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Butto T, Chongtham MC, Mungikar K, Hartwich D, Linke M, Ruffini N, Radyushkin K, Schweiger S, Winter J, Gerber S. Characterization of transcriptional profiles associated with stress-induced neuronal activation in Arc-GFP mice. Mol Psychiatry 2024:10.1038/s41380-024-02555-z. [PMID: 38649752 DOI: 10.1038/s41380-024-02555-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
Chronic stress has become a predominant factor associated with a variety of psychiatric disorders, such as depression and anxiety, in both human and animal models. Although multiple studies have looked at transcriptional changes after social defeat stress, these studies primarily focus on bulk tissues, which might dilute important molecular signatures of social interaction in activated cells. In this study, we employed the Arc-GFP mouse model in conjunction with chronic social defeat (CSD) to selectively isolate activated nuclei (AN) populations in the ventral hippocampus (vHIP) and prefrontal cortex (PFC) of resilient and susceptible animals. Nuclear RNA-seq of susceptible vs. resilient populations revealed distinct transcriptional profiles linked predominantly with neuronal and synaptic regulation mechanisms. In the vHIP, susceptible AN exhibited increased expression of genes related to the cytoskeleton and synaptic organization. At the same time, resilient AN showed upregulation of cell adhesion genes and differential expression of major glutamatergic subunits. In the PFC, susceptible mice exhibited upregulation of synaptotagmins and immediate early genes (IEGs), suggesting a potentially over-amplified neuronal activity state. Our findings provide a novel view of stress-exposed neuronal activation and the molecular response mechanisms in stress-susceptible vs. resilient animals, which may have important implications for understanding mental resilience.
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Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128, Mainz, Germany
| | | | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Dewi Hartwich
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Matthias Linke
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Nicolas Ruffini
- Leibniz Institute for Resilience Research, Wallstr 7, 55122, Mainz, Germany
| | | | - Susann Schweiger
- Leibniz Institute for Resilience Research, Wallstr 7, 55122, Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Jennifer Winter
- Leibniz Institute for Resilience Research, Wallstr 7, 55122, Mainz, Germany.
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany.
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany.
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2
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Zhong J, Wang C, Zhang D, Yao X, Zhao Q, Huang X, Lin F, Xue C, Wang Y, He R, Li XY, Li Q, Wang M, Zhao S, Afridi SK, Zhou W, Wang Z, Xu Y, Xu Z. PCDHA9 as a candidate gene for amyotrophic lateral sclerosis. Nat Commun 2024; 15:2189. [PMID: 38467605 PMCID: PMC10928119 DOI: 10.1038/s41467-024-46333-5] [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: 05/18/2023] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease. To identify additional genetic factors, we analyzed exome sequences in a large cohort of Chinese ALS patients and found a homozygous variant (p.L700P) in PCDHA9 in three unrelated patients. We generated Pcdhα9 mutant mice harboring either orthologous point mutation or deletion mutation. These mice develop progressive spinal motor loss, muscle atrophy, and structural/functional abnormalities of the neuromuscular junction, leading to paralysis and early lethality. TDP-43 pathology is detected in the spinal motor neurons of aged mutant mice. Mechanistically, we demonstrate that Pcdha9 mutation causes aberrant activation of FAK and PYK2 in aging spinal cord, and dramatically reduced NKA-α1 expression in motor neurons. Our single nucleus multi-omics analysis reveals disturbed signaling involved in cell adhesion, ion transport, synapse organization, and neuronal survival in aged mutant mice. Together, our results present PCDHA9 as a potential ALS gene and provide insights into its pathogenesis.
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Affiliation(s)
- Jie Zhong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaodong Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Disease, Beijing, 100053, China.
| | - Dan Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoli Yao
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Quanzhen Zhao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xusheng Huang
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Feng Lin
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Chun Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaqing Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruojie He
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xu-Ying Li
- Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Disease, Beijing, 100053, China
| | - Qibin Li
- Shenzhen Clabee Biotechnology Incorporation, Shenzhen, 518057, China
| | - Mingbang Wang
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, 201102, China
| | - Shaoli Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Shabbir Khan Afridi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenhao Zhou
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, 201102, China
| | - Zhanjun Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Disease, Beijing, 100053, China
| | - Yanming Xu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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3
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Gabriel GC, Yagi H, Tan T, Bais AS, Glennon BJ, Stapleton MC, Huang L, Reynolds WT, Shaffer MG, Ganapathiraju M, Simon D, Panigrahy A, Wu YL, Lo CW. Mitotic Block and Epigenetic Repression Underlie Neurodevelopmental Defects and Neurobehavioral Deficits in Congenital Heart Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.05.565716. [PMID: 38464057 PMCID: PMC10925221 DOI: 10.1101/2023.11.05.565716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Poor neurodevelopment is often observed with congenital heart disease (CHD), especially with mutations in chromatin modifiers. Here analysis of mice with hypoplastic left heart syndrome (HLHS) arising from mutations in Sin3A associated chromatin modifier Sap130 , and adhesion protein Pcdha9, revealed neurodevelopmental and neurobehavioral deficits reminiscent of those in HLHS patients. Microcephaly was associated with impaired cortical neurogenesis, mitotic block, and increased apoptosis. Transcriptional profiling indicated dysregulated neurogenesis by REST, altered CREB signaling regulating memory and synaptic plasticity, and impaired neurovascular coupling modulating cerebral blood flow. Many neurodevelopmental/neurobehavioral disease pathways were recovered, including autism and cognitive impairment. These same pathways emerged from genome-wide DNA methylation and Sap130 chromatin immunoprecipitation sequencing analyses, suggesting epigenetic perturbation. Mice with Pcdha9 mutation or forebrain-specific Sap130 deletion without CHD showed learning/memory deficits and autism-like behavior. These novel findings provide mechanistic insights indicating the adverse neurodevelopment in HLHS may involve cell autonomous/nonautonomous defects and epigenetic dysregulation and suggest new avenues for therapy.
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Vukic M, Chouaref J, Della Chiara V, Dogan S, Ratner F, Hogenboom JZM, Epp TA, Chawengsaksophak K, Vonk KKD, Breukel C, Ariyurek Y, San Leon Granado D, Kloet SL, Daxinger L. CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses. SCIENCE ADVANCES 2024; 10:eadk3384. [PMID: 38335290 PMCID: PMC10857554 DOI: 10.1126/sciadv.adk3384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
Disruption of cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting the deposition of H3K9 trimethylation (H3K9me3). CDCA7-associated aberrant DNA hypomethylation translated to localized, tissue-specific transcriptional dysregulation that affected large gene clusters. In the brain, we identify CDCA7 as a transcriptional repressor and epigenetic regulator of clustered protocadherin isoform choice. Increased protocadherin isoform expression frequency is accompanied by DNA methylation loss, gain of H3K4 trimethylation (H3K4me3), and increased binding of the transcriptional regulator CCCTC-binding factor (CTCF). Overall, our in vivo work identifies a key role for CDCA7 in safeguarding tissue-specific expression of gene clusters via the DNA methylation pathway.
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Affiliation(s)
- Maja Vukic
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Jihed Chouaref
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Serkan Dogan
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Fallon Ratner
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Trevor A. Epp
- Laboratory of Cell Differentiation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- CZ-OPENSCREEN, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kallayanee Chawengsaksophak
- Laboratory of Cell Differentiation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kelly K. D. Vonk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Cor Breukel
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Susan L. Kloet
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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5
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Bejaoui Y, Alresheq S, Durand S, Vilaire-Meunier M, Maillebouis L, Zen AAH, Mégarbané A, Hajj NE. DNA methylation profiling in Trisomy 21 females with and without breast cancer. Front Oncol 2023; 13:1203483. [PMID: 37538118 PMCID: PMC10395079 DOI: 10.3389/fonc.2023.1203483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
Background Down Syndrome (DS) is the most common chromosome anomaly in humans and occurs due to an extra copy of chromosome 21. The malignancy profile in DS is unique, since DS patients have a low risk of developing solid tumors such as breast cancer however they are at higher risk of developing acute myeloid leukemia and acute lymphoblastic leukemia. Methods In this study, we investigated DNA methylation signatures and epigenetic aging in DS individuals with and without breast cancer. We analyzed DNA methylation patterns in Trisomy 21 (T21) individuals without breast cancer (T21-BCF) and DS individuals with breast cancer (T21-BC), using the Infinium Methylation EPIC BeadChip array. Results Our results revealed several differentially methylated sites and regions in the T21-BC patients that were associated with changes in gene expression. The differentially methylated CpG sites were enriched for processes related to serine-type peptidase activity, epithelial cell development, GTPase activity, bicellular tight junction, Ras protein signal transduction, etc. On the other hand, the epigenetic age acceleration analysis showed no difference between T21-BC and T21-BCF patients. Conclusions This is the first study to investigate DNA methylation changes in Down syndrome women with and without breast cancer and it could help shed light on factors that protect against breast cancer in DS.
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Affiliation(s)
- Yosra Bejaoui
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Sara Alresheq
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | | | | | | | - Ayman Al Haj Zen
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - André Mégarbané
- Institut Jérôme Lejeune, Paris, France
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Nady El Hajj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
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6
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Shorey-Kendrick LE, Roberts VHJ, D'Mello RJ, Sullivan EL, Murphy SK, Mccarty OJT, Schust DJ, Hedges JC, Mitchell AJ, Terrobias JJD, Easley CA, Spindel ER, Lo JO. Prenatal delta-9-tetrahydrocannabinol exposure is associated with changes in rhesus macaque DNA methylation enriched for autism genes. Clin Epigenetics 2023; 15:104. [PMID: 37415206 PMCID: PMC10324248 DOI: 10.1186/s13148-023-01519-4] [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: 02/03/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND With the growing availability of cannabis and the popularization of additional routes of cannabis use beyond smoking, including edibles, the prevalence of cannabis use in pregnancy is rapidly increasing. However, the potential effects of prenatal cannabis use on fetal developmental programming remain unknown. RESULTS We designed this study to determine whether the use of edible cannabis during pregnancy is deleterious to the fetal and placental epigenome. Pregnant rhesus macaques consumed a daily edible containing either delta-9-tetrahydrocannabinol (THC) (2.5 mg/7 kg/day) or placebo. DNA methylation was measured in 5 tissues collected at cesarean delivery (placenta, lung, cerebellum, prefrontal cortex, and right ventricle of the heart) using the Illumina MethylationEPIC platform and filtering for probes previously validated in rhesus macaque. In utero exposure to THC was associated with differential methylation at 581 CpGs, with 573 (98%) identified in placenta. Loci differentially methylated with THC were enriched for candidate autism spectrum disorder (ASD) genes from the Simons Foundation Autism Research Initiative (SFARI) database in all tissues. The placenta demonstrated greatest SFARI gene enrichment, including genes differentially methylated in placentas from a prospective ASD study. CONCLUSIONS Overall, our findings reveal that prenatal THC exposure alters placental and fetal DNA methylation at genes involved in neurobehavioral development that may influence longer-term offspring outcomes. The data from this study add to the limited existing literature to help guide patient counseling and public health polices focused on prenatal cannabis use in the future.
