1
|
Belmonte KCD, Harman JC, Lanson NA, Gidday JM. Intra- and intergenerational changes in the cortical DNA methylome in response to therapeutic intermittent hypoxia in mice. Physiol Genomics 2019; 52:20-34. [PMID: 31762411 DOI: 10.1152/physiolgenomics.00094.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Recent evidence from our laboratory documents functional resilience to retinal ischemic injury in untreated mice derived from parents exposed to repetitive hypoxic conditioning (RHC) before breeding. To begin to understand the epigenetic basis of this intergenerational protection, we used methylated DNA immunoprecipitation and sequencing to identify genes with differentially methylated promoters (DMGPs) in the prefrontal cortex of mice treated directly with the same RHC stimulus (F0-RHC) and in the prefrontal cortex of their untreated F1-generation offspring (F1-*RHC). Subsequent bioinformatic analyses provided key mechanistic insights into how changes in gene expression secondary to promoter hypo- and hypermethylation might afford such protection within and across generations. We found extensive changes in DNA methylation in both generations consistent with the expression of many survival-promoting genes, with twice the number of DMGPs in the cortex of F1*RHC mice relative to their F0 parents that were directly exposed to RHC. In contrast to our hypothesis that similar epigenetic modifications would be realized in the cortices of both F0-RHC and F1-*RHC mice, we instead found relatively few DMGPs common to both generations; in fact, each generation manifested expected injury resilience via distinctly unique gene expression profiles. Whereas in the cortex of F0-RHC mice, predicted protein-protein interactions reflected activation of an anti-ischemic phenotype, networks activated in F1-*RHC cortex comprised networks indicative of a much broader cytoprotective phenotype. Altogether, our results suggest that the intergenerational transfer of an acquired phenotype to offspring does not necessarily require the faithful recapitulation of the conditioning-modified DNA methylome of the parent.
Collapse
Affiliation(s)
- Krystal Courtney D Belmonte
- Department of Ophthalmology, Louisiana State University School of Medicine, Health Sciences Center, New Orleans, Louisiana.,Department of Physiology, Louisiana State University School of Medicine, Health Sciences Center, New Orleans, Louisiana
| | - Jarrod C Harman
- Department of Ophthalmology, Louisiana State University School of Medicine, Health Sciences Center, New Orleans, Louisiana.,Neuroscience Center of Excellence, Louisiana State University School of Medicine, Health Sciences Center, New Orleans, Louisiana
| | - Nicholas A Lanson
- Department of Ophthalmology, Louisiana State University School of Medicine, Health Sciences Center, New Orleans, Louisiana
| | - Jeffrey M Gidday
- Department of Ophthalmology, Louisiana State University School of Medicine, Health Sciences Center, New Orleans, Louisiana.,Department of Physiology, Louisiana State University School of Medicine, Health Sciences Center, New Orleans, Louisiana.,Neuroscience Center of Excellence, Louisiana State University School of Medicine, Health Sciences Center, New Orleans, Louisiana
| |
Collapse
|
2
|
Masvekar R, Wu T, Kosa P, Barbour C, Fossati V, Bielekova B. Cerebrospinal fluid biomarkers link toxic astrogliosis and microglial activation to multiple sclerosis severity. Mult Scler Relat Disord 2019; 28:34-43. [PMID: 30553167 PMCID: PMC6411304 DOI: 10.1016/j.msard.2018.11.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/20/2018] [Accepted: 11/29/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Once multiple sclerosis (MS) reaches the progressive stage, immunomodulatory treatments have limited efficacy. This suggests that processes other than activation of innate immunity may at least partially underlie disability progression during late stages of MS. Pathology identified these alternative processes as aberrant activation of astrocytes and microglia, and subsequent degeneration of oligodendrocytes and neurons. However, we mostly lack biomarkers that could measure central nervous system (CNS) cell-specific intrathecal processes in living subjects. This prevents differentiating pathogenic processes from an epiphenomenon. Therefore, we sought to develop biomarkers of CNS cell-specific processes and link them to disability progression in MS. METHODS In a blinded manner, we measured over 1000 proteins in the cerebrospinal fluid (CSF) of 431 patients with neuroimmunological diseases and healthy volunteers using modified DNA-aptamers (SOMAscan®). We defined CNS cell type-enriched clusters using variable cluster analysis, combined with in vitro modeling. Differences between diagnostic categories were identified in the training cohort (n = 217) and their correlation to disability measures were assessed; results were validated in an independent validation cohort (n = 214). RESULTS Astrocyte cluster 8 (MMP7, SERPINA3, GZMA and CLIC1) and microglial cluster 2 (DSG2 and TNFRSF25) were reproducibly elevated in MS and had a significant and reproducible correlation with MS severity suggesting their pathogenic role. In vitro studies demonstrated that proteins of astrocyte cluster 8 are noticeably released upon stimulation with proinflammatory stimuli and overlap with the phenotype of recently described neuro-toxic (A1) astrocytes. CONCLUSION Microglial activation and toxic astrogliosis are associated with MS disease process and may partake in CNS tissue destruction. This hypothesis should be tested in new clinical trials.
