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van Wijnen AJ, Lewallen EA. Natural selection and evolution: evolving concepts. ACADEMIA BIOLOGY 2024; 2:10.20935/AcadBiol6245. [PMID: 38873024 PMCID: PMC11175172 DOI: 10.20935/acadbiol6245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Many recent studies in evolutionary biology have expanded and refined definitions of biological evolution and natural selection. Current evolutionary models incorporate different adaptive and non-adaptive processes based on molecular genetic changes and how DNA is modified over time in unicellular species, or in germline versus somatic cells in metazoan species. Cogent arguments can be raised for the view that natural selection should be considered a biological law, consistent with quantitative mathematical equations that describe the fitness of individuals, as well as variations within and among populations. Evolution is an overarching framework that incorporates the laws of natural selection and clarifies why phenotypic variation can increase in prevalence and result in species adaptations. The conceptual framework for biological evolution incorporates many cohesive principles that collectively have a predictive value. This framework will continue to evolve with improvements in high-resolution technologies that enable us to examine both adaptive and non-adaptive changes that drive biological phenotypes.
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Affiliation(s)
- Andre J. van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Eric A. Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, 23668, USA
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Rice RC, Gil DV, Baratta AM, Frawley RR, Hill SY, Farris SP, Homanics GE. Inter- and transgenerational heritability of preconception chronic stress or alcohol exposure: Translational outcomes in brain and behavior. Neurobiol Stress 2024; 29:100603. [PMID: 38234394 PMCID: PMC10792982 DOI: 10.1016/j.ynstr.2023.100603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/19/2024] Open
Abstract
Chronic stress and alcohol (ethanol) use are highly interrelated and can change an individual's behavior through molecular adaptations that do not change the DNA sequence, but instead change gene expression. A recent wealth of research has found that these nongenomic changes can be transmitted across generations, which could partially account for the "missing heritability" observed in genome-wide association studies of alcohol use disorder and other stress-related neuropsychiatric disorders. In this review, we summarize the molecular and behavioral outcomes of nongenomic inheritance of chronic stress and ethanol exposure and the germline mechanisms that could give rise to this heritability. In doing so, we outline the need for further research to: (1) Investigate individual germline mechanisms of paternal, maternal, and biparental nongenomic chronic stress- and ethanol-related inheritance; (2) Synthesize and dissect cross-generational chronic stress and ethanol exposure; (3) Determine cross-generational molecular outcomes of preconception ethanol exposure that contribute to alcohol-related disease risk, using cancer as an example. A detailed understanding of the cross-generational nongenomic effects of stress and/or ethanol will yield novel insight into the impact of ancestral perturbations on disease risk across generations and uncover actionable targets to improve human health.
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Affiliation(s)
- Rachel C. Rice
- Center for Neuroscience at the University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniela V. Gil
- Center for Neuroscience at the University of Pittsburgh, Pittsburgh, PA, USA
| | - Annalisa M. Baratta
- Center for Neuroscience at the University of Pittsburgh, Pittsburgh, PA, USA
| | - Remy R. Frawley
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shirley Y. Hill
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sean P. Farris
- Center for Neuroscience at the University of Pittsburgh, Pittsburgh, PA, USA
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gregg E. Homanics
- Center for Neuroscience at the University of Pittsburgh, Pittsburgh, PA, USA
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
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Sarkar S, Deyoung T, Ressler H, Chandler W. Brain Tumors: Development, Drug Resistance, and Sensitization - An Epigenetic Approach. Epigenetics 2023; 18:2237761. [PMID: 37499114 PMCID: PMC10376921 DOI: 10.1080/15592294.2023.2237761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023] Open
Abstract
In this article, we describe contrasting developmental aspects of paediatric and adult brain tumours. We hypothesize that the formation of cancer progenitor cells, for both paediatric and adult, could be due to epigenetic events. However, the progression of adult brain tumours selectively involves more mutations compared to paediatric tumours. We further discuss epigenetic switches, comprising both histone modifications and DNA methylation, and how they can differentially regulate transcription and expression of oncogenes and tumour suppressor genes. Next, we summarize the currently available therapies for both types of brain tumours, explaining the merits and failures leading to drug resistance. We analyse different mechanisms of drug resistance and the role of epigenetics in this process. We then provide a rationale for combination therapy, which includes epigenetic drugs. In the end, we postulate a concept which describes how a combination therapy could be initiated. The timing, doses, and order of individual drug regimens will depend on the individual case. This type of combination therapy will be part of a personalized medicine which will differ from patient to patient.
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Affiliation(s)
- Sibaji Sarkar
- Division of Biotechnology, Quincy College, Quincy, MA, USA
- Division of Biology, STEM, MBC College, Wellesley, MA, USA
- Division of Biology, STEM, RC College Boston, Boston, MA, USA
| | - Tara Deyoung
- Division of Biotechnology, Quincy College, Quincy, MA, USA
| | - Hope Ressler
- Division of Biology, STEM, MBC College, Wellesley, MA, USA
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Vedor JE. Revisiting Carl Jung's archetype theory a psychobiological approach. Biosystems 2023; 234:105059. [PMID: 37832929 DOI: 10.1016/j.biosystems.2023.105059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
This paper delves into the concept of archetypes, universal patterns of behavior and cognition, and proposes a novel tripartite model distinguishing between structural, regulatory, and representational archetypes. Drawing on insights from code biology, neuroscience, genetics, and epigenetics, the model provides a nuanced framework for understanding archetypes and their role in shaping cognition and behavior. The paper also explores the interplay between these elements to express representational archetypes. Furthermore, it addresses the informational capacity of the genome and its influence on post-natal development and the psyche. The paper concludes by discussing the future trajectory of psychology, emphasizing the need for an integrative approach that combines our understanding of social constructs with insights into our inherent organizational propensities or archetypes. This exploration holds the potential to advance our understanding of the human condition.
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Abraham LN, Croll D. Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen. BMC Biol 2023; 21:263. [PMID: 37981685 PMCID: PMC10658818 DOI: 10.1186/s12915-023-01763-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/07/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND In agricultural ecosystems, outbreaks of diseases are frequent and pose a significant threat to food security. A successful pathogen undergoes a complex and well-timed sequence of regulatory changes to avoid detection by the host immune system; hence, well-tuned gene regulation is essential for survival. However, the extent to which the regulatory polymorphisms in a pathogen population provide an adaptive advantage is poorly understood. RESULTS We used Zymoseptoria tritici, one of the most important pathogens of wheat, to generate a genome-wide map of regulatory polymorphism governing gene expression. We investigated genome-wide transcription levels of 146 strains grown under nutrient starvation and performed expression quantitative trait loci (eQTL) mapping. We identified cis-eQTLs for 65.3% of all genes and the majority of all eQTL loci are within 2kb upstream and downstream of the transcription start site (TSS). We also show that polymorphism in different gene elements contributes disproportionally to gene expression variation. Investigating regulatory polymorphism in gene categories, we found an enrichment of regulatory variants for genes predicted to be important for fungal pathogenesis but with comparatively low effect size, suggesting a separate layer of gene regulation involving epigenetics. We also show that previously reported trait-associated SNPs in pathogen populations are frequently cis-regulatory variants of neighboring genes with implications for the trait architecture. CONCLUSIONS Overall, our study provides extensive evidence that single populations segregate large-scale regulatory variation and are likely to fuel rapid adaptation to resistant hosts and environmental change.