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
| | - Victoria H J Roberts
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Rahul J D'Mello
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Elinor L Sullivan
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
- Department of Psychiatry, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Owen J T Mccarty
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Danny J Schust
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Jason C Hedges
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
- Department of Urology, Oregon Health and Science University, Portland, OR, 97239, USA
| | - A J Mitchell
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Jose Juanito D Terrobias
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Charles A Easley
- Department of Environmental Health Science, University of Georgia College of Public Health, Athens, GA, 30602, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Jamie O Lo
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Oregon Health and Science University, Portland, OR, 97239, USA
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7
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Siamoglou S, Boers R, Koromina M, Boers J, Tsironi A, Chatzilygeroudi T, Lazaris V, Verigou E, Kourakli A, van IJcken WFJ, Gribnau J, Symeonidis A, Patrinos GP. Genome-wide analysis toward the epigenetic aetiology of myelodysplastic syndrome disease progression and pharmacoepigenomic basis of hypomethylating agents drug treatment response. Hum Genomics 2023; 17:37. [PMID: 37098643 PMCID: PMC10127336 DOI: 10.1186/s40246-023-00483-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/05/2023] [Indexed: 04/27/2023] Open
Abstract
Myelodysplastic syndromes (MDS) consist of a group of hematological malignancies characterized by ineffective hematopoiesis, cytogenetic abnormalities, and often a high risk of transformation to acute myeloid leukemia (AML). So far, there have been only a very limited number of studies assessing the epigenetics component contributing to the pathophysiology of these disorders, but not a single study assessing this at a genome-wide level. Here, we implemented a generic high throughput epigenomics approach, using methylated DNA sequencing (MeD-seq) of LpnPI digested fragments to identify potential epigenomic targets associated with MDS subtypes. Our results highlighted that PCDHG and ZNF gene families harbor potential epigenomic targets, which have been shown to be differentially methylated in a variety of comparisons between different MDS subtypes. Specifically, CpG islands, transcription start sites and post-transcriptional start sites within ZNF124, ZNF497 and PCDHG family are differentially methylated with fold change above 3,5. Overall, these findings highlight important aspects of the epigenomic component of MDS syndromes pathogenesis and the pharmacoepigenomic basis to the hypomethylating agents drug treatment response, while this generic high throughput whole epigenome sequencing approach could be readily implemented to other genetic diseases with a strong epigenetic component.
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Affiliation(s)
- Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, 265 04, Rion, Patras, Greece
| | - Ruben Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Maria Koromina
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, 265 04, Rion, Patras, Greece
| | - Joachim Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Anna Tsironi
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, 265 04, Rion, Patras, Greece
| | - Theodora Chatzilygeroudi
- Hematology Division, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | - Vasileios Lazaris
- Hematology Division, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | - Evgenia Verigou
- Hematology Division, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | - Alexandra Kourakli
- Hematology Division, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | | | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Argiris Symeonidis
- Hematology Division, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, 265 04, Rion, Patras, Greece.
- Department of Genetics and Genomics, United Arab Emirates University, College of Medicine and Health Sciences, Al-Ain, Abu Dhabi, United Arab Emirates.
- Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi, United Arab Emirates.
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Navarrete-Meneses MDP, Salas-Labadía C, Juárez-Velázquez MDR, Moreno-Lorenzana D, Gómez-Chávez F, Olaya-Vargas A, Pérez-Vera P. Exposure to Insecticides Modifies Gene Expression and DNA Methylation in Hematopoietic Tissues In Vitro. Int J Mol Sci 2023; 24:6259. [PMID: 37047231 PMCID: PMC10094043 DOI: 10.3390/ijms24076259] [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: 01/30/2023] [Revised: 03/03/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
The evidence supporting the biological plausibility of the association of permethrin and malathion with hematological cancer is limited and contradictory; thus, further studies are needed. This study aimed to investigate whether in vitro exposure to 0.1 μM permethrin and malathion at 0, 24, 48 and 72 h after cell culture initiation induced changes in the gene expression and DNA methylation in mononuclear cells from bone marrow and peripheral blood (BMMCs, PBMCs). Both pesticides induced several gene expression modifications in both tissues. Through gene ontology analysis, we found that permethrin deregulates ion channels in PBMCs and BMMCs and that malathion alters genes coding proteins with nucleic acid binding capacity, which was also observed in PBMCs exposed to permethrin. Additionally, we found that both insecticides deregulate genes coding proteins with chemotaxis functions, ion channels, and cytokines. Several genes deregulated in this study are potentially associated with cancer onset and development, and some of them have been reported to be deregulated in hematological cancer. We found that permethrin does not induce DNA hypermethylation but can induce hypomethylation, and that malathion generated both types of events. Our results suggest that these pesticides have the potential to modify gene expression through changes in promoter DNA methylation and potentially through other mechanisms that should be investigated.
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Affiliation(s)
- María del Pilar Navarrete-Meneses
- Laboratorio de Genética y Cáncer, Instituto Nacional de Pediatría, Mexico City 04530, Mexico; (M.d.P.N.-M.); (C.S.-L.); (M.d.R.J.-V.); (D.M.-L.)
| | - Consuelo Salas-Labadía
- Laboratorio de Genética y Cáncer, Instituto Nacional de Pediatría, Mexico City 04530, Mexico; (M.d.P.N.-M.); (C.S.-L.); (M.d.R.J.-V.); (D.M.-L.)
| | - María del Rocío Juárez-Velázquez
- Laboratorio de Genética y Cáncer, Instituto Nacional de Pediatría, Mexico City 04530, Mexico; (M.d.P.N.-M.); (C.S.-L.); (M.d.R.J.-V.); (D.M.-L.)
| | - Dafné Moreno-Lorenzana
- Laboratorio de Genética y Cáncer, Instituto Nacional de Pediatría, Mexico City 04530, Mexico; (M.d.P.N.-M.); (C.S.-L.); (M.d.R.J.-V.); (D.M.-L.)
| | - Fernando Gómez-Chávez
- Maestría y Doctorado en Ciencia y Tecnología de Vacunas y Bioterapéuticos, Doctorado en Ciencias en Biotecnología, Laboratorio de Enfermedades Osteoarticulares e Inmunológicas, Instituto Politécnico Nacional-ENMyH, Mexico City 07738, Mexico;
| | - Alberto Olaya-Vargas
- Unidad de Trasplante de Células Hematopoyeticas y Terapia Celular, Instituto Nacional de Pediatría, Mexico City 04530, Mexico;
| | - Patricia Pérez-Vera
- Laboratorio de Genética y Cáncer, Instituto Nacional de Pediatría, Mexico City 04530, Mexico; (M.d.P.N.-M.); (C.S.-L.); (M.d.R.J.-V.); (D.M.-L.)
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9
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de Thonel A, Ahlskog JK, Daupin K, Dubreuil V, Berthelet J, Chaput C, Pires G, Leonetti C, Abane R, Barris LC, Leray I, Aalto AL, Naceri S, Cordonnier M, Benasolo C, Sanial M, Duchateau A, Vihervaara A, Puustinen MC, Miozzo F, Fergelot P, Lebigot É, Verloes A, Gressens P, Lacombe D, Gobbo J, Garrido C, Westerheide SD, David L, Petitjean M, Taboureau O, Rodrigues-Lima F, Passemard S, Sabéran-Djoneidi D, Nguyen L, Lancaster M, Sistonen L, Mezger V. CBP-HSF2 structural and functional interplay in Rubinstein-Taybi neurodevelopmental disorder. Nat Commun 2022; 13:7002. [PMID: 36385105 PMCID: PMC9668993 DOI: 10.1038/s41467-022-34476-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Patients carrying autosomal dominant mutations in the histone/lysine acetyl transferases CBP or EP300 develop a neurodevelopmental disorder: Rubinstein-Taybi syndrome (RSTS). The biological pathways underlying these neurodevelopmental defects remain elusive. Here, we unravel the contribution of a stress-responsive pathway to RSTS. We characterize the structural and functional interaction between CBP/EP300 and heat-shock factor 2 (HSF2), a tuner of brain cortical development and major player in prenatal stress responses in the neocortex: CBP/EP300 acetylates HSF2, leading to the stabilization of the HSF2 protein. Consequently, RSTS patient-derived primary cells show decreased levels of HSF2 and HSF2-dependent alteration in their repertoire of molecular chaperones and stress response. Moreover, we unravel a CBP/EP300-HSF2-N-cadherin cascade that is also active in neurodevelopmental contexts, and show that its deregulation disturbs neuroepithelial integrity in 2D and 3D organoid models of cerebral development, generated from RSTS patient-derived iPSC cells, providing a molecular reading key for this complex pathology.
