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Kitamura N, Ito Y, Kawai T, Kamura H, Yamamura M, Okubo H, Hasegawa A, Inoue M, Takahashi K, Miya M, Kawame H, Samura O, Okamoto A. Clinical course and genetic analysis of a case of the amniocentesis showing chromosome 6 trisomy mosaicism. Taiwan J Obstet Gynecol 2024; 63:418-421. [PMID: 38802211 DOI: 10.1016/j.tjog.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 05/29/2024] Open
Abstract
OBJECTIVE Herein, we present a case of mosaic trisomy 6 detected by amniocentesis. CASE REPORT Amniocentesis (G-banding) was performed at 17 weeks of gestation; the results were 47,XY,+6[3]/46,XY[12]. Fetal screening ultrasonography showed no morphological abnormalities, and the parents desired to continue the pregnancy. The infant was delivered vaginally at 39 weeks' gestation. The male infant weighed 3002 g at birth with no morphological abnormalities. G-banding karyotype analysis performed on the infant's peripheral blood revealed 46,XY[20]. FISH analysis revealed trisomy signals on chromosome 6 in 1-4 out of 100 cells from the placenta. The single nucleotide polymorphism microarray of the umbilical cord blood revealed no abnormalities. Methylation analysis of umbilical cord blood revealed no abnormalities in PLAGL1. No disorders were observed at one year of age. CONCLUSION When amniocentesis reveals chromosomal mosaicism, it is essential to provide a thorough fetal ultrasound examination and careful genetic counseling to support the couples' decision-making.
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Affiliation(s)
- Naoya Kitamura
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato Ku, Tokyo, Japan
| | - Yuki Ito
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato Ku, Tokyo, Japan; Department of Clinical Genetics, The Jikei University Hospital, Minato Ku, Tokyo, Japan.
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Hiromi Kamura
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Michihiro Yamamura
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Haruna Okubo
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato Ku, Tokyo, Japan
| | - Akihiro Hasegawa
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato Ku, Tokyo, Japan
| | - Momoko Inoue
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato Ku, Tokyo, Japan
| | - Ken Takahashi
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato Ku, Tokyo, Japan
| | - Michiko Miya
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato Ku, Tokyo, Japan
| | - Hiroshi Kawame
- Department of Clinical Genetics, The Jikei University Hospital, Minato Ku, Tokyo, Japan
| | - Osamu Samura
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato Ku, Tokyo, Japan; Department of Clinical Genetics, The Jikei University Hospital, Minato Ku, Tokyo, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato Ku, Tokyo, Japan
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Sun W, Wang Z, Wen S, Huang A, Li H, Jiang L, Feng Q, Fan D, Tian Q, Han D, Liu X. Technical strategy for monozygotic twin discrimination by single-nucleotide variants. Int J Legal Med 2024; 138:767-779. [PMID: 38197923 DOI: 10.1007/s00414-023-03150-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Monozygotic (MZ) twins are theoretically genetically identical. Although they are revealed to accumulate mutations after the zygote splits, discriminating between twin genomes remains a formidable challenge in the field of forensic genetics. Single-nucleotide variants (SNVs) are responsible for a substantial portion of genetic variation, thus potentially serving as promising biomarkers for the identification of MZ twins. In this study, we sequenced the whole genome of a pair of female MZ twins when they were 27 and 33 years old to approximately 30 × coverage using peripheral blood on an Illumina NovaSeq 6000 Sequencing System. Potentially discordant SNVs supported by whole-genome sequencing were validated extensively by amplicon-based targeted deep sequencing and Sanger sequencing. In total, we found nine bona fide post-twinning SNVs, all of which were identified in the younger genomes and found in the older genomes. None of the SNVs occurred within coding exons, three of which were observed in introns, supported by whole-exome sequencing results. A double-blind test was employed, and the reliability of MZ twin discrimination by discordant SNVs was endorsed. All SNVs were successfully detected when input DNA amounts decreased to 0.25 ng, and reliable detection was limited to seven SNVs below 0.075 ng input. This comprehensive analysis confirms that SNVs could serve as cost-effective biomarkers for MZ twin discrimination.
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Affiliation(s)
- Weifen Sun
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ziwei Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Shubo Wen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Ao Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Hui Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Lei Jiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Danlin Fan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qilin Tian
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Dingding Han
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China.
