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Breen C, Papale LA, Clark LR, Bergmann PE, Madrid A, Asthana S, Johnson SC, Keleş S, Alisch RS, Hogan KJ. Whole genome methylation sequencing in blood identifies extensive differential DNA methylation in late-onset dementia due to Alzheimer's disease. Alzheimers Dement 2024; 20:1050-1062. [PMID: 37856321 PMCID: PMC10916976 DOI: 10.1002/alz.13514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/17/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
INTRODUCTION DNA microarray-based studies report differentially methylated positions (DMPs) in blood between late-onset dementia due to Alzheimer's disease (AD) and cognitively unimpaired individuals, but interrogate < 4% of the genome. METHODS We used whole genome methylation sequencing (WGMS) to quantify DNA methylation levels at 25,409,826 CpG loci in 281 blood samples from 108 AD and 173 cognitively unimpaired individuals. RESULTS WGMS identified 28,038 DMPs throughout the human methylome, including 2707 differentially methylated genes (e.g., SORCS3, GABA, and PICALM) encoding proteins in biological pathways relevant to AD such as synaptic membrane, cation channel complex, and glutamatergic synapse. One hundred seventy-three differentially methylated blood-specific enhancers interact with the promoters of 95 genes that are differentially expressed in blood from persons with and without AD. DISCUSSION WGMS identifies differentially methylated CpGs in known and newly detected genes and enhancers in blood from persons with and without AD. HIGHLIGHTS Whole genome DNA methylation levels were quantified in blood from persons with and without Alzheimer's disease (AD). Twenty-eight thousand thirty-eight differentially methylated positions (DMPs) were identified. Two thousand seven hundred seven genes comprise DMPs. Forty-eight of 75 independent genetic risk loci for AD have DMPs. One thousand five hundred sixty-eight blood-specific enhancers comprise DMPs, 173 of which interact with the promoters of 95 genes that are differentially expressed in blood from persons with and without AD.
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Affiliation(s)
- Coleman Breen
- Department of StatisticsUniversity of Wisconsin, Medical Sciences CenterMadisonWisconsinUSA
| | - Ligia A. Papale
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Lindsay R. Clark
- Wisconsin Alzheimer's Disease Research CenterUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
- Geriatric Research Education and Clinical CenterWilliam S. Middleton Memorial Veterans HospitalMadisonWisconsinUSA
| | - Phillip E. Bergmann
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Andy Madrid
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Sanjay Asthana
- Geriatric Research Education and Clinical CenterWilliam S. Middleton Memorial Veterans HospitalMadisonWisconsinUSA
- Wisconsin Alzheimer's InstituteUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Sterling C. Johnson
- Wisconsin Alzheimer's Disease Research CenterUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
- Geriatric Research Education and Clinical CenterWilliam S. Middleton Memorial Veterans HospitalMadisonWisconsinUSA
- Wisconsin Alzheimer's InstituteUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Sündüz Keleş
- Department of StatisticsUniversity of Wisconsin, Medical Sciences CenterMadisonWisconsinUSA
- Department of Biostatistics and Medical InformaticsUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Reid S. Alisch
- Department of Neurological SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Kirk J. Hogan
- Wisconsin Alzheimer's InstituteUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
- Department of AnesthesiologyUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
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Ulschmid CM, Sun MR, Jabbarpour CR, Steward AC, Rivera-González KS, Cao J, Martin AA, Barnes M, Wicklund L, Madrid A, Papale LA, Joseph DB, Vezina CM, Alisch RS, Lipinski RJ. Disruption of DNA methylation-mediated cranial neural crest proliferation and differentiation causes orofacial clefts in mice. Proc Natl Acad Sci U S A 2024; 121:e2317668121. [PMID: 38194455 PMCID: PMC10801837 DOI: 10.1073/pnas.2317668121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/14/2023] [Indexed: 01/11/2024] Open
Abstract
Orofacial clefts of the lip and palate are widely recognized to result from complex gene-environment interactions, but inadequate understanding of environmental risk factors has stymied development of prevention strategies. We interrogated the role of DNA methylation, an environmentally malleable epigenetic mechanism, in orofacial development. Expression of the key DNA methyltransferase enzyme DNMT1 was detected throughout palate morphogenesis in the epithelium and underlying cranial neural crest cell (cNCC) mesenchyme, a highly proliferative multipotent stem cell population that forms orofacial connective tissue. Genetic and pharmacologic manipulations of DNMT activity were then applied to define the tissue- and timing-dependent requirement of DNA methylation in orofacial development. cNCC-specific Dnmt1 inactivation targeting initial palate outgrowth resulted in OFCs, while later targeting during palatal shelf elevation and elongation did not. Conditional Dnmt1 deletion reduced cNCC proliferation and subsequent differentiation trajectory, resulting in attenuated outgrowth of the palatal shelves and altered development of cNCC-derived skeletal elements. Finally, we found that the cellular mechanisms of cleft pathogenesis observed in vivo can be recapitulated by pharmacologically reducing DNA methylation in multipotent cNCCs cultured in vitro. These findings demonstrate that DNA methylation is a crucial epigenetic regulator of cNCC biology, define a critical period of development in which its disruption directly causes OFCs, and provide opportunities to identify environmental influences that contribute to OFC risk.
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Affiliation(s)
- Caden M. Ulschmid
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Miranda R. Sun
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Christopher R. Jabbarpour
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Austin C. Steward
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Kenneth S. Rivera-González
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
- Molecular and Environmental Toxicology Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Jocelyn Cao
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Alexander A. Martin
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Macy Barnes
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Lorena Wicklund
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Andy Madrid
- Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Ligia A. Papale
- Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Diya B. Joseph
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Chad M. Vezina
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
- Molecular and Environmental Toxicology Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Reid S. Alisch
- Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
- Molecular and Environmental Toxicology Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
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Alberca CD, Papale LA, Madrid A, Alisch RS. Hippocampal and peripheral blood DNA methylation signatures correlate at the gene and pathway level in a mouse model of autism. Hum Mol Genet 2023; 32:3312-3322. [PMID: 37658766 DOI: 10.1093/hmg/ddad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/02/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
Autism spectrum disorders (ASD) are polygenic multifactorial disorders influenced by environmental factors. ASD-related differential DNA methylation has been found in human peripheral tissues, such as placenta, paternal sperm, buccal epithelium, and blood. However, these data lack direct comparison of DNA methylation levels with brain tissue from the same individual to determine the extent that peripheral tissues are surrogates for behavior-related disorders. Here, whole genome methylation profiling at all the possible sites throughout the mouse genome (>25 million) from both brain and blood tissues revealed novel insights into the systemic contributions of DNA methylation to ASD. Sixty-six differentially methylated regions (DMRs) share the same genomic coordinates in these two tissues, many of which are linked to risk genes for neurodevelopmental disorders and intellectual disabilities (e.g. Prkch, Ptn, Hcfc1, Mid1, and Nfia). Gene ontological pathways revealed a significant number of common terms between brain and blood (N = 65 terms), and nearly half (30/65) were associated with brain/neuronal development. Furthermore, seven DMR-associated genes among these terms contain methyl-sensitive transcription factor sequence motifs within the DMRs of both tissues; four of them (Cux2, Kcnip2, Fgf13, and Mrtfa) contain the same methyl-sensitive transcription factor binding sequence motifs (HES1/2/5, TBX2 and TFAP2C), suggesting DNA methylation influences the binding of common transcription factors required for gene expression. Together, these findings suggest that peripheral blood is a good surrogate tissue for brain and support that DNA methylation contributes to altered gene regulation in the pathogenesis of ASD.
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Affiliation(s)
- Carolina D Alberca
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
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Balnis J, Lauria EJM, Yucel R, Singer HA, Alisch RS, Jaitovich A. Peripheral Blood Omics and Other Multiplex-based Systems in Pulmonary and Critical Care Medicine. Am J Respir Cell Mol Biol 2023; 69:383-390. [PMID: 37379507 PMCID: PMC10557924 DOI: 10.1165/rcmb.2023-0153ps] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023] Open
Abstract
Over the last years, the use of peripheral blood-derived big datasets in combination with machine learning technology has accelerated the understanding, prediction, and management of pulmonary and critical care conditions. The goal of this article is to provide readers with an introduction to the methods and applications of blood omics and other multiplex-based technologies in the pulmonary and critical care medicine setting to better appreciate the current literature in the field. To accomplish that, we provide essential concepts needed to rationalize this approach and introduce readers to the types of molecules that can be obtained from the circulating blood to generate big datasets; elaborate on the differences between bulk, sorted, and single-cell approaches; and the basic analytical pipelines required for clinical interpretation. Examples of peripheral blood-derived big datasets used in recent literature are presented, and limitations of that technology are highlighted to qualify both the current and future value of these methodologies.