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Affiliation(s)
- Aurélie de Thonel
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France.
| | - Johanna K Ahlskog
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Kevin Daupin
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Véronique Dubreuil
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Jérémy Berthelet
- Université de Paris, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
| | - Carole Chaput
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
- Ksilink, Strasbourg, France
| | - Geoffrey Pires
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Camille Leonetti
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Ryma Abane
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Lluís Cordón Barris
- Laboratory of Molecular Regulation of Neurogenesis, GIGA-Stem Cells and GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, CHU Sart Tilman, Liège, Belgium
| | - Isabelle Leray
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, F-44000, Nantes, France
| | - Anna L Aalto
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Sarah Naceri
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Marine Cordonnier
- INSERM, UMR1231, Laboratoire d'Excellence LipSTIC, Dijon, France
- University of Bourgogne Franche-Comté, Dijon, France
- Département d'Oncologie médicale, Centre Georges-François Leclerc, Dijon, France
| | - Carène Benasolo
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Matthieu Sanial
- CNRS, UMR 7592 Institut Jacques Monod, F-75205, Paris, France
| | - Agathe Duchateau
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Anniina Vihervaara
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mikael C Puustinen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Federico Miozzo
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
- Neuroscience Institute-CNR (IN-CNR), Milan, Italy
| | - Patricia Fergelot
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France and INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Élise Lebigot
- Service de Biochimie-pharmaco-toxicologie, Hôpital Bicêtre, Hopitaux Universitaires Paris-Sud, 94270 Le Kremlin Bicêtre, Paris-Sud, France
| | - Alain Verloes
- Université de Paris, INSERM, NeuroDiderot, Robert-Debré Hospital, F-75019, Paris, France
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Pierre Gressens
- Université de Paris, INSERM, NeuroDiderot, Robert-Debré Hospital, F-75019, Paris, France
| | - Didier Lacombe
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France and INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Jessica Gobbo
- INSERM, UMR1231, Laboratoire d'Excellence LipSTIC, Dijon, France
- University of Bourgogne Franche-Comté, Dijon, France
- Département d'Oncologie médicale, Centre Georges-François Leclerc, Dijon, France
| | - Carmen Garrido
- INSERM, UMR1231, Laboratoire d'Excellence LipSTIC, Dijon, France
- University of Bourgogne Franche-Comté, Dijon, France
- Département d'Oncologie médicale, Centre Georges-François Leclerc, Dijon, France
| | - Sandy D Westerheide
- Department of Cell Biology, Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida, Tampa, FL, USA
| | - Laurent David
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, F-44000, Nantes, France
| | - Michel Petitjean
- Université de Paris, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
| | - Olivier Taboureau
- Université de Paris, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
| | | | - Sandrine Passemard
- Université de Paris, INSERM, NeuroDiderot, Robert-Debré Hospital, F-75019, Paris, France
| | | | - Laurent Nguyen
- Laboratory of Molecular Regulation of Neurogenesis, GIGA-Stem Cells and GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, CHU Sart Tilman, Liège, Belgium
| | - Madeline Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical, Campus, Cambridge, UK
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Valérie Mezger
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France.
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10
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Borgenheimer E, Hamel K, Sheeler C, Moncada FL, Sbrocco K, Zhang Y, Cvetanovic M. Single nuclei RNA sequencing investigation of the Purkinje cell and glial changes in the cerebellum of transgenic Spinocerebellar ataxia type 1 mice. Front Cell Neurosci 2022; 16:998408. [PMID: 36457352 PMCID: PMC9706545 DOI: 10.3389/fncel.2022.998408] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Glial cells constitute half the population of the human brain and are essential for normal brain function. Most, if not all, brain diseases are characterized by reactive gliosis, a process by which glial cells respond and contribute to neuronal pathology. Spinocerebellar ataxia type 1 (SCA1) is a progressive neurodegenerative disease characterized by a severe degeneration of cerebellar Purkinje cells (PCs) and cerebellar gliosis. SCA1 is caused by an abnormal expansion of CAG repeats in the gene Ataxin1 (ATXN1). While several studies reported the effects of mutant ATXN1 in Purkinje cells, it remains unclear how cerebellar glia respond to dysfunctional Purkinje cells in SCA1. To address this question, we performed single nuclei RNA sequencing (snRNA seq) on cerebella of early stage Pcp2-ATXN1[82Q] mice, a transgenic SCA1 mouse model expressing mutant ATXN1 only in Purkinje cells. We found no changes in neuronal and glial proportions in the SCA1 cerebellum at this early disease stage compared to wild-type controls. Importantly, we observed profound non-cell autonomous and potentially neuroprotective reactive gene and pathway alterations in Bergmann glia, velate astrocytes, and oligodendrocytes in response to Purkinje cell dysfunction.
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11
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Hagelkruys A, Horrer M, Taubenschmid-Stowers J, Kavirayani A, Novatchkova M, Orthofer M, Pai TP, Cikes D, Zhuk S, Balmaña M, Esk C, Koglgruber R, Moeseneder P, Lazovic J, Zopf LM, Cronin SJ, Elling U, Knoblich JA, Penninger JM. The HUSH complex controls brain architecture and protocadherin fidelity. SCIENCE ADVANCES 2022; 8:eabo7247. [PMID: 36332029 PMCID: PMC9635835 DOI: 10.1126/sciadv.abo7247] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The HUSH (human silencing hub) complex contains the H3K9me3 binding protein M-phase phosphoprotein 8 (MPP8) and recruits the histone methyltransferase SETDB1 as well as Microrchidia CW-type zinc finger protein 2 (MORC2). Functional and mechanistic studies of the HUSH complex have hitherto been centered around SETDB1 while the in vivo functions of MPP8 and MORC2 remain elusive. Here, we show that genetic inactivation of Mphosph8 or Morc2a in the nervous system of mice leads to increased brain size, altered brain architecture, and behavioral changes. Mechanistically, in both mouse brains and human cerebral organoids, MPP8 and MORC2 suppress the repetitive-like protocadherin gene cluster in an H3K9me3-dependent manner. Our data identify MPP8 and MORC2, previously linked to silencing of repetitive elements via the HUSH complex, as key epigenetic regulators of protocadherin expression in the nervous system and thereby brain development and neuronal individuality in mice and humans.
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Affiliation(s)
- Astrid Hagelkruys
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Marion Horrer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | | | | | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Michael Orthofer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Tsung-Pin Pai
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Domagoj Cikes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Sergei Zhuk
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Meritxell Balmaña
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Christopher Esk
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Rubina Koglgruber
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Paul Moeseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Jelena Lazovic
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Lydia M. Zopf
- Vienna Biocenter Core Facilities (VBCF), Vienna, Austria
| | - Shane J.F. Cronin
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Jürgen A. Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Josef M. Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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12
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Derakhshan M, Kessler NJ, Ishida M, Demetriou C, Brucato N, Moore G, Fall CHD, Chandak GR, Ricaut FX, Prentice A, Hellenthal G, Silver M. Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo. Nucleic Acids Res 2022; 50:6735-6752. [PMID: 35713545 PMCID: PMC9749461 DOI: 10.1093/nar/gkac503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/06/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
We analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs ('hvCpGs') with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.
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Affiliation(s)
| | - Noah J Kessler
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, UK
| | - Miho Ishida
- UCL Great Ormond Street Institute of Child Health, UK
| | | | - Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | | | - Caroline H D Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton,
Southampton, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular
and Molecular Biology,Hyderabad, India
| | - Francois-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London,
Gower Street, London WC1E 6BT, UK
| | - Matt J Silver
- London School of Hygiene and Tropical Medicine, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
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13
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PCDH8 protects MPP+-induced neuronal injury in SH-SY5Y cells by inhibiting MAPK pathway. Mol Cell Toxicol 2022. [DOI: 10.1007/s13273-022-00257-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Liu Y, Zhang Y, Du D, Gu X, Zhou S. PCDH17 is regulated by methylation of DNMT3B and affects the malignant biological behavior of HCC through EMT. Exp Cell Res 2022; 418:113245. [DOI: 10.1016/j.yexcr.2022.113245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/19/2022] [Accepted: 06/04/2022] [Indexed: 11/26/2022]
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15
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Yang C, Shi Y, Li X, Guan L, Li H, Lin J. Cadherins and the pathogenesis of epilepsy. Cell Biochem Funct 2022; 40:336-348. [PMID: 35393670 DOI: 10.1002/cbf.3699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/22/2022] [Accepted: 03/12/2022] [Indexed: 12/13/2022]
Abstract
Epilepsy is a nervous system disease caused by abnormal discharge of brain neurons, which is characterized by recurrent seizures. The factors that induce epilepsy include genetic and environmental factors. Genetic factors are important pathogenic factors of epilepsy, such as epilepsy caused by protocadherin-19 (PCDH-19) mutation, which is an X-linked genetic disease. It is more common in female heterozygotes, which are caused by mutations in the PCDH-19 gene. Epilepsy caused by environmental factors is mainly caused by brain injury, which is commonly caused by brain tumors, brain surgery, or trauma to the brain. In addition, the pathogenesis of epilepsy is closely related to abnormalities in some signaling pathways. The Wnt/β-catenin signaling pathway is considered a new target for the treatment of epilepsy. This review summarizes these factors inducing epilepsy and the research hypotheses regarding the pathogenesis of epilepsy. The focus of this review centers on cadherins and the pathogenesis of epilepsy. We analyzed the pathogenesis of epilepsy induced by N-cadherin and PCDH-19 in the cadherin family members. Finally, we expect that in the future, new breakthroughs will be made in the study of the pathogenesis and mechanism of epilepsy at the cellular and molecular levels.
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Affiliation(s)
- Ciqing Yang
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China
| | - Yaping Shi
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Xiaoying Li
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Lihong Guan
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Han Li
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Juntang Lin
- Stem Cells & Biotherapy Engineering Research Center of Henan, College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China
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16
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Bejaoui Y, Razzaq A, Yousri NA, Oshima J, Megarbane A, Qannan A, Potabattula R, Alam T, Martin G, Horn HF, Haaf T, Horvath S, El Hajj N. DNA methylation signatures in Blood DNA of Hutchinson-Gilford Progeria syndrome. Aging Cell 2022; 21:e13555. [PMID: 35045206 PMCID: PMC8844112 DOI: 10.1111/acel.13555] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/17/2021] [Accepted: 01/05/2022] [Indexed: 12/30/2022] Open
Abstract
Hutchinson-Gilford Progeria Syndrome (HGPS) is an extremely rare genetic disorder caused by mutations in the LMNA gene and characterized by premature and accelerated aging beginning in childhood. In this study, we performed the first genome-wide methylation analysis on blood DNA of 15 patients with progeroid laminopathies using Infinium Methylation EPIC arrays including 8 patients with classical HGPS. We could observe DNA methylation alterations at 61 CpG sites as well as 32 significant regions following a 5 Kb tiling analysis. Differentially methylated probes were enriched for phosphatidylinositol biosynthetic process, phospholipid biosynthetic process, sarcoplasm, sarcoplasmic reticulum, phosphatase regulator activity, glycerolipid biosynthetic process, glycerophospholipid biosynthetic process, and phosphatidylinositol metabolic process. Differential methylation analysis at the level of promoters and CpG islands revealed no significant methylation changes in blood DNA of progeroid laminopathy patients. Nevertheless, we could observe significant methylation differences in classic HGPS when specifically looking at probes overlapping solo-WCGW partially methylated domains. Comparing aberrantly methylated sites in progeroid laminopathies, classic Werner syndrome, and Down syndrome revealed a common significantly hypermethylated region in close vicinity to the transcription start site of a long non-coding RNA located anti-sense to the Catenin Beta Interacting Protein 1 gene (CTNNBIP1). By characterizing epigenetically altered sites, we identify possible pathways/mechanisms that might have a role in the accelerated aging of progeroid laminopathies.