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Affiliation(s)
- Leen Nanchira Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland
- Present address: Institute of Plant Sciences, University of Cologne, Cologne, Germany
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland.
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Cheng H, Liu Y, Chen G. Identification of potential DNA methylation biomarkers related to diagnosis in patients with bladder cancer through integrated bioinformatic analysis. BMC Urol 2023; 23:135. [PMID: 37563710 PMCID: PMC10413619 DOI: 10.1186/s12894-023-01307-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Bladder cancer (BLCA) is one of the most common malignancies among tumors worldwide. There are no validated biomarkers to facilitate such treatment diagnosis. DNA methylation modification plays important roles in epigenetics. Identifying methylated differentially expressed genes is a common method for the discovery of biomarkers. METHODS Bladder cancer data were obtained from Gene Expression Omnibus (GEO), including the gene expression microarrays GSE37817( 18 patients and 3 normal ), GSE52519 (9 patients and 3 normal) and the gene methylation microarray GSE37816 (18 patients and 3 normal). Aberrantly expressed genes were obtained by GEO2R. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed using the DAVID database and KOBAS. Protein-protein interactions (PPIs) and hub gene networks were constructed by STRING and Cytoscape software. The validation of the results which was confirmed through four online platforms, including Gene Expression Profiling Interactive Analysis (GEPIA), Gene Set Cancer Analysis (GSCA), cBioProtal and MEXPRESS. RESULTS In total, 253 and 298 upregulated genes and 674 and 454 downregulated genes were identified for GSE37817 and GSE52519, respectively. For the GSE37816 dataset, hypermethylated and hypomethylated genes involving 778 and 3420 genes, respectively, were observed. Seventeen hypermethylated and low expression genes were enriched in biological processes associated with different organ development and morphogenesis. For molecular function, these genes showed enrichment in extracellular matrix structural constituents. Pathway enrichment showed drug metabolic enzymes and several amino acids metabolism, PI3K-Akt, Hedgehog signaling pathway. The top 3 hub genes screened by Cytoscape software were EFEMP1, SPARCL1 and ABCA8. The research results were verified using the GEPIA, GSCA, cBioProtal and EXPRESS databases, and the hub hypermethylated low expression genes were validated. CONCLUSION This study screened possible aberrantly methylated expression hub genes in BLCA by integrated bioinformatics analysis. The results may provide possible methylation-based biomarkers for the precise diagnosis and treatment of BLCA in the future.
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Affiliation(s)
- Hongxia Cheng
- School of Biological and Pharmaceutical Engineering, Wuhan Huaxia Institute of Technology, Wuhan, 430223, Hubei, China.
| | - Yuhua Liu
- School of Biological and Pharmaceutical Engineering, Wuhan Huaxia Institute of Technology, Wuhan, 430223, Hubei, China
| | - Gang Chen
- School of Biological and Pharmaceutical Engineering, Wuhan Huaxia Institute of Technology, Wuhan, 430223, Hubei, China
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Wang X, Yu D, Chen L. Antimicrobial resistance and mechanisms of epigenetic regulation. Front Cell Infect Microbiol 2023; 13:1199646. [PMID: 37389209 PMCID: PMC10306973 DOI: 10.3389/fcimb.2023.1199646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/26/2023] [Indexed: 07/01/2023] Open
Abstract
The rampant use of antibiotics in animal husbandry, farming and clinical disease treatment has led to a significant issue with pathogen resistance worldwide over the past decades. The classical mechanisms of resistance typically investigate antimicrobial resistance resulting from natural resistance, mutation, gene transfer and other processes. However, the emergence and development of bacterial resistance cannot be fully explained from a genetic and biochemical standpoint. Evolution necessitates phenotypic variation, selection, and inheritance. There are indications that epigenetic modifications also play a role in antimicrobial resistance. This review will specifically focus on the effects of DNA modification, histone modification, rRNA methylation and the regulation of non-coding RNAs expression on antimicrobial resistance. In particular, we highlight critical work that how DNA methyltransferases and non-coding RNAs act as transcriptional regulators that allow bacteria to rapidly adapt to environmental changes and control their gene expressions to resist antibiotic stress. Additionally, it will delve into how Nucleolar-associated proteins in bacteria perform histone functions akin to eukaryotes. Epigenetics, a non-classical regulatory mechanism of bacterial resistance, may offer new avenues for antibiotic target selection and the development of novel antibiotics.
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Affiliation(s)
- Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Donghong Yu
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Lu Chen
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
- National Health Commission Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
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Assessing the Core Variables of Business Managers’ Intuitive Decision Ability: A Review and Analysis. Behav Sci (Basel) 2022; 12:bs12110409. [DOI: 10.3390/bs12110409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Business decisions are frequently based on informed intuition in contrast to a formal analysis. Early man used simple intuition, but through time knowledge increases allowed decision makers (DMs) to move to ‘objectively informed intuition’ (OII). This uses inherent and learnt cognition at both unconscious and conscious levels. A model of business OII is proposed and evaluated using as variables the managers’ personal characteristics and their unique set of objectives. The resultant equation allows assessing decision quality and provides a framework for DMs to work on improvements relative to their objectives. The literature suggests OII stems from a DM’s makeup (business related phenotype), training and experience in a dynamic trio leading to the defining equation. Analyses show business related phenotype is the most important determinant as well as confirming the proposed theory on the determinants of OII success. Practical methods of improving OII are reviewed, and issues worth further investigation outlined. This research is the first encompassing quantitative relationships explaining business OII quality thus enabling improving OII. Suggested further research may refine the equation and expand its core base. This work involves a range of disciplines as different aspects of human characteristics impact on how decisions are made.