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Affiliation(s)
- Joseph Balnis
- Division of Pulmonary and Critical Care Medicine and
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Eitel J. M. Lauria
- School of Computer Science and Mathematics, Marist College, Poughkeepsie, New York
| | - Recai Yucel
- Department of Epidemiology and Biostatistics, Temple University, Philadelphia, Pennsylvania; and
| | - Harold A. Singer
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Reid S. Alisch
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine and
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
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Balnis J, Madrid A, Hogan KJ, Drake LA, Adhikari A, Vancavage R, Singer HA, Alisch RS, Jaitovich A. Whole-Genome Methylation Sequencing Reveals that COVID-19-induced Epigenetic Dysregulation Remains 1 Year after Hospital Discharge. Am J Respir Cell Mol Biol 2023; 68:594-597. [PMID: 37125894 PMCID: PMC10174161 DOI: 10.1165/rcmb.2022-0433le] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Affiliation(s)
| | - Andy Madrid
- University of Wisconsin School of Medicine and Public HealthMadison, Wisconsin
| | - Kirk J. Hogan
- Department of AnesthesiologyUniversity of WisconsinMadison, Wisconsin
| | | | | | | | | | - Reid S. Alisch
- University of Wisconsin School of Medicine and Public HealthMadison, Wisconsin
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Ozair A, Bhat V, Alisch RS, Khosla AA, Kotecha RR, Odia Y, McDermott MW, Ahluwalia MS. DNA Methylation and Histone Modification in Low-Grade Gliomas: Current Understanding and Potential Clinical Targets. Cancers (Basel) 2023; 15:cancers15041342. [PMID: 36831683 PMCID: PMC9954183 DOI: 10.3390/cancers15041342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Gliomas, the most common type of malignant primary brain tumor, were conventionally classified through WHO Grades I-IV (now 1-4), with low-grade gliomas being entities belonging to Grades 1 or 2. While the focus of the WHO Classification for Central Nervous System (CNS) tumors had historically been on histopathological attributes, the recently released fifth edition of the classification (WHO CNS5) characterizes brain tumors, including gliomas, using an integration of histological and molecular features, including their epigenetic changes such as histone methylation, DNA methylation, and histone acetylation, which are increasingly being used for the classification of low-grade gliomas. This review describes the current understanding of the role of DNA methylation, demethylation, and histone modification in pathogenesis, clinical behavior, and outcomes of brain tumors, in particular of low-grade gliomas. The review also highlights potential diagnostic and/or therapeutic targets in associated cellular biomolecules, structures, and processes. Targeting of MGMT promoter methylation, TET-hTDG-BER pathway, association of G-CIMP with key gene mutations, PARP inhibition, IDH and 2-HG-associated processes, TERT mutation and ARL9-associated pathways, DNA Methyltransferase (DNMT) inhibition, Histone Deacetylase (HDAC) inhibition, BET inhibition, CpG site DNA methylation signatures, along with others, present exciting avenues for translational research. This review also summarizes the current clinical trial landscape associated with the therapeutic utility of epigenetics in low-grade gliomas. Much of the evidence currently remains restricted to preclinical studies, warranting further investigation to demonstrate true clinical utility.
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Affiliation(s)
- Ahmad Ozair
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Faculty of Medicine, King George’s Medical University, Lucknow 226003, India
| | - Vivek Bhat
- St. John’s Medical College, Bangalore 560034, India
| | - Reid S. Alisch
- Department of Neurosurgery, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Atulya A. Khosla
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
| | - Rupesh R. Kotecha
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Yazmin Odia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Michael W. McDermott
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
- Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Correspondence: (M.W.M.); (M.S.A.)
| | - Manmeet S. Ahluwalia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Correspondence: (M.W.M.); (M.S.A.)
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Rizk E, Madrid A, Koueik J, Sun D, Stewart K, Chen D, Luo S, Hong F, Papale LA, Hariharan N, Alisch RS, Iskandar BJ. Purified regenerating retinal neurons reveal regulatory role of DNA methylation-mediated Na+/K+-ATPase in murine axon regeneration. Commun Biol 2023; 6:120. [PMID: 36717618 PMCID: PMC9886953 DOI: 10.1038/s42003-023-04463-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
While embryonic mammalian central nervous system (CNS) axons readily grow and differentiate, only a minority of fully differentiated mature CNS neurons are able to regenerate injured axons, leading to stunted functional recovery after injury and disease. To delineate DNA methylation changes specifically associated with axon regeneration, we used a Fluorescent-Activated Cell Sorting (FACS)-based methodology in a rat optic nerve transection model to segregate the injured retinal ganglion cells (RGCs) into regenerating and non-regenerating cell populations. Whole-genome DNA methylation profiling of these purified neurons revealed genes and pathways linked to mammalian RGC regeneration. Moreover, whole-methylome sequencing of purified uninjured adult and embryonic RGCs identified embryonic molecular profiles reactivated after injury in mature neurons, and others that correlate specifically with embryonic or adult axon growth, but not both. The results highlight the contribution to both embryonic growth and adult axon regeneration of subunits encoding the Na+/K+-ATPase. In turn, both biochemical and genetic inhibition of the Na+/K+-ATPase pump significantly reduced RGC axon regeneration. These data provide critical molecular insights into mammalian CNS axon regeneration, pinpoint the Na+/K+-ATPase as a key regulator of regeneration of injured mature CNS axons, and suggest that successful regeneration requires, in part, reactivation of embryonic signals.
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Affiliation(s)
- Elias Rizk
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA ,grid.240473.60000 0004 0543 9901Department of Neurological Surgery, Penn State Milton S. Hershey Medical Center, Hershey, PA 17033 USA
| | - Andy Madrid
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Joyce Koueik
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Dandan Sun
- grid.21925.3d0000 0004 1936 9000Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Krista Stewart
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - David Chen
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Susan Luo
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Felissa Hong
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Ligia A. Papale
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Nithya Hariharan
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Reid S. Alisch
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Bermans J. Iskandar
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
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Madrid A, Alisch RS, Rizk E, Papale LA, Hogan KJ, Iskandar BJ. Transgenerational epigenetic inheritance of axonal regeneration after spinal cord injury. Environ Epigenet 2023; 9:dvad002. [PMID: 36843857 PMCID: PMC9949995 DOI: 10.1093/eep/dvad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/01/2023] [Accepted: 01/14/2023] [Indexed: 05/14/2023]
Abstract
Human epidemiological studies reveal that dietary and environmental alterations influence the health of the offspring and that the effect is not limited to the F1 or F2 generations. Non-Mendelian transgenerational inheritance of traits in response to environmental stimuli has been confirmed in non-mammalian organisms including plants and worms and are shown to be epigenetically mediated. However, transgenerational inheritance beyond the F2 generation remains controversial in mammals. Our lab previously discovered that the treatment of rodents (rats and mice) with folic acid significantly enhances the regeneration of injured axons following spinal cord injury in vivo and in vitro, and the effect is mediated by DNA methylation. The potential heritability of DNA methylation prompted us to investigate the following question: Is the enhanced axonal regeneration phenotype inherited transgenerationally without exposure to folic acid supplementation in the intervening generations? In the present review, we condense our findings showing that a beneficial trait (i.e., enhanced axonal regeneration after spinal cord injury) and accompanying molecular alterations (i.e., DNA methylation), triggered by an environmental exposure (i.e., folic acid supplementation) to F0 animals only, are inherited transgenerationally and beyond the F3 generation.
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Affiliation(s)
- Andy Madrid
- Department of Neurological Surgery, University of Wisconsin—Madison, Madison, WI 53719, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin—Madison, Madison, WI 53719, USA
| | - Elias Rizk
- Department of Neurosurgery, Penn State Children’s Hospital, Hershey, PA 17033, USA
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin—Madison, Madison, WI 53719, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin—Madison, Madison, WI 53719, USA
- Wisconsin Alzheimer’s Institute, University of Wisconsin—Madison, Madison, WI 53719, USA
| | - Bermans J Iskandar
- Department of Neurological Surgery, University of Wisconsin—Madison, Madison, WI 53719, USA
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Balnis J, Madrid A, Hogan KJ, Drake LA, Adhikari A, Vancavage R, Singer HA, Alisch RS, Jaitovich A. Persistent blood DNA methylation changes one year after SARS-CoV-2 infection. Clin Epigenetics 2022; 14:94. [PMID: 35871090 PMCID: PMC9308917 DOI: 10.1186/s13148-022-01313-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/11/2022] [Indexed: 11/29/2022] Open
Abstract
We recently reported the COVID-19-induced circulating leukocytes DNA methylation profile. Here, we hypothesized that some of these genes would persist differentially methylated after disease resolution. Fifteen participants previously hospitalized for SARS-CoV-2 infection were epityped one year after discharge. Of the 1505 acute illness-induced differentially methylated regions (DMRs) previously identified, we found 71 regions with persisted differentially methylated, with an average of 7 serial CpG positions per DMR. Sixty-four DMRs persisted hypermethylated, and 7 DMR persisted hypomethylated. These data are the first reported evidence that DNA methylation changes in circulating leukocytes endure long after recovery from acute illness.
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Affiliation(s)
- Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA.,Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC91, Albany, New York, 12208, USA
| | - Andy Madrid
- Department of Neurological Surgery, Albany Medical College, Madison, Wisconsin, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lisa A Drake
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA
| | - Anish Adhikari
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA.,Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC91, Albany, New York, 12208, USA
| | - Rachel Vancavage
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA.,Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC91, Albany, New York, 12208, USA
| | - Harold A Singer
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA
| | - Reid S Alisch
- Department of Neurological Surgery, Albany Medical College, Madison, Wisconsin, USA
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA. .,Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC91, Albany, New York, 12208, USA.
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Papale LA, Madrid A, Zhang Q, Chen K, Sak L, Keleş S, Alisch RS. Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders. Genome Res 2022; 32:266-279. [PMID: 34949667 PMCID: PMC8805724 DOI: 10.1101/gr.276137.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/22/2021] [Indexed: 11/25/2022]
Abstract
Mouse knockouts of Cntnap2 show altered neurodevelopmental behavior, deficits in striatal GABAergic signaling, and a genome-wide disruption of an environmentally sensitive DNA methylation modification (5-hydroxymethylcytosine [5hmC]) in the orthologs of a significant number of genes implicated in human neurodevelopmental disorders. We tested adult Cntnap2 heterozygous mice (Cntnap2 +/-; lacking behavioral or neuropathological abnormalities) subjected to a prenatal stress and found that prenatally stressed Cntnap2 +/- female mice show repetitive behaviors and altered sociability, similar to the homozygote phenotype. Genomic profiling revealed disruptions in hippocampal and striatal 5hmC levels that are correlated to altered transcript levels of genes linked to these phenotypes (e.g., Reln, Dst, Trio, and Epha5). Chromatin immunoprecipitation coupled with high-throughput sequencing and hippocampal nuclear lysate pull-down data indicated that 5hmC abundance alters the binding of the transcription factor CLOCK near the promoters of these genes (e.g., Palld, Gigyf1, and Fry), providing a mechanistic role for 5hmC in gene regulation. Together, these data support gene-by-environment hypotheses for the origins of mental illness and provide a means to identify the elusive factors contributing to complex human diseases.
