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Chakraborty N, Meyerhoff J, Jett M, Hammamieh R. Genome to Phenome: A Systems Biology Approach to PTSD Using an Animal Model. Methods Mol Biol 2017; 1598:117-154. [PMID: 28508360 DOI: 10.1007/978-1-4939-6952-4_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Post-traumatic stress disorder (PTSD) is a debilitating illness that imposes significant emotional and financial burdens on military families. The understanding of PTSD etiology remains elusive; nonetheless, it is clear that PTSD is manifested by a cluster of symptoms including hyperarousal, reexperiencing of traumatic events, and avoidance of trauma reminders. With these characteristics in mind, several rodent models have been developed eliciting PTSD-like features. Animal models with social dimensions are of particular interest, since the social context plays a major role in the development and manifestation of PTSD.For civilians, a core trauma that elicits PTSD might be characterized by a singular life-threatening event such as a car accident. In contrast, among war veterans, PTSD might be triggered by repeated threats and a cumulative psychological burden that coalesced in the combat zone. In capturing this fundamental difference, the aggressor-exposed social stress (Agg-E SS) model imposes highly threatening conspecific trauma on naïve mice repeatedly and randomly.There is abundant evidence that suggests the potential role of genetic contributions to risk factors for PTSD. Specific observations include putatively heritable attributes of the disorder, the cited cases of atypical brain morphology, and the observed neuroendocrine shifts away from normative. Taken together, these features underscore the importance of multi-omics investigations to develop a comprehensive picture. More daunting will be the task of downstream analysis with integration of these heterogeneous genotypic and phenotypic data types to deliver putative clinical biomarkers. Researchers are advocating for a systems biology approach, which has demonstrated an increasingly robust potential for integrating multidisciplinary data. By applying a systems biology approach here, we have connected the tissue-specific molecular perturbations to the behaviors displayed by mice subjected to Agg-E SS. A molecular pattern that links the atypical fear plasticity to energy deficiency was thereby identified to be causally associated with many behavioral shifts and transformations.PTSD is a multifactorial illness sensitive to environmental influence. Accordingly, it is essential to employ the optimal animal model approximating the environmental condition that elicits PTSD-like symptoms. Integration of an optimal animal model with a systems biology approach can contribute to a more knowledge-driven and efficient next-generation care management system and, potentially, prevention of PTSD.
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Affiliation(s)
- Nabarun Chakraborty
- Integrative Systems Biology, Geneva Foundation, USACEHR, 568 Doughten Drive, Fredrick, MD, 21702-5010, USA
| | - James Meyerhoff
- Integrative Systems Biology, Geneva Foundation, USACEHR, 568 Doughten Drive, Fredrick, MD, 21702-5010, USA
| | - Marti Jett
- Integrative Systems Biology, US Army Center for Environmental Health Research, USACEHR, 568 Doughten Drive, Frederick, MD, 21702-5010, USA
| | - Rasha Hammamieh
- Integrative Systems Biology, US Army Center for Environmental Health Research, USACEHR, 568 Doughten Drive, Frederick, MD, 21702-5010, USA.
