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Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Hoolehan W, Kulpa AM, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. Epigenetics Chromatin 2023; 16:45. [PMID: 37953264 PMCID: PMC10642035 DOI: 10.1186/s13072-023-00522-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation, DNA modifications in particular, of gene expression between neurons and glia. RESULTS After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT-whole genome oxidative bisulfite sequencing (WGoxBS) to assess the neuronal translatome and epigenome in the hippocampus of young mice (4 months old). WGoxBS findings were validated with enzymatic methyl-Seq (EM-Seq) and nanopore sequencing. Comparing neuronal data to microglial and astrocytic data from NuTRAP models, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, rather than proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of gene body mCG and a positive relationship between distal promoter and gene body hmCG with gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. CONCLUSIONS Neurons, astrocytes, and microglia demonstrate different genome-wide levels of mCG, hmCG, and mCH that are reproducible across analytical methods. However, modification-gene expression relationships are conserved across cell types. Enrichment of differential modifications across cell types in gene bodies and distal regulatory elements, but not proximal promoters, highlights epigenomic patterning in these regions as potentially greater determinants of cell identity. These findings also demonstrate the importance of differentiating between mC and hmC in neuroepigenomic analyses, as up to 30% of what is conventionally interpreted as mCG can be hmCG, which often has a different relationship to gene expression than mCG.
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Affiliation(s)
- Kyla B Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Ana J Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Sarah R Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adeline H Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Kevin D Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Walker Hoolehan
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adam M Kulpa
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - David R Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Willard M Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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Jin Q, Xu L, Wang J, Lin J, Lin H. Pan-cancer analysis of Homeobox B9 as a predictor for prognosis and immunotherapy in human tumors. Aging (Albany NY) 2023; 15:204785. [PMID: 37301547 PMCID: PMC10292867 DOI: 10.18632/aging.204785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Although several animal and cell studies have described the association between HOXB9 and cancers, there is no pan-cancer investigation of HOXB9. In this article, we explored the expression levels and prognosis of HOXB9 in pan-cancer. We evaluated the correlation of HOXB9 expression level with the efficacy of immunotherapy. METHODS We conducted a survival analysis of HOXB9 in various types of cancer using publicly available databases. We also examined the relationship between HOXB9 expression levels and several factors including prognosis, immune infiltration, immune checkpoint genes, tumor mutational burden, microsatellite instability, mismatch repair, and DNA methylation. TIMER2.0 tool was conducted to explore the immune cell infiltrations related to HOXB9 in this analysis. RESULTS It was discovered through a comprehensive analysis of multiple public datasets that HOXB9 expression was highly expressed in most tumor tissues and cancer cell lines and that distinct associations exist between HOXB9 expression and tumor patient prognosis. Besides, HOXB9 expression was closely associated with immune cell infiltration and checkpoint genes in many cancers. Further, HOXB9 was associated with immune cell infiltration, TMB, MSI, MMR, and DNA methylation. It was also confirmed that HOXB9 was highly expressed in clinical GBM tissues. Experiments further revealed that knockdown of HOXB9 expression could suppress proliferation, migration, and invasion of glioma cells. CONCLUSIONS The results revealed that HOXB9, a robust tumor biomarker, has a significant prognostic value. HOXB9 may act as a new predictor to assess cancer prognosis and therapeutic efficacy of the immune in various cancers.
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Affiliation(s)
- Qingdong Jin
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian Province, China
- Department of Neurosurgery, The First Hospital of Putian City, Putian, Fujian Province, China
- Key Laboratory of Translational Tumor Medicine in Fujian Province, Putian University, Putian, Fujian Province, China
| | - Li Xu
- Key Laboratory of Translational Tumor Medicine in Fujian Province, Putian University, Putian, Fujian Province, China
| | - Jun Wang
- Department of Neurosurgery, The First Hospital of Putian City, Putian, Fujian Province, China
| | - Junling Lin
- Department of Neurosurgery, The First Hospital of Putian City, Putian, Fujian Province, China
| | - Huang Lin
- Department of Neurosurgery, The First Hospital of Putian City, Putian, Fujian Province, China
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Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543497. [PMID: 37333391 PMCID: PMC10274634 DOI: 10.1101/2023.06.05.543497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. This is especially true as for DNA modifications where most data are derived from bisulfite sequencing that cannot differentiate between DNA methylation and hydroxymethylation. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation of gene expression between neurons and glia. Results After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT whole genome oxidative bisulfite sequencing to assess the neuronal translatome and epigenome in the hippocampus of young mice (3 months old). These data were then compared to microglial and astrocytic data from NuTRAP models. When comparing the different cell types, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, with limited differences occurring within proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of mCG with gene expression within the gene body while a positive relationship between distal promoter and gene body hmCG and gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. Conclusions In this study, we identified differential usage of DNA modifications across CNS cell types, and assessed the relationship between DNA modifications and gene expression in neurons and glia. Despite having different global levels, the general modification-gene expression relationship was conserved across cell types. The enrichment of differential modifications in gene bodies and distal regulatory elements, but not proximal promoters, across cell types highlights epigenomic patterning in these regions as potentially greater determinants of cell identity.
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Affiliation(s)
- Kyla B. Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Ana J. Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Sarah R. Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Adeline H. Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Kevin D. Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - David R. Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Willard M. Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK USA
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Kaushik A, Chaudhary V, Longkumer I, Saraswathy KN, Jain S. Sex-specific variations in global DNA methylation levels with age: a population-based exploratory study from North India. Front Genet 2023; 14:1038529. [PMID: 37255712 PMCID: PMC10225692 DOI: 10.3389/fgene.2023.1038529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/03/2023] [Indexed: 06/01/2023] Open
Abstract
Purpose: Aging is one of the most important risk factors for a number of human diseases. Epigenetic alterations, including changes in DNA methylation patterns, have been reported to be one of the hallmarks of aging. Being a malleable process, the role of site-specific DNA methylation in aging is being extensively investigated; however, much less attention has been given to alterations in global DNA methylation with aging at the population level. The present study aims to explore overall and sex-specific variations in global DNA methylation patterns with age. Methods: A total of 1,127 adult individuals (792 females) aged 30-75 years belonging to Haryana, North India, were recruited. Socio-demographic data was collected using a pretested interview schedule. Global DNA methylation analysis, of peripheral blood leucocyte (PBL) DNA, was performed using the ELISA-based colorimetric technique. Results: Though the overall correlation analysis revealed a weak inverse trend between global DNA methylation and age, the adjusted regression model showed no significant association between global DNA methylation and age. In age-stratified analysis, global DNA methylation levels were found to be fairly stable until 60 years of age, followed by a decline in the above-60 age group. Further, no significant difference in DNA patterns methylation pattern was observed between males and females. Conclusion: Overall, the study suggests a lack of association between global DNA methylation and age, especially until 60 years of age, and a similar DNA methylation pattern between males and females with respect to age.
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Affiliation(s)
- Anshika Kaushik
- Laboratory of Molecular and Biochemical Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | - Vineet Chaudhary
- Laboratory of Molecular and Biochemical Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | - Imnameren Longkumer
- Laboratory of Molecular and Biochemical Anthropology, Department of Anthropology, University of Delhi, Delhi, India
| | | | - Sonal Jain
- Laboratory of Molecular and Biochemical Anthropology, Department of Anthropology, University of Delhi, Delhi, India
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Chalfun G, Araújo Brasil AD, Paravidino VB, Soares-Lima SC, Souza Almeida Lopes MD, Santos Salú MD, Barbosa E Dos Santos PV, P da Cunha Trompiere AC, Vieira Milone LT, Rodrigues-Santos G, Genuíno de Oliveira MB, Robaina JR, Lima-Setta F, Reis MM, Ledo Alves da Cunha AJ, Prata-Barbosa A, de Magalhães-Barbosa MC. NR3C1 gene methylation and cortisol levels in preterm and healthy full-term infants in the first 3 months of life. Epigenomics 2022; 14:1545-1561. [PMID: 36861354 DOI: 10.2217/epi-2022-0444] [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] [Indexed: 03/03/2023] Open
Abstract
Aim: To describe NR3C1 exon-1F methylation and cortisol levels in newborns. Materials & methods: Preterm ≤1500 g and full-term infants were included. Samples were collected at birth and at days 5, 30 and 90 (or at discharge). Results: 46 preterm and 49 full-term infants were included. Methylation was stable over time in full-term infants (p = 0.3116) but decreased in preterm infants (p = 0.0241). Preterm infants had higher cortisol levels on the fifth day, while full-term infants showed increasing levels (p = 0.0177) over time. Conclusion: Hypermethylated sites in NR3C1 at birth and higher cortisol levels on day 5 suggest that prematurity, reflecting prenatal stress, affects the epigenome. Methylation decrease over time in preterm infants suggests that postnatal factors may modify the epigenome, but their role needs to be clarified.
