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Kafida M, Karela M, Giakountis A. RNA-Independent Regulatory Functions of lncRNA in Complex Disease. Cancers (Basel) 2024; 16:2728. [PMID: 39123456 PMCID: PMC11311644 DOI: 10.3390/cancers16152728] [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: 07/06/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
During the metagenomics era, high-throughput sequencing efforts both in mice and humans indicate that non-coding RNAs (ncRNAs) constitute a significant fraction of the transcribed genome. During the past decades, the regulatory role of these non-coding transcripts along with their interactions with other molecules have been extensively characterized. However, the study of long non-coding RNAs (lncRNAs), an ncRNA regulatory class with transcript lengths that exceed 200 nucleotides, revealed that certain non-coding transcripts are transcriptional "by-products", while their loci exert their downstream regulatory functions through RNA-independent mechanisms. Such mechanisms include, but are not limited to, chromatin interactions and complex promoter-enhancer competition schemes that involve the underlying ncRNA locus with or without its nascent transcription, mediating significant or even exclusive roles in the regulation of downstream target genes in mammals. Interestingly, such RNA-independent mechanisms often drive pathological manifestations, including oncogenesis. In this review, we summarize selective examples of lncRNAs that regulate target genes independently of their produced transcripts.
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Affiliation(s)
| | | | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Mezourlo, 41500 Larissa, Greece
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2
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Ma X, Zhao LL, Yu YC, Cheng Y. Engrailed: Pathological and physiological effects of a multifunctional developmental gene. Genesis 2024; 62:e23557. [PMID: 37830136 DOI: 10.1002/dvg.23557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Engrailed-1 (EN1) is a developmental gene that encodes En1, a highly conserved transcription factor involved in regionalization during early embryogenesis and in the later maintenance of normal neurons. After birth, EN1 still plays a role in the development and physiology of the body; for example, it exerts a protective effect on midbrain dopaminergic (mDA) neurons, and loss of EN1 causes mDA neurons in the ventral midbrain to gradually die approximately 6 weeks after birth, resulting in motor and nonmotor symptoms similar to those observed in Parkinson's disease. Notably, EN1 has been identified as a possible susceptibility gene for idiopathic Parkinson's disease in humans. EN1 is involved in the processes of wound-healing scar production and tissue and organ fibrosis. Additionally, EN1 can lead to tumorigenesis and thus provides a target for the treatment of some tumors. In this review, we summarize the effects of EN1 on embryonic organ development, describe the consequences of the deletion or overexpression of the EN1 gene, and discuss the pathways in which EN1 is involved. We hope to clarify the role of EN1 as a developmental gene and present potential therapeutic targets for diseases involving the EN1 gene.
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Affiliation(s)
- Xiang Ma
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Liang-Liang Zhao
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Yi-Chun Yu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
| | - Yan Cheng
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, P.R. China
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3
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Wang H, Yin X, Xu J, Chen L, Karuppagounder SS, Xu E, Mao X, Dawson VL, Dawson TM. Interspecies chimerism with human embryonic stem cells generates functional human dopamine neurons at low efficiency. Stem Cell Reports 2024; 19:54-67. [PMID: 38134925 PMCID: PMC10828682 DOI: 10.1016/j.stemcr.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Interspecies chimeras offer great potential for regenerative medicine and the creation of human disease models. Whether human pluripotent stem cell-derived neurons in an interspecies chimera can differentiate into functional neurons and integrate into host neural circuity is not known. Here, we show, using Engrailed 1 (En1) as a development niche, that human naive-like embryonic stem cells (ESCs) can incorporate into embryonic and adult mouse brains. Human-derived neurons including tyrosine hydroxylase (TH)+ neurons integrate into the mouse brain at low efficiency. These TH+ neurons have electrophysiologic properties consistent with their human origin. In addition, these human-derived neurons in the mouse brain accumulate pathologic phosphorylated α-synuclein in response to α-synuclein preformed fibrils. Optimization of human/mouse chimeras could be used to study human neuronal differentiation and human brain disorders.