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Kreger J, Mooney JA, Shibata D, MacLean AL. Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.02.583106. [PMID: 38496542 PMCID: PMC10942294 DOI: 10.1101/2024.03.02.583106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Clonal hematopoiesis becomes increasingly common with age, but its cause is enigmatic because driver mutations are often absent. Serial observations infer weak selection indicating variants are acquired much earlier in life with unexplained initial growth spurts. Here we use fluctuating CpG methylation as a lineage marker to track stem cell clonal dynamics of hematopoiesis. We show, via the shared prenatal circulation of monozygotic twins, that weak selection conferred by stem cell variation created before birth can reliably yield clonal hematopoiesis later in life. Theory indicates weak selection will lead to dominance given enough time and large enough population sizes. Human hematopoiesis satisfies both these conditions. Stochastic loss of weakly selected variants is naturally prevented by the expansion of stem cell lineages during development. The dominance of stem cell clones created before birth is supported by blood fluctuating CpG methylation patterns that exhibit low correlation between unrelated individuals but are highly correlated between many elderly monozygotic twins. Therefore, clonal hematopoiesis driven by weak selection in later life appears to reflect variation created before birth.
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Affiliation(s)
- Jesse Kreger
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Jazlyn A. Mooney
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Darryl Shibata
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
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4
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Wang Z, Fu G, Ma G, Wang C, Wang Q, Lu C, Fu L, Zhang X, Cong B, Li S. The association between DNA methylation and human height and a prospective model of DNA methylation-based height prediction. Hum Genet 2024; 143:401-421. [PMID: 38507014 DOI: 10.1007/s00439-024-02659-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024]
Abstract
As a vital anthropometric characteristic, human height information not only helps to understand overall developmental status and genetic risk factors, but is also important for forensic DNA phenotyping. We utilized linear regression analysis to test the association between each CpG probe and the height phenotype. Next, we designed a methylation sequencing panel targeting 959 CpGs and subsequent height inference models were constructed for the Chinese population. A total of 11,730 height-associated sites were identified. By employing KPCA and deep neural networks, a prediction model was developed, of which the cross-validation RMSE, MAE and R2 were 5.62 cm, 4.45 cm and 0.64, respectively. Genetic factors could explain 39.4% of the methylation level variance of sites used in the height inference models. Collectively, we demonstrated an association between height and DNA methylation status through an EWAS analysis. Targeted methylation sequencing of only 959 CpGs combined with deep learning techniques could provide a model to estimate human height with higher accuracy than SNP-based prediction models.
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Affiliation(s)
- Zhonghua Wang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Guangping Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Guanju Ma
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Chunyan Wang
- Physical Examination Center of Shijiazhuang People's Hospital, Shijiazhuang, 050011, Hebei, China
| | - Qian Wang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Chaolong Lu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Lihong Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Xiaojing Zhang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China.
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5
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Mehta D, de Boer I, Sutherland HG, Pijpers JA, Bron C, Bainomugisa C, Haupt LM, van den Maagdenberg AMJM, Griffiths LR, Nyholt DR, Terwindt GM. Alterations in DNA methylation associate with reduced migraine and headache days after medication withdrawal treatment in chronic migraine patients: a longitudinal study. Clin Epigenetics 2023; 15:190. [PMID: 38087366 PMCID: PMC10717674 DOI: 10.1186/s13148-023-01604-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Chronic migraine, a highly disabling migraine subtype, affects nearly 2% of the general population. Understanding migraine chronification is vital for developing better treatment and prevention strategies. An important factor in the chronification of migraine is the overuse of acute headache medication. However, the mechanisms behind the transformation of episodic migraine to chronic migraine and vice versa have not yet been elucidated. We performed a longitudinal epigenome-wide association study to identify DNA methylation (DNAm) changes associated with treatment response in patients with chronic migraine and medication overuse as part of the Chronification and Reversibility of Migraine clinical trial. Blood was taken from patients with chronic migraine (n = 98) at baseline and after a 12-week medication withdrawal period. Treatment responders, patients with ≥ 50% reduction in monthly headache days (MHD), were compared with non-responders to identify DNAm changes associated with treatment response. Similarly, patients with ≥ 50% versus < 50% reduction in monthly migraine days (MMD) were compared. RESULTS At the epigenome-wide significant level (p < 9.42 × 10-8), a longitudinal reduction in DNAm at an intronic CpG site (cg14377273) within the HDAC4 gene was associated with MHD response following the withdrawal of acute medication. HDAC4 is highly expressed in the brain, plays a major role in synaptic plasticity, and modulates the expression and release of several neuroinflammation markers which have been implicated in migraine pathophysiology. Investigating whether baseline DNAm associated with treatment response, we identified lower baseline DNAm at a CpG site (cg15205829) within MARK3 that was significantly associated with MMD response at 12 weeks. CONCLUSIONS Our findings of a longitudinal reduction in HDAC4 DNAm status associated with treatment response and baseline MARK3 DNAm status as an early biomarker for treatment response, provide support for a role of pathways related to chromatin structure and synaptic plasticity in headache chronification and introduce HDAC4 and MARK3 as novel therapeutic targets.