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Affiliation(s)
- Yosra Bejaoui
- College of Health and Life SciencesQatar FoundationHamad Bin Khalifa UniversityDohaQatar
| | - Aleem Razzaq
- College of Health and Life SciencesQatar FoundationHamad Bin Khalifa UniversityDohaQatar
| | | | - Junko Oshima
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
- Department of Clinical Cell Biology and MedicineGraduate School of MedicineChiba UniversityChibaJapan
| | - Andre Megarbane
- Department of Human GeneticsGilbert and Rose‐Marie Ghagoury School of MedicineLebanese American UniversityByblosLebanon
- Institut Jérôme LejeuneParisFrance
| | - Abeer Qannan
- College of Health and Life SciencesQatar FoundationHamad Bin Khalifa UniversityDohaQatar
| | - Ramya Potabattula
- Institute of Human GeneticsJulius Maximilians UniversityWürzburgGermany
| | - Tanvir Alam
- College of Science and EngineeringHamad Bin Khalifa UniversityDohaQatar
| | - George M. Martin
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Henning F. Horn
- College of Health and Life SciencesQatar FoundationHamad Bin Khalifa UniversityDohaQatar
| | - Thomas Haaf
- Institute of Human GeneticsJulius Maximilians UniversityWürzburgGermany
| | - Steve Horvath
- Department of Human GeneticsDavid Geffen School of MedicineUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Department of BiostatisticsFielding School of Public HealthUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Nady El Hajj
- College of Health and Life SciencesQatar FoundationHamad Bin Khalifa UniversityDohaQatar
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17
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COP1 Acts as a Ubiquitin Ligase for PCDH9 Ubiquitination and Degradation in Human Glioma. Mol Neurobiol 2022; 59:2378-2388. [PMID: 35084653 DOI: 10.1007/s12035-021-02634-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
Constitutive photomorphogenic 1 (COP1, also known as RFWD2), a ring-finger-type E3 ubiquitin ligase, has been reported to play a pivotal role in the regulation of cell growth, apoptosis, and DNA repair. Accumulating evidence has suggested that COP1 plays a role in tumorigenesis by triggering the ubiquitination and degradation of its substrates, but the potential mechanism remains unclear. In this study, COP1 was used as a bait in a yeast two-hybrid experiment to screen COP1-interacting proteins in a human brain cDNA library, and the results indicated that protocadherin 9 (PCDH9) was a potential binding protein of COP1. The interaction between and colocalization of COP1 and PCDH9 was further confirmed by coimmunoprecipitation (co-IP) assay and immunofluorescent staining. Subsequently, we demonstrated that COP1 acted as an E3 ligase to promote the ubiquitination and degradation of PCDH9 through the proteasome pathway in glioma cells. Furthermore, we identified that the type of COP1 mediated PCDH9 ubiquitination was Lys48-linked polyubiquitination. Finally, we found that the COP1 protein level was inversely correlated with the PCDH9 protein level in human glioma tissues. Taken together, our results suggest that COP1 is an E3 ubiquitin ligase for PCDH9 and reveal an important mechanism for PCDH9 regulation in human glioma.
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18
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A Genome-Wide Profiling of Glioma Patients with an IDH1 Mutation Using the Catalogue of Somatic Mutations in Cancer Database. Cancers (Basel) 2021; 13:cancers13174299. [PMID: 34503108 PMCID: PMC8428353 DOI: 10.3390/cancers13174299] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Glioma patients that present a somatic mutation in the isocitrate dehydrogenase 1 (IDH1) gene have a significantly better prognosis and overall survival than patients with the wild-type genotype. An IDH1 mutation is hypothesized to occur early during cellular transformation and leads to further genetic instability. A genome-wide profiling of glioma patients in the Catalogue of Somatic Mutations in Cancer (COSMIC) database was performed to classify the genetic differences in IDH1-mutant versus IDH1-wildtype patients. This classification will aid in a better understanding of how this specific mutation influences the genetic make-up of glioma and the resulting prognosis. Key differences in co-mutation and gene expression levels were identified that correlate with an improved prognosis. Abstract Gliomas are differentiated into two major disease subtypes, astrocytoma or oligodendroglioma, which are then characterized as either IDH (isocitrate dehydrogenase)-wild type or IDH-mutant due to the dramatic differences in prognosis and overall survival. Here, we investigated the genetic background of IDH1-mutant gliomas using the Catalogue of Somatic Mutations in Cancer (COSMIC) database. In astrocytoma patients, we found that IDH1 is often co-mutated with TP53, ATRX, AMBRA1, PREX1, and NOTCH1, but not CHEK2, EGFR, PTEN, or the zinc finger transcription factor ZNF429. The majority of the mutations observed in these genes were further confirmed to be either drivers or pathogenic by the Cancer-Related Analysis of Variants Toolkit (CRAVAT). Gene expression analysis showed down-regulation of DRG2 and MSN expression, both of which promote cell proliferation and invasion. There was also significant over-expression of genes such as NDRG3 and KCNB1 in IDH1-mutant astrocytoma patients. We conclude that IDH1-mutant glioma is characterized by significant genetic changes that could contribute to a better prognosis in glioma patients.
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19
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LaMassa N, Sverdlov H, Mambetalieva A, Shapiro S, Bucaro M, Fernandez-Monreal M, Phillips GR. Gamma-protocadherin localization at the synapse is associated with parameters of synaptic maturation. J Comp Neurol 2021; 529:2407-2417. [PMID: 33381867 DOI: 10.1002/cne.25102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/16/2020] [Accepted: 12/20/2020] [Indexed: 11/07/2022]
Abstract
Clustered protocadherins (Pcdhs) are a family of ~60 cadherin-like proteins (divided into subclasses α, β, and γ) that regulate dendrite morphology and neural connectivity. Their expression is controlled through epigenetic regulation at a gene cluster encoding the molecules. During neural development, Pcdhs mediate dendrite self-avoidance in some neuronal types through an uncharacterized anti-adhesive mechanism. Pcdhs are also important for dendritic complexity in cortical neurons likely through a pro-adhesive mechanism. Pcdhs have also been postulated to participate in synaptogenesis and connectivity. Some synaptic defects were noted in knockout animals, including synaptic number and physiology, but the role of these molecules in synaptic development is not understood. The effect of Pcdh knockout on dendritic patterning may present a confound to studying synaptogenesis. We showed previously that Pcdh-γs are highly enriched in intracellular compartments in dendrites and spines with localization at only a few synaptic clefts. To gain insight into how Pcdh-γs might affect synapses, we compared synapses that harbored Pcdh-γs versus those that did not for parameters of synaptic maturation including pre- and postsynaptic size, postsynaptic perforations, and spine morphology by light microscopy in cultured hippocampal neurons and by serial section immuno-electron microscopy in hippocampal CA1. In mature neurons, synapses immunopositive for Pcdh-γs were larger in diameter with more frequent perforations. Analysis of spines in cultured neurons revealed that mushroom spines were more frequently immunopositive for Pcdh-γs at their tips than thin spines. These results suggest that Pcdh-γ function at the synapse may be related to promotion of synaptic maturation and stabilization.
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Affiliation(s)
- Nicole LaMassa
- Program in Biology, Neuroscience Subprogram, CUNY Graduate Center, New York, New York, USA.,Department of Biology, College of Staten Island, CUNY, New York, New York, USA
| | - Hanna Sverdlov
- Department of Biology, College of Staten Island, CUNY, New York, New York, USA
| | - Aliya Mambetalieva
- Department of Biology, College of Staten Island, CUNY, New York, New York, USA
| | - Stacy Shapiro
- Department of Biology, College of Staten Island, CUNY, New York, New York, USA
| | - Michael Bucaro
- Department of Biology, College of Staten Island, CUNY, New York, New York, USA
| | - Monica Fernandez-Monreal
- University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, F-33000 Bordeaux, France
| | - Greg R Phillips
- Program in Biology, Neuroscience Subprogram, CUNY Graduate Center, New York, New York, USA.,Department of Biology, College of Staten Island, CUNY, New York, New York, USA.,Center for Developmental Neuroscience, College of Staten Island, CUNY, New York, New York, USA
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20
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Alberry B, Laufer BI, Chater-Diehl E, Singh SM. Epigenetic Impacts of Early Life Stress in Fetal Alcohol Spectrum Disorders Shape the Neurodevelopmental Continuum. Front Mol Neurosci 2021; 14:671891. [PMID: 34149355 PMCID: PMC8209299 DOI: 10.3389/fnmol.2021.671891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/30/2021] [Indexed: 12/24/2022] Open
Abstract
Neurodevelopment in humans is a long, elaborate, and highly coordinated process involving three trimesters of prenatal development followed by decades of postnatal development and maturation. Throughout this period, the brain is highly sensitive and responsive to the external environment, which may provide a range of inputs leading to positive or negative outcomes. Fetal alcohol spectrum disorders (FASD) result from prenatal alcohol exposure (PAE). Although the molecular mechanisms of FASD are not fully characterized, they involve alterations to the regulation of gene expression via epigenetic marks. As in the prenatal stages, the postnatal period of neurodevelopment is also sensitive to environmental inputs. Often this sensitivity is reflected in children facing adverse conditions, such as maternal separation. This exposure to early life stress (ELS) is implicated in the manifestation of various behavioral abnormalities. Most FASD research has focused exclusively on the effect of prenatal ethanol exposure in isolation. Here, we review the research into the effect of prenatal ethanol exposure and ELS, with a focus on the continuum of epigenomic and transcriptomic alterations. Interestingly, a select few experiments have assessed the cumulative effect of prenatal alcohol and postnatal maternal separation stress. Regulatory regions of different sets of genes are affected by both treatments independently, and a unique set of genes are affected by the combination of treatments. Notably, epigenetic and gene expression changes converge at the clustered protocadherin locus and oxidative stress pathway. Functional studies using epigenetic editing may elucidate individual contributions of regulatory regions for hub genes and further profiling efforts may lead to the development of non-invasive methods to identify children at risk. Taken together, the results favor the potential to improve neurodevelopmental outcomes by epigenetic management of children born with FASD using favorable postnatal conditions with or without therapeutic interventions.