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Affiliation(s)
- Hu Wang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xiling Yin
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jinchong Xu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Li Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Senthilkumar S Karuppagounder
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Enquan Xu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xiaobo Mao
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Bhardwaj V, Yadav D, Dhankhar M, Saini K. A novel approach for identification of mirror repeats within the Engrailed Homeobox-1 gene of Xenopus tropicalis. BIOMEDICAL AND BIOTECHNOLOGY RESEARCH JOURNAL (BBRJ) 2022. [DOI: 10.4103/bbrj.bbrj_281_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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5
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Mc Auley MT. DNA methylation in genes associated with the evolution of ageing and disease: A critical review. Ageing Res Rev 2021; 72:101488. [PMID: 34662746 DOI: 10.1016/j.arr.2021.101488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/30/2021] [Accepted: 10/12/2021] [Indexed: 12/28/2022]
Abstract
Ageing is characterised by a physical decline in biological functioning which results in a progressive risk of mortality with time. As a biological phenomenon, it is underpinned by the dysregulation of a myriad of complex processes. Recently, however, ever-increasing evidence has associated epigenetic mechanisms, such as DNA methylation (DNAm) with age-onset pathologies, including cancer, cardiovascular disease, and Alzheimer's disease. These diseases compromise healthspan. Consequently, there is a medical imperative to understand the link between epigenetic ageing, and healthspan. Evolutionary theory provides a unique way to gain new insights into epigenetic ageing and health. This review will: (1) provide a brief overview of the main evolutionary theories of ageing; (2) discuss recent genetic evidence which has revealed alleles that have pleiotropic effects on fitness at different ages in humans; (3) consider the effects of DNAm on pleiotropic alleles, which are associated with age related disease; (4) discuss how age related DNAm changes resonate with the mutation accumulation, disposable soma and programmed theories of ageing; (5) discuss how DNAm changes associated with caloric restriction intersect with the evolution of ageing; and (6) conclude by discussing how evolutionary theory can be used to inform investigations which quantify age-related DNAm changes which are linked to age onset pathology.
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Affiliation(s)
- Mark Tomás Mc Auley
- Faculty of Science and Engineering, University of Chester, Exton Park, Chester CH1 4BJ, UK.
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6
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Electrochemically detecting DNA methylation in the EN1 gene promoter: implications for understanding ageing and disease. Biosci Rep 2021; 40:226876. [PMID: 33135722 PMCID: PMC7670582 DOI: 10.1042/bsr20202571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/29/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
There is a growing need for biomarkers which predict age-onset pathology. Although this is challenging, the methylome offers significant potential. Cancer is associated with the hypermethylation of many gene promoters, among which are developmental genes. Evolutionary theory suggests developmental genes arbitrate early-late life trade-offs, causing epimutations that increase disease vulnerability. Such genes could predict age-related disease. The aim of this work was to optimise an electrochemical procedure for the future investigation of a broad range of ageing-related pathologies. An electrochemical approach, which adopted three analytical techniques, was used to investigate DNA methylation in the engrailed-1 (EN1) gene promoter. Using synthetic single-stranded DNA, one technique was able to detect DNA at concentrations as low as 10 nM, with methylation status distinguishable at concentrations >25 nM. A negative correlation could be observed between % methylation of a heterogeneous solution and the key electrochemical parameter, charge transfer resistance (Rct; r = -0.982, P<0.01). The technique was applied to the breast cancer cell line Michigan Cancer Foundation-7 (MCF-7), where a similar correlation was observed (r = -0.965, P<0.01). These results suggest electrochemistry can effectively measure DNA methylation at low concentrations of DNA. This has implications for the future detection of age-related disease.