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Affiliation(s)
- Georgia Chalfun
- Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, 22281-100, Brazil
- Department of Neonatology, Maternity School, Federal University of Rio de Janeiro (UFRJ), RJ, 22240-000, Brazil
| | - Aline de Araújo Brasil
- Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, 22281-100, Brazil
| | - Vitor Barreto Paravidino
- Department of Epidemiology, Institute of Social Medicine, University of the State of Rio de Janeiro (UERJ), 20550-013, Brazil
- Department of Physical Education & Sports, Naval Academy, Brazilian Navy, Rio de Janeiro, RJ, 20021-010, Brazil
| | - Sheila Coelho Soares-Lima
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rio de Janeiro, RJ, 20230-130, Brazil
| | | | - Margarida Dos Santos Salú
- Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, 22281-100, Brazil
| | | | | | - Leo Travassos Vieira Milone
- Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, 22281-100, Brazil
| | - Gustavo Rodrigues-Santos
- Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, 22281-100, Brazil
| | | | - Jaqueline Rodrigues Robaina
- Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, 22281-100, Brazil
| | - Fernanda Lima-Setta
- Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, 22281-100, Brazil
| | - Marcelo Martins Reis
- Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, 22281-100, Brazil
| | - Antônio José Ledo Alves da Cunha
- Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, 22281-100, Brazil
- Postgraduate Program in Perinatal Health, Maternity School, Federal University of Rio de Janeiro (UFRJ), RJ, 22240-000, Brazil
| | - Arnaldo Prata-Barbosa
- Department of Pediatrics, D'Or Institute for Research & Education (IDOR), Rio de Janeiro, RJ, 22281-100, Brazil
- Postgraduate Program in Perinatal Health, Maternity School, Federal University of Rio de Janeiro (UFRJ), RJ, 22240-000, Brazil
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Chucair-Elliott AJ, Ocañas SR, Pham K, Van Der Veldt M, Cheyney A, Stanford D, Gurley J, Elliott MH, Freeman WM. Translatomic response of retinal Müller glia to acute and chronic stress. Neurobiol Dis 2022; 175:105931. [PMID: 36423879 PMCID: PMC9875566 DOI: 10.1016/j.nbd.2022.105931] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 11/14/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Analysis of retina cell type-specific epigenetic and transcriptomic signatures is crucial to understanding the pathophysiology of retinal degenerations such as age-related macular degeneration (AMD) and delineating cell autonomous and cell-non-autonomous mechanisms. We have discovered that Aldh1l1 is specifically expressed in the major macroglia of the retina, Müller glia, and, unlike the brain, is not expressed in retinal astrocytes. This allows use of Aldh1l1 cre drivers and Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) constructs for temporally controlled labeling and paired analysis of Müller glia epigenomes and translatomes. As validated through a variety of approaches, the Aldh1l1cre/ERT2-NuTRAP model provides Müller glia specific translatomic and epigenomic profiles without the need to isolate whole cells. Application of this approach to models of acute injury (optic nerve crush) and chronic stress (aging) uncovered few common Müller glia-specific transcriptome changes in inflammatory pathways, and mostly differential signatures for each stimulus. The expression of members of the IL-6 and integrin-linked kinase signaling pathways was enhanced in Müller glia in response to optic nerve crush but not aging. Unique changes in neuroinflammation and fibrosis signaling pathways were observed in response to aging but not with optic nerve crush. The Aldh1l1cre/ERT2-NuTRAP model allows focused molecular analyses of a single, minority cell type within the retina, providing more substantial effect sizes than whole tissue analyses. The NuTRAP model, nucleic acid isolation, and validation approaches presented here can be applied to any retina cell type for which a cell type-specific cre is available.
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Affiliation(s)
- Ana J. Chucair-Elliott
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Corresponding authors at: Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA. (A.J. Chucair-Elliott), (W.M. Freeman)
| | - Sarah R. Ocañas
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin Pham
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael Van Der Veldt
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Ashley Cheyney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - David Stanford
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Jami Gurley
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael H. Elliott
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M. Freeman
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA,Corresponding authors at: Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA. (A.J. Chucair-Elliott), (W.M. Freeman)
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Varma SJ, Calvani E, Grüning NM, Messner CB, Grayson N, Capuano F, Mülleder M, Ralser M. Global analysis of cytosine and adenine DNA modifications across the tree of life. eLife 2022; 11:81002. [PMID: 35900202 PMCID: PMC9333990 DOI: 10.7554/elife.81002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022] Open
Abstract
Interpreting the function and metabolism of enzymatic DNA modifications requires both position-specific and global quantities. Sequencing-based techniques that deliver the former have become broadly accessible, but analytical methods for the global quantification of DNA modifications have thus far been applied mostly to individual problems. We established a mass spectrometric method for the sensitive and accurate quantification of multiple enzymatic DNA modifications. Then, we isolated DNA from 124 archean, bacterial, fungal, plant, and mammalian species, and several tissues and created a resource of global DNA modification quantities. Our dataset provides insights into the general nature of enzymatic DNA modifications, reveals unique biological cases, and provides complementary quantitative information to normalize and assess the accuracy of sequencing-based detection of DNA modifications. We report that only three of the studied DNA modifications, methylcytosine (5mdC), methyladenine (N6mdA) and hydroxymethylcytosine (5hmdC), were detected above a picomolar detection limit across species, and dominated in higher eukaryotes (5mdC), in bacteria (N6mdA), or the vertebrate central nervous systems (5hmdC). All three modifications were detected simultaneously in only one of the tested species, Raphanus sativus. In contrast, these modifications were either absent or detected only at trace quantities, across all yeasts and insect genomes studied. Further, we reveal interesting biological cases. For instance, in Allium cepa, Helianthus annuus, or Andropogon gerardi, more than 35% of cytosines were methylated. Additionally, next to the mammlian CNS, 5hmdC was also detected in plants like Lepidium sativum and was found on 8% of cytosines in the Garra barreimiae brain samples. Thus, identifying unexpected levels of DNA modifications in several wild species, our resource underscores the need to address biological diversity for studying DNA modifications.
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Affiliation(s)
| | - Enrica Calvani
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Nana-Maria Grüning
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas Grayson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Michael Mülleder
- Core Facility-High Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany.,The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
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8
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Erofeeva TV, Grigorenko AP, Gusev FE, Kosevich IA, Rogaev EI. Studying of Molecular Regulation of Developmental Processes of Lower Metazoans Exemplified by Cnidaria Using High-Throughput Sequencing. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:269-293. [PMID: 35526848 DOI: 10.1134/s0006297922030075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/13/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
A unique set of features and characteristics of species of the Cnidaria phylum is the one reason that makes them a model for a various studies. The plasticity of a life cycle and the processes of cell differentiation and development of an integral multicellular organism associated with it are of a specific scientific interest. A new stage of development of molecular genetic methods, including methods for high-throughput genome, transcriptome, and epigenome sequencing, both at the level of the whole organism and at the level of individual cells, makes it possible to obtain a detailed picture of the development of these animals. This review examines some modern approaches and advances in the reconstruction of the processes of ontogenesis of cnidarians by studying the regulatory signal transduction pathways and their interactions.
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Affiliation(s)
- Taisia V Erofeeva
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasia P Grigorenko
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Fedor E Gusev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Igor A Kosevich
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Evgeny I Rogaev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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9
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Liu Y, Xiang J, Peng G, Shen C. Omics- and Pharmacogenomic Evidence for the Prognostic, Regulatory, and Immune-Related Roles of PBK in a Pan-Cancer Cohort. Front Mol Biosci 2021; 8:785370. [PMID: 34859058 PMCID: PMC8632063 DOI: 10.3389/fmolb.2021.785370] [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: 09/29/2021] [Accepted: 10/27/2021] [Indexed: 01/05/2023] Open
Abstract
PDZ-binding kinase (PBK) is known to regulate tumor progression in some cancer types. However, its relationship to immune cell infiltration and prognosis in different cancers is unclear. This was investigated in the present study by analyzing data from TCGA, GEO, GETx, TIMER, CPTAC, GEPIA2, cBioPortal, GSCALite, PROGNOSCAN, PharmacoDB, STRING, and ENCORI databases. PBK was overexpressed in most tumors including adenocortical carcinoma (hazard ratio [HR] = 2.178, p < 0.001), kidney renal clear cell carcinoma (KIRC; HR = 1.907, p < 0.001), kidney renal papillary cell carcinoma (HR = 3.024, p < 0.001), and lung adenocarcinoma (HR = 1.255, p < 0.001), in which it was associated with poor overall survival and advanced pathologic stage. PBK methylation level was a prognostic marker in thyroid carcinoma (THCA). PBK expression was positively correlated with the levels of BIRC5, CCNB1, CDC20, CDK1, DLGAP5, MAD2L1, MELK, PLK1, TOP2A, and TTK in 32 tumor types; and with the levels of the transcription factors E2F1 and MYC, which regulate apoptosis, the cell cycle, cell proliferation and invasion, tumorigenesis, and metastasis. It was also negatively regulated by the microRNAs hsa-miR-101-5p, hsa-miR-145-5p, and hsa-miR-5694. PBK expression in KIRC, liver hepatocellular carcinoma, THCA, and thymoma was positively correlated with the infiltration of immune cells including B cells, CD4+T cells, CD8+ T cells, macrophages, monocytes, and neutrophils. The results of the functional enrichment analysis suggested that PBK and related genes contribute to tumor development via cell cycle regulation. We also identified 20 drugs that potentially inhibit PBK expression. Thus, PBK is associated with survival outcome in a variety of cancers and may promote tumor development and progression by increasing immune cell infiltration into the tumor microenvironment. These findings indicate that PBK is a potential therapeutic target and has prognostic value in cancer treatment.