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Affiliation(s)
- Bonnie Alberry
- Department of Biology, Faculty of Science, The University of Western Ontario, London, ON, Canada
| | - Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA, United States.,Genome Center, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States
| | - Eric Chater-Diehl
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Shiva M Singh
- Department of Biology, Faculty of Science, The University of Western Ontario, London, ON, Canada
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21
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Abstract
OBJECTIVE Comprehensive molecular profiling of radioresistant and cystic vestibular schwannoma (VS) subtypes. STUDY DESIGN Our study utilized whole-exome sequencing (WES), RNA-sequencing (RNAseq), and correlated clinical data from 12 samples (2 samples of solid sporadic subtype, 8 with cystic changes, and 2 previously irradiated). SETTING Academic medical center. PATIENTS Patients diagnosed with VS who required surgical treatment. Inclusion: Cystic and radioresistant tumors matched to age and tumor volume, with solid sporadic VS samples as control; Exclusion: NF-2 patients. INTERVENTION(S) WES using custom probes for copy number analysis. A modified version of the Agilent Human Whole Exome sequencing hybrid capture system was used to process samples. Recurrent variants were identified and compared between groups. Leukocyte-derived DNA was utilized as internal control to reduce false-positives. MAIN OUTCOME MEASURE(S) Analysis of genetic landscape of VS subtypes (naive solid VS, cystic VS, and previously irradiated VS) by performing deep next-generation sequencing. RESULTS WES data achieved a mean coverage of 202X and RNAseq generated an average of 74 million total reads. As a group, 25% of samples had 22q loss. Somatic analysis identified previously reported genes and multiple novel mutations across samples. Differential expression analysis of RNAseq data found significantly mutated genes such as COL6A3, CLMP, ART4, Lumican that were shared by both cystic VS and irradiated VS, but not seen in sporadic VS. CONCLUSIONS Using WES we were able to demonstrate that cystic and irradiated samples are subtypes of VS with an increased mutation burden and a unique genetic fingerprint. We identified differences between the genomic and molecular profile of cystic VS and radioresistant VS. Our results help advance the understanding of the pathophysiology of these tumor subtypes and suggest possible molecular targets for novel treatment strategies.
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22
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Koldobskiy MA, Jenkinson G, Abante J, Rodriguez DiBlasi VA, Zhou W, Pujadas E, Idrizi A, Tryggvadottir R, Callahan C, Bonifant CL, Rabin KR, Brown PA, Ji H, Goutsias J, Feinberg AP. Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis. Nat Biomed Eng 2021; 5:360-376. [PMID: 33859388 PMCID: PMC8370714 DOI: 10.1038/s41551-021-00703-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/18/2021] [Indexed: 02/02/2023]
Abstract
In cancer, linking epigenetic alterations to drivers of transformation has been difficult, in part because DNA methylation analyses must capture epigenetic variability, which is central to tumour heterogeneity and tumour plasticity. Here, by conducting a comprehensive analysis, based on information theory, of differences in methylation stochasticity in samples from patients with paediatric acute lymphoblastic leukaemia (ALL), we show that ALL epigenomes are stochastic and marked by increased methylation entropy at specific regulatory regions and genes. By integrating DNA methylation and single-cell gene-expression data, we arrived at a relationship between methylation entropy and gene-expression variability, and found that epigenetic changes in ALL converge on a shared set of genes that overlap with genetic drivers involved in chromosomal translocations across the disease spectrum. Our findings suggest that an epigenetically driven gene-regulation network, with UHRF1 (ubiquitin-like with PHD and RING finger domains 1) as a central node, links genetic drivers and epigenetic mediators in ALL.
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Affiliation(s)
- Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Garrett Jenkinson
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Varenka A Rodriguez DiBlasi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Cancer Immunology and Immune Modulation, Boehringer Ingelheim, Ridgefield, CT, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Elisabet Pujadas
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Colin Callahan
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Challice L Bonifant
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen R Rabin
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Patrick A Brown
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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23
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Saadatmand F, Gurdziel K, Jackson L, Kwabi-Addo B, Ruden DM. DNA methylation and exposure to violence among African American young adult males. Brain Behav Immun Health 2021; 14:100247. [PMID: 34589758 PMCID: PMC8474503 DOI: 10.1016/j.bbih.2021.100247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 02/02/2023] Open
Abstract
Exposure to violence (ETV) has been linked to epigenomics mechanisms such as DNA methylation (DNAm). We used epigenetic profiling of blood collected from 32 African American young adult males who lived in Washington DC to determine if changes in DNAm at CpG sites affiliated with nervous and immune system were associated with exposure to violence. Pathway analysis of differentially methylated regions comparing high and low ETV groups revealed an enrichment of gene sets annotated to nervous system and immune ontologies. Many of these genes are known to interact with each other which suggests DNAm alters gene function in the nervous and immune system in response to ETV. Using data from a unique age group, young African American adult males, we provide evidence that lifetime ETV could impact DNA methylation in genes impacted at Central Nervous System and Immune Function sites. METHOD Methylation analysis was performed on DNA collected from the blood of participants classified with either high or low lifetime ETV. Illumina®MethylationEPIC Beadchips (~850k CpG sites) were processed on the iScan System to examine whole-genome methylation differences. Differentially methylated CpG-sites between high (n = 19) and low (n = 13) groups were identified using linear regression with violence and substance abuse as model covariates. Gene ontology analysis was used to identify enrichment categories from probes annotated to the nearest gene. RESULTS A total of 595 probes (279 hypermethylated; 316 hypomethylated) annotated to 383 genes were considered differentially methylated in association with ETV. Males with high ETV showed elevated methylation in several signaling pathways but were most impacted at Central Nervous System and Immune Function affiliated sites. Eight candidate genes were identified that play important biological roles in stress response to violence with HDAC4 (10%), NR4A3 (11%), NR4A2 (12%), DSCAML1(12%), and ELAVL3 (13%) exhibiting higher levels in the low ETV group and DLGAP1 (10%), SHANK2 (10%), and NRG1(11%) having increased methylation in the high ETV group. These findings suggest that individuals subjected to high ETV may be at risk for poor health outcomes that have not been reported previously.
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Affiliation(s)
- Forough Saadatmand
- Department of Pediatrics, College of Medicine, Howard University, Washington, DC, USA,Corresponding author.
| | - Katherine Gurdziel
- Office of the Vice President of Research, Wayne State University, Detroit, MI, USA
| | - Latifa Jackson
- Department of Pediatrics, College of Medicine, Howard University, Washington, DC, USA,W. Montague Cobb Research Laboratory, College of Arts and Sciences, Howard University, Washington, DC, USA
| | - Bernard Kwabi-Addo
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC, USA
| | - Douglas M. Ruden
- Department of Ob/Gyn, CS Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI, USA,Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, MI, USA
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24
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Zhang S, Zhang X, Purmann C, Ma S, Shrestha A, Davis KN, Ho M, Huang Y, Pattni R, Hung Wong W, Bernstein JA, Hallmayer J, Urban AE. Network Effects of the 15q13.3 Microdeletion on the Transcriptome and Epigenome in Human-Induced Neurons. Biol Psychiatry 2021; 89:497-509. [PMID: 32919612 PMCID: PMC9359316 DOI: 10.1016/j.biopsych.2020.06.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND The 15q13.3 microdeletion is associated with several neuropsychiatric disorders, including autism and schizophrenia. Previous association and functional studies have investigated the potential role of several genes within the deletion in neuronal dysfunction, but the molecular effects of the deletion as a whole remain largely unknown. METHODS Induced pluripotent stem cells, from 3 patients with the 15q13.3 microdeletion and 3 control subjects, were generated and converted into induced neurons. We analyzed the effects of the 15q13.3 microdeletion on genome-wide gene expression, DNA methylation, chromatin accessibility, and sensitivity to cisplatin-induced DNA damage. Furthermore, we measured gene expression changes in induced neurons with CRISPR (clustered regularly interspaced short palindromic repeats) knockouts of individual 15q13.3 microdeletion genes. RESULTS In both induced pluripotent stem cells and induced neurons, gene copy number change within the 15q13.3 microdeletion was accompanied by significantly decreased gene expression and no compensatory changes in DNA methylation or chromatin accessibility, supporting the model that haploinsufficiency of genes within the deleted region drives the disorder. Furthermore, we observed global effects of the microdeletion on the transcriptome and epigenome, with disruptions in several neuropsychiatric disorder-associated pathways and gene families, including Wnt signaling, ribosome function, DNA binding, and clustered protocadherins. Individual gene knockouts mirrored many of the observed changes in an overlapping fashion between knockouts. CONCLUSIONS Our multiomics analysis of the 15q13.3 microdeletion revealed downstream effects in pathways previously associated with neuropsychiatric disorders and indications of interactions between genes within the deletion. This molecular systems analysis can be applied to other chromosomal aberrations to further our etiological understanding of neuropsychiatric disorders.
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Affiliation(s)
- Siming Zhang
- Department of Genetics, School of Humanities and Science, Stanford University, Stanford, California
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Carolin Purmann
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Shining Ma
- Department of Pediatrics, School of Humanities and Sciences, Stanford University, Stanford, California
| | - Anima Shrestha
- School of Medicine, Stanford University, and Department of Statistics, School of Humanities and Sciences, Stanford University, Stanford, California
| | - Kasey N Davis
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Marcus Ho
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Yiling Huang
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Wing Hung Wong
- Department of Pediatrics, School of Humanities and Sciences, Stanford University, Stanford, California
| | - Jonathan A Bernstein
- Department of Human Biology, School of Humanities and Science, Stanford University, Stanford, California
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California
| | - Alexander E Urban
- Department of Genetics, School of Humanities and Science, Stanford University, Stanford, California; Department of Psychiatry and Behavioral Sciences, School of Humanities and Science, Stanford University, Stanford, California.