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Shi Y, Wang G, Lau HCH, Yu J. Metagenomic Sequencing for Microbial DNA in Human Samples: Emerging Technological Advances. Int J Mol Sci 2022; 23:ijms23042181. [PMID: 35216302 PMCID: PMC8877284 DOI: 10.3390/ijms23042181] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/06/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Whole genome metagenomic sequencing is a powerful platform enabling the simultaneous identification of all genes from entirely different kingdoms of organisms in a complex sample. This technology has revolutionised multiple areas from microbiome research to clinical diagnoses. However, one of the major challenges of a metagenomic study is the overwhelming non-microbial DNA present in most of the host-derived specimens, which can inundate the microbial signals and reduce the sensitivity of microorganism detection. Various host DNA depletion methods to facilitate metagenomic sequencing have been developed and have received considerable attention in this context. In this review, we present an overview of current host DNA depletion approaches along with explanations of their underlying principles, advantages and disadvantages. We also discuss their applications in laboratory microbiome research and clinical diagnoses and, finally, we envisage the direction of the further perfection of metagenomic sequencing in samples with overabundant host DNA.
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Affiliation(s)
| | | | | | - Jun Yu
- Correspondence: ; Tel.: +852-37636099; Fax:+852-21445330
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Robin AN, Denton KK, Horna Lowell ES, Dulay T, Ebrahimi S, Johnson GC, Mai D, O’Fallon S, Philson CS, Speck HP, Zhang XP, Nonacs P. Major Evolutionary Transitions and the Roles of Facilitation and Information in Ecosystem Transformations. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.711556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A small number of extraordinary “Major Evolutionary Transitions” (METs) have attracted attention among biologists. They comprise novel forms of individuality and information, and are defined in relation to organismal complexity, irrespective of broader ecosystem-level effects. This divorce between evolutionary and ecological consequences qualifies unicellular eukaryotes, for example, as a MET although they alone failed to significantly alter ecosystems. Additionally, this definition excludes revolutionary innovations not fitting into either MET type (e.g., photosynthesis). We recombine evolution with ecology to explore how and why entire ecosystems were newly created or radically altered – as Major System Transitions (MSTs). In doing so, we highlight important morphological adaptations that spread through populations because of their immediate, direct-fitness advantages for individuals. These are Major Competitive Transitions, or MCTs. We argue that often multiple METs and MCTs must be present to produce MSTs. For example, sexually-reproducing, multicellular eukaryotes (METs) with anisogamy and exoskeletons (MCTs) significantly altered ecosystems during the Cambrian. Therefore, we introduce the concepts of Facilitating Evolutionary Transitions (FETs) and Catalysts as key events or agents that are insufficient themselves to set a MST into motion, but are essential parts of synergies that do. We further elucidate the role of information in MSTs as transitions across five levels: (I) Encoded; (II) Epigenomic; (III) Learned; (IV) Inscribed; and (V) Dark Information. The latter is ‘authored’ by abiotic entities rather than biological organisms. Level IV has arguably allowed humans to produce a MST, and V perhaps makes us a FET for a future transition that melds biotic and abiotic life into one entity. Understanding the interactive processes involved in past major transitions will illuminate both current events and the surprising possibilities that abiotically-created information may produce.
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Sibilia V, Bottai D, Maggi R, Pagani F, Chiaramonte R, Giannandrea D, Citro V, Platonova N, Casati L. Sex Steroid Regulation of Oxidative Stress in Bone Cells: An In Vitro Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182212168. [PMID: 34831936 PMCID: PMC8621144 DOI: 10.3390/ijerph182212168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 01/02/2023]
Abstract
Environmental stimuli, including sex hormones and oxidative stress (OS), affect bone balance, modifying the epigenetic profiles of key osteogenic genes. Nonetheless, the interplay between sex steroids, epigenome and OS has yet be fully elucidated. This paper aims to study in vitro the role of sex steroids in OS-induced alteration in bone cells’ homeostasis, and to assess the possible contribution of epigenetic modifications. Toward this purpose, osteoblast (MC3T3-E1) and osteocyte (MLOY-4) cell lines were exposed to two different sources of free oxygen radicals, i.e., tert-butyl hydroperoxide and dexamethasone, and the protective effect of pre-treatment with androgens and estrogens was evaluated. In particular, we analyzed parameters that reflect bone cell homeostasis such as cell viability, cell migration, transcriptomic profile, transcriptional activity, and epigenetic signature. Our findings indicate that estrogens and androgens counteract OS effects. Using partially overlapping strategies, they reduce OS outcomes regarding cell viability, cell migration, the transcriptomic profile of gene families involved in bone remodeling, and epigenetic profile, i.e., H3K4me3 level. Additionally, we demonstrated that the protective effect of steroids against OS on bone homeostasis is partially mediated by the Akt pathway. Overall, these results suggest that the hormonal milieu may influence the mechanisms of age-related bone disease.
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Affiliation(s)
- Valeria Sibilia
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129 Milano, Italy; (V.S.); (F.P.)
| | - Daniele Bottai
- Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (D.B.); (R.C.); (D.G.); (V.C.); (N.P.)
| | - Roberto Maggi
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, 20133 Milano, Italy;
| | - Francesca Pagani
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129 Milano, Italy; (V.S.); (F.P.)
| | - Raffaella Chiaramonte
- Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (D.B.); (R.C.); (D.G.); (V.C.); (N.P.)
| | - Domenica Giannandrea
- Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (D.B.); (R.C.); (D.G.); (V.C.); (N.P.)
| | - Valentina Citro
- Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (D.B.); (R.C.); (D.G.); (V.C.); (N.P.)
| | - Natalia Platonova
- Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (D.B.); (R.C.); (D.G.); (V.C.); (N.P.)
| | - Lavinia Casati
- Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (D.B.); (R.C.); (D.G.); (V.C.); (N.P.)
- Correspondence:
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Jian H, Xu G, Yi Y, Hao Y, Wang Y, Xiong L, Wang S, Liu S, Meng C, Wang J, Zhang Y, Chen C, Feng X, Luo H, Zhang H, Zhang X, Wang L, Wang Z, Deng Z, Xiao X. The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes. Nat Commun 2021; 12:6382. [PMID: 34737280 PMCID: PMC8569181 DOI: 10.1038/s41467-021-26636-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and constitute an epigenetic system with multiple functions, including antioxidant ability, restriction modification, and virus resistance. Despite these advantages for hosting dnd systems, they are surprisingly distributed sporadically among contemporary prokaryotic genomes. To address this ecological paradox, we systematically investigate the occurrence and phylogeny of dnd systems, and they are suggested to have originated in ancient Cyanobacteria after the Great Oxygenation Event. Interestingly, the occurrence of dnd systems and prophages is significantly negatively correlated. Further, we experimentally confirm that PT modification activates the filamentous phage SW1 by altering the binding affinity of repressor and the transcription level of its encoding gene. Competition assays, concurrent epigenomic and transcriptomic sequencing subsequently show that PT modification affects the expression of a variety of metabolic genes, which reduces the competitive fitness of the marine bacterium Shewanella piezotolerans WP3. Our findings strongly suggest that a series of negative effects on microorganisms caused by dnd systems limit horizontal gene transfer, thus leading to their sporadic distribution. Overall, our study reveals putative evolutionary scenario of the dnd system and provides novel insights into the physiological and ecological influences of PT modification.
