirsten K Davison
- Boston College School of Social Work, 140 Commonwealth Ave, Chestnut Hill, MA, 20467, USA
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146
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D'Amico-Willman KM, Niederhuth CE, Sovic MG, Anderson ES, Gradziel TM, Fresnedo-Ramírez J. Hypermethylation and small RNA expression are associated with increased age in almond (Prunus dulcis [Mill.] D.A. Webb) accessions. Plant Sci 2024; 338:111918. [PMID: 37956826 DOI: 10.1016/j.plantsci.2023.111918] [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: 07/24/2023] [Revised: 10/20/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023]
Abstract
The focus of this study is to profile changes in DNA methylation and small RNA expression occurring with increased age in almond breeding germplasm to identify possible biomarkers of age that can be used to assess the potential of individuals to develop aging-related disorders. To profile DNA methylation in almond germplasm, 70 methylomes were generated from almond individuals representing three age cohorts (11, 7, and 2 years old) using an enzymatic methyl-seq approach followed by analysis to call differentially methylated regions (DMRs) within these cohorts. Small RNA (sRNA) expression was profiled in three breeding selections, each from two age cohorts (1 and 6 years old), using sRNA-Seq followed by differential expression analysis. Weighted chromosome-level methylation analysis reveals hypermethylation in 11-year-old almond breeding selections when compared to 2-year-old selections in the CG and CHH contexts. Seventeen consensus DMRs were identified in all age contrasts. sRNA expression differed significantly between the two age cohorts tested, with significantly decreased expression in sRNAs in the 6-year-old selections compared to the 1-year-old. Almond shows a pattern of hypermethylation and decreased sRNA expression with increased age. Identified DMRs and differentially expressed sRNAs could function as putative biomarkers of age following validation in additional age groups.
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Affiliation(s)
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Michael G Sovic
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Elizabeth S Anderson
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Thomas M Gradziel
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jonathan Fresnedo-Ramírez
- Translational Plant Sciences, The Ohio State University, Columbus, OH 43210, USA; Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA; Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA.
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Zarate-Lopez D, Torres-Chávez AL, Gálvez-Contreras AY, Gonzalez-Perez O. Three Decades of Valproate: A Current Model for Studying Autism Spectrum Disorder. Curr Neuropharmacol 2024; 22:260-289. [PMID: 37873949 PMCID: PMC10788883 DOI: 10.2174/1570159x22666231003121513] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 10/25/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder with increased prevalence and incidence in recent decades. Its etiology remains largely unclear, but it seems to involve a strong genetic component and environmental factors that, in turn, induce epigenetic changes during embryonic and postnatal brain development. In recent decades, clinical studies have shown that inutero exposure to valproic acid (VPA), a commonly prescribed antiepileptic drug, is an environmental factor associated with an increased risk of ASD. Subsequently, prenatal VPA exposure in rodents has been established as a reliable translational model to study the pathophysiology of ASD, which has helped demonstrate neurobiological changes in rodents, non-human primates, and brain organoids from human pluripotent stem cells. This evidence supports the notion that prenatal VPA exposure is a valid and current model to replicate an idiopathic ASD-like disorder in experimental animals. This review summarizes and describes the current features reported with this animal model of autism and the main neurobiological findings and correlates that help elucidate the pathophysiology of ASD. Finally, we discuss the general framework of the VPA model in comparison to other environmental and genetic ASD models.
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Affiliation(s)
- David Zarate-Lopez
- Laboratory of Neuroscience, School of Psychology, University of Colima, Colima 28040, México
- Physiological Science Ph.D. Program, School of Medicine, University of Colima, Colima 28040, Mexico
| | - Ana Laura Torres-Chávez
- Laboratory of Neuroscience, School of Psychology, University of Colima, Colima 28040, México
- Physiological Science Ph.D. Program, School of Medicine, University of Colima, Colima 28040, Mexico
| | - Alma Yadira Gálvez-Contreras
- Department of Neuroscience, Centro Universitario de Ciencias de la Salud, University of Guadalajara, Guadalajara 44340, México
| | - Oscar Gonzalez-Perez
- Laboratory of Neuroscience, School of Psychology, University of Colima, Colima 28040, México
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Lucas MC, Pryszcz LP, Medina R, Milenkovic I, Camacho N, Marchand V, Motorin Y, Ribas de Pouplana L, Novoa EM. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. Nat Biotechnol 2024; 42:72-86. [PMID: 37024678 DOI: 10.1038/s41587-023-01743-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [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: 06/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023]
Abstract
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to Saccharomyces cerevisiae tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress.