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Affiliation(s)
- Yi Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Juan Xiang
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Gang Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Chenfu Shen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
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10
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Van Remmen H, Freeman WM, Miller BF, Kinter M, Wren JD, Chiao A, Towner RA, Snider TA, Sonntag WE, Richardson A. Oklahoma Nathan Shock Aging Center - assessing the basic biology of aging from genetics to protein and function. GeroScience 2021; 43:2183-2203. [PMID: 34606039 PMCID: PMC8599778 DOI: 10.1007/s11357-021-00454-7] [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: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 01/21/2023] Open
Abstract
The Oklahoma Shock Nathan Shock Center is designed to deliver unique, innovative services that are not currently available at most institutions. The focus of the Center is on geroscience and the development of careers of young investigators. Pilot grants are provided through the Research Development Core to junior investigators studying aging/geroscience throughout the USA. However, the services of our Center are available to the entire research community studying aging and geroscience. The Oklahoma Nathan Shock Center provides researchers with unique services through four research cores. The Multiplexing Protein Analysis Core uses the latest mass spectrometry technology to simultaneously measure the levels, synthesis, and turnover of hundreds of proteins associated with pathways of importance to aging, e.g., metabolism, antioxidant defense system, proteostasis, and mitochondria function. The Genomic Sciences Core uses novel next-generation sequencing that allows investigators to study the effect of age, or anti-aging manipulations, on DNA methylation, mitochondrial genome heteroplasmy, and the transcriptome of single cells. The Geroscience Redox Biology Core provides investigators with a comprehensive state-of-the-art assessment of the oxidative stress status of a cell, e.g., measures of oxidative damage and redox couples, which are important in aging as well as many major age-related diseases as well as assays of mitochondrial function. The GeroInformatics Core provides investigators assistance with data analysis, which includes both statistical support as well as analysis of large datasets. The Core also has developed number of unique software packages to help with interpretation of results and discovery of new leads relevant to aging. In addition, the Geropathology Research Resource in the Program Enhancement Core provides investigators with pathological assessments of mice using the recently developed Geropathology Grading Platform.
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Affiliation(s)
- Holly Van Remmen
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
- Biochemistry & Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma, City, OK, USA.
| | - Willard M Freeman
- Biochemistry & Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma, City, OK, USA
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Benjamin F Miller
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
- Biochemistry & Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma, City, OK, USA
| | - Michael Kinter
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Jonathan D Wren
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Ann Chiao
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Rheal A Towner
- Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Timothy A Snider
- Department of Veterinary Pathology, Center for Veterinary Health Sciences at, Oklahoma State University, Stillwater, OK, USA
| | - William E Sonntag
- Biochemistry & Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma, City, OK, USA
| | - Arlan Richardson
- Biochemistry & Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma, City, OK, USA
- Oklahoma City VA Medical Center, Oklahoma City, OK, USA
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11
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Zeng Y, Li N, Zheng Z, Chen R, Liu W, Zhu J, Zeng M, Cheng J, Peng M, Hong C. A Pan-Cancer Analysis of the Prognostic Value and Expression of Adenylate Cyclase 7 (ADCY7) in Human Tumors. Int J Gen Med 2021; 14:5415-5429. [PMID: 34539183 PMCID: PMC8445103 DOI: 10.2147/ijgm.s330680] [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: 07/29/2021] [Accepted: 08/31/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The role of adenylate cyclase 7 (ADCY7) in cancer is still unclear. This study analyzed the interrelationship between the expression and immune function of ADCY7. METHODS ADCY7 expression in multiple human cancers was analyzed using the databases of Genotype-Tissue Expression Project (GTEx), Cancer Cell Line Encyclopedia (CCLE), and The Cancer Genome Atlas (TCGA). Correlations among ADCY7 gene expression, mismatch repair (MMR) gene expression, and DNA methyltransferase (DNMT) expression were assessed using Spearman correlation analysis. Univariate survival analysis and Kaplan-Meier (KM) curve were used to examine the effect of ADCY7 expression on prognosis. The Tumor Immune Estimation Resource (TIMER) database was used to evaluate the relationship between ADCY7 gene expression and tumor immune invasion or immune checkpoint gene (ICG) expression. RESULTS ADCY7 was abnormally expressed in multiple human cancers and was correlated with MMR genes and DNMT expression. Univariate survival analysis and KM curve showed that ADCY7 expression influences the overall survival (OS) of six types of cancer, disease-specific survival (DSS) of eight, and progression-free interval (PFI) of three. The high expression of ADCY7 in OS, DSS, and PFI was strongly associated with poor outcomes in patients with breast cancer and lung squamous cell carcinoma. ADCY7 expression was strongly associated with immune cell infiltration and ICG expression. CONCLUSION The results of this study indicated that ADCY7 may be a prognostic biomarker of tumorigenesis. The study may also provide a new perspective on the role of ADCY7 in human cancers.
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Affiliation(s)
- Yu Zeng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, People’s Republic of China
| | - Nanhong Li
- Department of Pathology and Pathophysiology, Southern Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Zhenzhen Zheng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, People’s Republic of China
| | - Riken Chen
- China State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Wang Liu
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, People’s Republic of China
| | - Jinru Zhu
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, People’s Republic of China
| | - Mingqing Zeng
- First Clinical School of Medicine, Guangdong Medical University, Zhanjiang, Guangdong, People’s Republic of China
| | - Junfen Cheng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, People’s Republic of China
| | - Min Peng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, People’s Republic of China
| | - Cheng Hong
- China State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People’s Republic of China
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12
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Insights of fibroblast growth factor receptor 3 aberrations in pan-cancer and their roles in potential clinical treatment. Aging (Albany NY) 2021; 13:16541-16566. [PMID: 34160364 PMCID: PMC8266346 DOI: 10.18632/aging.203175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/02/2021] [Indexed: 02/05/2023]
Abstract
Fibroblast growth factor receptor 3 (FGFR3) alters frequently across various cancer types and is a common therapeutic target in bladder urothelial carcinoma (BLCA) with FGFR3 variants. Although emerging evidence supports the role of FGFR3 in individual cancer types, no pan-cancer analysis is available. In this work, we used the open comprehensive datasets, covering a total of 10,953 patients with 10,967 samples across 32 TCGA cancer types, to identify the full alteration spectrum of FGFR3. FGFR3 abnormal expression, methylation patterns, alteration frequency, mutation location distribution, functional impact, and prognostic implications differed greatly from cancer to cancer. The overall alteration frequency of FGFR3 was relatively low in all cancers. Targetable mutations were mainly detected in BLCA, and S249C, Y373C, G370C, and R248C were hotspot mutations that could be targeted by an FDA approved erdafitinib. Genetic fusions were mainly observed in glioma, followed by BLCA. FGFR3-TACC3 was the most common fusion type which was proposed as novel therapeutic targets in glioma and was targetable with erdafitinib in BLCA. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) were two lung cancer subtypes, FGFR3 fusion and hotspot mutation like S249C were observed more commonly in LUSC but not in LUAD. DNA methylation was correlated with the expression of FGFR3 and its downstream genes in some tumors. FGFG3 abnormal expression and alterations exhibited clinical correlations with patient prognosis in several tumors. This work exhibited the full alteration spectrum of FGFR3 and indicated several new clues for their application as potential therapeutic targets and prognostic indicators.