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Allou L, Balzano S, Magg A, Quinodoz M, Royer-Bertrand B, Schöpflin R, Chan WL, Speck-Martins CE, Carvalho DR, Farage L, Lourenço CM, Albuquerque R, Rajagopal S, Nampoothiri S, Campos-Xavier B, Chiesa C, Niel-Bütschi F, Wittler L, Timmermann B, Spielmann M, Robson MI, Ringel A, Heinrich V, Cova G, Andrey G, Prada-Medina CA, Pescini-Gobert R, Unger S, Bonafé L, Grote P, Rivolta C, Mundlos S, Superti-Furga A. Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator. Nature 2021; 592:93-98. [DOI: 10.1038/s41586-021-03208-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/07/2021] [Indexed: 11/09/2022]
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Di Nardo AA, Joliot A, Prochiantz A. Homeoprotein transduction in neurodevelopment and physiopathology. SCIENCE ADVANCES 2020; 6:6/44/eabc6374. [PMID: 33115744 PMCID: PMC7608782 DOI: 10.1126/sciadv.abc6374] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/11/2020] [Indexed: 05/28/2023]
Abstract
Homeoproteins were originally identified for embryonic cell-autonomous transcription activity, but they also have non-cell-autonomous activity owing to transfer between cells. This Review discusses transfer mechanisms and focuses on some established functions, such as neurodevelopmental regulation of axon guidance, and postnatal critical periods of brain plasticity that affect sensory processing and cognition. Homeoproteins are present across all eukaryotes, and intercellular transfer occurs in plants and animals. Proposed functions have evolutionary relevance, such as morphogenetic activity and sexual exchange during the mating of unicellular eukaryotes, while others have physiopathological relevance, such as regulation of mood and cognition by influencing brain compartmentalization, connectivity, and plasticity. There are more than 250 known homeoproteins with conserved transfer domains, suggesting that this is a common mode of signal transduction but with many undiscovered functions.
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Affiliation(s)
- Ariel A Di Nardo
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, 75005 Paris, France.
| | - Alain Joliot
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, 75005 Paris, France
| | - Alain Prochiantz
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, 75005 Paris, France.
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Simkin J, Sammarco MC, Dawson LA, Schanes PP, Yu L, Muneoka K. The mammalian blastema: regeneration at our fingertips. ACTA ACUST UNITED AC 2015; 2:93-105. [PMID: 27499871 PMCID: PMC4895320 DOI: 10.1002/reg2.36] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/14/2015] [Accepted: 03/16/2015] [Indexed: 02/06/2023]
Abstract
In the mouse, digit tip regeneration progresses through a series of discrete stages that include inflammation, histolysis, epidermal closure, blastema formation, and redifferentiation. Recent studies reveal how each regenerative stage influences subsequent stages to establish a blastema that directs the successful regeneration of a complex mammalian structure. The focus of this review is on early events of healing and how an amputation wound transitions into a functional blastema. The stepwise formation of a mammalian blastema is proposed to provide a model for how specific targeted treatments can enhance regenerative performance in humans.
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Affiliation(s)
- Jennifer Simkin
- Division of Developmental Biology, Department of Cell and Molecular Biology Tulane University New Orleans Louisiana 70118 USA
| | - Mimi C Sammarco
- Division of Developmental Biology, Department of Cell and Molecular Biology Tulane University New Orleans Louisiana 70118 USA
| | - Lindsay A Dawson
- Division of Developmental Biology, Department of Cell and Molecular Biology Tulane University New Orleans Louisiana 70118 USA
| | - Paula P Schanes
- Division of Developmental Biology, Department of Cell and Molecular Biology Tulane University New Orleans Louisiana 70118 USA
| | - Ling Yu
- Division of Developmental Biology, Department of Cell and Molecular Biology Tulane University New Orleans Louisiana 70118 USA
| | - Ken Muneoka
- Division of Developmental Biology, Department of Cell and Molecular Biology Tulane University New Orleans Louisiana 70118 USA
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