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Affiliation(s)
- Divya Mehta
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
- Centre for Data Science, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
| | - Irene de Boer
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Heidi G Sutherland
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
| | - Judith A Pijpers
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Charlene Bron
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
| | - Charlotte Bainomugisa
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
- Centre for Data Science, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
| | - Larisa M Haupt
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
| | - Arn M J M van den Maagdenberg
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Lyn R Griffiths
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
| | - Dale R Nyholt
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia.
- Centre for Data Science, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia.
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia.
| | - Gisela M Terwindt
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands.
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6
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Varshavsky M, Harari G, Glaser B, Dor Y, Shemer R, Kaplan T. Accurate age prediction from blood using a small set of DNA methylation sites and a cohort-based machine learning algorithm. CELL REPORTS METHODS 2023; 3:100567. [PMID: 37751697 PMCID: PMC10545910 DOI: 10.1016/j.crmeth.2023.100567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/18/2023] [Accepted: 08/03/2023] [Indexed: 09/28/2023]
Abstract
Chronological age prediction from DNA methylation sheds light on human aging, health, and lifespan. Current clocks are mostly based on linear models and rely upon hundreds of sites across the genome. Here, we present GP-age, an epigenetic non-linear cohort-based clock for blood, based upon 11,910 methylomes. Using 30 CpG sites alone, GP-age outperforms state-of-the-art models, with a median accuracy of ∼2 years on held-out blood samples, for both array and sequencing-based data. We show that aging-related changes occur at multiple neighboring CpGs, with implications for using fragment-level analysis of sequencing data in aging research. By training three independent clocks, we show enrichment of donors with consistent deviation between predicted and actual age, suggesting individual rates of biological aging. Overall, we provide a compact yet accurate alternative to array-based clocks for blood, with applications in longitudinal aging research, forensic profiling, and monitoring epigenetic processes in transplantation medicine and cancer.
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Affiliation(s)
- Miri Varshavsky
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; The Center for Computational Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil Harari
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel; The Center for Computational Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel; The Center for Computational Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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7
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Alameda L, Liu Z, Sham PC, Aas M, Trotta G, Rodriguez V, Di Forti M, Stilo SA, Kandaswamy R, Arango C, Arrojo M, Bernardo M, Bobes J, de Haan L, Del-Ben CM, Gayer-Anderson C, Sideli L, Jones PB, Jongsma HE, Kirkbride JB, La Cascia C, Lasalvia A, Tosato S, Llorca PM, Menezes PR, van Os J, Quattrone D, Rutten BP, Santos JL, Sanjuán J, Selten JP, Szöke A, Tarricone I, Tortelli A, Velthorst E, Morgan C, Dempster E, Hannon E, Burrage J, Dwir D, Arumuham A, Mill J, Murray RM, Wong CCY. Exploring the mediation of DNA methylation across the epigenome between childhood adversity and First Episode of Psychosis-findings from the EU-GEI study. Mol Psychiatry 2023; 28:2095-2106. [PMID: 37062770 DOI: 10.1038/s41380-023-02044-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/04/2023] [Accepted: 03/20/2023] [Indexed: 04/18/2023]
Abstract
ABTRACT Studies conducted in psychotic disorders have shown that DNA-methylation (DNAm) is sensitive to the impact of Childhood Adversity (CA). However, whether it mediates the association between CA and psychosis is yet to be explored. Epigenome wide association studies (EWAS) using the Illumina Infinium-Methylation EPIC array in peripheral blood tissue from 366 First-episode of psychosis and 517 healthy controls was performed. Adversity scores were created for abuse, neglect and composite adversity with the Childhood Trauma Questionnaire (CTQ). Regressions examining (I) CTQ scores with psychosis; (II) with DNAm EWAS level and (III) between DNAm and caseness, adjusted for a variety of confounders were conducted. Divide-Aggregate Composite-null Test for the composite null-hypothesis of no mediation effect was conducted. Enrichment analyses were conducted with missMethyl package and the KEGG database. Our results show that CA was associated with psychosis (Composite: OR = 1.68; p = <0.001; abuse: OR = 2.16; p < 0.001; neglect: OR = 2.27; p = <0.001). None of the CpG sites significantly mediated the adversity-psychosis association