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25
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Liu Y, Chang X, Qu HQ, Tian L, Glessner J, Qu J, Li D, Qiu H, Sleiman P, Hakonarson H. Rare Recurrent Variants in Noncoding Regions Impact Attention-Deficit Hyperactivity Disorder (ADHD) Gene Networks in Children of both African American and European American Ancestry. Genes (Basel) 2021; 12:310. [PMID: 33671795 PMCID: PMC7927037 DOI: 10.3390/genes12020310] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022] Open
Abstract
Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with poorly understood molecular mechanisms that results in significant impairment in children. In this study, we sought to assess the role of rare recurrent variants in non-European populations and outside of coding regions. We generated whole genome sequence (WGS) data on 875 individuals, including 205 ADHD cases and 670 non-ADHD controls. The cases included 116 African Americans (AA) and 89 European Americans (EA), and the controls included 408 AA and 262 EA. Multiple novel rare recurrent variants were identified in exonic regions, functionally classified as stop-gains and frameshifts for known ADHD genes. Deletion in introns of the protocadherins families and the ncRNA HGB8P were identified in two independent EA ADHD patients. A meta-analysis of the two ethnicities for differential ADHD recurrent variants compared to controls shows a small number of overlaps. These results suggest that rare recurrent variants in noncoding regions may be involved in the pathogenesis of ADHD in children of both AA and EA ancestry; thus, WGS could be a powerful discovery tool for studying the molecular mechanisms of ADHD.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Xiao Chang
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Hui-Qi Qu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Lifeng Tian
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Joseph Glessner
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Jingchun Qu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Dong Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Haijun Qiu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Patrick Sleiman
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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26
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Luo R, Mukherjee N, Chen S, Jiang Y, Arshad SH, Holloway JW, Hedman A, Gruzieva O, Andolf E, Pershagen G, Almqvist C, Karmaus WJ. Paternal DNA Methylation May Be Associated With Gestational Age at Birth. Epigenet Insights 2020; 13:2516865720930701. [PMID: 32964196 PMCID: PMC7488897 DOI: 10.1177/2516865720930701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/09/2020] [Indexed: 11/15/2022] Open
Abstract
Background: How epigenetic modifications of DNA are associated with gestational age at birth is not fully understood. We investigated potential effects of differential paternal DNA methylation (DNAm) on offspring gestational age at birth by conducting an epigenome-wide search for cytosine-phosphate-guanine (CpG) sites. Methods: Study participants in this study consist of male cohort members or partners of the F1-generation of the Isle of Wight Birth Cohort (IoWBC). DNAm levels in peripheral blood from F1-fathers (n = 92) collected around pregnancy of their spouses were analyzed using the Illumina 450K array. A 5-step statistical analysis was performed. First, a training-testing screening approach was applied to select CpG sites that are potentially associated with gestational age at birth. Second, functional enrichment analysis was employed to identify biological processes. Third, by centralizing on biologically informative genes, Cox proportional hazards models were used to assess the hazard ratios of individual paternal CpGs on gestational age adjusting for confounders. Fourth, to assess the validity of our results, we compared our CpG-gestational age correlations within a Born into Life Study in Sweden (n = 15). Finally, we investigated the correlation between the detected CpGs and differential gene expression in F2 cord blood in the IoWBC. Results: Analysis of DNAm of fathers collected around their partner’s pregnancy identified 216 CpG sites significantly associated with gestational age at birth. Functional enrichment pathways analyses of the annotated genes revealed 2 biological pathways significantly related to cell-cell membrane adhesion molecules. Differential methylation of 9 cell membrane adhesion pathway-related CpGs were significantly associated with gestational age at birth after adjustment for confounders. The replication sample showed correlation coefficients of 2 pathway-related CpGs with gestational age at birth within 95% confidence intervals of correlation coefficients in IoWBC. Finally, CpG sites of protocadherin (PCDH) gene clusters were associated with gene expression of PCDH in F2 cord blood. Conclusions: Our findings suggest that differential paternal DNAm may affect gestational age at birth through cell-cell membrane adhesion molecules. The results are novel but require future replication in a larger cohort.
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Affiliation(s)
- Rui Luo
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Nandini Mukherjee
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Su Chen
- Department of Mathematical Sciences, University of Memphis, Memphis, TN, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - S Hasan Arshad
- The David Hide Asthma and Allergy Research Centre, Newport, UK.,Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Anna Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Ellika Andolf
- Department of Clinical Sciences, Danderyd Hospital, Stockholm, Sweden
| | - Goran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Unit of Pediatric Allergy and Pulmonology at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Wilfried Jj Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
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27
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Flaherty E, Maniatis T. The role of clustered protocadherins in neurodevelopment and neuropsychiatric diseases. Curr Opin Genet Dev 2020; 65:144-150. [PMID: 32679536 DOI: 10.1016/j.gde.2020.05.041] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/15/2020] [Accepted: 05/31/2020] [Indexed: 12/17/2022]
Abstract
During development, individual neurons extend highly branched arbors that innervate the surrounding territory, enabling the formation of appropriate synaptic connections. The clustered protocadherins (cPCDH), a family of diverse cell-surface homophilic proteins, provide each neuron with a cell specific identity required for distinguishing between self versus non-self. While only 52 unique cPcdh isoforms are encoded in the human genome, a combination of stochastic promoter choice and the formation of a protein lattice through engagement of adjacent cPCDH protein cis/trans-tetramers confer the high degree of cellular specificity required for self-recognition. Studies of mice bearing deletions of individual cPcdh gene clustees have identified deficits in circuit formation and behavior. In humans, single nucleotide variants scattered across the cPCDH locus have been identified, which associate with multiple neurodevelopmental disorders, including autism and schizophrenia. To advance our understanding of cPCDH stochastic choice and maintenance, function across cell types, and contribution to neuropsychiatric disease pathogenesis, hiPSC-based models have been developed. Ultimately, integration of human genetic data, biochemical assays, and functional studies is needed to uncover the mechanism underlying neurite repulsion, which has been implicated in neurodevelopmental disorders.
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Affiliation(s)
- Erin Flaherty
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, United States; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, 10027, United States
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, United States; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, 10027, United States; New York Genome Center, New York, NY 10013, United States.
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28
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Pancho A, Aerts T, Mitsogiannis MD, Seuntjens E. Protocadherins at the Crossroad of Signaling Pathways. Front Mol Neurosci 2020; 13:117. [PMID: 32694982 PMCID: PMC7339444 DOI: 10.3389/fnmol.2020.00117] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/08/2020] [Indexed: 12/25/2022] Open
Abstract
Protocadherins (Pcdhs) are cell adhesion molecules that belong to the cadherin superfamily, and are subdivided into clustered (cPcdhs) and non-clustered Pcdhs (ncPcdhs) in vertebrates. In this review, we summarize their discovery, expression mechanisms, and roles in neuronal development and cancer, thereby highlighting the context-dependent nature of their actions. We furthermore provide an extensive overview of current structural knowledge, and its implications concerning extracellular interactions between cPcdhs, ncPcdhs, and classical cadherins. Next, we survey the known molecular action mechanisms of Pcdhs, emphasizing the regulatory functions of proteolytic processing and domain shedding. In addition, we outline the importance of Pcdh intracellular domains in the regulation of downstream signaling cascades, and we describe putative Pcdh interactions with intracellular molecules including components of the WAVE complex, the Wnt pathway, and apoptotic cascades. Our overview combines molecular interaction data from different contexts, such as neural development and cancer. This comprehensive approach reveals potential common Pcdh signaling hubs, and points out future directions for research. Functional studies of such key factors within the context of neural development might yield innovative insights into the molecular etiology of Pcdh-related neurodevelopmental disorders.
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Affiliation(s)
- Anna Pancho
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Tania Aerts
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuela D Mitsogiannis
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
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29
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Yu H, Jiang X, Jiang L, Zhou H, Bao J, Zhu X, Liu F, Huang J. Protocadherin 8 (PCDH8) Inhibits Proliferation, Migration, Invasion, and Angiogenesis in Esophageal Squamous Cell Carcinoma. Med Sci Monit 2020; 26:e920665. [PMID: 32330123 PMCID: PMC7197227 DOI: 10.12659/msm.920665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Protocadherin 8 (PCDH8) functions as a tumor-suppressor gene in many types of cancer. This study aimed to investigate the role of PCDH8 in esophageal squamous cell carcinoma (ESCC). MATERIAL AND METHODS Cell proliferation, apoptosis, transwell assay, tube formation assays, and tumor xenograft experiment were performed to explore the role of PCDH8 in the progression of ESCC. RESULTS PCDH8 was found to be downregulated in ESCC cells. Ectopic expression of PCDH8 blocked proliferation, invasion, and migration and induced apoptosis in ESCC cells. Furthermore, vascular endothelial growth factor A (VEGFA) secretion and the AKT signaling pathway were also inhibited when PCDH8 was upregulated. PCDH8 overexpression suppressed epithelial-mesenchymal transition (EMT) and pro-angiogenic activity of ESCC cells. In a mouse model of ESCC xenograft tumors, PCDH8 overexpression remarkably restrained tumor cell growth, with the tumor inhibition rate of 75.2%. PCDH8 was the target of miR-200c and had a negative correlation with miR-200c. CONCLUSIONS PCDH8 exerts a tumor-suppressive effect against ESCC cells. However, further studies are required to elucidate the exact molecular mechanism underlying the antitumor activity of PCDH8 in ESCC.
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Affiliation(s)
- Hong Yu
- Department of Pathology, Taizhou People's Hospital, Taizhou, Jiangsu, China (mainland)
| | - Xiaoqin Jiang
- Department of Pathology, Taizhou People's Hospital, Taizhou, Jiangsu, China (mainland)
| | - Lin Jiang
- Department of Anesthesiology, Taizhou People's Hospital, Taizhou, Jiangsu, China (mainland)
| | - Huiling Zhou
- Department of Pathology, Taizhou People's Hospital, Taizhou, Jiangsu, China (mainland)
| | - Jingjing Bao
- Department of Pathology, Taizhou People's Hospital, Taizhou, Jiangsu, China (mainland)
| | - Xiaowei Zhu
- Department of Pathology, Taizhou People's Hospital, Taizhou, Jiangsu, China (mainland)
| | - Fuxing Liu
- Department of Pathology, Taizhou People's Hospital, Taizhou, Jiangsu, China (mainland)
| | - Junxing Huang
- Department of Oncology, Taizhou People's Hospital, Taizhou, Jiangsu, China (mainland)
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30
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Zhu L, Liang J, Xia B, Xu Y, Qian Z, Ma S, Zhang S. Identification of somatic copy number variations in plasma cell free DNA correlating with intrinsic resistances to EGFR targeted therapy in T790M negative non-small cell lung cancer. J Thorac Dis 2020; 12:883-892. [PMID: 32274156 PMCID: PMC7138977 DOI: 10.21037/jtd.2019.12.97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Background About 20–30% EGFR-mutant non-small lung cancer show intrinsic resistance to EGFR targeted therapies. Compared to T790M positive in acquired resistance patients, little is known about EGFR-TKI intrinsic resistance for T790M negative patients. Methods Thirty-one patients with advanced stage lung cancer, including 18 patients with intrinsic resistance (PFS <6 months) and 13 patients with acquired resistance (PFS >36 months) but are negative for plasma T790M were recruited in the study. Plasma cell free DNA was profiled by low coverage whole genome sequencing with median genome coverage of 1.86X by Illumina X10. Sequencing coverage across chromosomes was summarized by samtools, and normalized by segmentation analysis as provided by R package ‘DNACopy’. Results The most frequent chromosomal changes were found on chr7, chr1 and chr8. Among them, chr7p gains were found in 12 (66.7%) intrinsic resistance and 4 (30.7%) acquired resistance patients. The gene EGFR was found located on the focal amplification peak of chr7p. The performance of 7p gain to predict intrinsic resistance reaches AUC =0.902. Similarly, focal amplifications were also found on chromosome 5, 16 and 22, where tumor related gene PCDHA@, ADAMTS18 and CRKL were located. Focal deletions were also found in chr1, 8, 10 and 16, where genes SFTPA1/2, DLC1, PTEN and CDH1 are located. Conclusions The results suggest cell free DNA copy number might be a useful peripheral blood tumor biomarker for predicting intrinsic resistance of EGFR targeted therapy and prognosis.