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13
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Lin S, Tian C, Li J, Liu B, Ma T, Chen K, Gong W, Wang JM, Huang J. Differential MUC22 expression by epigenetic alterations in human lung squamous cell carcinoma and adenocarcinoma. Oncol Rep 2021; 45:78. [PMID: 33786615 PMCID: PMC8020203 DOI: 10.3892/or.2021.8029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/24/2021] [Indexed: 12/24/2022] Open
Abstract
Disruption in mucins (MUCs) is involved in cancer development and metastasis and is thus used as a biomarker. Non‑small cell lung carcinoma (NSCLC) is characterized by heterogeneous genetic and epigenetic alterations. Lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) are the two primary subtypes of NSCLC that require different therapeutic interventions. Here, we report distinct expression and epigenetic alterations in mucin 22 (MUC22), a new MUC family member, in LUSC vs. LUAD. In lung cancer cell lines and tissues, MUC22 was downregulated in LUSC (MUC22Low) but upregulated in LUAD (MUC22High) with co‑expression of MUC21. The aberrant expression of MUC22 was inversely correlated with its promoter hypermethylation in LUSC and hypomethylation in LUAD cells and tissues, respectively. Decreased MUC22 expression in NSCLC cell lines was restored upon treatment with epigenetic modifiers 5‑aza‑2'‑deoxycytidine (5‑Aza) or trichostatin A (TSA), accompanied by reduction in global protein level of histone deacetylase 1 (HDAC1) but increased enrichment of histone H3 lysine 9 acetylation (H3K9ac) specifically in the MUC22 promoter in the SK‑MES‑1 cell line. MUC22 knockdown increased the growth and motility of lung cancer cells and an immortalized human bronchial epithelial BEAS‑2B cell line via NF‑κB activation. Clinically, MUC22Low in LUSC and MUC22High in LUAD were shown to be indicators of unfavorable overall survival for patients with early cancer stages. Our study reveals that changes in MUC22 expression due to epigenetic alterations in NSCLC may have important biological significance and prognostic potential in LUSC when compared to LUAD. Thus, MUC22 expression and epigenetic alterations may be used for molecular subtyping of NSCLC in precision medicine.
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MESH Headings
- Adenocarcinoma of Lung/diagnosis
- Adenocarcinoma of Lung/genetics
- Adenocarcinoma of Lung/mortality
- Adenocarcinoma of Lung/therapy
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Carcinoma, Non-Small-Cell Lung/diagnosis
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/mortality
- Carcinoma, Non-Small-Cell Lung/therapy
- Carcinoma, Squamous Cell/diagnosis
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/mortality
- Carcinoma, Squamous Cell/therapy
- Cell Line, Tumor
- DNA Methylation
- Datasets as Topic
- Down-Regulation
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Neoplastic
- Gene Knockdown Techniques
- Genetic Heterogeneity
- Humans
- Kaplan-Meier Estimate
- Lung/pathology
- Lung Neoplasms/diagnosis
- Lung Neoplasms/genetics
- Lung Neoplasms/mortality
- Lung Neoplasms/therapy
- Male
- Middle Aged
- Mucins/genetics
- Neoplasm Staging
- Precision Medicine/methods
- Prognosis
- Promoter Regions, Genetic/genetics
- RNA-Seq
- Up-Regulation
- Young Adult
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Affiliation(s)
- Shuye Lin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
| | - Cuimeng Tian
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Jianhui Li
- Department of Pathology, Xuchang Central Hospital, Affiliated to Henan University of Science and Technology, Xuchang, Henan 461000, P.R. China
| | - Bin Liu
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
| | - Teng Ma
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
| | - Keqiang Chen
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Wanghua Gong
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Ji Ming Wang
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Jiaqiang Huang
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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14
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Li J, Hu K, Huang J, Zhou L, Yan Y, Xu Z. A Pancancer Analysis of the Expression Landscape and Clinical Relevance of Fibroblast Growth Factor Receptor 2 in Human Cancers. Front Oncol 2021; 11:644854. [PMID: 33968743 PMCID: PMC8097147 DOI: 10.3389/fonc.2021.644854] [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: 12/23/2020] [Accepted: 02/23/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Fibroblast growth factor receptor 2 (FGFR2) is frequently altered in tumors and one of the top therapeutic targets in cholangiocarcinoma (CHOL) with FGFR2 fusions. Although there have been several studies on individual tumors, a comprehensive analysis of FGFR2 genetic aberrations and their simultaneous clinical implications across different tumors have not been reported. Methods: In this study, we used the large comprehensive datasets available, covering over 10,000 tumor samples across more than 30 cancer types, to analyze FGFR2 abnormal expression, methylation, alteration (mutations/fusions and amplification/deletion), and their clinical associations. Results: Alteration frequency, mutation location distribution, oncogenic effects, and therapeutic implications varied among different cancers. The overall mutation rate of FGFR2 is low in pancancer. CHOL had the highest mutation frequency, and fusion accounted for the major proportion. All these fusion aberrations in CHOL were targetable, and an FDA-approved drug was approved recently. Uterine corpus endometrial carcinoma (UCEC) had the highest number of FGFR2 mutations, and the most frequently mutated positions were S252W and N549K, where the functional impact was oncogenic, but targeted therapy was less effective. Additionally, DNA methylation was associated with FGFR2 expression in several cancers. Moreover, FGFG2 expression and genetic aberrations showed clinical associations with patient survival in several cancers, indicating their potential for application as new tumor markers and therapeutic targets. Conclusions: This study showed the full FGFR2 alteration spectrum and provided a broad molecular perspective of FGFR2 in a comprehensive manner, suggesting some new directions for clinical targeted therapy of cancers.
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Affiliation(s)
- Juanni Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Kuan Hu
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, United States
| | - Lei Zhou
- Department of Anesthesiology, Third Xiangya Hospital of Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
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15
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Long Y, Li H, Jin Z, Zhang X. LncRNA SLC16A1-AS1 is Upregulated in Glioblastoma and Promotes Cancer Cell Proliferation by Regulating miR-149 Methylation. Cancer Manag Res 2021; 13:1215-1223. [PMID: 33603467 PMCID: PMC7882451 DOI: 10.2147/cmar.s264613] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/18/2020] [Indexed: 12/13/2022] Open
Abstract
Introduction LncRNA SLC16A1-AS1 has been characterized as a critical player in lung cancer, while its role in glioblastoma (GBM) is unknown. By analyzing the TCGA dataset, we observed the upregulation of SLC16A1-AS1 expression in GBM. Therefore, we aimed to investigate the role of SLC16A1-AS1 in this cancer. Methods GBM tissues and paired non-tumor tissues were collected from 62 GBM patients through biopsy. RT-qPCR was performed to determine the expression of SLC16A1-AS1 and miR-149. Linear regression was used to analyze their correlations. The relationship between SLC16A1-AS1 and miR-149 was assessed by gain and loss of function experiments. Methylation-specific PCR (MSP) and bisulfite sequencing PCR (BSP) were performed to analyze the methylation status of miR-149. Cell proliferation was evaluated by CCK-8 assay and colony formation experiments in GBM cells. Results We found that SLC16A1-AS1 expression was upregulated in GBM tissues, and the upregulated expression of SLC16A1-AS1 predicted poor survival of GBM patients. MiR-149 was downregulated in GBM tissues and inversely correlated with the expression of SLC16A1-AS1. In GBM cells, overexpression of SLC16A1-AS1 downregulated the expression of miR-149 and increased the methylation of miR-149 gene. In cell proliferation and colony formation assay, overexpression of SLC16A1-AS1 reduced the inhibitory effects of miR-149 on GBM cell proliferation. Conclusion SLC16A1-AS1 may promote GBM cell proliferation by regulating miR-149 methylation. SLC16A1-AS1 can be considered as a potential diagnostic marker in GBM.
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Affiliation(s)
- Yinbo Long
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou City, Hebei Province, 061000, People's Republic of China
| | - Heyang Li
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou City, Hebei Province, 061000, People's Republic of China
| | - Zhibin Jin
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou City, Hebei Province, 061000, People's Republic of China
| | - Xiang Zhang
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou City, Hebei Province, 061000, People's Republic of China
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16
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Multi-omics characterization and validation of MSI-related molecular features across multiple malignancies. Life Sci 2021; 270:119081. [PMID: 33516699 DOI: 10.1016/j.lfs.2021.119081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/09/2021] [Accepted: 01/10/2021] [Indexed: 01/17/2023]
Abstract
HEADINGS AIMS To establish a microsatellite instability (MSI) predictive model in pan-cancer and compare the multi-omics characterization of MSI-related molecular features. MATERIALS AND METHODS We established a 15-gene signature for predicting MSI status and performed a systematic assessment of MSI-related molecular features including gene and miRNA expression, DNA methylation, and somatic mutation, in approximately 10,000 patients across 30 cancer types from The Cancer Genome Atlas, Gene Expression Omnibus database, and our institution. Then we identified common MSI-associated dysregulated molecular features across six cancers and explored their mutual interfering relationships and the drug sensitivity. KEY FINDINGS we demonstrated the model's high prediction performance and found the samples with high-MSI were mainly distributed in six cancers: BRCA, COAD, LUAD, LIHC, STAD, and UCEC. We found RPL22L1 was up-regulated in the high-MSI group of 5/6 cancer types. CYP27A1 and RAI2 were down-regulated in 4/6 cancer types. More than 20 miRNAs and 39 DMGs were found up-regulated in MSI-H at least three cancers. We discovered some drugs, including OSI-027 and AZD8055 had a higher sensitivity in the high MSI-score group. Functional enrichment analysis revealed the correlation between MSI score and APM score, HLA score, or glycolysis score. The complicated regulatory mechanism of tumor MSI status in multiple dimensions was explored by an integrated analysis of the correlations among MSI-related genes, miRNAs, methylation, and drug response data. SIGNIFICANCE Our pan-cancer study provides a valuable predictive model and a comprehensive atlas of tumor MSI, which may guide more precise and personalized therapeutic strategies for tumor patients.