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Affiliation(s)
- Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Guanpeng Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Xiong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Siyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Canxing Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xiaoyuan Feng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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Gerdol M, La Vecchia C, Strazzullo M, De Luca P, Gorbi S, Regoli F, Pallavicini A, D’Aniello E. Evolutionary History of DNA Methylation Related Genes in Bivalvia: New Insights From Mytilus galloprovincialis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is an essential epigenetic mechanism influencing gene expression in all organisms. In metazoans, the pattern of DNA methylation changes during embryogenesis and adult life. Consequently, differentiated cells develop a stable and unique DNA methylation pattern that finely regulates mRNA transcription during development and determines tissue-specific gene expression. Currently, DNA methylation remains poorly investigated in mollusks and completely unexplored in Mytilus galloprovincialis. To shed light on this process in this ecologically and economically important bivalve, we screened its genome, detecting sequences homologous to DNA methyltransferases (DNMTs), methyl-CpG-binding domain (MBD) proteins and Ten-eleven translocation methylcytosine dioxygenase (TET) previously described in other organisms. We characterized the gene architecture and protein domains of the mussel sequences and studied their phylogenetic relationships with the ortholog sequences from other bivalve species. We then comparatively investigated their expression levels across different adult tissues in mussel and other bivalves, using previously published transcriptome datasets. This study provides the first insights on DNA methylation regulators in M. galloprovincialis, which may provide fundamental information to better understand the complex role played by this mechanism in regulating genome activity in bivalves.
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14
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Alves N, Neuparth T, Barros S, Santos MM. The anti-lipidemic drug simvastatin modifies epigenetic biomarkers in the amphipod Gammarus locusta. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111849. [PMID: 33387775 DOI: 10.1016/j.ecoenv.2020.111849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
The adverse effects of certain environmental chemicals have been recently associated with the modulation of the epigenome. Although changes in the epigenetic signature have yet to be integrated into hazard and risk assessment, they are interesting candidates to link environmental exposures and altered phenotypes, since these changes may be passed across multiple non-exposed generations. Here, we addressed the effects of simvastatin (SIM), one of the most prescribed pharmaceuticals in the world, on epigenetic regulation using the amphipod Gammarus locusta as a proxy, to support its integration into hazard and environmental risk assessment. SIM is a known modulator of the epigenome in mammalian cell lines and has been reported to impact G. locusta ecological endpoints at environmentally relevant levels. G. locusta juveniles were exposed to three SIM environmentally relevant concentrations (0.32, 1.6 and 8 µg L-1) for 15 days. Gene transcription levels of selected epigenetic regulators, i.e., dnmt1, dmap1, usp7, kat5 and uhrf1 were assessed, along with the quantification of DNA methylation levels and evaluation of key ecological endpoints: survival and growth. Exposure to 0.32 and 8 µg L-1 SIM induced significant downregulation of DNA methyltransferase 1 (dnmt1), concomitant with global DNA hypomethylation and growth impacts. Overall, this work is the first to validate the basal expression of key epigenetic regulators in a keystone marine crustacean, supporting the integration of epigenetic biomarkers into hazard assessment frameworks.
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Affiliation(s)
- Nélson Alves
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Endocrine Disruptors and Emerging Contaminants Group, University of Porto, Avenida General Norton de Matos S/N, 4450-208 Matosinhos, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre nº 1021/1055, 4169-007 Porto, Portugal
| | - Teresa Neuparth
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Endocrine Disruptors and Emerging Contaminants Group, University of Porto, Avenida General Norton de Matos S/N, 4450-208 Matosinhos, Portugal.
| | - Susana Barros
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Endocrine Disruptors and Emerging Contaminants Group, University of Porto, Avenida General Norton de Matos S/N, 4450-208 Matosinhos, Portugal
| | - Miguel M Santos
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Endocrine Disruptors and Emerging Contaminants Group, University of Porto, Avenida General Norton de Matos S/N, 4450-208 Matosinhos, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre nº 1021/1055, 4169-007 Porto, Portugal.
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15
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Long Y, Ubych K, Jagu E, Neely RK. FRET-Based Method for Direct, Real-Time Measurement of DNA Methyltransferase Activity. Bioconjug Chem 2020; 32:192-198. [PMID: 33306345 DOI: 10.1021/acs.bioconjchem.0c00612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA methyltransferase activity is associated with a host of diseases, including cancers, where global hypomethylation of the genome, as well as marked changes in local DNA methylation patterns, can be both diagnostic and prognostic for the disease. Despite this, we currently lack a method for directly measuring the activity of the DNA methyltransferases, which would support the development of DNA methyltransferase-targeted therapies. Here, we demonstrate an assay for the direct measurement of methyltransferase activity, in real time. We employ a fluorescent methyltransferase cofactor analogue, which when bound by the enzyme to a labeled target DNA sequence results in fluorescence resonance energy transfer (FRET) between the donor dye (DNA) and the acceptor dye (cofactor). We demonstrate that the method can be used to monitor the activity of DNA MTases in real time and can be applied to screen inhibitors of the DNA methyltransferases. We show this in both bulk phase and single molecule imaging experiments, highlighting the potential application of the assay in screening and biophysical studies of methyltransferase function.
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Affiliation(s)
- Yi Long
- The University of Birmingham, School of Chemistry, Edgbaston, Birmingham, B15 2TT, United Kingdom.,Medical Research Center, Southern University of Science and Technology Hospital, Shenzhen, Guangdong Province, 518055, China
| | - Krystian Ubych
- The University of Birmingham, School of Chemistry, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Elodie Jagu
- The University of Birmingham, School of Chemistry, Edgbaston, Birmingham, B15 2TT, United Kingdom.,ICCF, SIGMA Clermont, Université Clermont Auvergne, CNRS, Clermont-Ferrand, 63178 Aubière, France
| | - Robert K Neely
- The University of Birmingham, School of Chemistry, Edgbaston, Birmingham, B15 2TT, United Kingdom
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16
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Navarro-Martín L, Martyniuk CJ, Mennigen JA. Comparative epigenetics in animal physiology: An emerging frontier. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100745. [PMID: 33126028 DOI: 10.1016/j.cbd.2020.100745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 12/19/2022]
Abstract
The unprecedented access to annotated genomes now facilitates the investigation of the molecular basis of epigenetic phenomena in phenotypically diverse animals. In this critical review, we describe the roles of molecular epigenetic mechanisms in regulating mitotically and meiotically stable spatiotemporal gene expression, phenomena that provide the molecular foundation for the intra-, inter-, and trans-generational emergence of physiological phenotypes. By focusing principally on emerging comparative epigenetic roles of DNA-level and transcriptome-level epigenetic mark dynamics in the emergence of phenotypes, we highlight the relationship between evolutionary conservation and innovation of specific epigenetic pathways, and their interplay as a priority for future study. This comparative approach is expected to significantly advance our understanding of epigenetic phenomena, as animals show a diverse array of strategies to epigenetically modify physiological responses. Additionally, we review recent technological advances in the field of molecular epigenetics (single-cell epigenomics and transcriptomics and editing of epigenetic marks) in order to (1) investigate environmental and endogenous factor dependent epigenetic mark dynamics in an integrative manner; (2) functionally test the contribution of specific epigenetic marks for animal phenotypes via genome and transcript-editing tools. Finally, we describe advantages and limitations of emerging animal models, which under the Krogh principle, may be particularly useful in the advancement of comparative epigenomics and its potential translational applications in animal science, ecotoxicology, ecophysiology, climate change science and wild-life conservation, as well as organismal health.