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Affiliation(s)
- Lucheng Zhu
- Center for Translational Medicine, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou 310006, China.,Department of Oncology, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou 310006, China.,Department of Oncology, Hangzhou Cancer Hospital, Hangzhou 310002, China
| | - Jiafeng Liang
- Center for Translational Medicine, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou 310006, China.,Department of Oncology, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou 310006, China
| | - Bing Xia
- Department of Oncology, Hangzhou Cancer Hospital, Hangzhou 310002, China
| | - Yasi Xu
- Center for Translational Medicine, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou 310006, China.,Center for Translational Medicine, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | | | - Shenglin Ma
- Center for Translational Medicine, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou 310006, China.,Department of Oncology, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou 310006, China.,Department of Oncology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Shirong Zhang
- Center for Translational Medicine, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou 310006, China.,Center for Translational Medicine, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.,Department of Oncology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
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31
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Haertle L, Müller T, Lardenoije R, Maierhofer A, Dittrich M, Riemens RJM, Stora S, Roche M, Leber M, Riedel-Heller S, Wagner M, Scherer M, Ravel A, Mircher C, Cieuta-Walti C, Durand S, van de Hove DLA, Hoffmann P, Ramirez A, Haaf T, El Hajj N, Mégarbané A. Methylomic profiling in trisomy 21 identifies cognition- and Alzheimer's disease-related dysregulation. Clin Epigenetics 2019; 11:195. [PMID: 31843015 PMCID: PMC6916110 DOI: 10.1186/s13148-019-0787-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 11/25/2019] [Indexed: 11/28/2022] Open
Abstract
Abstract Background Trisomy 21 (T21) is associated with intellectual disability that ranges from mild to profound with an average intellectual quotient of around 50. Furthermore, T21 patients have a high risk of developing Alzheimer’s disease (AD) early in life, characterized by the presence of senile plaques of amyloid protein and neurofibrillary tangles, leading to neuronal loss and cognitive decline. We postulate that epigenetic factors contribute to the observed variability in intellectual disability, as well as at the level of neurodegeneration seen in T21 individuals. Materials and Methods A genome-wide DNA methylation study was performed using Illumina Infinium® MethylationEPIC BeadChips on whole blood DNA of 3 male T21 patients with low IQ, 8 T21 patients with high IQ (4 males and 4 females), and 21 age- and sex-matched control samples (12 males and 9 females) in order to determine whether DNA methylation alterations could help explain variation in cognitive impairment between individuals with T21. In view of the increased risk of developing AD in T21 individuals, we additionally investigated the T21-associated sites in published blood DNA methylation data from the AgeCoDe cohort (German study on Ageing, Cognition, and Dementia). AgeCoDe represents a prospective longitudinal study including non-demented individuals at baseline of which a part develops AD dementia at follow-up. Results Two thousand seven hundred sixteen differentially methylated sites and regions discriminating T21 and healthy individuals were identified. In the T21 high and low IQ comparison, a single CpG located in the promoter of PELI1 was differentially methylated after multiple testing adjustment. For the same contrast, 69 differentially methylated regions were identified. Performing a targeted association analysis for the significant T21-associated CpG sites in the AgeCoDe cohort, we found that 9 showed significant methylation differences related to AD dementia, including one in the ADAM10 gene. This gene has previously been shown to play a role in the prevention of amyloid plaque formation in the brain. Conclusion The differentially methylated regions may help understand the interaction between methylation alterations and cognitive function. In addition, ADAM10 might be a valuable blood-based biomarker for at least the early detection of AD.
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Affiliation(s)
- Larissa Haertle
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,Division of Hematology and Oncology, Department of Internal Medicine II, University Hospital, Wuerzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilian University, Wuerzburg, Germany
| | - Roy Lardenoije
- Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, the Netherlands.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Anna Maierhofer
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,Department of Bioinformatics, Julius Maximilian University, Wuerzburg, Germany
| | - Renzo J M Riemens
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, the Netherlands
| | - Samantha Stora
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Mathilde Roche
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Markus Leber
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937, Cologne, Germany.,Department of Neurodegeneration and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, 04103, Leipzig, Germany
| | - Michael Wagner
- Department of Neurodegeneration and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Martin Scherer
- Department of Primary Medical Care, University Medical Centre Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Aimé Ravel
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Clotilde Mircher
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | | | - Sophie Durand
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France
| | - Daniel L A van de Hove
- Department of Psychiatry & Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, the Netherlands.,Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 53127, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, 53127, Bonn, Germany.,Division of Medical Genetics, University Hospital and Department of Biomedicine, University of Basel, CH-4058, Basel, Switzerland
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937, Cologne, Germany.,Department of Neurodegeneration and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany.,College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - André Mégarbané
- Institut Jérôme Lejeune, CRB BioJeL, 37 rue des Volontaires, Paris, France.
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32
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Paul JL, Dashtipour K, Chen Z, Wang C. DNA methylome study of human cerebellar tissues identified genes and pathways possibly involved in essential tremor. PRECISION CLINICAL MEDICINE 2019; 2:221-234. [PMID: 31886034 PMCID: PMC6927097 DOI: 10.1093/pcmedi/pbz028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/30/2019] [Accepted: 12/01/2019] [Indexed: 01/13/2023] Open
Abstract
Background Essential tremor (ET) is a neurological syndrome of unknown origin with poorly understood etiology and pathogenesis. It is suggested that the cerebellum and its tracts may be involved in the pathophysiology of ET. DNA methylome interrogation of cerebellar tissue may help shine some light on the understanding of the mechanism of the development of ET. Our study used postmortem human cerebellum tissue samples collected from 12 ET patients and 11 matched non-ET controls for DNA methylome study to identify differentially methylated genes in ET. Results Using Nugen’s Ovation reduced representation bisulfite sequencing (RRBS), we identified 753 genes encompassing 938 CpG sites with significant differences in DNA methylation between the ET and the control group. Identified genes were further analyzed with Ingenuity Pathway Analysis (IPA) by which we identified certain significant pathways, upstream regulators, diseases and functions, and networks associated with ET. Conclusions Our study provides evidence that there are significant differences in DNA methylation patterns between the ET and control samples, suggesting that the methylation alteration of certain genes in the cerebellum may be associated with ET pathogenesis. The identified genes allude to the GABAergic hypothesis which supports the notation that ET is a neurodegenerative disease, particularly involving the cerebellum.
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Affiliation(s)
- Jennifer L Paul
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Khashayar Dashtipour
- Division of Movement Disorders, Department of Neurology, Loma Linda University Medical Center, Loma Linda, CA 92350, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA.,Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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33
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Chromatin establishes an immature version of neuronal protocadherin selection during the naive-to-primed conversion of pluripotent stem cells. Nat Genet 2019; 51:1691-1701. [PMID: 31740836 PMCID: PMC7061033 DOI: 10.1038/s41588-019-0526-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/30/2019] [Indexed: 01/09/2023]
Abstract
In the mammalian genome, the clustered protocadherin (cPcdh) locus is a paradigm of stochastic gene expression with the potential to generate a unique cPcdh combination in every neuron. Here, we report a chromatin-based mechanism emerging during the transition from the naive to the primed states of cell pluripotency that reduces by orders of magnitude the combinatorial potential in the human cPcdh locus. This mechanism selectively increases the frequency of stochastic selection of a small subset of cPcdh genes after neuronal differentiation in monolayers, months-old organoids, and engrafted cells in the rat spinal cord. Signs of these frequent selections can be observed in the brain throughout fetal development and disappear after birth, unless there is a condition of delayed maturation such as Down Syndrome. We therefore propose that a pattern of limited cPcdh diversity is maintained while human neurons still retain fetal-like levels of maturation. Short and long-term cultures of human stem cell-derived neurons reveal that a pattern of restricted selection of clustered protocadherin isoforms, pre-established in pluripotent cells, distinguishes immature from mature neurons.
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34
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Canzio D, Maniatis T. The generation of a protocadherin cell-surface recognition code for neural circuit assembly. Curr Opin Neurobiol 2019; 59:213-220. [PMID: 31710891 DOI: 10.1016/j.conb.2019.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
The assembly of functional neural circuits in vertebrate organisms requires complex mechanisms of self-recognition and self-avoidance. Neurites (axons and dendrites) from the same neuron recognize and avoid self, but engage in synaptic interactions with other neurons. Vertebrate neural self-avoidance requires the expression of distinct repertoires of clustered Protocadherin (Pcdh) cell-surface protein isoforms, which act as cell-surface molecular barcodes that mediate highly specific homophilic self-recognition, followed by repulsion. The generation of sufficiently diverse cell-surface barcodes is achieved by the stochastic and combinatorial activation of a subset of clustered Pcdh promoters in individual neurons. This remarkable mechanism leads to the generation of enormous molecular diversity at the cell surface. Here we review recent studies showing that stochastic expression of individual Pcdhα isoforms is accomplished through an extraordinary mechanism involving the activation of 'antisense strand' promoter within Pcdhα 'variable' exons, antisense transcription of a long non-coding RNA through the upstream 'sense strand' promoter, demethylation of this promoter, binding of the CTCF/cohesin complex and DNA looping to a distant enhancer through a mechanism of chromatin 'extrusion'.
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Affiliation(s)
- Daniele Canzio
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94143, United States; Department of Neurology, University of California San Francisco, San Francisco, CA, 94143, United States; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94143, United States; Department of Psychiatry, University of California San Francisco, San Francisco, CA, 94143, United States.
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, United States; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, 10027, United States; New York Genome Center, New York, NY 10013, United States.