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Affiliation(s)
- Morghan C Lucas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rebeca Medina
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivan Milenkovic
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Virginie Marchand
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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149
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Lizárraga D, Gómez-Gil B, García-Gasca T, Ávalos-Soriano A, Casarini L, Salazar-Oroz A, García-Gasca A. Gestational diabetes mellitus: genetic factors, epigenetic alterations, and microbial composition. Acta Diabetol 2024; 61:1-17. [PMID: 37660305 DOI: 10.1007/s00592-023-02176-y] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Gestational diabetes mellitus (GDM) is a common metabolic disorder, usually diagnosed during the third trimester of pregnancy that usually disappears after delivery. In GDM, the excess of glucose, fatty acids, and amino acids results in foetuses large for gestational age. Hyperglycaemia and insulin resistance accelerate the metabolism, raising the oxygen demand, and creating chronic hypoxia and inflammation. Women who experienced GDM and their offspring are at risk of developing type-2 diabetes, obesity, and other metabolic or cardiovascular conditions later in life. Genetic factors may predispose the development of GDM; however, they do not account for all GDM cases; lifestyle and diet also play important roles in GDM development by modulating epigenetic signatures and the body's microbial composition; therefore, this is a condition with a complex, multifactorial aetiology. In this context, we revised published reports describing GDM-associated single-nucleotide polymorphisms (SNPs), DNA methylation and microRNA expression in different tissues (such as placenta, umbilical cord, adipose tissue, and peripheral blood), and microbial composition in the gut, oral cavity, and vagina from pregnant women with GDM, as well as the bacterial composition of the offspring. Altogether, these reports indicate that a number of SNPs are associated to GDM phenotypes and may predispose the development of the disease. However, extrinsic factors (lifestyle, nutrition) modulate, through epigenetic mechanisms, the risk of developing the disease, and some association exists between the microbial composition with GDM in an organ-specific manner. Genes, epigenetic signatures, and microbiota could be transferred to the offspring, increasing the possibility of developing chronic degenerative conditions through postnatal life.
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Affiliation(s)
- Dennise Lizárraga
- Laboratory of Molecular and Cell Biology, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico
| | - Bruno Gómez-Gil
- Laboratory of Microbial Genomics, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico
| | - Teresa García-Gasca
- Laboratory of Molecular and Cellular Biology, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias s/n, 76230, Juriquilla, Querétaro, Mexico
| | - Anaguiven Ávalos-Soriano
- Laboratory of Molecular and Cell Biology, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico
| | - Livio Casarini
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41125, Modena, Italy
| | - Azucena Salazar-Oroz
- Maternal-Fetal Department, Instituto Vidalia, Hospital Sharp Mazatlán, Avenida Rafael Buelna y Dr. Jesús Kumate s/n, 82126, Mazatlán, Sinaloa, Mexico
| | - Alejandra García-Gasca
- Laboratory of Molecular and Cell Biology, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico.
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150
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Lee JM, Park SU, Lee SD, Lee HY. Application of array-based age prediction models to post-mortem tissue samples. Forensic Sci Int Genet 2024; 68:102940. [PMID: 37857127 DOI: 10.1016/j.fsigen.2023.102940] [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: 05/23/2023] [Revised: 09/03/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
Since DNA methylation at specific CpG sites exhibits a strong age association, researchers have developed numerous age prediction models based on the methylation BeadChip array. These models harness epigenetic clocks that hold the potential to narrow down the search range for unknown suspects and unidentified victims. This study collected 180 post-mortem tissue samples comprising nine tissue types (blood, brain, heart, lung, liver, kidney, muscle, epidermis, and dermis) from autopsies of 20 Koreans aged 18-78. Subsequently, DNA methylation profiling was conducted using the Infinium MethylationEPIC array. We tested several array-based age prediction models using the data obtained from various tissues. The pan-tissue clock exhibited a moderately accurate prediction across all nine tissue types (MAE = 8.7 years, r = 0.88). Notably, the DNAm ages of the Hannum clock, the skin & blood clock, and the Zhang clock strongly correlated with the actual age in blood samples (MAE < approximately 5 years, r > 0.9). PhenoAge yielded an MAE of 10.1 years and an r-value of 0.92. The muscle-specific epigenetic clock, the MEAT package, demonstrated high prediction accuracy in muscle samples (MAE = 4.7 years, r = 0.93). Those previously reported array-based age prediction models were mainly constructed in Europeans but performed well in Koreans. In addition, tests involving various quantities of DNA and fragmented DNA have shown that DNA quantity and quality affected methylation measurements and age prediction results. However, robust age prediction models exist under low amounts of DNA and fragmented DNA conditions.
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Affiliation(s)
- Jeong Min Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Un Park
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea.
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