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Affiliation(s)
- Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON K1N6N5, Canada
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17
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Kansara S, Pandey V, Lobie PE, Sethi G, Garg M, Pandey AK. Mechanistic Involvement of Long Non-Coding RNAs in Oncotherapeutics Resistance in Triple-Negative Breast Cancer. Cells 2020; 9:cells9061511. [PMID: 32575858 PMCID: PMC7349003 DOI: 10.3390/cells9061511] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most lethal forms of breast cancer (BC), with a significant disease burden worldwide. Chemoresistance and lack of targeted therapeutics are major hindrances to effective treatments in the clinic and are crucial causes of a worse prognosis and high rate of relapse/recurrence in patients diagnosed with TNBC. In the last decade, long non-coding RNAs (lncRNAs) have been found to perform a pivotal role in most cellular functions. The aberrant functional expression of lncRNAs plays an ever-increasing role in the progression of diverse malignancies, including TNBC. Therefore, lncRNAs have been recently studied as predictors and modifiers of chemoresistance. Our review discusses the potential involvement of lncRNAs in drug-resistant mechanisms commonly found in TNBC and highlights various therapeutic strategies to target lncRNAs in this malignancy.
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Affiliation(s)
- Samarth Kansara
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India;
| | - Vijay Pandey
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518005, China; (V.P.); (P.E.L.)
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Peter E. Lobie
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518005, China; (V.P.); (P.E.L.)
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- Correspondence: (G.S.); (A.K.P.)
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Sector-125, Noida 201313, India;
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India;
- Correspondence: (G.S.); (A.K.P.)
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18
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Abstract
Following the success of and the high demand for recombinant protein-based therapeutics during the last 25 years, the pharmaceutical industry has invested significantly in the development of novel treatments based on biologics. Mammalian cells are the major production systems for these complex biopharmaceuticals, with Chinese hamster ovary (CHO) cell lines as the most important players. Over the years, various engineering strategies and modeling approaches have been used to improve microbial production platforms, such as bacteria and yeasts, as well as to create pre-optimized chassis host strains. However, the complexity of mammalian cells curtailed the optimization of these host cells by metabolic engineering. Most of the improvements of titer and productivity were achieved by media optimization and large-scale screening of producer clones. The advances made in recent years now open the door to again consider the potential application of systems biology approaches and metabolic engineering also to CHO. The availability of a reference genome sequence, genome-scale metabolic models and the growing number of various “omics” datasets can help overcome the complexity of CHO cells and support design strategies to boost their production performance. Modular design approaches applied to engineer industrially relevant cell lines have evolved to reduce the time and effort needed for the generation of new producer cells and to allow the achievement of desired product titers and quality. Nevertheless, important steps to enable the design of a chassis platform similar to those in use in the microbial world are still missing. In this review, we highlight the importance of mammalian cellular platforms for the production of biopharmaceuticals and compare them to microbial platforms, with an emphasis on describing novel approaches and discussing still open questions that need to be resolved to reach the objective of designing enhanced modular chassis CHO cell lines.
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19
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The complex phylogenetic relationships of a 4mC/6mA DNA methyltransferase in prokaryotes. Mol Phylogenet Evol 2020; 149:106837. [PMID: 32304827 DOI: 10.1016/j.ympev.2020.106837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 01/30/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023]
Abstract
DNA methyltransferases are proteins that modify DNA via attachment of methyl groups to nucleobases and are ubiquitous across the bacterial, archaeal, and eukaryotic domains of life. Here, we investigated the complex evolutionary history of the large and consequential 4mC/6mA DNA methyltransferase protein family using phylogenetic reconstruction of amino acid sequences. We present a well-supported phylogeny of this family based on systematic sampling of taxa across superphyla of bacteria and archaea. We compared the phylogeny to a current representation of the species tree of life and found that the 4mC/6mA methyltransferase family has a strikingly complex evolutionary history that likely began sometime after the last universal common ancestor of life diverged into the bacterial and archaeal lineages and probably involved many horizontal gene transfers within and between domains. Despite the complexity of its evolutionary history, we inferred that only one significant shift in molecular evolutionary rate characterizes the diversification of this protein family.
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20
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Xiong X, Wu G, Wei Y, Liu L, Zhang Y, Su R, Jiang X, Li M, Gao H, Tian X, Zhang Y, Hu L, Chen S, Tang Y, Jiang S, Huang R, Li Z, Wang Y, Deng Z, Wang J, Dedon PC, Chen S, Wang L. SspABCD-SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities. Nat Microbiol 2020; 5:917-928. [PMID: 32251370 DOI: 10.1038/s41564-020-0700-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 03/02/2020] [Indexed: 01/07/2023]
Abstract
Bacteria have evolved diverse mechanisms to fend off predation by bacteriophages. We previously identified the Dnd system, which uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification, and DndFGH, a restriction component. Here, we describe an unusual SspABCD-SspE PT system in Vibrio cyclitrophicus, Escherichia coli and Streptomyces yokosukanensis, which has distinct genetic organization, biochemical functions and phenotypic behaviour. SspABCD confers single-stranded and high-frequency PTs with SspB acting as a nickase and possibly introducing nicks to facilitate sulfur incorporation. Strikingly, SspABCD coupled with SspE provides protection against phages in unusual ways: (1) SspE senses sequence-specific PTs by virtue of its PT-stimulated NTPase activity to exert its anti-phage activity, and (2) SspE inhibits phage propagation by introducing nicking damage to impair phage DNA replication. These results not only expand our knowledge about the diversity and functions of DNA PT modification but also enhance our understanding of the known arsenal of defence systems.