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Affiliation(s)
- Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
- Neuroscience Training Program, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Qi Zhang
- Department Mathematics and Statistics, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Kailei Chen
- Department of Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Lara Sak
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Sündüz Keleş
- Department of Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
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11
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Plante DT, Papale LA, Madrid A, Cook JD, Prairie ML, Alisch RS. PAX8/PAX8-AS1 DNA methylation levels are associated with objective sleep duration in persons with unexplained hypersomnolence using a deep phenotyping approach. Sleep 2021; 44:6305146. [PMID: 34145460 DOI: 10.1093/sleep/zsab108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
STUDY OBJECTIVES Patients with unexplained hypersomnolence have significant impairment related to daytime sleepiness and excessive sleep duration, the biological bases of which are poorly understood. This investigation sought to examine relationships between objectively measured hypersomnolence phenotypes and epigenetic modification of candidate hypersomnolence genes to advance this line of inquiry. METHODS Twenty-eight unmedicated clinical patients with unexplained hypersomnolence were evaluated using overnight ad libitum polysomnography, multiple sleep latency testing, infrared pupillometry, and the psychomotor vigilance task. DNA methylation levels on CpG sites annotated to 11 a priori hypersomnolence candidate genes were assessed for statistical association with hypersomnolence measures using independent regression models with adjusted local index of significance (aLIS) P-value threshold of 0.05. RESULTS Nine CpG sites exhibited significant associations between DNA methylation levels and total sleep time measured using ad libitum polysomnography (aLIS p-value < .05). All nine differentially methylated CpG sites were annotated to the paired box 8 (PAX8) gene and its related antisense gene (PAX8-AS1). Among these nine differentially methylated positions was a cluster of five CpG sites located in the body of the PAX8 gene and promoter of PAX8-AS1. CONCLUSIONS This study demonstrates that PAX8/PAX8-AS1 DNA methylation levels are associated with total sleep time in persons with unexplained hypersomnolence. Given prior investigations that have implicated single nucleotide polymorphisms in PAX8/PAX8-AS1 with habitual sleep duration, further research that clarifies the role of DNA methylation levels on these genes in the phenotypic expression of total sleep time is warranted.
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Affiliation(s)
| | | | - Andy Madrid
- Department of Neurological Surgery, Madison, WI.,Neuroscience Training Program, University of Wisconsin - Madison, Madison, WI
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12
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Dean DC, Madrid A, Planalp EM, Moody JF, Papale LA, Knobel KM, Wood EK, McAdams RM, Coe CL, Hill Goldsmith H, Davidson RJ, Alisch RS, Kling PJ. Cord blood DNA methylation modifications in infants are associated with white matter microstructure in the context of prenatal maternal depression and anxiety. Sci Rep 2021; 11:12181. [PMID: 34108589 PMCID: PMC8190282 DOI: 10.1038/s41598-021-91642-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/17/2021] [Indexed: 12/12/2022] Open
Abstract
Maternal and environmental factors influence brain networks and architecture via both physiological pathways and epigenetic modifications. In particular, prenatal maternal depression and anxiety symptoms appear to impact infant white matter (WM) microstructure, leading us to investigate whether epigenetic modifications (i.e., DNA methylation) contribute to these WM differences. To determine if infants of women with depression and anxiety symptoms exhibit epigenetic modifications linked to neurodevelopmental changes, 52 umbilical cord bloods (CBs) were profiled. We observed 219 differentially methylated genomic positions (DMPs; FDR p < 0.05) in CB that were associated with magnetic resonance imaging measures of WM microstructure at 1 month of age and in regions previously described to be related to maternal depression and anxiety symptoms. Genomic characterization of these associated DMPs revealed 143 unique genes with significant relationships to processes involved in neurodevelopment, GTPase activity, or the canonical Wnt signaling pathway. Separate regression models for female (n = 24) and male (n = 28) infants found 142 associated DMPs in females and 116 associated DMPs in males (nominal p value < 0.001, R > 0.5), which were annotated to 98 and 81 genes, respectively. Together, these findings suggest that umbilical CB DNA methylation levels at birth are associated with 1-month WM microstructure.
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Affiliation(s)
- Douglas C Dean
- Department of Pediatrics, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, USA.,Department of Medical Physics, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Waisman Center, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Andy Madrid
- Department of Neurosurgery, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth M Planalp
- Waisman Center, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Psychology, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason F Moody
- Department of Medical Physics, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ligia A Papale
- Department of Neurosurgery, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Karla M Knobel
- Waisman Center, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth K Wood
- Harlow Center for Biological Psychology, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan M McAdams
- Department of Pediatrics, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, USA
| | - Christopher L Coe
- Waisman Center, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Psychology, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Harlow Center for Biological Psychology, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - H Hill Goldsmith
- Waisman Center, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Psychology, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Richard J Davidson
- Waisman Center, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Psychology, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Center for Healthy Minds, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Psychiatry, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Reid S Alisch
- Department of Neurosurgery, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, WI, USA.
| | - Pamela J Kling
- Department of Pediatrics, School of Medicine & Public Health, University of Wisconsin-Madison, Madison, USA
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13
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Balnis J, Madrid A, Hogan KJ, Drake LA, Chieng HC, Tiwari A, Vincent CE, Chopra A, Vincent PA, Robek MD, Singer HA, Alisch RS, Jaitovich A. Blood DNA methylation and COVID-19 outcomes. Clin Epigenetics 2021; 13:118. [PMID: 34034806 PMCID: PMC8148415 DOI: 10.1186/s13148-021-01102-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/11/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There are no prior reports that compare differentially methylated regions of DNA in blood samples from COVID-19 patients to samples collected before the SARS-CoV-2 pandemic using a shared epigenotyping platform. We performed a genome-wide analysis of circulating blood DNA CpG methylation using the Infinium Human MethylationEPIC BeadChip on 124 blood samples from hospitalized COVID-19-positive and COVID-19-negative patients and compared these data with previously reported data from 39 healthy individuals collected before the pandemic. Prospective outcome measures such as COVID-19-GRAM risk-score and mortality were combined with methylation data. RESULTS Global mean methylation levels did not differ between COVID-19 patients and healthy pre-pandemic controls. About 75% of acute illness-associated differentially methylated regions were located near gene promoter regions and were hypo-methylated in comparison with healthy pre-pandemic controls. Gene ontology analyses revealed terms associated with the immune response to viral infections and leukocyte activation; and disease ontology analyses revealed a predominance of autoimmune disorders. Among COVID-19-positive patients, worse outcomes were associated with a prevailing hyper-methylated status. Recursive feature elimination identified 77 differentially methylated positions predictive of COVID-19 severity measured by the GRAM-risk score. CONCLUSION Our data contribute to the awareness that DNA methylation may influence the expression of genes that regulate COVID-19 progression and represent a targetable process in that setting.
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Affiliation(s)
- Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin, Madison, WI, USA
| | - Lisa A Drake
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Hau C Chieng
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Anupama Tiwari
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Catherine E Vincent
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Amit Chopra
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Peter A Vincent
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Michael D Robek
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Harold A Singer
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA.
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA.
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA.
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14
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Ensink JBM, Keding TJ, Henneman P, Venema A, Papale LA, Alisch RS, Westerman Y, van Wingen G, Zantvoord J, Middeldorp CM, Mannens MMAM, Herringa RJ, Lindauer RJL. Differential DNA Methylation Is Associated With Hippocampal Abnormalities in Pediatric Posttraumatic Stress Disorder. Biol Psychiatry Cogn Neurosci Neuroimaging 2021; 6:1063-1070. [PMID: 33964519 DOI: 10.1016/j.bpsc.2021.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/01/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Recent findings in neuroimaging and epigenetics offer important insights into brain structures and biological pathways of altered gene expression associated with posttraumatic stress disorder (PTSD). However, it is unknown to what extent epigenetic mechanisms are associated with PTSD and its neurobiology in youth. METHODS In this study, we combined a methylome-wide association study and structural neuroimaging measures in a Dutch cohort of youths with PTSD (8-18 years of age). We aimed to replicate findings in a similar independent U.S. cohort. RESULTS We found significant methylome-wide associations for pediatric PTSD (false discovery rate p < .05) compared with non-PTSD control groups (traumatized and nontraumatized youths). Methylation differences on nine genes were replicated, including genes related to glucocorticoid functioning. In both cohorts, methylation on OLFM3 gene was further associated with anterior hippocampal volume. CONCLUSIONS These findings point to molecular pathways involved in inflammation, stress response, and neuroplasticity as potential contributors to neural abnormalities and provide potentially unique biomarkers and treatment targets for pediatric PTSD.