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Hwang JJ, Kim YS, Kim MJ, Kim DE, Jeong IG, Kim CS. Histone Deacetylase Inhibitor Potentiates Anticancer Effect of Docetaxel via Modulation of Bcl-2 Family Proteins and Tubulin in Hormone Refractory Prostate Cancer Cells. J Urol 2010; 184:2557-64. [DOI: 10.1016/j.juro.2010.07.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Indexed: 01/20/2023]
Affiliation(s)
| | - Yong Sook Kim
- Institute for Innovative Cancer Research, Seoul, Korea
| | - Mi Joung Kim
- Institute for Innovative Cancer Research, Seoul, Korea
| | - Dong Eun Kim
- Institute for Innovative Cancer Research, Seoul, Korea
| | | | - Choung-Soo Kim
- University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
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Ronzoni S, Faretta M, Ballarini M, Pelicci P, Minucci S. Assessment of Histone Acetylation Levels in Relation to Cell Cycle Phase. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.35. [DOI: 10.1002/0471142956.cy0735s46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Simona Ronzoni
- Department of Experimental Oncology, European Institute of Oncology Milan Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology Milan Italy
| | - Marco Ballarini
- Department of Experimental Oncology, European Institute of Oncology Milan Italy
| | | | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology Milan Italy
- Department of Biomolecular Sciences and Biotechnology, University of Milan Milan Italy
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Scognamiglio A, Nebbioso A, Manzo F, Valente S, Mai A, Altucci L. HDAC-class II specific inhibition involves HDAC proteasome-dependent degradation mediated by RANBP2. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:2030-8. [PMID: 18691615 DOI: 10.1016/j.bbamcr.2008.07.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Revised: 07/06/2008] [Accepted: 07/10/2008] [Indexed: 12/20/2022]
Abstract
Discovered for their ability to deacetylate histones and repress transcription, HDACs are a promising target for therapy of human diseases. The class II HDACs are mainly involved in developmental and differentiation processes, such as myogenesis. We report here that class I and class II HDAC inhibitors such as SAHA or the class II selective inhibitor MC1568 induce down-regulation of class II HDACs in human cells. In particular, both SAHA and MC1568 induce HDAC 4 down-regulation by increasing its specific sumoylation followed by activation of proteasomal pathways of degradation. Sumoylation that corresponds to HDAC 4 nuclear localization results in a transient increase of the HDAC 4 repressive action on target genes such as RARalpha and TNFalpha. The HDAC 4 degradation that follows to its sumoylation results in gene target activation. Silencing of the RANBP2 E3 ligase reverts HDAC 4 repression by blocking its own sumoylation. These findings identify a crosstalk occurring between acetylation, deacetylation and sumoylation pathways and suggest that class II specific HDAC inhibitors may affect different epigenetic pathways.
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Affiliation(s)
- Annamaria Scognamiglio
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Vico L. De Crecchio 7, 80138 Napoli, Italy
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Skinner MK. What is an epigenetic transgenerational phenotype? F3 or F2. Reprod Toxicol 2008; 25:2-6. [PMID: 17949945 PMCID: PMC2249610 DOI: 10.1016/j.reprotox.2007.09.001] [Citation(s) in RCA: 324] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 07/26/2007] [Accepted: 09/05/2007] [Indexed: 01/02/2023]
Abstract
The ability of an environmental exposure to induce an epigenetic transgenerational adult onset disease phenotype is discussed in the current mini-review in the context of defining this phenomenon and the associated reproductive toxicology. A gestating female (F0 generation) exposure to an environmental compound results in the F1 generation embryo and F2 generation germ-line being directly exposed, such that the F3 generation is the first not directly exposed to the environmental compound. In contrast, postnatal or adult exposure (F0 generation) results in the F1 generation germ-line being exposed, such that F2 generation is the first to not be directly exposed to the environmental compound. The unequivocal transgenerational transmission of an adult onset disease phenotype through the germ-line requires assessment of the F3 generation for embryonic exposure, and F2 generation for postnatal exposure. This is in contrast to a number of F1 and F2 generation studies referred to as transgenerational. The reproductive toxicology associated with this transgenerational phenotype generally involves the reprogramming of the germ-line epigenome. The biological phenomenon involved in this reproductive toxicology deals with embryonic gonadal development and germ-line differentiation, or postnatally the gametogenesis process and germ cell development. The ability of an environmental compound (e.g. endocrine disruptor) to promote this reprogramming of the germ-line appears to be the causal factor in the epigenetic transgenerational phenotype.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4231, USA.
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Taylor KH, Pena-Hernandez KE, Davis JW, Arthur GL, Duff DJ, Shi H, Rahmatpanah FB, Sjahputera O, Caldwell CW. Large-Scale CpG Methylation Analysis Identifies Novel Candidate Genes and Reveals Methylation Hotspots in Acute Lymphoblastic Leukemia. Cancer Res 2007; 67:2617-25. [PMID: 17363581 DOI: 10.1158/0008-5472.can-06-3993] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study examined DNA methylation associated with acute lymphoblastic leukemia (ALL) and showed that selected molecular targets can be pharmacologically modulated to reverse gene silencing. A CpG island (CGI) microarray containing more than 3,400 unique clones that span all human chromosomes was used for large-scale discovery experiments and led to 262 unique CGI loci being statistically identified as methylated in ALL lymphoblasts. The methylation status of 10 clones encompassing 11 genes (DCC, DLC-1, DDX51, KCNK2, LRP1B, NKX6-1, NOPE, PCDHGA12, RPIB9, ABCB1, and SLC2A14) identified as differentially methylated between ALL patients and controls was independently verified. Consequently, the methylation status of DDX51 was found to differentiate patients with B- and T-ALL subtypes (P = 0.011, Fisher's exact test). Next, the relationship between methylation and expression of these genes was examined in ALL cell lines (NALM-6 and Jurkat) before and after treatments with 5-aza-2-deoxycytidine and trichostatin A. More than a 10-fold increase in mRNA expression was observed for two previously identified tumor suppressor genes (DLC-1 and DCC) and also for RPIB9 and PCDHGA12. Although the mechanisms that lead to the CGI methylation of these genes are unknown, bisulfite sequencing of the promoter of RPIB9 suggests that expression is inhibited by methylation within SP1 and AP2 transcription factor binding motifs. Finally, specific chromosomal methylation hotspots were found to be associated with ALL. This study sets the stage for acquiring a better biological understanding of ALL and for the identification of epigenetic biomarkers useful for differential diagnosis, therapeutic monitoring, and the detection of leukemic relapse.