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Affiliation(s)
- Xiaolin Xiong
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Wei
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Liqiong Liu
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Yubing Zhang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Su
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xianyue Jiang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Mengxue Li
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Haiyan Gao
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Xihao Tian
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yizhou Zhang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Li Hu
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Si Chen
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - You Tang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Susu Jiang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Ruolin Huang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yunfu Wang
- Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zixin Deng
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shi Chen
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.,Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Lianrong Wang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China. .,Taihe Hospital, Hubei University of Medicine, Shiyan, China. .,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, China.
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21
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Tang P, Miri K, Varmuza S. Unique trophoblast chromatin environment mediated by the PcG protein SFMBT2. Biol Open 2019; 8:bio043638. [PMID: 31391163 PMCID: PMC6737984 DOI: 10.1242/bio.043638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/29/2019] [Indexed: 12/22/2022] Open
Abstract
Stem/progenitor cells are maintained by a chromatin environment, mediated in part by Polycomb group (PcG) proteins, which depress differentiation. The trophoblast-specific PcG protein SFMBT2 is known to be required for maintenance of trophoblast progenitors. Rather than binding to trophoblast-specific genes repressed in TSC, SFMBT2 is concentrated at chromocentres and regions rich in repetitive elements, specifically LINE sequences and major satellites, suggesting that it is involved in higher-order organization of the trophoblast genome. It is also found enriched at a subset of ncRNAs. Comparison of ChIP-seq datasets for other chromatin proteins reveals several stereotypical distribution patterns, suggesting that SFMBT2 interacts with several different types of chromatin complexes specific to the trophoblast lineage.
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Affiliation(s)
- Priscilla Tang
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord St., Toronto, Ontario M5S 3G5, Canada
| | - Kamelia Miri
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord St., Toronto, Ontario M5S 3G5, Canada
| | - Susannah Varmuza
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord St., Toronto, Ontario M5S 3G5, Canada
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22
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The Regulatory Role of Rac1, a Small Molecular Weight GTPase, in the Development of Diabetic Retinopathy. J Clin Med 2019; 8:jcm8070965. [PMID: 31277234 PMCID: PMC6678477 DOI: 10.3390/jcm8070965] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/24/2019] [Accepted: 06/27/2019] [Indexed: 12/16/2022] Open
Abstract
Diabetic retinopathy, a microvascular complication of diabetes, remains the leading cause of vision loss in working age adults. Hyperglycemia is considered as the main instigator for its development, around which other molecular pathways orchestrate. Of these multiple pathways, oxidative stress induces many metabolic, functional and structural changes in the retinal cells, leading to the development of pathological features characteristic of this blinding disease. An increase in cytosolic reactive oxygen species (ROS), produced by cytosolic NADPH oxidase 2 (Nox2), is an early event in the pathogenesis of diabetic retinopathy, which leads to mitochondrial damage and retinal capillary cell apoptosis. Activation of Nox2 is mediated through an obligatory small molecular weight GTPase, Ras-related C3 botulinum toxin substrate 1 (Rac1), and subcellular localization of Rac1 and its activation are regulated by several regulators, rendering it a complex biological process. In diabetes, Rac1 is functionally activated in the retina and its vasculature, and, via Nox2-ROS, contributes to mitochondrial damage and the development of retinopathy. In addition, Rac1 is also transcriptionally activated, and epigenetic modifications play a major role in this transcriptional activation. This review focusses on the role of Rac1 and its regulation in the development and progression of diabetic retinopathy, and discusses some possible avenues for therapeutic interventions.
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23
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Gurung PMS, Barnett AR, Wilson JS, Hudson J, Ward DG, Messing EM, Bryan RT. Prognostic DNA Methylation Biomarkers in High-risk Non-muscle-invasive Bladder Cancer: A Systematic Review to Identify Loci for Prospective Validation. Eur Urol Focus 2019; 6:683-697. [PMID: 30803927 DOI: 10.1016/j.euf.2019.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
CONTEXT High-risk non-muscle-invasive bladder cancer (HR-NMIBC) represents over 30% of all incident urothelial bladder cancers (BCs); patients are at risk of progression, and 20-30% will die from BC within 5 yr. Current guidelines recommend induction and maintenance of intravesical bacillus Calmette-Guérin (BCG) or upfront radical cystectomy for highest-risk disease, treatments with markedly different morbidity, mortality, and patient burden. There are no validated biomarkers to facilitate such treatment decisions. Alterations in DNA methylation are commonplace in BC; hence, measurable changes in DNA methylation represent an opportunity for the discovery of such biomarkers. OBJECTIVE To systematically assess the evidence regarding DNA methylation markers as prognosticators for HR-NMIBC. EVIDENCE ACQUISITION Standard systematic review methods were employed with searches undertaken in MEDLINE, EMBASE, and PubMed up to January 2019. Studies that included patients with HR-NMIBC and investigated the utility of DNA methylation biomarkers as prognostic tools were included. EVIDENCE SYNTHESIS Of 63 prognostic biomarker studies identified, 21 met the protocol-driven inclusion criteria and were directly relevant to HR-NMIBC patient outcomes: tumour recurrence (TR), tumour progression (TP), disease-specific survival (DSS), and overall survival (OS). These studies described 140 methylation markers; of these, the most promising were cadherin-13 (CDH13; hazard ratios [HRs]: 5.1 for TR, 6.6 for TP, 3.8-8.0 for OS), protocadherins (PCDHs; HRs: 4.7 for TR, 2.5 for TP, 3.0-4.8 for OS), Runt domain transcription factor 3 (RUNX3; HR: 5.1 for TP), Homeobox 9 (HOXA9; HR: 1.9 for TR), Islet-1 (ISL1; HRs: 1.7 for TR, 3.3 for TP), and PAX6 (HR: 2.2 for TR). CONCLUSIONS This systematic review identifies a number of potentially useful prognostic methylation markers for HR-NMIBC. These loci (CDH13, PCDHs, RUNX3, HOXA9, ISL1, and PAX6) should be validated in prospective studies in order to translate benefit to patients. PATIENT SUMMARY Early bladder cancer represents a more complex spectrum of disease than can be assessed by conventional methods Emerging studies on molecular markers will improve our understanding of this disease, and may enable more precise and personalised treatment.
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Affiliation(s)
- Pratik M S Gurung
- University of Rochester Medical Center, Rochester, New York, NY, USA
| | - Abigail R Barnett
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Jayne S Wilson
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Douglas G Ward
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Edward M Messing
- University of Rochester Medical Center, Rochester, New York, NY, USA
| | - Richard T Bryan
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK.