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17
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Chucair-Elliott AJ, Ocañas SR, Stanford DR, Ansere VA, Buettner KB, Porter H, Eliason NL, Reid JJ, Sharpe AL, Stout MB, Beckstead MJ, Miller BF, Richardson A, Freeman WM. Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia. Commun Biol 2020; 3:693. [PMID: 33214681 PMCID: PMC7678837 DOI: 10.1038/s42003-020-01418-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
Epigenetic regulation of gene expression occurs in a cell type-specific manner. Current cell-type specific neuroepigenetic studies rely on cell sorting methods that can alter cell phenotype and introduce potential confounds. Here we demonstrate and validate a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach for temporally controlled labeling and isolation of ribosomes and nuclei, and thus RNA and DNA, from specific central nervous system cell types. Analysis of gene expression and DNA modifications in astrocytes or microglia from the same animal demonstrates differential usage of DNA methylation and hydroxymethylation in CpG and non-CpG contexts that corresponds to cell type-specific gene expression. Application of this approach in LPS treated mice uncovers microglia-specific transcriptome and epigenome changes in inflammatory pathways that cannot be detected with tissue-level analysis. The NuTRAP model and the validation approaches presented can be applied to any brain cell type for which a cell type-specific cre is available. Ana Chucair-Elliott, Sarah Ocaňas et al. present a NuTRAP approach for simultaneous analysis of transcript expression and DNA modifications in two specific mouse brain cell types, astrocytes and microglia. They further apply this approach to identify molecular changes in microglia following LPS treatment and identify both transcriptomic and epigenomic alterations not apparent in tissue-level analyses.
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Affiliation(s)
- Ana J Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sarah R Ocañas
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - David R Stanford
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Victor A Ansere
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kyla B Buettner
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Hunter Porter
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.,Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Nicole L Eliason
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Justin J Reid
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Amanda L Sharpe
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael B Stout
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael J Beckstead
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Benjamin F Miller
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Arlan Richardson
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA. .,Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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18
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Yan Y, Yan Q, Qian L, Jiang Y, Chen X, Zeng S, Xu Z, Gong Z. S-adenosylmethionine administration inhibits levodopa-induced vascular endothelial growth factor-A expression. Aging (Albany NY) 2020; 12:21290-21307. [PMID: 33170152 PMCID: PMC7695432 DOI: 10.18632/aging.103863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023]
Abstract
Background: Studies have demonstrated that S-adenosylmethionine could effectively affect the clinical wearing-off phenomena of levodopa, an antiparkinsonian agent; however, the detailed mechanisms for this effect need to be further clarified. Results: S-adenosylmethionine and levodopa had opposite effects on the protein stability of vascular endothelial growth factor-A. The analysis of tube formation and cell viability also showed the nonconforming functions of S-adenosylmethionine and levodopa on cell angiogenesis and proliferation. Meanwhile, S-adenosylmethionine could significantly abolish the increased angiogenesis and cell viability induced by levodopa. S-adenosylmethionine resulted in G1/S phase arrest, with decreased cyclin dependent kinase 4/6 and increased p16, a specific cyclin dependent kinase inhibitor. Mechanically, the different effects of levodopa and S-adenosylmethionine were dependent on the phosphorylation and activation of extracellular signal-regulated kinase. S-adenosylmethionine could be fitted into the predicted docking pocket in the crystal structure of vascular endothelial growth factor-A, enhancing its acetylation level and reducing half-life. Conclusions: These observations suggested that methyl donor S-adenosylmethionine could act as a potential agent against vascular endothelial growth factor-A-related diseases induced by levodopa treatment. Methods: We performed in vitro cytological analyses to assess whether S-adenosylmethionine intake could influence levodopa-induced vascular endothelial growth factor-A expression in human umbilical vein endothelial cells.
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Affiliation(s)
- Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, China
| | - Qijia Yan
- Department of Pathology, Xiangya Hospital, Central South University, Hunan, China
| | - Long Qian
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, China
| | - Yueping Jiang
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, China
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, China
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Ju Q, Li XM, Zhang H, Zhao YJ. BRCA1-Associated Protein Is a Potential Prognostic Biomarker and Is Correlated With Immune Infiltration in Liver Hepatocellular Carcinoma: A Pan-Cancer Analysis. Front Mol Biosci 2020; 7:573619. [PMID: 33240929 PMCID: PMC7667264 DOI: 10.3389/fmolb.2020.573619] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/09/2020] [Indexed: 11/30/2022] Open
Abstract
Background BRCA1-associated protein (BRAP) is a critical gene that regulates inflammation-related signaling pathway and affects patients’ prognosis in esophageal squamous cell carcinoma (ESCC). However, its roles in different cancers remain largely unknown. Methods BRAP expression in human pan-cancer was analyzed via the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) database. Pearson correlation analysis was used to evaluate the association between BRAP expression with mismatch repair (MMR) gene mutation and DNA methyltransferase. We evaluated the influence of BRAP on clinical prognosis by univariate survival analysis. Moreover, the correlation between BRAP and tumor immune infiltration was analyzed via the Tumor Immune Evaluation Resource (TIMER) database. Pearson correlation analysis was used to investigate the correlation between BRAP expression and immune checkpoint genes expression. Results BRAP is abnormally overexpressed and significantly correlated with MMR gene mutation level and DNA methyltransferase expression in human pan-cancer. Univariate survival analysis showed that BRAP was significant with patients’ overall survival (OS) in six cancer types, disease-free interval (DFI) in three cancer types, and progression-free interval (PFI) in two cancer types. Remarkably, increased BRAP expression was strongly correlated with patients’ poor prognosis in liver hepatocellular carcinoma (LIHC), whether OS (P < 0.0001, hazard ratio (HR) = 1.1), DFI (P = 0.00099, HR = 1.06), or PFI (P = 0.00025, HR = 1.07). Moreover, a positive relationship was found between BRAP expression and immune infiltrating cells including B cell, CD4 + T cell, CD8 + T cell, dendritic cell, macrophage cell, and neutrophil cell in colon adenocarcinoma (COAD), kidney renal clear cell carcinoma (KIRC), and LIHC. Additionally, BRAP expression showed strong correlations with immune checkpoint genes in LIHC. Conclusion BRAP expression is increased in human pan-cancer samples compared with normal tissues. Overexpression of BRAP is correlated with poor prognosis and immune infiltration in multiple cancers, especially in LIHC. These findings suggest that BRAP may be used as a potential molecular biomarker for determining prognosis and immune infiltration in LIHC.
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Affiliation(s)
- Qiang Ju
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Xin-Mei Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Heng Zhang
- School of Public Health, Qingdao University, Qingdao, China
| | - Yan-Jie Zhao
- School of Public Health, Qingdao University, Qingdao, China
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20
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An epigenome-wide association study of early-onset major depression in monozygotic twins. Transl Psychiatry 2020; 10:301. [PMID: 32843619 PMCID: PMC7447798 DOI: 10.1038/s41398-020-00984-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 06/18/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022] Open
Abstract
Major depression (MD) is a debilitating mental health condition with peak prevalence occurring early in life. Genome-wide examination of DNA methylation (DNAm) offers an attractive complement to studies of allelic risk given it can reflect the combined influence of genes and environment. The current study used monozygotic twins to identify differentially and variably methylated regions of the genome that distinguish twins with and without a lifetime history of early-onset MD. The sample included 150 Caucasian monozygotic twins between the ages of 15 and 20 (73% female; Mage = 17.52 SD = 1.28) who were assessed during a developmental stage characterized by relatively distinct neurophysiological changes. All twins were generally healthy and currently free of medications with psychotropic effects. DNAm was measured in peripheral blood cells using the Infinium Human BeadChip 450 K Array. MD associations with early-onset MD were detected at 760 differentially and variably methylated probes/regions that mapped to 428 genes. Genes and genomic regions involved neural circuitry formation, projection, functioning, and plasticity. Gene enrichment analyses implicated genes related to neuron structures and neurodevelopmental processes including cell-cell adhesion genes (e.g., PCDHA genes). Genes previously implicated in mood and psychiatric disorders as well as chronic stress (e.g., NRG3) also were identified. DNAm regions associated with early-onset MD were found to overlap genetic loci identified in the latest Psychiatric Genomics Consortium meta-analysis of depression. Understanding the time course of epigenetic influences during emerging adulthood may clarify developmental phases where changes in the DNA methylome may modulate individual differences in MD risk.