after Bonferroni correction (p < 8.1 × 10-8). However, 28, 34 and 29 differentially methylated probes associated with 21, 27, 20 genes passed a less stringent discovery threshold (p < 5 × 10-5) for composite, abuse and neglect respectively, with a lack of overlap between abuse and neglect. These included genes previously associated to psychosis in EWAS studies, such as PANK1, SPEG TBKBP1, TSNARE1 or H2R. Downstream gene ontology analyses did not reveal any biological pathways that survived false discovery rate correction. Although at a non-significant level, DNAm changes in genes previously associated with schizophrenia in EWAS studies may mediate the CA-psychosis association. These results and associated involved processes such as mitochondrial or histaminergic disfunction, immunity or neural signalling requires replication in well powered samples. The lack of overlap between mediating genes associated with abuse and neglect suggests differential biological trajectories linking CA subtypes and psychosis.
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Affiliation(s)
- Luis Alameda
- Service of General Psychiatry, Treatment and Early Intervention in Psychosis Program, Lausanne University Hospital (CHUV), Lausanne, Switzerland.
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK.
- Instituto de Investigación Sanitaria de Sevilla, IbiS, Hospital Universitario Virgen del Rocío, Department of Psychiatry, Universidad de Sevilla, Seville, Spain.
| | - Zhonghua Liu
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Pak C Sham
- Department of Psychiatry, State Key Laboratory of Brain and Cognitive Sciences, and Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Monica Aas
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Giulia Trotta
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Victoria Rodriguez
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
| | - Marta Di Forti
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Simona A Stilo
- Department of Mental Health and Addiction Services, ASP Crotone, Crotone, Italy
| | - Radhika Kandaswamy
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, Madrid, Spain
| | - Manuel Arrojo
- Department of Psychiatry, Psychiatric Genetic Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago de Compostela, Santiago, Spain
| | - Miguel Bernardo
- Barcelona Clinic Schizophrenia Unit, Neuroscience Institute, Hospital Clinic of Barcelona, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, Biomedical Research Networking Centre in Mental Health (CIBERSAM), Barcelona, Spain
| | - Julio Bobes
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Department of Medicine, Psychiatry Area, School of Medicine, Universidad de Oviedo, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Oviedo, Spain
| | - Lieuwe de Haan
- Department of Psychiatry, Early Psychosis Section, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Cristina Marta Del-Ben
- Neuroscience and Behaviour Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Lucia Sideli
- LUMSA University, Department of Human Science and Department of Psychosis Studies, KCL, Rome, Italy
| | - Peter B Jones
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- CAMEO Early Intervention Service, Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, UK
| | - Hannah E Jongsma
- Psylife Group, Division of Psychiatry, University College London, London, UK
| | - James B Kirkbride
- Psylife Group, Division of Psychiatry, University College London, London, UK
| | - Caterina La Cascia
- Section of Psychiatry, Department of Biomedicine, Neuroscience and advanced Diagnostic (BiND), University of Palermo, Palermo, Italy
| | - Antonio Lasalvia
- Section of Psychiatry, Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Sarah Tosato
- Section of Psychiatry, Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | | | - Paulo Rossi Menezes
- Department of Preventive Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Jim van Os
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, South Limburg Mental Health Research and Teaching Network, Maastricht University Medical Centre, Maastricht, The Netherlands
- Department Psychiatry, Brain Centre Rudolf Magnus, Utrecht University Medical Centre, Utrecht, The Netherlands
| | - Diego Quattrone
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Bart P Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, South Limburg Mental Health Research and Teaching Network, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Jose Luis Santos
- Department of Psychiatry, Servicio de Psiquiatría Hos"ital "Virgen de"a Luz", C/Hermandad de Donantes de Sangre, 16002, Cuenca, Spain
| | - Julio Sanjuán
- Department of Psychiatry, School of Medicine, Universidad de Valencia, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), C/Avda. Blasco Ibáñez 15, 46010, Valencia, Spain
| | - Jean-Paul Selten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, South Limburg Mental Health Research and Teaching Network, Maastricht University Medical Centre, Maastricht, The Netherlands
- Rivierduinen Institute for Mental Health Care, Leiden, The Netherlands
| | - Andrei Szöke
- University of Paris Est Creteil, INSERM, IMRB, AP-HP, Hôpitaux Universitaires, H. Mondor, DMU IMPACT, Creteil, France
| | - Ilaria Tarricone