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24
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Podolich O, Kukharenko O, Haidak A, Zaets I, Zaika L, Storozhuk O, Palchikovska L, Orlovska I, Reva O, Borisova T, Khirunenko L, Sosnin M, Rabbow E, Kravchenko V, Skoryk M, Kremenskoy M, Demets R, Olsson-Francis K, Kozyrovska N, de Vera JPP. Multimicrobial Kombucha Culture Tolerates Mars-Like Conditions Simulated on Low-Earth Orbit. ASTROBIOLOGY 2019; 19:183-196. [PMID: 30484685 DOI: 10.1089/ast.2017.1746] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A kombucha multimicrobial culture (KMC) was exposed to simulated Mars-like conditions in low-Earth orbit (LEO). The study was part of the Biology and Mars Experiment (BIOMEX), which was accommodated in the European Space Agency's EXPOSE-R2 facility, outside the International Space Station. The aim of the study was to investigate the capability of a KMC microecosystem to survive simulated Mars-like conditions in LEO. During the 18-month exposure period, desiccated KMC samples, represented by living cellulose-based films, were subjected to simulated anoxic Mars-like conditions and ultraviolet (UV) radiation, as prevalent at the surface of present-day Mars. Postexposure analysis demonstrated that growth of both the bacterial and yeast members of the KMC community was observed after 60 days of incubation; whereas growth was detected after 2 days in the initial KMC. The KMC that was exposed to extraterrestrial UV radiation showed degradation of DNA, alteration in the composition and structure of the cellular membranes, and an inhibition of cellulose synthesis. In the "space dark control" (exposed to LEO conditions without the UV radiation), the diversity of the microorganisms that survived in the biofilm was reduced compared with the ground-based controls. This was accompanied by structural dissimilarities in the extracellular membrane vesicles. After a series of subculturing, the revived communities restored partially their structure and associated activities.
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Affiliation(s)
- Olga Podolich
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Olga Kukharenko
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Andriy Haidak
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Iryna Zaets
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Leonid Zaika
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Olha Storozhuk
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Iryna Orlovska
- 1 Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Oleg Reva
- 2 Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | | | | | | | - Elke Rabbow
- 5 German Aerospace Center (DLR) Cologne, Institute of Aerospace Medicine, Radiation Biology, Berlin, Germany
| | | | | | | | | | - Karen Olsson-Francis
- 8 School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, United Kingdom
| | | | - Jean-Pierre Paul de Vera
- 9 Astrobiological Laboratories, German Aerospace Center (DLR) Berlin, Institute of Planetary Research, Management and Infrastructure, Berlin, Germany
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25
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Sensitization of Drug Resistant Cancer Cells: A Matter of Combination Therapy. Cancers (Basel) 2018; 10:cancers10120483. [PMID: 30518036 PMCID: PMC6315347 DOI: 10.3390/cancers10120483] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/12/2018] [Accepted: 11/21/2018] [Indexed: 02/07/2023] Open
Abstract
Cancer drug resistance is an enormous problem. It is responsible for most relapses in cancer patients following apparent remission after successful therapy. Understanding cancer relapse requires an understanding of the processes underlying cancer drug resistance. This article discusses the causes of cancer drug resistance, the current combination therapies, and the problems with the combination therapies. The rational design of combination therapy is warranted to improve the efficacy. These processes must be addressed by finding ways to sensitize the drug-resistant cancers cells to chemotherapy, and to prevent formation of drug resistant cancer cells. It is also necessary to prevent the formation of cancer progenitor cells by epigenetic mechanisms, as cancer progenitor cells are insensitive to standard therapies. In this article, we emphasize the role for the rational development of combination therapy, including epigenetic drugs, in achieving these goals.
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26
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Cross-species interference of gene expression. Nat Commun 2018; 9:5019. [PMID: 30479328 PMCID: PMC6258686 DOI: 10.1038/s41467-018-07353-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/18/2018] [Indexed: 11/09/2022] Open
Abstract
Microbes can contribute to protection of animals and plants against diseases. A recent study reveals a mechanism by which a bacterium controls fungal infection in wheat, involving secretion of a metabolite that affects histone acetyltransferase activity of a plant pathogenic fungus.
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Bhushan B, Erdmann A, Zhang Y, Belle R, Johannson C, Oppermann U, Hopkinson RJ, Schofield CJ, Kawamura A. Investigations on small molecule inhibitors targeting the histone H3K4 tri-methyllysine binding PHD-finger of JmjC histone demethylases. Bioorg Med Chem 2018; 26:2984-2991. [PMID: 29764755 PMCID: PMC6380468 DOI: 10.1016/j.bmc.2018.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/10/2018] [Accepted: 03/18/2018] [Indexed: 12/12/2022]
Abstract
Plant homeodomain (PHD) containing proteins are important epigenetic regulators and are of interest as potential drug targets. Inspired by the amiodarone derivatives reported to inhibit the PHD finger 3 of KDM5A (KDM5A(PHD3)), a set of compounds were synthesised. Amiodarone and its derivatives were observed to weakly disrupt the interactions of a histone H3K4me3 peptide with KDM5A(PHD3). Selected amiodarone derivatives inhibited catalysis of KDM5A, but in a PHD-finger independent manner. Amiodarone derivatives also bind to H3K4me3-binding PHD-fingers from the KDM7 subfamily. Further work is required to develop potent and selective PHD finger inhibitors.
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Affiliation(s)
- Bhaskar Bhushan
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Alexandre Erdmann
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Yijia Zhang
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Roman Belle
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Catrine Johannson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, United Kingdom
| | - Udo Oppermann
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, United Kingdom
| | - Richard J Hopkinson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Akane Kawamura
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.
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28
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Jeremias G, Barbosa J, Marques SM, Asselman J, Gonçalves FJM, Pereira JL. Synthesizing the role of epigenetics in the response and adaptation of species to climate change in freshwater ecosystems. Mol Ecol 2018; 27:2790-2806. [DOI: 10.1111/mec.14727] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/27/2018] [Accepted: 05/02/2018] [Indexed: 12/23/2022]
Affiliation(s)
| | - João Barbosa
- Department of Biology; University of Aveiro; Aveiro Portugal
| | - Sérgio M. Marques
- Department of Biology; University of Aveiro; Aveiro Portugal
- CESAM - Centre for Environmental and Marine Studies; University of Aveiro; Aveiro Portugal
| | - Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab); Ghent University; Ghent Belgium
| | - Fernando J. M. Gonçalves
- Department of Biology; University of Aveiro; Aveiro Portugal
- CESAM - Centre for Environmental and Marine Studies; University of Aveiro; Aveiro Portugal
| | - Joana L. Pereira
- Department of Biology; University of Aveiro; Aveiro Portugal
- CESAM - Centre for Environmental and Marine Studies; University of Aveiro; Aveiro Portugal
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29
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Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 140:49-73. [PMID: 29685747 DOI: 10.1016/j.pbiomolbio.2018.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/12/2018] [Indexed: 02/07/2023]
Abstract
Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity.