Collapse
Affiliation(s)
- Ruturaj Masvekar
- Neuroimmunological Diseases Section (NDS), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5N248, 10 Center Drive, MSC1444, Bethesda, MD 20892, United States
| | - Tianxia Wu
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Peter Kosa
- Neuroimmunological Diseases Section (NDS), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5N248, 10 Center Drive, MSC1444, Bethesda, MD 20892, United States
| | - Christopher Barbour
- Neuroimmunological Diseases Section (NDS), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5N248, 10 Center Drive, MSC1444, Bethesda, MD 20892, United States; Department of Mathematical Sciences, Montana State University, Bozeman, MT, United States
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
| | - Bibiana Bielekova
- Neuroimmunological Diseases Section (NDS), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5N248, 10 Center Drive, MSC1444, Bethesda, MD 20892, United States.
| |
Collapse
|
3
|
Bereman MS, Beri J, Enders JR, Nash T. Machine Learning Reveals Protein Signatures in CSF and Plasma Fluids of Clinical Value for ALS. Sci Rep 2018; 8:16334. [PMID: 30397248 PMCID: PMC6218542 DOI: 10.1038/s41598-018-34642-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/23/2018] [Indexed: 11/14/2022] Open
Abstract
We use shotgun proteomics to identify biomarkers of diagnostic and prognostic value in individuals diagnosed with amyotrophic lateral sclerosis. Matched cerebrospinal and plasma fluids were subjected to abundant protein depletion and analyzed by nano-flow liquid chromatography high resolution tandem mass spectrometry. Label free quantitation was used to identify differential proteins between individuals with ALS (n = 33) and healthy controls (n = 30) in both fluids. In CSF, 118 (p-value < 0.05) and 27 proteins (q-value < 0.05) were identified as significantly altered between ALS and controls. In plasma, 20 (p-value < 0.05) and 0 (q-value < 0.05) proteins were identified as significantly altered between ALS and controls. Proteins involved in complement activation, acute phase response and retinoid signaling pathways were significantly enriched in the CSF from ALS patients. Subsequently various machine learning methods were evaluated for disease classification using a repeated Monte Carlo cross-validation approach. A linear discriminant analysis model achieved a median area under the receiver operating characteristic curve of 0.94 with an interquartile range of 0.88–1.0. Three proteins composed a prognostic model (p = 5e-4) that explained 49% of the variation in the ALS-FRS scores. Finally we investigated the specificity of two promising proteins from our discovery data set, chitinase-3 like 1 protein and alpha-1-antichymotrypsin, using targeted proteomics in a separate set of CSF samples derived from individuals diagnosed with ALS (n = 11) and other neurological diseases (n = 15). These results demonstrate the potential of a panel of targeted proteins for objective measurements of clinical value in ALS.