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Affiliation(s)
- Judith B M Ensink
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Department of Child and Adolescent Psychiatry, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Academic Centre for Child and Adolescent Psychiatry, De Bascule, Amsterdam, the Netherlands; Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Taylor J Keding
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin
| | - Peter Henneman
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Andrea Venema
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Ligia A Papale
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Yousha Westerman
- Academic Centre for Child and Adolescent Psychiatry, De Bascule, Amsterdam, the Netherlands
| | - Guido van Wingen
- Department of Psychiatry, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands
| | - Jasper Zantvoord
- Department of Psychiatry, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands
| | - Christel M Middeldorp
- Children's Health Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Marcel M A M Mannens
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Ryan J Herringa
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin.
| | - Ramon J L Lindauer
- Department of Child and Adolescent Psychiatry, Amsterdam University Medical Center, location AMC, Amsterdam, the Netherlands; Academic Centre for Child and Adolescent Psychiatry, De Bascule, Amsterdam, the Netherlands
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15
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Alberca CD, Papale LA, Madrid A, Gianatiempo O, Cánepa ET, Alisch RS, Chertoff M. Perinatal protein malnutrition results in genome-wide disruptions of 5-hydroxymethylcytosine at regions that can be restored to control levels by an enriched environment. Epigenetics 2020; 16:1085-1101. [PMID: 33172347 DOI: 10.1080/15592294.2020.1841871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Maternal malnutrition remains one of the major adversities affecting brain development and long-term mental health outcomes, increasing the risk to develop anxiety and depressive disorders. We have previously shown that malnutrition-induced anxiety-like behaviours can be rescued by a social and sensory stimulation (enriched environment) in male mice. Here, we expand these findings to adult female mice and profiled genome-wide ventral hippocampal 5hmC levels related to malnutrition-induced anxiety-like behaviours and their rescue by an enriched environment. This approach revealed 508 differentially hydroxymethylated genes associated with protein malnutrition and that several genes (N = 34) exhibited a restored 5hmC abundance to control levels following exposure to an enriched environment, including genes involved in neuronal functions like dendrite outgrowth, axon guidance, and maintenance of neuronal circuits (e.g. Fltr3, Itsn1, Lman1, Lsamp, Nav, and Ror1) and epigenetic mechanisms (e.g. Hdac9 and Dicer1). Sequence motif predictions indicated that 5hmC may be modulating the binding of transcription factors for several of these transcripts, suggesting a regulatory role for 5hmC in response to perinatal malnutrition and exposure to an enriched environment. Together, these findings establish a role for 5hmC in early-life malnutrition and reveal genes linked to malnutrition-induced anxious behaviours that are mitigated by an enriched environment.
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Affiliation(s)
- Carolina D Alberca
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Neuroepigenetica, Buenos Aires, Argentina
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA.,Neuroscience Training Program, University of Wisconsin, Madison, WI, USA
| | - Octavio Gianatiempo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Neuroepigenetica, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales - CONICET (IQUIBICEN), Buenos Aires, Argentina
| | - Eduardo T Cánepa
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Neuroepigenetica, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales - CONICET (IQUIBICEN), Buenos Aires, Argentina
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Mariela Chertoff
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Neuroepigenetica, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales - CONICET (IQUIBICEN), Buenos Aires, Argentina
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16
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Madrid A, Borth LE, Hogan KJ, Hariharan N, Papale LA, Alisch RS, Iskandar BJ. DNA methylation and hydroxymethylation have distinct genome-wide profiles related to axonal regeneration. Epigenetics 2020; 16:64-78. [PMID: 32633672 DOI: 10.1080/15592294.2020.1786320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Alterations in environmentally sensitive epigenetic mechanisms (e.g., DNA methylation) influence axonal regeneration in the spinal cord following sharp injury. Conventional DNA methylation detection methods using sodium bisulphite treatment do not distinguish between methylated and hydroxymethylated forms of cytosine, meaning that past studies report a composite of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). To identify the distinct contributions of DNA methylation modifications to axonal regeneration, we collected spinal cord tissue after sharp injury from untreated adult F3 male rats with enhanced regeneration of injured spinal axons or controls, derived from folate- or water-treated F0 lineages, respectively. Genomic DNA was profiled for genome-wide 5hmC levels, revealing 658 differentially hydroxymethylated regions (DhMRs). Genomic profiling with whole genome bisulphite sequencing disclosed regeneration-related alterations in composite 5mC + 5hmC DNA methylation levels at 2,260 differentially methylated regions (DMRs). While pathway analyses revealed that differentially hydroxymethylated and methylated genes are linked to biologically relevant axon developmental pathways, only 22 genes harbour both DhMR and DMRs. Since these differential modifications were more than 60 kilobases on average away from each other, the large majority of differential hydroxymethylated and methylated regions are unique with distinct functions in the axonal regeneration phenotype. These data highlight the importance of distinguishing independent contributions of 5mC and 5hmC levels in the central nervous system, and denote discrete roles for DNA methylation modifications in spinal cord injury and regeneration in the context of transgenerational inheritance.
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Affiliation(s)
- Andy Madrid
- Department of Neurological Surgery, University of Wisconsin - Madison , Madison, WI, USA.,Neuroscience Training Program, University of Wisconsin - Madison , Madison, WI, USA
| | - Laura E Borth
- Department of Neurological Surgery, University of Wisconsin - Madison , Madison, WI, USA.,Interdepartmental Graduate Program in Nutritional Science, University of Wisconsin - Madison , Madison, WI, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin - Madison , Madison, WI, USA
| | - Nithya Hariharan
- Department of Neurological Surgery, University of Wisconsin - Madison , Madison, WI, USA
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin - Madison , Madison, WI, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin - Madison , Madison, WI, USA
| | - Bermans J Iskandar
- Department of Neurological Surgery, University of Wisconsin - Madison , Madison, WI, USA
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17
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Westmark CJ, Maloney B, Alisch RS, Sokol DK, Lahiri DK. FMRP Regulates the Nuclear Export of Adam9 and Psen1 mRNAs: Secondary Analysis of an N 6-Methyladenosine Dataset. Sci Rep 2020; 10:10781. [PMID: 32612155 PMCID: PMC7329887 DOI: 10.1038/s41598-020-66394-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/19/2020] [Indexed: 01/19/2023] Open
Abstract
Fragile X mental retardation protein (FMRP) binds to and regulates the translation of amyloid-β protein precursor (App) mRNA, but the detailed mechanism remains to be determined. Differential methylation of App mRNA could underlie FMRP binding, message localization and translation efficiency. We sought to determine the role of FMRP and N6-methyladeonsine (m6A) on nuclear export of App mRNA. We utilized the m6A dataset by Hsu and colleagues to identify m6A sites in App mRNA and to determine if the abundance of message in the cytoplasm relative to the nucleus is altered in Fmr1 knockout mouse brain cortex. Given that processing of APP to Aβ and soluble APP alpha (sAPPα) contributes to disease phenotypes, we also investigated whether Fmr1KO associates with nuclear export of the mRNAs for APP protein processing enzymes, including β-site amyloid cleaving enzyme (Bace1), A disintegrin and metalloproteinases (Adams), and presenilins (Psen). Fmr1KO did not alter the nuclear/cytoplasmic abundance of App mRNA. Of 36 validated FMRP targets, 35 messages contained m6A peaks but only Agap2 mRNA was selectively enriched in Fmr1KO nucleus. The abundance of the APP processing enzymes Adam9 and Psen1 mRNA, which code for a minor alpha-secretase and gamma-secretase, respectively, were selectively enriched in wild type cytoplasm.
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Affiliation(s)
- Cara J Westmark
- Department of Neurology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Bryan Maloney
- Department of Psychiatry, Indiana Alzheimer Disease Center, Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA
| | - Deborah K Sokol
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Debomoy K Lahiri
- Department of Psychiatry, Indiana Alzheimer Disease Center, Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
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18
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Madrid A, Hogan KJ, Papale LA, Clark LR, Asthana S, Johnson SC, Alisch RS. DNA Hypomethylation in Blood Links B3GALT4 and ZADH2 to Alzheimer's Disease. J Alzheimers Dis 2019; 66:927-934. [PMID: 30372681 DOI: 10.3233/jad-180592] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Differentially methylated positions (DMPs) between persons with and without late-onset Alzheimer's disease (LOAD) were observed at 477 of 769,190 loci in a plurality of genes. Of these, 17 were shared with DMPs identified using clinical LOAD markers analyzed independently as continuous variables comprising Rey Auditory Verbal Learning Test scores, cerebrospinal fluid total tau (t-tau) and phosphorylated tau 181 (p-tau181) levels, and t-tau/Aβ1-42 (Aβ42), p-tau181/Aβ42, and Aβ42/Aβ1-40 (Aβ40) ratios. In patients with LOAD, 12 of the shared 17 DMPs were hypomethylated in B3GALT4 (Beta-1,3-galatcosyltransferase 4) (EC 2.4.1.62), and 5 were hypomethylated in ZADH2 (Prostaglandin reductase 3) (EC 1.3.1.48).
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Affiliation(s)
- Andy Madrid
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Neuroscience Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ligia A Papale
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lindsay R Clark
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Sanjay Asthana
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Sterling C Johnson
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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19
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Abstract
Mapping patterns of DNA methylation throughout the epigenome are critical to our understanding of several important biological and regulatory functions, such as transcriptional regulation, genomic imprinting, and embryonic development. The development and rapid advancement of next-generation sequencing (NGS) technologies have provided clinicians and researchers with accurate and reliable read-outs of genomic and epigenomic information at the nucleotide level. Such improvements have significantly lowered the cost required for genome-wide sequencing, facilitating the vast acquisition of data that has led to many improvements in patient care. However, the torrid rate of NGS data generation has left targeted validation approaches behind, including the confirmation of epigenetic marks such as DNA methylation. To overcome these shortcomings, we present a rapid and robust protocol for the parallel examination of multiple methylated sequences that we have termed simultaneous targeted methylation sequencing (sTM-Seq). Key features of this technique include the elimination of the need for large amounts of high-molecular weight DNA and the nucleotide specific distinction of both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Moreover, sTM-Seq is scalable and can be used to investigate multiple loci in dozens of samples within a single sequencing run. By utilizing freely available web-based software and universal primers for multipurpose barcoding, library preparation, and customized sequencing, sTM-Seq is affordable, efficient, and widely applicable. Together, these features enable sTM-Seq to have wide-reaching clinical applications that will greatly improve turnaround rates for same-day procedures and allow clinicians to collect high-resolution data that can be used in a variety of patient settings. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Natalie Asmus
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin.,Neuroscience Training Program, University of Wisconsin, Madison, Wisconsin
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin.,Neuroscience Training Program, University of Wisconsin, Madison, Wisconsin
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20
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Abstract
Environmentally sensitive molecular mechanisms in the brain, such as DNA methylation, have become a significant focus of neuroscience research because of mounting evidence indicating that they are critical in response to social situations, stress, threats, and behavior. The recent identification of 5-hydroxymethylcytosine (5hmC), which is enriched in the brain (tenfold over peripheral tissues), raises new questions as to the role of this base in mediating epigenetic effects in the brain. The development of genome-wide methods capable of distinguishing 5-methylcytosine (5mC) from 5hmC has revealed that a growing number of behaviors are linked to independent disruptions of 5mC and 5hmC levels, further emphasizing the unique importance of both of these modifications in the brain. Here, we review the recent links that indicate DNA methylation (both 5mC and 5hmC) is highly dynamic and that perturbations in this modification may contribute to behaviors related to psychiatric disorders and hold clinical relevance.