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21
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Arthur-Farraj P, Moyon S. DNA methylation in Schwann cells and in oligodendrocytes. Glia 2020; 68:1568-1583. [PMID: 31958184 DOI: 10.1002/glia.23784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/17/2019] [Accepted: 01/10/2020] [Indexed: 12/12/2022]
Abstract
DNA methylation is one of many epigenetic marks, which directly modifies base residues, usually cytosines, in a multiple-step cycle. It has been linked to the regulation of gene expression and alternative splicing in several cell types, including during cell lineage specification and differentiation processes. DNA methylation changes have also been observed during aging, and aberrant methylation patterns have been reported in several neurological diseases. We here review the role of DNA methylation in Schwann cells and oligodendrocytes, the myelin-forming glia of the peripheral and central nervous systems, respectively. We first address how methylation and demethylation are regulating myelinating cells' differentiation during development and repair. We then mention how DNA methylation dysregulation in diseases and cancers could explain their pathogenesis by directly influencing myelinating cells' proliferation and differentiation capacities.
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Affiliation(s)
- Peter Arthur-Farraj
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Sarah Moyon
- Neuroscience Initiative Advanced Science Research Center, CUNY, New York, New York
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22
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Li Q, Cai M, Wang J, Gao Q, Guo X, Jia X, Xu S, Zhu H. Decreased ovarian function and autophagy gene methylation in aging rats. J Ovarian Res 2020; 13:12. [PMID: 32014030 PMCID: PMC6998822 DOI: 10.1186/s13048-020-0615-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/22/2020] [Indexed: 01/23/2023] Open
Abstract
Background Degeneration of ovarian function is an obvious feature of female aging. In addition, studies have shown that autophagy decreases with age, and DNA methylation is a hallmark epigenetic pattern during aging. However, it is not clear whether the expression and DNA methylation of autophagy genes are involved in the declines in ovarian function that occur during aging. Results Three groups of rats were used: 6-month-old (6 M) rats, 12-month-old (12 M) rats and 24-month-old (24 M) rats. Serum E2 levels and the mRNA and protein expression levels of Atg5, Atg12, Atg16L, Beclin1 and Lc3B were significantly decreased in aged rats. In addition, the methylation levels of the Atg5 gene were significantly increased in aged rats. The expression of the Dnmt1 and Dnmt2 genes decreased with aging; however, the expression of the Dnmt3A and Dnmt3B genes gradually increased with aging. Conclusions Decreased autophagic activity was involved in the declines in ovarian function in aging rats. Upregulation of the DNA methyltransferases Dnmt3A and Dnmt3B may have led to methylation of the autophagy genes Atg5 and Lc3B to ultimately cause the observed decreases in autophagic activity.
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Affiliation(s)
- Qiuyuan Li
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Minghui Cai
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Jiao Wang
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Qiang Gao
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Xiaocheng Guo
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Xiaotong Jia
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Shanshan Xu
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Hui Zhu
- Department of Physiology, Harbin Medical University, Harbin, 150086, China.
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23
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Wiedenhoeft T, Tarantini S, Nyúl-Tóth Á, Yabluchanskiy A, Csipo T, Balasubramanian P, Lipecz A, Kiss T, Csiszar A, Csiszar A, Ungvari Z. Fusogenic liposomes effectively deliver resveratrol to the cerebral microcirculation and improve endothelium-dependent neurovascular coupling responses in aged mice. GeroScience 2019; 41:711-725. [PMID: 31654270 PMCID: PMC6925096 DOI: 10.1007/s11357-019-00102-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Abstract
Adjustment of cerebral blood flow (CBF) to the increased oxygen and nutrient demands of active brain regions via neurovascular coupling (NVC) has an essential role in maintenance of healthy cognitive function. In advanced age, cerebromicrovascular oxidative stress and endothelial dysfunction impair neurovascular coupling, contributing to age-related cognitive decline. Recently we developed a resveratrol (3,4',5-trihydroxystilbene)-containing fusogenic liposome (FL-RSV)-based molecular delivery system that can effectively target cultured cerebromicrovascular endothelial cells, attenuating age-related oxidative stress. To assess the cerebromicrovascular protective effects of FL-RSV in vivo, aged (24-month-old) C57BL/6 mice were treated with FL-RSV for four days. To demonstrate effective cellular uptake of FL-RSV, accumulation of the lipophilic tracer dyes in cells of the neurovascular unit was confirmed using two-photon imaging (through a chronic cranial window). NVC was assessed by measuring CBF responses (laser speckle contrast imaging) evoked by contralateral whisker stimulation. We found that NVC responses were significantly impaired in aged mice. Treatment with FL-RSV significantly improved NVC responses by increasing NO-mediated vasodilation. These findings are paralleled by the protective effects of FL-RSV on endothelium-dependent relaxation in the aorta. Thus, treatment with FL-RSV rescues endothelial function and NVC responses in aged mice. We propose that resveratrol containing fusogenic liposomes could also be used for combined delivery of various anti-geronic factors, including proteins, small molecules, DNA vectors and mRNAs targeting key pathways involved in microvascular aging and neurovascular dysfunction for the prevention/treatment of age-related cerebromicrovascular pathologies and development of vascular cognitive impairment (VCI) in aging.
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Affiliation(s)
- Tabea Wiedenhoeft
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging/Oklahoma Center for Geroscience, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Stefano Tarantini
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging/Oklahoma Center for Geroscience, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- International Training Program in Geroscience, Doctoral School of Basic and Translational Medicine/Department of Public Health, Semmelweis University, Budapest, Hungary
| | - Ádám Nyúl-Tóth
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging/Oklahoma Center for Geroscience, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Andriy Yabluchanskiy
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging/Oklahoma Center for Geroscience, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Tamas Csipo
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging/Oklahoma Center for Geroscience, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- International Training Program in Geroscience, Doctoral School of Basic and Translational Medicine/Department of Public Health, Semmelweis University, Budapest, Hungary
- International Training Program in Geroscience, Division of Clinical Physiology, Department of Cardiology/ Kalman Laki Doctoral School, Faculty of Medicine, University of Debrecen, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Priya Balasubramanian
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging/Oklahoma Center for Geroscience, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Agnes Lipecz
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging/Oklahoma Center for Geroscience, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- International Training Program in Geroscience, Doctoral School of Basic and Translational Medicine/Department of Public Health, Semmelweis University, Budapest, Hungary
| | - Tamas Kiss
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging/Oklahoma Center for Geroscience, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- International Training Program in Geroscience,Theoretical Medicine Doctoral School/Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary
| | - Anna Csiszar
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging/Oklahoma Center for Geroscience, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- International Training Program in Geroscience,Theoretical Medicine Doctoral School/Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary
- Doctoral School of Basic and Translational Medicine/Institute of Clinical Experimental Research, Semmelweis University, Budapest, Hungary
| | - Agnes Csiszar
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Zoltan Ungvari
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging/Oklahoma Center for Geroscience, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- International Training Program in Geroscience, Doctoral School of Basic and Translational Medicine/Department of Public Health, Semmelweis University, Budapest, Hungary.
- Doctoral School of Basic and Translational Medicine/Institute of Clinical Experimental Research, Semmelweis University, Budapest, Hungary.
- Department of Health Promotion Sciences, College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA.
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24
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Kiss T, Balasubramanian P, Valcarcel-Ares MN, Tarantini S, Yabluchanskiy A, Csipo T, Lipecz A, Reglodi D, Zhang XA, Bari F, Farkas E, Csiszar A, Ungvari Z. Nicotinamide mononucleotide (NMN) treatment attenuates oxidative stress and rescues angiogenic capacity in aged cerebromicrovascular endothelial cells: a potential mechanism for the prevention of vascular cognitive impairment. GeroScience 2019; 41:619-630. [PMID: 31144244 PMCID: PMC6885080 DOI: 10.1007/s11357-019-00074-2] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 05/11/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022] Open
Abstract
Age-related impairment of angiogenesis likely has a critical role in cerebromicrovascular rarefaction and development of vascular cognitive impairment and dementia (VCID) in the elderly. Recently, we demonstrated that aging is associated with NAD+ depletion in the vasculature and that administration of NAD+ precursors exerts potent anti-aging vascular effects, rescuing endothelium-mediated vasodilation in the cerebral circulation and improving cerebral blood supply. The present study was designed to elucidate how treatment with nicotinamide mononucleotide (NMN), a key NAD+ intermediate, impacts age-related impairment of endothelial angiogenic processes. Using cerebromicrovascular endothelial cells (CMVECs) isolated from young and aged F344xBN rats, we demonstrated that compared with young cells, aged CMVECs exhibit impaired proliferation, cellular migration (measured by a wound-healing assay using electric cell-substrate impedance sensing [ECIS] technology), impaired ability to form capillary-like structures, and increased oxidative stress. NMN treatment in aged CMVECs significantly improved angiogenic processes and attenuated H2O2 production. We also found that pre-treatment with EX-527, a pharmacological inhibitor of SIRT1, prevented NMN-mediated restoration of angiogenic processes in aged CMVECs. Collectively, we find that normal cellular NAD+ levels are essential for normal endothelial angiogenic processes, suggesting that age-related cellular NAD+ depletion and consequential SIRT1 dysregulation may be a potentially reversible mechanism underlying impaired angiogenesis and cerebromicrovascular rarefaction in aging. We recommend that pro-angiogenic effects of NAD+ boosters should be considered in both preclinical and clinical studies.