Collapse
Affiliation(s)
- Michael S Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA. .,Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA. .,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Joshua Beri
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jeffrey R Enders
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
| | - Tara Nash
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
| |
Collapse
|
4
|
Park J, Masaki T, Mezaki Y, Yokoyama H, Nakamura M, Maehashi H, Fujimi TJ, Gouraud SS, Nagatsuma K, Nakagomi M, Kimura N, Matsuura T. Alpha-1 antichymotrypsin is involved in astrocyte injury in concert with arginine-vasopressin during the development of acute hepatic encephalopathy. PLoS One 2017; 12:e0189346. [PMID: 29216295 PMCID: PMC5720809 DOI: 10.1371/journal.pone.0189346] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/24/2017] [Indexed: 01/09/2023] Open
Abstract
Background and aims We developed a bio-artificial liver (BAL) using a radial-flow bioreactor and rescued mini-pig models with lethal acute liver failure (ALF). The point of the rescue is the recovery from hepatic encephalopathy (HE). HE on ALF has sometimes resulted in brain death following brain edema with astrocyte swelling. Several factors, including ammonia and glutamine, have been reported to induce astrocyte swelling and injury. However, many clinicians believe that there are any other factors involved in the development of HE. Therefore, the aim of this study was to identify novel HE-inducible factors, particularly those inducing astrocyte dysfunction. Methods Mini-pig plasma samples were collected at three time points: before the administration of toxins (α-amanitin and LPS), when HE occurred after the administration of toxins, and after treatment with extracorporeal circulation (EC) by the BAL. To identify the causative factors of HE, each plasma sample was subjected to a comparative proteome analysis with two-dimensional gel electrophoresis and mass spectrometry. To assess the direct effects of candidate factors on the astrocyte function and injury, in vitro experiments with human astrocytes were performed. Results Using a proteome analysis, we identified alpha-1 antichymotrypsin (ACT), which was increased in plasma samples from mini-pigs with HE and decreased in those after treatment with EC by BAL. In in vitro experiments with human astrocytes, ACT showed growth-inhibitory and cytotoxic effects on astrocytes. In addition, the expression of water channel protein aquaporin-4, which is induced in injured astrocytes, was increased following ACT treatment. Interestingly, these effects of ACT were additively enhanced by adding arginine-vasopressin (AVP) and were canceled by adding an AVP receptor antagonist. Conclusions These results suggest that ACT is involved in astrocyte injury and dysfunction in concert with AVP during the development of acute HE.
Collapse
Affiliation(s)
- Jonghyuk Park
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | - Takahiro Masaki
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | - Yoshihiro Mezaki
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | - Hiroshi Yokoyama
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | - Mariko Nakamura
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | - Haruka Maehashi
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | - Takahiko J. Fujimi
- Faculty of Health and Nutrition, Bunkyo University, Chigasaki, Kanagawa, Japan
| | - Sabine S. Gouraud
- Department of Biology, Faculty of Science, Ochanomizu University, Bunkyo-ku, Tokyo, Japan
| | - Keisuke Nagatsuma
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | - Madoka Nakagomi
- Hatano Research Institute, Food and Drug Safety Center, Hadano, Kanagawa, Japan
| | - Naofumi Kimura
- Department of Pharmacology, The Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | - Tomokazu Matsuura
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, Japan
- * E-mail:
| |
Collapse
|
5
|
Chelbi ST, Wilson ML, Veillard AC, Ingles SA, Zhang J, Mondon F, Gascoin-Lachambre G, Doridot L, Mignot TM, Rebourcet R, Carbonne B, Concordet JP, Barbaux S, Vaiman D. Genetic and epigenetic mechanisms collaborate to control SERPINA3 expression and its association with placental diseases. Hum Mol Genet 2012; 21:1968-78. [PMID: 22246292 DOI: 10.1093/hmg/dds006] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
SERPINA3 (Serpin peptidase inhibitor clade A member 3), also known as a1-antichymotrypsin, is a serine protease inhibitor involved in a wide range of biological processes. Recently, it has been shown to be up-regulated in human placental diseases in association with a hypomethylation of the 5' region of the gene. In the present study, we show that the promoter of SERPINA3 is transcriptionally activated by three transcription factors (TFs) (SP1, MZF1 and ZBTB7B), the level of induction being dependent on the rs1884082 single nucleotide polymorphism (SNP) located inside the promoter, the T allele being consistently induced to a higher level than the G, with or without added TFs. When the promoter was methylated, the response to ZBTB7B was allele specific (the G allele was strongly induced, while the T allele was strongly down-regulated). We propose an adaptive model to explain the interest of such a regulation for placental function and homeostasis. Overexpression of SERPINA3 in JEG-3 cells, a trophoblast cell model, decreased cell adhesion to the extracellular matrix and to neighboring cells, but protects them from apoptosis, suggesting a way by which this factor could be deleterious at high doses. In addition, we show in different human populations that the T allele appears to predispose to Intra Uterine Growth Restriction (IUGR), while a G allele at a second SNP located in the second exon (rs4634) increases the risk of preeclampsia. Our results provide mechanistic views inside the involvement of SERPINA3 in placental diseases, through its regulation by a combination of epigenetic, genetic and TF-mediated regulations.
