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Cevik SE, Skaar DA, Jima DD, Liu AJ, Østbye T, Whitson HE, Jirtle RL, Hoyo C, Planchart A. DNA methylation of imprint control regions associated with Alzheimer's disease in non-Hispanic Blacks and non-Hispanic Whites. Clin Epigenetics 2024; 16:58. [PMID: 38658973 PMCID: PMC11043040 DOI: 10.1186/s13148-024-01672-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/13/2024] [Indexed: 04/26/2024] Open
Abstract
Alzheimer's disease (AD) prevalence is twice as high in non-Hispanic Blacks (NHBs) as in non-Hispanic Whites (NHWs). The objective of this study was to determine whether aberrant methylation at imprint control regions (ICRs) is associated with AD. Differentially methylated regions (DMRs) were bioinformatically identified from whole-genome bisulfite sequenced DNA derived from brain tissue of 9 AD (5 NHBs and 4 NHWs) and 8 controls (4 NHBs and 4 NHWs). We identified DMRs located within 120 regions defined as candidate ICRs in the human imprintome ( https://genome.ucsc.edu/s/imprintome/hg38.AD.Brain_track ). Eighty-one ICRs were differentially methylated in NHB-AD, and 27 ICRs were differentially methylated in NHW-AD, with two regions common to both populations that are proximal to the inflammasome gene, NLRP1, and a known imprinted gene, MEST/MESTIT1. These findings indicate that early developmental alterations in DNA methylation of regions regulating genomic imprinting may contribute to AD risk and that this epigenetic risk differs between NHBs and NHWs.
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Affiliation(s)
- Sebnem E Cevik
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - David A Skaar
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Andy J Liu
- Department of Neurology, School of Medicine, Duke University, Durham, NC, USA
| | - Truls Østbye
- Department of Family Medicine and Community Health, Duke University, Durham, NC, USA
| | - Heather E Whitson
- Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
- Duke Center for the Study of Aging and Human Development, Durham, NC, USA
- Duke/UNC Alzheimer's Disease Research Center (ADRC), Durham, NC, USA
| | - Randy L Jirtle
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
| | - Cathrine Hoyo
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
| | - Antonio Planchart
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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Slavotinek A, Misceo D, Htun S, Mathisen L, Frengen E, Foreman M, Hurtig JE, Enyenihi L, Sterrett MC, Leung SW, Schneidman-Duhovny D, Estrada-Veras J, Duncan JL, Haaxma CA, Kamsteeg EJ, Xia V, Beleford D, Si Y, Douglas G, Treidene HE, van Hoof A, Fasken MB, Corbett AH. Biallelic variants in the RNA exosome gene EXOSC5 are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness. Hum Mol Genet 2021; 29:2218-2239. [PMID: 32504085 DOI: 10.1093/hmg/ddaa108] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/10/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022] Open
Abstract
The RNA exosome is an essential ribonuclease complex required for processing and/or degradation of both coding and non-coding RNAs. We identified five patients with biallelic variants in EXOSC5, which encodes a structural subunit of the RNA exosome. The clinical features of these patients include failure to thrive, short stature, feeding difficulties, developmental delays that affect motor skills, hypotonia and esotropia. Brain MRI revealed cerebellar hypoplasia and ventriculomegaly. While we ascertained five patients, three patients with distinct variants of EXOSC5 were studied in detail. The first patient had a deletion involving exons 5-6 of EXOSC5 and a missense variant, p.Thr114Ile, that were inherited in trans, the second patient was homozygous for p.Leu206His and the third patient had paternal isodisomy for chromosome 19 and was homozygous for p.Met148Thr. The additional two patients ascertained are siblings who had an early frameshift mutation in EXOSC5 and the p.Thr114Ile missense variant that were inherited in trans. We employed three complementary approaches to explore the requirement for EXOSC5 in brain development and assess consequences of pathogenic EXOSC5 variants. Loss of function for exosc5 in zebrafish results in shortened and curved tails/bodies, reduced eye/head size and edema. We modeled pathogenic EXOSC5 variants in both budding yeast and mammalian cells. Some of these variants cause defects in RNA exosome function as well as altered interactions with other RNA exosome subunits. These findings expand the number of genes encoding RNA exosome subunits linked to human disease while also suggesting that disease mechanism varies depending on the specific pathogenic variant.
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Affiliation(s)
- Anne Slavotinek
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Stephanie Htun
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Linda Mathisen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo 0450, Norway
| | - Michelle Foreman
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Jennifer E Hurtig
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Liz Enyenihi
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | | | - Sara W Leung
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering and the Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Juvianee Estrada-Veras
- Department of Pediatrics-Medical Genetics and Metabolism, Uniformed Services University/Walter Reed NMMC Bethesda, MD 20889, USA
| | - Jacque L Duncan
- Department of Ophthalmology, University of California, San Francisco, CA 94143, USA
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Vivian Xia
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Daniah Beleford
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Yue Si
- GeneDx Inc., MD 20877, USA
| | | | - Hans Einar Treidene
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo 0450, Norway
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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Song J, Zhu L, Zhou T, Wang B. A rare case of uniparental isodisomy of chromosome 19 with no phenotypic abnormalities. Taiwan J Obstet Gynecol 2021; 60:376-377. [PMID: 33678349 DOI: 10.1016/j.tjog.2021.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/25/2020] [Indexed: 11/25/2022] Open
Affiliation(s)
- Jieping Song
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, PR China
| | - Ling Zhu
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, PR China
| | - Ting Zhou
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, PR China
| | - Bo Wang
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, PR China.
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Characterization of Prevalence and Health Consequences of Uniparental Disomy in Four Million Individuals from the General Population. Am J Hum Genet 2019; 105:921-932. [PMID: 31607426 PMCID: PMC6848996 DOI: 10.1016/j.ajhg.2019.09.016] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/13/2019] [Indexed: 12/30/2022] Open
Abstract
Meiotic nondisjunction and resulting aneuploidy can lead to severe health consequences in humans. Aneuploidy rescue can restore euploidy but may result in uniparental disomy (UPD), the inheritance of both homologs of a chromosome from one parent with no representative copy from the other. Current understanding of UPD is limited to ∼3,300 case subjects for which UPD was associated with clinical presentation due to imprinting disorders or recessive diseases. Thus, the prevalence of UPD and its phenotypic consequences in the general population are unknown. We searched for instances of UPD across 4,400,363 consented research participants from the personal genetics company 23andMe, Inc., and 431,094 UK Biobank participants. Using computationally detected DNA segments identical-by-descent (IBD) and runs of homozygosity (ROH), we identified 675 instances of UPD across both databases. We estimate that UPD is twice as common as previously thought, and we present a machine-learning framework to detect UPD using ROH. While we find a nominally significant association between UPD of chromosome 22 and autism risk, we do not find significant associations between UPD and deleterious traits in the 23andMe database.
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