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Affiliation(s)
- Tamas Kiss
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK 73104 USA
- Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary
- Theoretical Medicine Doctoral School, University of Szeged, Szeged, Hungary
| | - Priya Balasubramanian
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK 73104 USA
| | - Marta Noa Valcarcel-Ares
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK 73104 USA
| | - Stefano Tarantini
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK 73104 USA
| | - Andriy Yabluchanskiy
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK 73104 USA
| | - Tamas Csipo
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK 73104 USA
- Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary
| | - Agnes Lipecz
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK 73104 USA
- Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary
| | - Dora Reglodi
- Department of Anatomy, MTA-PTE PACAP Research Team, University of Pecs Medical School, Pecs, Hungary
| | - Xin A. Zhang
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Ferenc Bari
- Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary
- Theoretical Medicine Doctoral School, University of Szeged, Szeged, Hungary
| | - Eszter Farkas
- Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary
- Theoretical Medicine Doctoral School, University of Szeged, Szeged, Hungary
| | - Anna Csiszar
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK 73104 USA
- Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary
- Theoretical Medicine Doctoral School, University of Szeged, Szeged, Hungary
| | - Zoltan Ungvari
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK 73104 USA
- Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary
- Theoretical Medicine Doctoral School, University of Szeged, Szeged, Hungary
- Department of Public Health, Semmelweis University, Budapest, Hungary
- Department of Health Promotion Sciences, the Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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25
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Chucair-Elliott AJ, Ocanas SR, Stanford DR, Hadad N, Wronowski B, Otalora L, Stout MB, Freeman WM. Tamoxifen induction of Cre recombinase does not cause long-lasting or sexually divergent responses in the CNS epigenome or transcriptome: implications for the design of aging studies. GeroScience 2019; 41:691-708. [PMID: 31493147 PMCID: PMC6885072 DOI: 10.1007/s11357-019-00090-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 12/27/2022] Open
Abstract
The systemic delivery of tamoxifen (Tam) to activate inducible CreERT2-loxP transgenic mouse systems is now widely used in neuroscience studies. This critical technological advancement allows temporal control of DNA-cre recombination, avoidance of embryonically lethal phenotypes, and minimization of residual cell labeling encountered in constitutively active drivers. Despite its advantages, the use of Tam has the potential to cause long-lasting, uncharacterized side effects on the transcriptome and epigenome in the CNS, given its mixed estrogen receptor (ER) agonist/antagonist actions. With the welcome focus on including both sexes in biomedical studies and efforts to understand sex differences, Tam administration could also cause sexually divergent responses that would confound studies. To examine these issues, epigenetic and transcriptomic profiles were compared in C57BL/6 J female and male hippocampus, cortex, and retina 1 month after a 5-day Tam treatment typical for cre induction, or vehicle control (sunflower seed oil). Cytosine methylation and hydroxymethylation levels, in both CG and non-CG contexts, were unchanged as determined by oxidative bisulfite sequencing. Long-lasting Tam transcriptomic effects were also not evident/minimal. Furthermore, there is no evidence of sexually divergent responses with Tam administration and Tam did not alter sex differences evident in controls. Combined with recently reported data that Tam alone does not cause long-lasting changes in behavior and neurogenesis, our findings provide confidence that Tam can be used as a cre-recombinase inducer without introducing significant confounds in transcriptomic and epigenomic neuroscience studies, particularly those focused on genomic and transcriptomic aspects of the aging brain.
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Affiliation(s)
- Ana J Chucair-Elliott
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, OK, 73104, USA
| | - Sarah R Ocanas
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, OK, 73104, USA
| | - David R Stanford
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, OK, 73104, USA
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Benjamin Wronowski
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Laura Otalora
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, OK, 73104, USA
| | - Michael B Stout
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Physiology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, OK, 73104, USA.
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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26
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Abstract
Ageing is the main risk factor for the development of cardiovascular diseases. A central mechanism by which ageing promotes vascular pathologies is compromising endothelial health. The age-related attenuation of endothelium-dependent dilator responses (endothelial dysfunction) associated with impairment of angiogenic processes and the subsequent pathological remodelling of the microcirculation contribute to compromised tissue perfusion and exacerbate functional decline in older individuals. This Review focuses on cellular, molecular, and functional changes that occur in the endothelium during ageing. We explore the links between oxidative and nitrative stress and the conserved molecular pathways affecting endothelial dysfunction and impaired angiogenesis during ageing. We also speculate on how these pathological processes could be therapeutically targeted. An improved understanding of endothelial biology in older patients is crucial for all cardiologists because maintenance of a competently functioning endothelium is critical for adequate tissue perfusion and long-term cardiac health.
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27
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Fernandez E, Ross C, Liang H, Javors M, Tardif S, Salmon AB. Evaluation of the pharmacokinetics of metformin and acarbose in the common marmoset. PATHOBIOLOGY OF AGING & AGE RELATED DISEASES 2019; 9:1657756. [PMID: 31497263 PMCID: PMC6719263 DOI: 10.1080/20010001.2019.1657756] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/15/2019] [Indexed: 12/31/2022]
Abstract
Metformin has beneficial effects on several age-related diseases (e.g., diabetes, obesity, cancer) and extends lifespan in nematodes and mice. Acarbose, an FDA-approved agent for treating type 2 diabetes, prevents breakdown of complex carbohydrates. Both compounds have been suggested as potential anti-aging interventions and acarbose has been shown to extend mouse longevity by the Intervention Testing Program (ITP). One potential next step is to assess the effect of these interventions on healthspan and lifespan in non-human primates. The common marmoset (Callithrix jacchus) is a small new world monkey with a relatively short life span and small size, both valuable for the translation potential of this nonhuman primate species for the study of aging and chronic disease. However, the dosing and assessment of potential side effects of either metformin or acarbose in this species have yet to be assessed. This study evaluated the pharmacokinetics of two dosage levels each of metformin or acarbose (given separately) in two small groups of young marmosets (n = 5/group) treated for 24 h to define the pharmacokinetics of each drug. The ability to rapidly and reliably dose socially housed marmosets with an oral form of acarbose or metformin that is well tolerated indicates that this species is a reliable model for testing acarbose and metformin in a safe and efficient way in a long-term intervention.
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Affiliation(s)
- Elizabeth Fernandez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX, USA.,Geriatric Research, Education and Clinical Center, South Texas Veteran's Health Care System, San Antonio.,Department of Pharmacology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Corinna Ross
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX, USA.,Department of Arts & Sciences, Texas A&M-San Antonio, San Antonio, TX, USA
| | - Hanyu Liang
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX, USA.,Geriatric Research, Education and Clinical Center, South Texas Veteran's Health Care System, San Antonio
| | - Martin Javors
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX, USA.,Department of Pharmacology, University of Texas Health Science Center, San Antonio, TX, USA.,Department of Psychiatry, University of Texas Health Science Center, San Antonio, TX, USA
| | - Suzette Tardif
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX, USA.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Adam B Salmon
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX, USA.,Geriatric Research, Education and Clinical Center, South Texas Veteran's Health Care System, San Antonio.,Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
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Wei Y, Sun Z, Wang Y, Xie Z, Xu S, Xu Y, Zhou X, Bi J, Zhu Z. Methylation in the TP53 promoter is associated with ischemic stroke. Mol Med Rep 2019; 20:1404-1410. [PMID: 31173230 DOI: 10.3892/mmr.2019.10348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 03/06/2019] [Indexed: 11/05/2022] Open
Abstract
Cerebral ischemic stroke (IS) is a disease presenting high morbidity and mortality rates worldwide. Understanding of the pathogenesis underlying IS may facilitate the development of effective clinical therapeutic strategies and improve the prevention of this disease, decreasing its occurrence rate. Epigenetic alterations have recently attracted attention as possible mechanisms underlying IS. Additionally, tumor protein p53 (TP53) was identified to be involved in the pathophysiology of cerebral stroke. In the present study, the methylation status of the TP53 promoter was investigated in patients with IS and in age‑matched healthy controls. The methylation status of the promoter of TP53 was significantly increased in patients with IS compared with healthy subjects. Additionally, the methylation level of the TP53 promoter was identified to be associated with carotid intima‑media thickness, the degree of carotid atherosclerosis and the circulating levels of homocysteine in peripheral blood. The present findings may improve the understanding of the role of the epigenetic modifications of the TP53 promoter in IS pathogenesis.