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Affiliation(s)
- Kristen H Taylor
- Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri-Columbia School of Medicine, Columbia, Missouri 65212, USA
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Quina AS, Buschbeck M, Di Croce L. Chromatin structure and epigenetics. Biochem Pharmacol 2006; 72:1563-9. [PMID: 16836980 DOI: 10.1016/j.bcp.2006.06.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 06/11/2006] [Accepted: 06/13/2006] [Indexed: 12/20/2022]
Abstract
In eukaryotic cells, the DNA molecule is found in the form of a nucleoprotein complex named chromatin. The basic unit of the chromatin is the nucleosome, which comprises 147 base pairs of DNA wrapped around an octamer of core histones (made of two molecules of each H2A, H2B, H3, and H4 histones). Each nucleosome is linked to the next by small segments of linker DNA. Most chromatin is further condensated by winding in a polynucleosome fibre, which may be stabilized through the binding of histone H1 to each nucleosome and to the linker DNA. The modulation of the structure of the chromatin fibre is critical for the regulation of gene expression since it determines the accessibility and the sequential recruitment of regulatory factors to the underlying DNA. Depending on the different transcriptional states, the structure of the chromatin may be altered in its constituents (e.g. the presence of repressors, activators, chromatin remodelling complexes, and/or incorporation of histone variants), and in covalent modifications of its constituents (such as DNA methylation at cytosine residues, and posttranslational modifications of histone tails). Here, we give an overview of the molecular mechanisms involved in chromatin regulation and the epigenetic transmission of its state, both in normal and pathological scenarios.
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Affiliation(s)
- A S Quina
- Center for Genomic Regulation, Passeig Maritim 37-49, 08003 Barcelona, Spain
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Carbone R, Botrugno OA, Ronzoni S, Insinga A, Di Croce L, Pelicci PG, Minucci S. Recruitment of the histone methyltransferase SUV39H1 and its role in the oncogenic properties of the leukemia-associated PML-retinoic acid receptor fusion protein. Mol Cell Biol 2006; 26:1288-96. [PMID: 16449642 PMCID: PMC1367206 DOI: 10.1128/mcb.26.4.1288-1296.2006] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leukemia-associated fusion proteins establish aberrant transcriptional programs, which result in the block of hematopoietic differentiation, a prominent feature of the leukemic phenotype. The dissection of the mechanisms of deregulated transcription by leukemia fusion proteins is therefore critical for the design of tailored antileukemic strategies, aimed at reestablishing the differentiation program of leukemic cells. The acute promyelocytic leukemia (APL)-associated fusion protein PML-retinoic acid receptor (RAR) behaves as an aberrant transcriptional repressor, due to its ability to induce chromatin modifications (histone deacetylation and DNA methylation) and silencing of PML-RAR target genes. Here, we indicate that the ultimate result of PML-RAR action is to impose a heterochromatin-like structure on its target genes, thereby establishing a permanent transcriptional silencing. This effect is mediated by the previously described association of PML-RAR with chromatin-modifying enzymes (histone deacetylases and DNA methyltransferases) and by recruitment of the histone methyltransferase SUV39H1, responsible for trimethylation of lysine 9 of histone H3.