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Affiliation(s)
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA. .,Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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21
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Andrews SV, Sheppard B, Windham GC, Schieve LA, Schendel DE, Croen LA, Chopra P, Alisch RS, Newschaffer CJ, Warren ST, Feinberg AP, Fallin MD, Ladd-Acosta C. Case-control meta-analysis of blood DNA methylation and autism spectrum disorder. Mol Autism 2018; 9:40. [PMID: 29988321 PMCID: PMC6022498 DOI: 10.1186/s13229-018-0224-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/21/2018] [Indexed: 11/10/2022] Open
Abstract
Background Several reports have suggested a role for epigenetic mechanisms in ASD etiology. Epigenome-wide association studies (EWAS) in autism spectrum disorder (ASD) may shed light on particular biological mechanisms. However, studies of ASD cases versus controls have been limited by post-mortem timing and severely small sample sizes. Reports from in-life sampling of blood or saliva have also been very limited in sample size and/or genomic coverage. We present the largest case-control EWAS for ASD to date, combining data from population-based case-control and case-sibling pair studies. Methods DNA from 968 blood samples from children in the Study to Explore Early Development (SEED 1) was used to generate epigenome-wide array DNA methylation (DNAm) data at 485,512 CpG sites for 453 cases and 515 controls, using the Illumina 450K Beadchip. The Simons Simplex Collection (SSC) provided 450K array DNAm data on an additional 343 cases and their unaffected siblings. We performed EWAS meta-analysis across results from the two data sets, with adjustment for sex and surrogate variables that reflect major sources of biological variation and technical confounding such as cell type, batch, and ancestry. We compared top EWAS results to those from a previous brain-based analysis. We also tested for enrichment of ASD EWAS CpGs for being targets of meQTL associations using available SNP genotype data in the SEED sample. Findings In this meta-analysis of blood-based DNA from 796 cases and 858 controls, no single CpG met a Bonferroni discovery threshold of p < 1.12 × 10− 7. Seven CpGs showed differences at p < 1 × 10− 5 and 48 at 1 × 10− 4. Of the top 7, 5 showed brain-based ASD associations as well, often with larger effect sizes, and the top 48 overall showed modest concordance (r = 0.31) in direction of effect with cerebellum samples. Finally, we observed suggestive evidence for enrichment of CpG sites controlled by SNPs (meQTL targets) among the EWAS CpG hits, which was consistent across EWAS and meQTL discovery p value thresholds. Conclusions No single CpG site showed a large enough DNAm difference between cases and controls to achieve epigenome-wide significance in this sample size. However, our results suggest the potential to observe disease associations from blood-based samples. Among the seven sites achieving suggestive statistical significance, we observed consistent, and stronger, effects at the same sites among brain samples. Discovery-oriented EWAS for ASD using blood samples will likely need even larger samples and unified genetic data to further understand DNAm differences in ASD. Electronic supplementary material The online version of this article (10.1186/s13229-018-0224-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shan V Andrews
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Brooke Sheppard
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Gayle C Windham
- 3California Department of Public Health, Environmental Health Investigations Branch, 850 Marina Bay Parkway, Richmond, CA 94804 USA
| | - Laura A Schieve
- 4National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, MS E-86, 1600 Clifton Road, Atlanta, GA 30333 USA
| | - Diana E Schendel
- 5Deparment of Public Health, Section of Epidemiology, Aarhus University, Aarhus, Denmark.,6Department of Economics and Business, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,7Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Lisa A Croen
- 8Kaiser Permanente Division of Research, 2000 Broadway, Oakland, CA 94612 USA
| | - Pankaj Chopra
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Reid S Alisch
- 10Department of Psychiatry, University of Wisconsin-Madison, 6001 Research Park Blvd, Madison, WI 53719 USA
| | - Craig J Newschaffer
- 11Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA 19104 USA.,A.J. Drexel Autism Institute, 3020 Market Street Suite 560, Philadelphia, PA 19104 USA
| | - Stephen T Warren
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,13Department of Biochemistry, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,14Department of Pediatrics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Andrew P Feinberg
- 15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,16Department of Medicine, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA
| | - M Daniele Fallin
- 2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA.,15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,17Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH850, Baltimore, MD 21205 USA
| | - Christine Ladd-Acosta
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
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22
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Madrid A, Chopra P, Alisch RS. Species-Specific 5 mC and 5 hmC Genomic Landscapes Indicate Epigenetic Contribution to Human Brain Evolution. Front Mol Neurosci 2018; 11:39. [PMID: 29491831 PMCID: PMC5817089 DOI: 10.3389/fnmol.2018.00039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/29/2018] [Indexed: 12/01/2022] Open
Abstract
Human evolution from non-human primates has seen substantial change in the central nervous system, with the molecular mechanisms underlying human brain evolution remaining largely unknown. Methylation of cytosine at the fifth carbon (5-methylcytosine; 5 mC) is an essential epigenetic mark linked to neurodevelopment, as well as neurological disease. The emergence of another modified form of cytosine (5-hydroxymethylcytosine; 5 hmC) that is enriched in the brain further substantiates a role for these epigenetic marks in neurodevelopment, yet little is known about the evolutionary importance of these marks in brain development. Here, human and monkey brain tissue were profiled, identifying 5,516 and 4,070 loci that were differentially methylated and hydroxymethylated, respectively, between the species. Annotation of these loci to the human genome revealed genes critical for the development of the nervous system and that are associated with intelligence and higher cognitive functioning, such as RELN and GNAS. Moreover, ontological analyses of these differentially methylated and hydroxymethylated genes revealed a significant enrichment of neuronal/immunological-related processes, including neurogenesis and axon development. Finally, the sequences flanking the differentially methylated/hydroxymethylated loci contained a significant enrichment of binding sites for neurodevelopmentally important transcription factors (e.g., OTX1 and PITX1), suggesting that DNA methylation may regulate gene expression by mediating transcription factor binding on these transcripts. Together, these data support dynamic species-specific epigenetic contributions in the evolution and development of the human brain from non-human primates.
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Affiliation(s)
- Andy Madrid
- Department of Psychiatry, University of Wisconsin–Madison, Madison, WI, United States
- Neuroscience Training Program, University of Wisconsin–Madison, Madison, WI, United States
| | - Pankaj Chopra
- Department Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Reid S. Alisch
- Department of Psychiatry, University of Wisconsin–Madison, Madison, WI, United States
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23
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Alisch RS, Van Hulle C, Chopra P, Bhattacharyya A, Zhang SC, Davidson RJ, Kalin NH, Goldsmith HH. A multi-dimensional characterization of anxiety in monozygotic twin pairs reveals susceptibility loci in humans. Transl Psychiatry 2017; 7:1282. [PMID: 29225348 PMCID: PMC5802687 DOI: 10.1038/s41398-017-0047-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023] Open
Abstract
The etiology of individual differences in human anxiousness is complex and includes contributions from genetic, epigenetic (i.e., DNA methylation) and environmental factors. Past genomic approaches have been limited in their ability to detect human anxiety-related differences in these factors. To overcome these limitations, we employed both a multi-dimensional characterization method, to select monozygotic twin pairs discordant for anxiety, and whole genome DNA methylation sequencing. This approach revealed 230 anxiety-related differentially methylated loci that were annotated to 183 genes, including several known stress-related genes such as NAV1, IGF2, GNAS, and CRTC1. As an initial validation of these findings, we tested the significance of an overlap of these data with anxiety-related differentially methylated loci that we previously reported from a key neural circuit of anxiety (i.e., the central nucleus of the amygdala) in young monkeys and found a significant overlap (P-value < 0.05) of anxiety-related differentially methylated genes, including GNAS, SYN3, and JAG2. Finally, sequence motif predictions of all the human differentially methylated regions indicated an enrichment of five transcription factor binding motifs, suggesting that DNA methylation may regulate gene expression by mediating transcription factor binding of these transcripts. Together, these data demonstrate environmentally sensitive factors that may underlie the development of human anxiety.