Collapse
Affiliation(s)
- Sonia T Chelbi
- Institut Cochin, Université Paris Descartes, CNRS, UMR 8104, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Di Domenico F, Owen JB, Sultana R, Sowell RA, Perluigi M, Cini C, Cai J, Pierce WM, Butterfield DA. The wheat germ agglutinin-fractionated proteome of subjects with Alzheimer's disease and mild cognitive impairment hippocampus and inferior parietal lobule: Implications for disease pathogenesis and progression. J Neurosci Res 2010; 88:3566-77. [PMID: 20936705 DOI: 10.1002/jnr.22528] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 08/28/2010] [Accepted: 09/03/2010] [Indexed: 01/07/2023]
Abstract
Lectin affinity chromatography is a powerful separation technique that fractionates proteins by selectively binding to specific carbohydrate moieties characteristic of protein glycosylation type. Wheat germ agglutinin (WGA) selectively binds terminal N-acetylglucosamine (O-GlcNAc) and sialic acid moieties characteristic of O-linked glycosylation. The current study utilizes WGA affinity chromatography to fractionate proteins from hippocampus and inferior parietal lobule (IPL) from subjects with Alzheimer's disease (AD) and arguably its earliest form, mild cognitive impairment (MCI). Proteins identified by proteomics that were fractionated from MCI and AD hippocampus by WGA affinity chromatography with altered levels compared with age-matched controls included GP96, γ-enolase, glutamate dehydrogenase, glucosidase IIα, 14-3-3ϵ, 14-3-3γ, 14-3-3ζ, tropomyosin-2, calmodulin 2, gelsolin, β-synuclein, α1-antichymotrypsin, and dimethylguanosine tRNA methyltransferase. Proteins identified by proteomics that were fractionated from MCI and AD IPL by WGA affinity chromatography showing altered levels compared with age-matched controls included protein disulfide isomerase, calreticulin, and GP96. The proteins described in this study are involved in diverse processes, including glucose metabolism, endoplasmic reticulum (ER) functions, chaperoning, cytoskeletal assembly, and proteolysis, all of which are affected in AD. This study, the first to use proteomics to identify WGA-fractionated proteins isolated from brains from subjects with MCI and AD, provides additional information about the active proteome of the brain throughout AD progression.
Collapse
Affiliation(s)
- Fabio Di Domenico
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Yu G, Jia J. Is there an association of regulatory region polymorphism in the alpha-1-antichymotrypsin gene with sporadic Alzheimer’s disease in the northern Han-Chinese population? J Clin Neurosci 2010; 17:766-9. [DOI: 10.1016/j.jocn.2009.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 08/06/2009] [Accepted: 10/11/2009] [Indexed: 12/22/2022]
|
8
|
The alpha-1-antitrypsin gene promoter in human A549 lung derived cells, and a novel transcription initiation site. Int J Biochem Cell Biol 2008; 41:1157-64. [PMID: 19010440 DOI: 10.1016/j.biocel.2008.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 10/17/2008] [Accepted: 10/22/2008] [Indexed: 11/20/2022]
Abstract
Alpha-1-antitrypsin (AAT), also called serine proteinase inhibitor A1 (Serpin A1), is the most abundant serpin in human plasma. A major physiological role of AAT is to protect the lung from the destructive effects of excess uninhibited neutrophil elastase. During inflammation, circulating levels of AAT may increase twofold-to-threefold as part of the acute-phase response. The liver is the main contributor to this increase. However, local synthesis may provide an important mechanism for controlling neutrophil elastase activity at sites of inflammation, and previous studies have shown a marked increase in production after cytokine stimulation. In the current study we report a distinct transcription initiation site for AAT expression in the lung alveolar epithelial cell line A549, which is located nine bases upstream of the previously mapped full-length monocyte transcription start-site, and show using site-directed mutagenesis that two Sp1 sites and a putative TATA box are functional. EMSA experiments provide evidence for Sp1 and Sp3 binding to these two Sp1 sites. We have also mapped the minimal promoter region and a cell-specific element essential for expression in A549 cells, both of which reside in an 865bp fragment upstream of the transcription start-site. Understanding the mechanisms of AAT gene regulation in a lung-derived cell line has important implications for understanding the control of localised lung tissue damage which occurs as a result of excess proteolytic activity.
Collapse
|