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MESH Headings
- Cell Differentiation
- DNA Methylation
- Gene Silencing
- Histone Methyltransferases
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Histones/chemistry
- Histones/metabolism
- Humans
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/metabolism
- Leukemia, Promyelocytic, Acute/pathology
- Methylation
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Models, Biological
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promyelocytic Leukemia Protein
- Protein Methyltransferases
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Transfection
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
- U937 Cells
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Affiliation(s)
- Roberta Carbone
- Department of Experimental Oncology, European Institute of Oncology, and Department of Biomolecular Sciences and Biotechnologies, University of Milan, Italy
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Minucci S, Pelicci PG. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat Rev Cancer 2006; 6:38-51. [PMID: 16397526 DOI: 10.1038/nrc1779] [Citation(s) in RCA: 1695] [Impact Index Per Article: 94.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Histone deacetylases (HDACs) are considered to be among the most promising targets in drug development for cancer therapy, and first-generation histone deacetylase inhibitors (HDACi) are currently being tested in phase I/II clinical trials. A wide-ranging knowledge of the role of HDACs in tumorigenesis, and of the action of HDACi, has been achieved. However, several basic aspects are not yet fully understood. Investigating these aspects in the context of what we now understand about HDACi action both in vitro and in vivo will further improve the design of optimized clinical protocols.
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Affiliation(s)
- Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology, Via Ripamanti 435, 20141, Milan, Italy.
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Ushmorov A, Leithäuser F, Sakk O, Weinhaüsel A, Popov SW, Möller P, Wirth T. Epigenetic processes play a major role in B-cell-specific gene silencing in classical Hodgkin lymphoma. Blood 2005; 107:2493-500. [PMID: 16304050 DOI: 10.1182/blood-2005-09-3765] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Many B-lineage-specific genes are down-regulated in Hodgkin and Reed-Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL). We investigated the involvement of epigenetic modifications in gene silencing in cHL cell lines and in microdissected primary HRS cells. We assessed the expression and methylation status of CD19, CD20, CD79B, SYK, PU.1, BOB.1/OBF.1, BCMA, and LCK, all of which are typically down-regulated in cHL. We could reactivate gene expression in cHL cell lines with the DNA demethylating agent 5-aza-deoxycytidine (5-aza-dC). Using methylation-specific polymerase chain reaction (MSP), bisulfite genomic sequencing, and digestion with methylation-sensitive endonuclease followed by polymerase chain reaction (PCR), we determined the methylation status of promoter regions of PU.1, BOB.1/OBF.1, CD19, SYK, and CD79B. Down-regulation of transcription typically correlated with hypermethylation. Using bisulfite genomic sequencing we found that in microdissected HRS cells of primary cHL SYK, BOB.1/OBF.1, and CD79B promoters were also hypermethylated. Ectopic expression of both Oct2 and PU.1 in a cHL cell line potentiated endogenous PU.1 and SYK expression after 5-aza-dC treatment. These observations indicate that silencing of the B-cell-specific genes in cHL may be the consequence of a compromised regulatory network where down-regulation of a few master transcription factors results in silencing of numerous genes.
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Affiliation(s)
- Alexey Ushmorov
- Department of Physiological Chemistry, University of Ulm, D-89069 Ulm, Germany
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Di Croce L. Chromatin modifying activity of leukaemia associated fusion proteins. Hum Mol Genet 2005; 14 Spec No 1:R77-84. [PMID: 15809276 DOI: 10.1093/hmg/ddi109] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The leukaemias, which are divided into chronic and acute forms, are malignant diseases of haematopoietic cells in which the proper balance between proliferation, differentiation and apoptosis is no longer operative. Genes, such as those of mixed-lineage leukaemia, AML1 and retinoic acid receptor alpha, have been found to be aberrantly fused to different partners, which often encode transcription factors or other chromatin modifying enzymes, in numerous types of acute lymphoid and myeloid leukaemias. These chimeric fusion oncoproteins, generated by reciprocal chromosomal translocations, are responsible for chromatin alterations on target genes whose expression is critical to stem cell development or lineage specification in haematopoiesis. Alterations in the 'histone code' or in the DNA methylation content occur as consequence of aberrant targeting of the corresponding enzymatic activities. Here, the author will review the most recent progress in the field, focusing on how fusion proteins generated by chromosomal translocation are responsible for chromatin alterations, gene deregulation and haematopoietic differentiation block and their implication for clinical treatment.
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Affiliation(s)
- Luciano Di Croce
- ICREA and Centre de Regulació Genòmica (CRG), Passeig Maritim 37-49, 08003 Barcelona, Spain.
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