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Affiliation(s)
- Reid S. Alisch
- 0000 0001 0701 8607grid.28803.31Departments of Psychiatry, University of Wisconsin, Madison, WI USA ,0000 0001 2167 3675grid.14003.36Neuroscience Training Program, University of Wisconsin, Madison, WI USA
| | - Carol Van Hulle
- 0000 0001 2167 3675grid.14003.36Waisman Center, University of Wisconsin, Madison, WI USA
| | - Pankaj Chopra
- 0000 0001 0941 6502grid.189967.8Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Anita Bhattacharyya
- 0000 0001 2167 3675grid.14003.36Waisman Center, University of Wisconsin, Madison, WI USA
| | - Su-Chun Zhang
- 0000 0001 2167 3675grid.14003.36Neuroscience Training Program, University of Wisconsin, Madison, WI USA ,0000 0001 2167 3675grid.14003.36Waisman Center, University of Wisconsin, Madison, WI USA ,0000 0001 0701 8607grid.28803.31Departments of Neuroscience, University of Wisconsin, Madison, WI USA ,0000 0001 0701 8607grid.28803.31Departments of Neurology, University of Wisconsin, Madison, WI USA
| | - Richard J. Davidson
- 0000 0001 0701 8607grid.28803.31Departments of Psychiatry, University of Wisconsin, Madison, WI USA ,0000 0001 2167 3675grid.14003.36Neuroscience Training Program, University of Wisconsin, Madison, WI USA ,0000 0001 2167 3675grid.14003.36Waisman Center, University of Wisconsin, Madison, WI USA ,0000 0001 0701 8607grid.28803.31Departments of Psychology, University of Wisconsin, Madison, WI USA ,Center for Healthy Minds, Madison, WI USA
| | - Ned H. Kalin
- 0000 0001 0701 8607grid.28803.31Departments of Psychiatry, University of Wisconsin, Madison, WI USA ,0000 0001 2167 3675grid.14003.36Neuroscience Training Program, University of Wisconsin, Madison, WI USA
| | - H. Hill Goldsmith
- 0000 0001 2167 3675grid.14003.36Waisman Center, University of Wisconsin, Madison, WI USA ,0000 0001 0701 8607grid.28803.31Departments of Psychology, University of Wisconsin, Madison, WI USA
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Abstract
Environmental stress contributes to the development of psychiatric disorders, including posttraumatic stress disorder and anxiety. While even acute stress alters gene expression, the molecular mechanisms underlying these changes remain largely unknown. 5-hydroxymethylcytosine (5hmC) is a novel environmentally sensitive DNA modification that is highly enriched in the brain and is associated with active transcription of neuronal genes. Here we examined behavioral and molecular alterations in adult mice that experienced an early-life stress before weaning (postnatal day 12 to 18) and found anxiety-like behaviors in adult female mice that were accompanied by correlated disruptions of hypothalamic 5hmC and gene expression in 118 genes, revealing potentially functional 5hmC (i.e., gene regulation). These genes are known and potentially novel stress-related targets, including Nr3c2, Nrxn1, Nfia, and Clip1, that have a significant enrichment for neuronal ontological functions, such as neuronal development and differentiation. Sequence motif predictions indicated that 5hmC may regulate gene expression by mediating transcription factor binding and alternative splicing of many of these transcripts. Together, these findings represent a critical step toward understanding the effects of early environment on the neuromolecular mechanisms that underlie the risk to develop anxiety disorders.
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Affiliation(s)
- Ligia A Papale
- a Department of Psychiatry , University of Wisconsin , Madison , WI , USA
| | - Andy Madrid
- a Department of Psychiatry , University of Wisconsin , Madison , WI , USA.,b Neuroscience Training Program , University of Wisconsin , Madison , WI , USA
| | - Sisi Li
- a Department of Psychiatry , University of Wisconsin , Madison , WI , USA.,b Neuroscience Training Program , University of Wisconsin , Madison , WI , USA
| | - Reid S Alisch
- a Department of Psychiatry , University of Wisconsin , Madison , WI , USA
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25
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Papale LA, Li S, Madrid A, Zhang Q, Chen L, Chopra P, Jin P, Keleş S, Alisch RS. Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress. Neurobiol Dis 2016; 96:54-66. [PMID: 27576189 DOI: 10.1016/j.nbd.2016.08.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 01/18/2023] Open
Abstract
Environmental stress is among the most important contributors to increased susceptibility to develop psychiatric disorders. While it is well known that acute environmental stress alters gene expression, the molecular mechanisms underlying these changes remain largely unknown. 5-hydroxymethylcytosine (5hmC) is a novel environmentally sensitive epigenetic modification that is highly enriched in neurons and is associated with active neuronal transcription. Recently, we reported a genome-wide disruption of hippocampal 5hmC in male mice following acute stress that was correlated to altered transcript levels of genes in known stress related pathways. Since sex-specific endocrine mechanisms respond to environmental stimulus by altering the neuronal epigenome, we examined the genome-wide profile of hippocampal 5hmC in female mice following exposure to acute stress and identified 363 differentially hydroxymethylated regions (DhMRs) linked to known (e.g., Nr3c1 and Ntrk2) and potentially novel genes associated with stress response and psychiatric disorders. Integration of hippocampal expression data from the same female mice found stress-related hydroxymethylation correlated to altered transcript levels. Finally, characterization of stress-induced sex-specific 5hmC profiles in the hippocampus revealed 778 sex-specific acute stress-induced DhMRs some of which were correlated to altered transcript levels that produce sex-specific isoforms in response to stress. Together, the alterations in 5hmC presented here provide a possible molecular mechanism for the adaptive sex-specific response to stress that may augment the design of novel therapeutic agents that will have optimal effectiveness in each sex.
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Affiliation(s)
- Ligia A Papale
- Department of Psychiatry, University of Wisconsin, Madison, WI, USA
| | - Sisi Li
- Department of Psychiatry, University of Wisconsin, Madison, WI, USA; Neuroscience Training Program, University of Wisconsin, Madison, WI, USA
| | - Andy Madrid
- Department of Psychiatry, University of Wisconsin, Madison, WI, USA; Neuroscience Training Program, University of Wisconsin, Madison, WI, USA
| | - Qi Zhang
- Department of Statistics, University of Nebraska, Lincoln, NE, USA
| | - Li Chen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sündüz Keleş
- Department of Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin, Madison, WI, USA.
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26
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Abstract
Historically biomedical research has examined genetic influences on mental health but these approaches have been limited, likely due to the broad heritability of brain-related disorders (e.g., 30–90%). Epigenetic modifications, such as DNA methylation, are environmentally sensitive mechanisms that may play a role in the origins and progression of mental illness. Recently, genome-wide disruptions of 5-hydroxymethylcytosine (5hmC) were associated with the development of early and late onset mental illnesses such as autism and Alzheimer’s disease, bringing new hope to the field of psychiatry. Here, we review the recent links of 5hmC to mental illness and discuss several putative functions of 5hmC in the context of its promising clinical relevance.
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Affiliation(s)
- Andy Madrid
- Department of Psychiatry, University of Wisconsin, Madison, WI 53719, USA
- Neuroscience training program, University of Wisconsin, Madison, WI 53719, USA
| | - Ligia A Papale
- Department of Psychiatry, University of Wisconsin, Madison, WI 53719, USA
| | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin, Madison, WI 53719, USA
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27
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Li S, Papale LA, Zhang Q, Madrid A, Chen L, Chopra P, Keleş S, Jin P, Alisch RS. Genome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress. Neurobiol Dis 2015; 86:99-108. [PMID: 26598390 DOI: 10.1016/j.nbd.2015.11.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/11/2015] [Indexed: 12/15/2022] Open
Abstract
Environmental stress is among the most important contributors to increased susceptibility to develop psychiatric disorders, including anxiety and post-traumatic stress disorder. While even acute stress alters gene expression, the molecular mechanisms underlying these changes remain largely unknown. 5-hydroxymethylcytosine (5hmC) is a novel environmentally sensitive DNA modification that is highly enriched in post-mitotic neurons and is associated with active transcription of neuronal genes. Recently, we found a hippocampal increase of 5hmC in the glucocorticoid receptor gene (Nr3c1) following acute stress, warranting a deeper investigation of stress-related 5hmC levels. Here we used an established chemical labeling and affinity purification method coupled with high-throughput sequencing technology to generate the first genome-wide profile of hippocampal 5hmC following exposure to acute restraint stress and a one-hour recovery. This approach found a genome-wide disruption in 5hmC associated with acute stress response, primarily in genic regions, and identified known and potentially novel stress-related targets that have a significant enrichment for neuronal ontological functions. Integration of these data with hippocampal gene expression data from these same mice found stress-related hydroxymethylation correlated to altered transcript levels and sequence motif predictions indicated that 5hmC may function by mediating transcription factor binding to these transcripts. Together, these data reveal an environmental impact on this newly discovered epigenetic mark in the brain and represent a critical step toward understanding stress-related epigenetic mechanisms that alter gene expression and can lead to the development of psychiatric disorders.
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Affiliation(s)
- Sisi Li
- Department of Psychiatry University of Wisconsin, Madison, WI, USA; Neuroscience Training Program, University of Wisconsin, Madison, WI, USA
| | - Ligia A Papale
- Department of Psychiatry University of Wisconsin, Madison, WI, USA
| | - Qi Zhang
- Department Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Andy Madrid
- Department of Psychiatry University of Wisconsin, Madison, WI, USA; Endocrinology and Reproductive Physiology Training Program, University of Wisconsin, Madison, WI, USA
| | - Li Chen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sündüz Keleş
- Department Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Reid S Alisch
- Department of Psychiatry University of Wisconsin, Madison, WI, USA.