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A computational method using the random walk with restart algorithm for identifying novel epigenetic factors. Mol Genet Genomics 2017; 293:293-301. [PMID: 28932904 DOI: 10.1007/s00438-017-1374-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/11/2017] [Indexed: 12/31/2022]
Abstract
Epigenetic regulation has long been recognized as a significant factor in various biological processes, such as development, transcriptional regulation, spermatogenesis, and chromosome stabilization. Epigenetic alterations lead to many human diseases, including cancer, depression, autism, and immune system defects. Although efforts have been made to identify epigenetic regulators, it remains a challenge to systematically uncover all the components of the epigenetic regulation in the genome level using experimental approaches. The advances of constructing protein-protein interaction (PPI) networks provide an excellent opportunity to identify novel epigenetic factors computationally in the genome level. In this study, we identified potential epigenetic factors by using a computational method that applied the random walk with restart (RWR) algorithm on a protein-protein interaction (PPI) network using reported epigenetic factors as seed nodes. False positives were identified by their specific roles in the PPI network or by a low-confidence interaction and a weak functional relationship with epigenetic regulators. After filtering out the false positives, 26 candidate epigenetic factors were finally accessed. According to previous studies, 22 of these are thought to be involved in epigenetic regulation, suggesting the robustness of our method. Our study provides a novel computational approach which successfully identified 26 potential epigenetic factors, paving the way on deepening our understandings on the epigenetic mechanism.
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Ashraf W, Ibrahim A, Alhosin M, Zaayter L, Ouararhni K, Papin C, Ahmad T, Hamiche A, Mély Y, Bronner C, Mousli M. The epigenetic integrator UHRF1: on the road to become a universal biomarker for cancer. Oncotarget 2017; 8:51946-51962. [PMID: 28881702 PMCID: PMC5584303 DOI: 10.18632/oncotarget.17393] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/02/2017] [Indexed: 12/12/2022] Open
Abstract
Cancer is one of the deadliest diseases in the world causing record number of mortalities in both developed and undeveloped countries. Despite a lot of advances and breakthroughs in the field of oncology still, it is very hard to diagnose and treat the cancers at early stages. Here in this review we analyze the potential of Ubiquitin-like containing PHD and Ring Finger domain 1 (UHRF1) as a universal biomarker for cancers. UHRF1 is an important epigenetic regulator maintaining DNA methylation and histone code in the cell. It is highly expressed in a variety of cancers and is a well-known oncogene that can disrupt the epigenetic code and override the senescence machinery. Many studies have validated UHRF1 as a powerful diagnostic and prognostic tool to differentially diagnose cancer, predict the therapeutic response and assess the risk of tumor progression and recurrence. Highly sensitive, non-invasive and cost effective approaches are therefore needed to assess the level of UHRF1 in patients, which can be deployed in diagnostic laboratories to detect cancer and monitor disease progression.
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Affiliation(s)
- Waseem Ashraf
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Abdulkhaleg Ibrahim
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Mahmoud Alhosin
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer Metabolism and Epigenetic Unit, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer and Mutagenesis Unit, King Fahd Centre for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Liliyana Zaayter
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Khalid Ouararhni
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Christophe Papin
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Tanveer Ahmad
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Ali Hamiche
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Yves Mély
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Christian Bronner
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Marc Mousli
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
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33
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Peedicayil J. Epigenetics and developmental psychiatry. Int J Soc Psychiatry 2017; 63:378. [PMID: 28504044 DOI: 10.1177/0020764017693656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, Vellore, India
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Abbaoui B, Telu KH, Lucas CR, Thomas-Ahner JM, Schwartz SJ, Clinton SK, Freitas MA, Mortazavi A. The impact of cruciferous vegetable isothiocyanates on histone acetylation and histone phosphorylation in bladder cancer. J Proteomics 2017; 156:94-103. [PMID: 28132875 DOI: 10.1016/j.jprot.2017.01.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 12/07/2016] [Accepted: 01/25/2017] [Indexed: 12/17/2022]
Abstract
Cruciferous vegetable intake is associated with reduced risk of bladder cancer, yet mechanisms remain unclear. Cruciferous vegetable isothiocyanates (ITCs), namely sulforaphane (SFN) and erucin (ECN), significantly inhibit histone deacetylase (HDAC) activity in human bladder cancer cells representing superficial to invasive biology (59-83% inhibition with 20μM, 48h treatment), and in bladder cancer xenografts (59±3% ECN inhibition). Individual HDACs inhibited by SFN and ECN include HDACs 1, 2, 4 and 6. Interestingly, global acetylation status of histones H3 or H4 remain unaltered. The interplay between HDAC inhibition and modest modulation of AcH3 and AcH4 status is partially explained by decreased histone acetyl transferase activity (48.8±5.3%). In contrast, a significant decrease in phosphorylation status of all isoforms of histone H1 was observed, concomitant with increased phosphatase PP1β and PP2A activity. Together, these findings suggest that ITCs modulate histone status via HDAC inhibition and phosphatase enhancement. This allows for reduced levels of histone H1 phosphorylation, a marker correlated with human bladder cancer progression. Therefore, ITC-mediated inhibition of histone H1 phosphorylation presents a novel direction of research in elucidating epidemiological relationships and supports future food-based prevention strategies. SIGNIFICANCE Collectively, our findings suggest that the cruciferous vegetable isothiocyanates: sulforaphane (SFN) and erucin (ECN), impact histones status in bladder cancer cells by modulating specific HDACs and HATs, and enhancing phosphatase activity, resulting in reduction of histone H1 phosphorylation. These findings are significant due to the fact that our previous work positively correlated histone H1 phosphorylation with bladder cancer carcinogenesis and progression. Therefore, we propose that SFN and ECN may inhibit bladder carcinogenesis via epigenetic modulation of gene expression associated with histone H1 phosphorylation. These efforts may elucidate biomarkers useful in epidemiologic studies related to cruciferous vegetable intake and cancer risk or provide intermediate biomarkers for food-based clinical intervention studies in high-risk cohorts.
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Affiliation(s)
- Besma Abbaoui
- The Integrated Biomedical Science Graduate Program, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kelly H Telu
- Department of Chemistry, College of Arts and Sciences, The Ohio State University, Columbus, OH 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Christopher R Lucas
- The Integrated Biomedical Science Graduate Program, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | | | - Steven J Schwartz
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Food Science and Technology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Steven K Clinton
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Division of Medical Oncology, Department of Internal Medicine, College of Medicine; The Ohio State University, Columbus, OH 43210, USA
| | - Michael A Freitas
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Amir Mortazavi
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Division of Medical Oncology, Department of Internal Medicine, College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
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