- Bologna Transcultural Psychosomatic Team (BoTPT), Department of Medical and Surgical Science, Alma Mater Studiorum Università di Bologna, Bologna, Italy
| | | | - Eva Velthorst
- GGZ (Mental Health Services) Noord Holland Noord, Heerhugowaard, the Netherlands
| | - Craig Morgan
- ESRC Centre for Society and Mental Health, King's College London, London, UK
| | - Emma Dempster
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Eilis Hannon
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Joe Burrage
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Daniella Dwir
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Atheeshaan Arumuham
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
- Psychiatric Imaging Group, MRC London Institute of Medical Sciences, London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Jonathan Mill
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Robin M Murray
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
| | - Chloe C Y Wong
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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8
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Martin CL, Ghastine L, Lodge EK, Dhingra R, Ward-Caviness CK. Understanding Health Inequalities Through the Lens of Social Epigenetics. Annu Rev Public Health 2022; 43:235-254. [PMID: 35380065 PMCID: PMC9584166 DOI: 10.1146/annurev-publhealth-052020-105613] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Longstanding racial/ethnic inequalities in morbidity and mortality persist in the United States. Although the determinants of health inequalities are complex, social and structural factors produced by inequitable and racialized systems are recognized as contributing sources. Social epigenetics is an emerging area of research that aims to uncover biological pathways through which social experiences affect health outcomes. A growing body of literature links adverse social exposures to epigenetic mechanisms, namely DNA methylation, offering a plausible pathway through which health inequalities may arise. This review provides an overview of social epigenetics and highlights existing literature linking social exposures—i.e., psychosocial stressors, racism, discrimination, socioeconomic position, and neighborhood social environment—to DNA methylation in humans.We conclude with a discussion of social epigenetics as a mechanistic link to health inequalities and provide suggestions for future social epigenetics research on health inequalities.
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Affiliation(s)
- Chantel L Martin
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; .,Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lea Ghastine
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA;
| | - Evans K Lodge
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; .,Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Radhika Dhingra
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Institute of Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cavin K Ward-Caviness
- Center for Public Health and Environmental Assessment, US Environmental Protection Agency, Chapel Hill, North Carolina, USA
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9
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Kitazawa S, Ohno T, Haraguchi R, Kitazawa R. Histochemistry, Cytochemistry and Epigenetics. Acta Histochem Cytochem 2022; 55:1-7. [PMID: 35444348 PMCID: PMC8913277 DOI: 10.1267/ahc.21-00095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/27/2021] [Indexed: 12/23/2022] Open
Abstract
Over the past few decades, many researchers have individually identified tumor-related genes, and have accumulated information on their basic research in a database. With the development of technology that can comprehensively test the expression status within a short time, oncogene panel testing has become attainable. On the other hand, changes in gene expression that do not depend on changes in base sequences, that is, epigenetics, or more comprehensively, epigenomes, are also highly involved in the development and progression of disease. Oncogene panel tests tend to focus on DNA base mutations such as point mutations, deletions, duplications, and chimera formation. Elucidation leads to correct interpretation of diseases and treatment choices, and we are in an era where integrated understanding of the genome and epigenome is indispensable. In this review, we make every effort to cover a wide range of knowledge, including data on histone protein modification, non-coding (nc)RNA and DNA methylation, and recent application trials for demonstrating epigenetic alterations in histologic and cytologic specimens. We hope this review will help marshal the knowledge accumulated by researchers involved in genomic and epigenomic studies.
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Affiliation(s)
- Sohei Kitazawa
- Department of Molecular Pathology, Ehime University Graduate School of Medicine
| | - Teruyuki Ohno
- Division of Diagnostic Pathology, Ehime University Hospital
| | - Ryuma Haraguchi
- Department of Molecular Pathology, Ehime University Graduate School of Medicine
| | - Riko Kitazawa
- Division of Diagnostic Pathology, Ehime University Hospital
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