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28
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Papale LA, Zhang Q, Li S, Chen K, Keleş S, Alisch RS. Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism. Hum Mol Genet 2015; 24:7121-31. [PMID: 26423458 DOI: 10.1093/hmg/ddv411] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/28/2015] [Indexed: 01/29/2023] Open
Abstract
The autism spectrum disorders (ASD) comprise a broad group of behaviorally related neurodevelopmental disorders affecting as many as 1 in 68 children. The hallmarks of ASD consist of impaired social and communication interactions, pronounced repetitive behaviors and restricted patterns of interests. Family, twin and epidemiological studies suggest a polygenetic and epistatic susceptibility model involving the interaction of many genes; however, the etiology of ASD is likely to be complex and include both epigenetic and environmental factors. 5-hydroxymethylcytosine (5hmC) is a novel environmentally sensitive DNA modification that is highly enriched in post-mitotic neurons and is associated with active transcription of neuronal genes. Here, we used an established chemical labeling and affinity purification method coupled with high-throughput sequencing technology to generate a genome-wide profile of striatal 5hmC in an autism mouse model (Cntnap2(-/-) mice) and found that at 9 weeks of age the Cntnap2(-/-) mice have a genome-wide disruption in 5hmC, primarily in genic regions and repetitive elements. Annotation of differentially hydroxymethylated regions (DhMRs) to genes revealed a significant overlap with known ASD genes (e.g. Nrxn1 and Reln) that carried an enrichment of neuronal ontological functions, including axonogenesis and neuron projection morphogenesis. Finally, sequence motif predictions identified associations with transcription factors that have a high correlation with important genes in neuronal developmental and functional pathways. Together, our data implicate a role for 5hmC-mediated epigenetic modulation in the pathogenesis of autism and represent a critical step toward understanding the genome-wide molecular consequence of the Cntnap2 mutation, which results in an autism-like phenotype.
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Affiliation(s)
| | - Qi Zhang
- Department of Statistics, Biostatistics, and Medical Informatics and
| | - Sisi Li
- Department of Psychiatry, Neuroscience training program, University of Wisconsin, Madison, WI 53719, USA
| | - Kailei Chen
- Department of Statistics, Biostatistics, and Medical Informatics and
| | - Sündüz Keleş
- Department of Statistics, Biostatistics, and Medical Informatics and
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29
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Li S, Papale LA, Kintner DB, Sabat G, Barrett-Wilt GA, Cengiz P, Alisch RS. Hippocampal increase of 5-hmC in the glucocorticoid receptor gene following acute stress. Behav Brain Res 2015; 286:236-240. [PMID: 25746451 DOI: 10.1016/j.bbr.2015.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 11/17/2022]
Abstract
5-Hydroxymethylcytosine (5-hmC) is a novel environmentally sensitive DNA modification that is highly enriched in post-mitotic neurons and is associated with active transcription of neuronal genes. Recently, 5-hmC was functionally linked to learning and cognition and these studies revealed an accumulation of 5-hmC in the prefrontal cortex of mice undergoing fear extinction. These studies led us to hypothesize a role for 5-hmC in response to stress. To test this hypothesis, we combined immunohistochemistry, tandem mass spectrometry, and tet-assisted sodium bisulfite sequencing (TAB-seq) analyses on tissue and DNA from the hippocampus of 7-week old male mice exposed to a single 30-min restraint stress. After first identifying that the broad neuronal distribution of 5-hmC is not disrupted by acute stress, we used TAB-seq to find a stress-induced increase of 5-hmC in the 3'UTR of the glucocorticoid receptor gene (Nr3c1). Nr3c1 has a well-defined role in the stress pathway and these data suggest that 5-hmC contributes to these processes. Together, these data indicate that a deeper investigation of stress-related 5-hmC levels may reveal an environmental impact on this newly discovered epigenetic mark in the brain.
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Affiliation(s)
- Sisi Li
- Neuroscience training program, Departments of, University of Wisconsin, Madison, WI, USA
- Department of Psychiatry, University of Wisconsin, Madison, WI, USA
| | - Ligia A Papale
- Department of Psychiatry, University of Wisconsin, Madison, WI, USA
| | - Douglas B Kintner
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
- The Waisman Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin, Madison, WI, USA
| | | | - Pelin Cengiz
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
- The Waisman Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin, Madison, WI, USA
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30
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Chopra P, Papale LA, White ATJ, Hatch A, Brown RM, Garthwaite MA, Roseboom PH, Golos TG, Warren ST, Alisch RS. Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice. BMC Genomics 2014; 15:131. [PMID: 24524199 PMCID: PMC3930898 DOI: 10.1186/1471-2164-15-131] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 02/05/2014] [Indexed: 11/12/2022] Open
Abstract
Background Methylation on the fifth position of cytosine (5-mC) is an essential epigenetic mark that is linked to both normal neurodevelopment and neurological diseases. The recent identification of another modified form of cytosine, 5-hydroxymethylcytosine (5-hmC), in both stem cells and post-mitotic neurons, raises new questions as to the role of this base in mediating epigenetic effects. Genomic studies of these marks using model systems are limited, particularly with array-based tools, because the standard method of detecting DNA methylation cannot distinguish between 5-mC and 5-hmC and most methods have been developed to only survey the human genome. Results We show that non-human data generated using the optimization of a widely used human DNA methylation array, designed only to detect 5-mC, reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R2 > 0.99). Genome-wide methylation analysis, using this approach, reveals 6,102 differentially methylated loci between rhesus placental and fetal tissues with pathways analysis significantly overrepresented for developmental processes. Restricting the analysis to oncogenes and tumor suppressor genes finds 76 differentially methylated loci, suggesting that rhesus placental tissue carries a cancer epigenetic signature. Similarly, adapting the assay to detect 5-hmC finds highly reproducible 5-hmC levels within human, rhesus, and mouse brain tissue that is species-specific with a hierarchical abundance among the three species (human > rhesus >> mouse). Annotation of 5-hmC with respect to gene structure reveals a significant prevalence in the 3'UTR and an association with chromatin-related ontological terms, suggesting an epigenetic feedback loop mechanism for 5-hmC. Conclusions Together, these data show that this array-based methylation assay is generalizable to all mammals for the detection of both 5-mC and 5-hmC, greatly improving the utility of mammalian model systems to study the role of epigenetics in human health, disease, and evolution.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin-Madison, 6001 Research Park Blvd,, Madison, Wisconsin 53719, USA.
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Alisch RS, Wang T, Chopra P, Visootsak J, Conneely KN, Warren ST. Genome-wide analysis validates aberrant methylation in fragile X syndrome is specific to the FMR1 locus. BMC Med Genet 2013; 14:18. [PMID: 23356558 PMCID: PMC3599197 DOI: 10.1186/1471-2350-14-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/25/2013] [Indexed: 02/07/2023]
Abstract
Background Fragile X syndrome (FXS) is a common form of inherited intellectual disability caused by an expansion of CGG repeats located in the 5′ untranslated region (UTR) of the FMR1 gene, which leads to hypermethylation and silencing of this locus. Although a dramatic increase in DNA methylation of the FMR1 full mutation allele is well documented, the extent to which these changes affect DNA methylation throughout the rest of the genome has gone unexplored. Methods Here we examined genome-wide methylation in both peripheral blood (N = 62) and induced pluripotent stem cells (iPSCs; N = 10) from FXS individuals and controls. Results We not only found the expected significant DNA methylation differences in the FMR1 promoter and 5′ UTR, we also saw that these changes inverse in the FMR1 gene body. Importantly, we found no other differentially methylated loci throughout the remainder of the genome, indicating the aberrant methylation of FMR1 in FXS is locus-specific. Conclusions This study provides a comprehensive methylation profile of FXS and helps refine our understanding of the mechanisms behind FMR1 silencing.
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Affiliation(s)
- Reid S Alisch
- Departments of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
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Gordon L, Joo JE, Powell JE, Ollikainen M, Novakovic B, Li X, Andronikos R, Cruickshank MN, Conneely KN, Smith AK, Alisch RS, Morley R, Visscher PM, Craig JM, Saffery R. Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence. Genome Res 2012; 22:1395-406. [PMID: 22800725 PMCID: PMC3409253 DOI: 10.1101/gr.136598.111] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Comparison between groups of monozygotic (MZ) and dizygotic (DZ) twins enables an estimation of the relative contribution of genetic and shared and nonshared environmental factors to phenotypic variability. Using DNA methylation profiling of ∼20,000 CpG sites as a phenotype, we have examined discordance levels in three neonatal tissues from 22 MZ and 12 DZ twin pairs. MZ twins exhibit a wide range of within-pair differences at birth, but show discordance levels generally lower than DZ pairs. Within-pair methylation discordance was lowest in CpG islands in all twins and increased as a function of distance from islands. Variance component decomposition analysis of DNA methylation in MZ and DZ pairs revealed a low mean heritability across all tissues, although a wide range of heritabilities was detected for specific genomic CpG sites. The largest component of variation was attributed to the combined effects of nonshared intrauterine environment and stochastic factors. Regression analysis of methylation on birth weight revealed a general association between methylation of genes involved in metabolism and biosynthesis, providing further support for epigenetic change in the previously described link between low birth weight and increasing risk for cardiovascular, metabolic, and other complex diseases. Finally, comparison of our data with that of several older twins revealed little evidence for genome-wide epigenetic drift with increasing age. This is the first study to analyze DNA methylation on a genome scale in twins at birth, further highlighting the importance of the intrauterine environment on shaping the neonatal epigenome.