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Affiliation(s)
- Yan Wei
- Department of Neurology Medicine, Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Zhongzheng Sun
- Department of Neurosurgery, Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Yun Wang
- Department of Neurology Medicine, Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Zhaohong Xie
- Department of Neurology Medicine, Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Shunliang Xu
- Department of Neurology Medicine, Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Yingying Xu
- Department of Neurology Medicine, Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Xiaoyan Zhou
- Department of Neurology Medicine, Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Jianzhong Bi
- Department of Neurology Medicine, Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Zhengyu Zhu
- Department of Neurology Medicine, Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
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Csiszar A, Tarantini S, Yabluchanskiy A, Balasubramanian P, Kiss T, Farkas E, Baur JA, Ungvari Z. Role of endothelial NAD + deficiency in age-related vascular dysfunction. Am J Physiol Heart Circ Physiol 2019; 316:H1253-H1266. [PMID: 30875255 PMCID: PMC6620681 DOI: 10.1152/ajpheart.00039.2019] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/26/2019] [Accepted: 03/12/2019] [Indexed: 12/23/2022]
Abstract
Age-related alterations in endothelium and the resulting vascular dysfunction critically contribute to a range of pathological conditions associated with old age. To develop therapies rationally that improve vascular health and thereby increase health span and life span in older adults, it will be essential to understand the cellular and molecular mechanisms contributing to vascular aging. Preclinical studies in model organisms demonstrate that NAD+ availability decreases with age in multiple tissues and that supplemental NAD+ precursors can ameliorate many age-related cellular impairments. Here, we provide a comprehensive overview of NAD+-dependent pathways [including the NAD+-using silent information regulator-2-like enzymes and poly(ADP-ribose) polymerase enzymes] and the potential consequences of endothelial NAD+ deficiency in vascular aging. The multifaceted vasoprotective effects of treatments that reverse the age-related decline in cellular NAD+ levels, as well as their potential limitations, are discussed. The preventive and therapeutic potential of NAD+ intermediates as effective, clinically relevant interventions in older adults at risk for ischemic heart disease, vascular cognitive impairment, and other common geriatric conditions and diseases that involve vascular pathologies (e.g., sarcopenia, frailty) are critically discussed. We propose that NAD+ precursors [e.g., nicotinamide (Nam) riboside, Nam mononucleotide, niacin] should be considered as critical components of combination therapies to slow the vascular aging process and increase cardiovascular health span.
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Affiliation(s)
- Anna Csiszar
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center , Oklahoma City, Oklahoma
- Department of Medical Physics and Informatics, University of Szeged , Szeged , Hungary
| | - Stefano Tarantini
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center , Oklahoma City, Oklahoma
| | - Andriy Yabluchanskiy
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center , Oklahoma City, Oklahoma
| | - Priya Balasubramanian
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center , Oklahoma City, Oklahoma
| | - Tamas Kiss
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center , Oklahoma City, Oklahoma
- Department of Medical Physics and Informatics, University of Szeged , Szeged , Hungary
- Theoretical Medicine Doctoral School, University of Szeged , Szeged , Hungary
| | - Eszter Farkas
- Department of Medical Physics and Informatics, University of Szeged , Szeged , Hungary
| | - Joseph A Baur
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Zoltan Ungvari
- Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center , Oklahoma City, Oklahoma
- Department of Medical Physics and Informatics, University of Szeged , Szeged , Hungary
- Theoretical Medicine Doctoral School, University of Szeged , Szeged , Hungary
- Department of Pulmonology, Semmelweis University , Budapest , Hungary
- Department of Health Promotion Sciences, Hudson College of Public Health, University of Oklahoma Health Sciences Center , Oklahoma City, Oklahoma
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Abstract
Recent research suggests that epigenetics, especially DNA methylation, plays a mechanistic role in aging. Epigenetic clocks, which measure changes in a few hundred specific CpG sites, can accurately predict chronological age in a variety of species, including humans. These clocks are currently the bestbiomarkers for predicting mortality in humans. Additionally, several studies have characterized the effects of aging across the methylome in a wide variety of tissues from humans and mice. A small fraction (~2%) of the CpG sites show age-related changes, either hypermethylation or hypomethylation with aging. Evaluation of non-CpG site methylation has only been examined in a few studies, with about ~0.5% of these sites showing achange with age. Therefore, while only a small fraction of cytosines in the genome show changes in DNA methylation with age, this represents 2 to 3 million cytosines in the genome. Importantly, the only study to compare the effect of aging on DNA methylation in male and female mice and humans found that N95% of the age-related changes in DNA methylation in the hippocampus were sexually divergent, i.e., the methylation did not differ between males and females atyoung age but age-related changes occurred in one sex but not the other. The age-related changes in DNA methylation tend to be enriched and under-represented in specific genomic contexts, with some commonalities between tissues and species that require further investigation. The strongest evidence that the age-related changes in DNA methylation play a role in aging comes from studies of anti-aging interventions (e.g., caloric restriction, dwarfism, and rapamycin treatment) in mice. These anti-aging interventions deaccelerate the epigenetic clocks and reverse/prevent 20 to 40% of the age-related changes in DNA methylation. It will be important in the future to demonstrate that at least some of the age-related changes in DNA methylation directly lead to alterations in the transcriptome of cells/tissues that could potentially contribute to aging.
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Imperio CG, McFalls AJ, Hadad N, Blanco-Berdugo L, Masser DR, Colechio EM, Coffey AA, Bixler GV, Stanford DR, Vrana KE, Grigson PS, Freeman WM. Exposure to environmental enrichment attenuates addiction-like behavior and alters molecular effects of heroin self-administration in rats. Neuropharmacology 2018; 139:26-40. [PMID: 29964093 PMCID: PMC6067959 DOI: 10.1016/j.neuropharm.2018.06.037] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/25/2018] [Accepted: 06/27/2018] [Indexed: 01/11/2023]
Abstract
Environmental factors profoundly affect the addictive potential of drugs of abuse and may also modulate the neuro-anatomical/neuro-chemical impacts of uncontrolled drug use and relapse propensity. This study examined the impact of environmental enrichment on heroin self-administration, addiction-related behaviors, and molecular processes proposed to underlie these behaviors. Male Sprague-Dawley rats in standard and enriched housing conditions intravenously self-administered similar amounts of heroin over 14 days. However, environmental enrichment attenuated progressive ratio, extinction, and reinstatement session responding after 14 days of enforced abstinence. Molecular mechanisms, namely DNA methylation and gene expression, are proposed to underlie abstinence-persistent behaviors. A global reduction in methylation is reported to coincide with addiction, but no differences in total genomic methylation or repeat element methylation were observed in CpG or non-CpG (CH) contexts across the mesolimbic circuitry as assessed by multiple methods including whole genome bisulfite sequencing. Immediate early gene expression associated with drug seeking, taking, and abstinence also were examined. EGR1 and EGR2 were suppressed in mesolimbic regions with heroin-taking and environmental enrichment. Site-specific methylation analysis of EGR1 and EGR2 promoter regions using bisulfite amplicon sequencing (BSAS) revealed hypo-methylation in the EGR2 promoter region and EGR1 intragenic CpG sites with heroin-taking and environmental enrichment that was associated with decreased mRNA expression. Taken together, these findings illuminate the impact of drug taking and environment on the epigenome in a locus and gene-specific manner and highlight the need for positive, alternative rewards in the treatment and prevention of drug addiction.
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Affiliation(s)
- Caesar G. Imperio
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Ashley J. McFalls
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Niran Hadad
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | | | - Dustin R. Masser
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Elizabeth M. Colechio
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Alissa A. Coffey
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Georgina V. Bixler
- Genome Sciences Facility, Penn State College of Medicine, Hershey, Pennsylvania
| | - David R. Stanford
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Kent. E. Vrana
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Patricia S. Grigson
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Willard M. Freeman
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
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Fibrosis: Lessons from OMICS analyses of the human lung. Matrix Biol 2018; 68-69:422-434. [PMID: 29567123 DOI: 10.1016/j.matbio.2018.03.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 12/30/2022]
Abstract
In recent decades there has been a significant shift in our understanding of idiopathic pulmonary fibrosis (IPF), a progressive and lethal disorder. While initially much of the mechanistic understanding was derived from hypotheses generated from animal models of disease, in recent decades new insights derived from humans with IPF have taken precedence. This is mainly because of the establishment of large collections of IPF lung tissues and patient cohorts, and the emergence of high throughput profiling technologies collectively termed 'omics' technologies based on their shared suffix. In this review we describe impacts of 'omics' analyses of human IPF samples on our understanding of the disease. In particular, we discuss the results of genomics and transcriptomics studies, as well as proteomics, epigenomics and metabolomics. We then describe how these findings can be integrated in a modified paradigm of human idiopathic pulmonary fibrosis, that introduces the 'hallmarks of aging' as a central theme in the IPF lung. This allows resolution of all the disparate cellular and molecular features in IPF, from the central role of epithelial cells, through the dramatic phenotypic alterations observed in fibroblasts and the numerous aberrations that inflammatory cells exhibit. We end with reiterating a call for renewed efforts to collect and analyze carefully characterized human tissues, in ways that would facilitate implementation of novel technologies for high resolution single cell omics profiling.
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