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Affiliation(s)
- Lavinia Gordon
- Bioinformatics Unit, Murdoch Childrens Research Institute, Parkville, Victoria 3052, Australia
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Rovin ML, Boss-Williams KA, Alisch RS, Ritchie JC, Weinshenker D, West CH, Weiss JM. Influence of chronic administration of antidepressant drugs on mRNA for galanin, galanin receptors, and tyrosine hydroxylase in catecholaminergic and serotonergic cell-body regions in rat brain. Neuropeptides 2012; 46:81-91. [PMID: 22317959 PMCID: PMC3759228 DOI: 10.1016/j.npep.2012.01.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 11/11/2011] [Accepted: 01/02/2012] [Indexed: 11/19/2022]
Abstract
Activity of locus coeruleus (LC) neurons and release of the peptide galanin (GAL), which is colocalized with norepinephrine (NE) in LC neurons, has been implicated in depression and, conversely, in antidepressant action. The present study examined the influence of chronic administration (for 14days, via subcutaneously-implanted minipump) of antidepressant (AD) drugs representing three different classes (tricyclic [desipramine], selective serotonin reuptake inhibitor [SSRI] [paroxetine], and monoamine oxidase inhibitor [MAOI] [phenelzine]) on mRNA for GAL, GAL receptors (GalR1, GalR2, and GalR3), and tyrosine hydroxylase (TH), the rate-limiting enzyme for NE synthesis, in four brain regions--LC, A1/C1, dorsal raphe (DRN), and ventral tegmentum (VTA) of rats. Consistent with previous findings that chronic administration of AD drugs decreases activity of LC neurons, administration of AD drugs reduced mRNA for both GAL and TH in LC neurons. GAL and TH mRNA in LC neurons was highly correlated. AD drugs also reduced GAL and TH mRNA in A1/C1 and VTA but effects were smaller than in LC. The largest change in mRNA for GAL receptors produced by AD administration was to decrease mRNA for GalR2 receptors in the VTA region. Also, mRNA for GalR2 and GalR3 receptors was significantly (positively) correlated in all three predominantly catecholaminergic brain regions (LC, A1/C1, and VTA). Relative to these three brain regions, unique effects were seen in the DRN region, with the SSRI elevating GAL mRNA and with mRNA for GalR1 and GalR3 being highly correlated in this brain region. The findings show that chronic administration of AD drugs, which produces effective antidepressant action, results in changes in mRNA for GAL, GAL receptors, and TH in brain regions that likely participate in depression and antidepressant effects.
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Affiliation(s)
| | | | | | - James C. Ritchie
- Department of Pathology Emory University School of Medicine Atlanta, GA, USA
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Abstract
DNA methylation (DNAm) plays diverse roles in human biology, but this dynamic epigenetic mark remains far from fully characterized. Although earlier studies uncovered loci that undergo age-associated DNAm changes in adults, little is known about such changes during childhood. Despite profound DNAm plasticity during embryogenesis, monozygotic twins show indistinguishable childhood methylation, suggesting that DNAm is highly coordinated throughout early development. Here we examine the methylation of 27,578 CpG dinucleotides in peripheral blood DNA from a cross-sectional study of 398 boys, aged 3-17 yr, and find significant age-associated changes in DNAm at 2078 loci. These findings correspond well with pyrosequencing data and replicate in a second pediatric population (N = 78). Moreover, we report a deficit of age-related loci on the X chromosome, a preference for specific nucleotides immediately surrounding the interrogated CpG dinucleotide, and a primary association with developmental and immune ontological functions. Meta-analysis (N = 1158) with two adult populations reveals that despite a significant overlap of age-associated loci, most methylation changes do not follow a lifelong linear pattern due to a threefold to fourfold higher rate of change in children compared with adults; consequently, the vast majority of changes are more accurately modeled as a function of logarithmic age. We therefore conclude that age-related DNAm changes in peripheral blood occur more rapidly during childhood and are imperfectly accounted for by statistical corrections that are linear in age, further suggesting that future DNAm studies should be matched closely for age.
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Affiliation(s)
- Reid S Alisch
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Abstract
Recent genome-wide interrogations of transcribed RNA have yielded compelling evidence for pervasive and complex transcription throughout a large majority of the human genome. Tens of thousands of noncoding RNA transcripts have been identified, most of which have yet to be functionally characterized. Along with the revelation that noncoding RNAs in the human genome are surprisingly abundant, there has been a surge in molecular and genetic data showing important and diverse regulatory roles for noncoding RNA. In this report, we summarize the potential roles that noncoding RNAs may play in the molecular pathogenesis of different mental retardation disorders. We suspect that these findings are just the tip of the iceberg, with noncoding RNAs possibly being involved in disease pathogenesis at different levels and through multiple distinct mechanisms.
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Affiliation(s)
- K E Szulwach
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Alisch RS, Jin P, Epstein M, Caspary T, Warren ST. Argonaute2 is essential for mammalian gastrulation and proper mesoderm formation. PLoS Genet 2007; 3:e227. [PMID: 18166081 PMCID: PMC2323323 DOI: 10.1371/journal.pgen.0030227] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 11/05/2007] [Indexed: 11/19/2022] Open
Abstract
Mammalian Argonaute proteins (EIF2C1-4) play an essential role in RNA-induced silencing. Here, we show that the loss of eIF2C2 (Argonaute2 or Ago2) results in gastrulation arrest, ectopic expression of Brachyury (T), and mesoderm expansion. We identify a genetic interaction between Ago2 and T, as Ago2 haploinsufficiency partially rescues the classic T/+ short-tail phenotype. Finally, we demonstrate that the ectopic T expression and concomitant mesoderm expansion result from disrupted fibroblast growth factor signaling, likely due to aberrant expression of Eomesodermin. Together, these data indicate that a factor best known as a key component of the RNA-induced silencing complex is required for proper fibroblast growth factor signaling during gastrulation, suggesting a possible micro-RNA function in the formation of a mammalian germ layer.
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Affiliation(s)
- Reid S Alisch
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Michael Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
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Abstract
Long Interspersed Element-1 (LINE-1 or L1) retrotransposons encode proteins required for their mobility (ORF1p and ORF2p), yet little is known about how L1 mRNA is translated. Here, we show that ORF2 translation generally initiates from the first in-frame methionine codon of ORF2, and that both ORF1 and the inter-ORF spacer are dispensable for ORF2 translation. Remarkably, changing the ORF2 AUG codon to any other coding triplet is compatible with retrotransposition. However, introducing a premature termination codon in ORF1 or a thermostable hairpin in the inter-ORF spacer reduces ORF2p translation or L1 retrotransposition to approximately 5% of wild-type levels. Similar data obtained from "natural" and codon optimized "synthetic" mouse L1s lead us to propose that ORF2 is translated by an unconventional termination/reinitiation mechanism.
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Affiliation(s)
- Reid S Alisch
- Department of Human Genetics and Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA
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Abstract
Fragile X syndrome is caused by the loss of an RNA-binding protein called FMRP (for fragile X mental retardation protein). FMRP seems to influence synaptic plasticity through its role in mRNA transport and translational regulation. Recent advances include the identification of mRNA ligands, FMRP-mediated mRNA transport and the neuronal consequence of FMRP deficiency. FMRP was also recently linked to the microRNA pathway. These advances provide mechanistic insight into this disorder, and into learning and memory in general.
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Affiliation(s)
- Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Badge RM, Alisch RS, Moran JV. ATLAS: a system to selectively identify human-specific L1 insertions. Am J Hum Genet 2003; 72:823-38. [PMID: 12632328 PMCID: PMC1180347 DOI: 10.1086/373939] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2002] [Accepted: 12/30/2002] [Indexed: 11/03/2022] Open
Abstract
Retrotransposition of L1 LINEs (long interspersed elements) continues to sculpt the human genome. However, because recent insertions are dimorphic, they are not fully represented in sequence databases. Here, we have developed a system, termed "ATLAS" (amplification typing of L1 active subfamilies), that enables the selective amplification and display of DNA fragments containing the termini of human-specific L1s and their respective flanking sequences. We demonstrate that ATLAS is robust and that the resultant display patterns are highly reproducible, segregate in Centre d'Etude du Polymorphisme Humain pedigrees, and provide an individual-specific fingerprint. ATLAS also allows the identification of L1s that are absent from current genome databases, and we show that some of these L1s can retrotranspose at high frequencies in cultured human cells. Finally, we demonstrate that ATLAS also can identify single-nucleotide polymorphisms within a subset of older, primate-specific L1s. Thus, ATLAS provides a simple, high-throughput means to assess genetic variation associated with L1 retrotransposons.
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Affiliation(s)
- Richard M. Badge
- Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, Ann Arbor; and Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Reid S. Alisch
- Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, Ann Arbor; and Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - John V. Moran
- Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, Ann Arbor; and Department of Genetics, University of Leicester, Leicester, United Kingdom
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Brunkow ME, Gardner JC, Van Ness J, Paeper BW, Kovacevich BR, Proll S, Skonier JE, Zhao L, Sabo PJ, Fu Y, Alisch RS, Gillett L, Colbert T, Tacconi P, Galas D, Hamersma H, Beighton P, Mulligan J. Bone dysplasia sclerosteosis results from loss of the SOST gene product, a novel cystine knot-containing protein. Am J Hum Genet 2001; 68:577-89. [PMID: 11179006 PMCID: PMC1274471 DOI: 10.1086/318811] [Citation(s) in RCA: 688] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2000] [Accepted: 01/19/2001] [Indexed: 12/11/2022] Open
Abstract
Sclerosteosis is an autosomal recessive sclerosing bone dysplasia characterized by progressive skeletal overgrowth. The majority of affected individuals have been reported in the Afrikaner population of South Africa, where a high incidence of the disorder occurs as a result of a founder effect. Homozygosity mapping in Afrikaner families along with analysis of historical recombinants localized sclerosteosis to an interval of approximately 2 cM between the loci D17S1787 and D17S930 on chromosome 17q12-q21. Here we report two independent mutations in a novel gene, termed "SOST." Affected Afrikaners carry a nonsense mutation near the amino terminus of the encoded protein, whereas an unrelated affected person of Senegalese origin carries a splicing mutation within the single intron of the gene. The SOST gene encodes a protein that shares similarity with a class of cystine knot-containing factors including dan, cerberus, gremlin, prdc, and caronte. The specific and progressive effect on bone formation observed in individuals affected with sclerosteosis, along with the data presented in this study, together suggest that the SOST gene encodes an important new regulator of bone homeostasis.
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Wei W, Morrish TA, Alisch RS, Moran JV. A transient assay reveals that cultured human cells can accommodate multiple LINE-1 retrotransposition events. Anal Biochem 2000; 284:435-8. [PMID: 10964437 DOI: 10.1006/abio.2000.4675] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- W Wei
- Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
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