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35
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Bhak Y, Jeong HO, Cho YS, Jeon S, Cho J, Gim JA, Jeon Y, Blazyte A, Park SG, Kim HM, Shin ES, Paik JW, Lee HW, Kang W, Kim A, Kim Y, Kim BC, Ham BJ, Bhak J, Lee S. Depression and suicide risk prediction models using blood-derived multi-omics data. Transl Psychiatry 2019; 9:262. [PMID: 31624227 PMCID: PMC6797735 DOI: 10.1038/s41398-019-0595-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/09/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
More than 300 million people worldwide experience depression; annually, ~800,000 people die by suicide. Unfortunately, conventional interview-based diagnosis is insufficient to accurately predict a psychiatric status. We developed machine learning models to predict depression and suicide risk using blood methylome and transcriptome data from 56 suicide attempters (SAs), 39 patients with major depressive disorder (MDD), and 87 healthy controls. Our random forest classifiers showed accuracies of 92.6% in distinguishing SAs from MDD patients, 87.3% in distinguishing MDD patients from controls, and 86.7% in distinguishing SAs from controls. We also developed regression models for predicting psychiatric scales with R2 values of 0.961 and 0.943 for Hamilton Rating Scale for Depression-17 and Scale for Suicide Ideation, respectively. Multi-omics data were used to construct psychiatric status prediction models for improved mental health treatment.
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Affiliation(s)
- Youngjune Bhak
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea ,Clinomics Inc., Ulsan, 44919 Republic of Korea
| | - Hyoung-oh Jeong
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea
| | | | - Sungwon Jeon
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea
| | - Juok Cho
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea
| | - Jeong-An Gim
- 0000 0004 0470 5905grid.31501.36Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University, Suwon, 16229 Republic of Korea
| | - Yeonsu Jeon
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea
| | - Asta Blazyte
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Seung Gu Park
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Hak-Min Kim
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea ,Clinomics Inc., Ulsan, 44919 Republic of Korea
| | - Eun-Seok Shin
- Division of Cardiology, Department of Internal Medicine, Ulsan Medical Center, Ulsan, Republic of Korea
| | - Jong-Woo Paik
- 0000 0001 2171 7818grid.289247.2Department of Neuropsychiatry, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hae-Woo Lee
- 0000 0004 0642 340Xgrid.415520.7Department of Psychiatry, Seoul Medical Center, Seoul, Republic of Korea
| | - Wooyoung Kang
- 0000 0001 0840 2678grid.222754.4Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Aram Kim
- 0000 0001 0840 2678grid.222754.4Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yumi Kim
- Clinomics Inc., Ulsan, 44919 Republic of Korea
| | | | - Byung-Joo Ham
- 0000 0001 0840 2678grid.222754.4Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea ,0000 0004 0474 0479grid.411134.2Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea ,0000 0004 0474 0479grid.411134.2Brain Convergence Research Center, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Jong Bhak
- Korean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. .,Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919, Republic of Korea. .,Clinomics Inc., Ulsan, 44919, Republic of Korea. .,Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.
| | - Semin Lee
- Korean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. .,Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919, Republic of Korea.
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Shi C, Yang Y, Zhang L, Yu J, Qin S, Xu H, Gao Y. MiR-200a-3p promoted the malignant behaviors of ovarian cancer cells through regulating PCDH9. Onco Targets Ther 2019; 12:8329-8338. [PMID: 31632082 PMCID: PMC6790212 DOI: 10.2147/ott.s220339] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/13/2019] [Indexed: 12/25/2022] Open
Abstract
Background Increasing evidence has revealed that the aberrant expression of microRNAs (miRNAs) plays vital roles in the development and progression of ovarian cancer. MiR-200a-3p was found to act as an oncogene in a variety of cancers, however, the expression and function of miR-200a-3p in ovarian cancer has not been characterized. Materials and methods The expression of miR-200a-3p in ovarian cancer tissues and cell lines was detected by the RT-qPCR. The influence of miR-200a-3p on the growth of ovarian cancer cells was determined with the Cell Counting Kit-8 assay, colony formation and cell invasion assay. The binding of miR-200a-3p with the 3ʹ-untranslated region (UTR) of PDCH9 was detected by luciferase reporter assay. The expression of PCDH9 was investigated by RT-qPCR and Western blot analysis. Results miR-200a-3p was up-regulated in ovarian cancer tissues and cell lines. Highly expressed miR-200a-3p was significantly associated with the tumor size, tumor metastasis and TNM stage. Overexpression of miR-200a-3p markedly promoted the proliferation, colony formation and invasion of ovarian cancer cells. Functional study uncovered that miR-200a-3p bound the 3ʹ-untranslated region (UTR) of PCDH9 and decreased the expression of PCDH9 in ovarian cancer cells. The expression of miR-200a-3p in ovarian cancer tissues was significantly negatively correlated with that of PCDH9. Restored PCDH9 inhibited the promoting effect of miR-200a-3p on the proliferation of ovarian cancer cells. Conclusion Our results suggested the potential oncogenic function of miR-200a-3p via modulating PCDH9 in ovarian cancer.
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Affiliation(s)
- Can Shi
- Department of Obstetrics and Gynecology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, People's Republic of China
| | - Yijun Yang
- Department of Obstetrics and Gynecology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, People's Republic of China
| | - Lei Zhang
- Department of Obstetrics and Gynecology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, People's Republic of China
| | - Juanpeng Yu
- Department of Obstetrics and Gynecology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, People's Republic of China
| | - Shanshan Qin
- Department of Obstetrics and Gynecology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, People's Republic of China
| | - Hongge Xu
- Department of Obstetrics and Gynecology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, People's Republic of China
| | - Yingchun Gao
- Department of Obstetrics and Gynecology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, People's Republic of China
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Wang CY, Brand H, Shaw ND, Talkowski ME, Lee JT. Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans. Genetics 2019; 213:685-703. [PMID: 31420322 PMCID: PMC6781896 DOI: 10.1534/genetics.119.302600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an architectural factor critical for X-chromosome inactivation (XCI) and the repression of select autosomal gene clusters. In mice, homozygous nonsense mutations in Smchd1 cause female-specific embryonic lethality due to an XCI defect. However, although human mutations in SMCHD1 are associated with congenital arhinia and facioscapulohumeral muscular dystrophy type 2 (FSHD2), the diseases do not show a sex-specific bias, despite the essential nature of XCI in humans. To investigate whether there is a dosage imbalance for the sex chromosomes, we here analyze transcriptomic data from arhinia and FSHD2 patient blood and muscle cells. We find that X-linked dosage compensation is maintained in these patients. In mice, SMCHD1 controls not only protocadherin (Pcdh) gene clusters, but also Hox genes critical for craniofacial development. Ablating Smchd1 results in aberrant expression of these genes, coinciding with altered chromatin states and three-dimensional (3D) topological organization. In a subset of FSHD2 and arhinia patients, we also found dysregulation of clustered PCDH, but not HOX genes. Overall, our study demonstrates preservation of XCI in arhinia and FSHD2, and implicates SMCHD1 in the regulation of the 3D organization of select autosomal gene clusters.
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Affiliation(s)
- Chen-Yu Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Harrison Brand
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Natalie D Shaw
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Michael E Talkowski
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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38
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Vega-Benedetti AF, Loi E, Moi L, Blois S, Fadda A, Antonelli M, Arcella A, Badiali M, Giangaspero F, Morra I, Columbano A, Restivo A, Zorcolo L, Gismondi V, Varesco L, Bellomo SE, Giordano S, Canale M, Casadei-Gardini A, Faloppi L, Puzzoni M, Scartozzi M, Ziranu P, Cabras G, Cocco P, Ennas MG, Satta G, Zucca M, Canzio D, Zavattari P. Clustered protocadherins methylation alterations in cancer. Clin Epigenetics 2019; 11:100. [PMID: 31288858 PMCID: PMC6617643 DOI: 10.1186/s13148-019-0695-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/11/2019] [Indexed: 01/29/2023] Open
Abstract
Background Clustered protocadherins (PCDHs) map in tandem at human chromosome 5q31 and comprise three multi-genes clusters: α-, β- and γ-PCDH. The expression of this cluster consists of a complex mechanism involving DNA hub formation through DNA-CCTC binding factor (CTCF) interaction. Methylation alterations can affect this interaction, leading to transcriptional dysregulation. In cancer, clustered PCDHs undergo a mechanism of long-range epigenetic silencing by hypermethylation. Results In this study, we detected frequent methylation alterations at CpG islands associated to these clustered PCDHs in all the solid tumours analysed (colorectal, gastric and biliary tract cancers, pilocytic astrocytoma), but not hematologic neoplasms such as chronic lymphocytic leukemia. Importantly, several altered CpG islands were associated with CTCF binding sites. Interestingly, our analysis revealed a hypomethylation event in pilocytic astrocytoma, suggesting that in neuronal tissue, where PCDHs are highly expressed, these genes become hypomethylated in this type of cancer. On the other hand, in tissues where PCDHs are lowly expressed, these CpG islands are targeted by DNA methylation. In fact, PCDH-associated CpG islands resulted hypermethylated in gastrointestinal tumours. Conclusions Our study highlighted a strong alteration of the clustered PCDHs methylation pattern in the analysed solid cancers and suggested these methylation aberrations in the CpG islands associated with PCDH genes as powerful diagnostic biomarkers. Electronic supplementary material The online version of this article (10.1186/s13148-019-0695-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Loredana Moi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Sylvain Blois
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Antonio Fadda
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Manila Antonelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, University Sapienza of Rome, Rome, Italy
| | | | - Manuela Badiali
- Genetic and Genomic Laboratory, Microcitemico Children's Hospital, Cagliari, Italy
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, University Sapienza of Rome, Rome, Italy.,IRCCS Neuromed, Pozzilli, Italy
| | - Isabella Morra
- Department of Pathology OIRM-S, Anna Hospital, A.O.U. City of Health and Science, Turin, Italy
| | - Amedeo Columbano
- Department of Biomedical Sciences, Unit of Oncology and Molecular Pathology, University of Cagliari, Cagliari, Italy
| | - Angelo Restivo
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Luigi Zorcolo
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Viviana Gismondi
- Unit of Hereditary Cancer, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Liliana Varesco
- Unit of Hereditary Cancer, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Silvia Giordano
- Department of Oncology, University of Turin, Turin, Italy.,Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Matteo Canale
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Andrea Casadei-Gardini
- Department of Medical and Surgical Sciences for Children and Adults, Division of Medical Oncology, Policlinico di Modena Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
| | - Luca Faloppi
- Department of Medical Oncology, University Hospital of Cagliari, Cagliari, Italy.,Medical Oncology Unit, Macerata General Hospital, ASUR Marche AV3, Macerata, Italy
| | - Marco Puzzoni
- Department of Medical Oncology, University Hospital of Cagliari, Cagliari, Italy
| | - Mario Scartozzi
- Department of Medical Oncology, University Hospital of Cagliari, Cagliari, Italy
| | - Pina Ziranu
- Department of Medical Oncology, University Hospital of Cagliari, Cagliari, Italy
| | | | - Pierluigi Cocco
- Department of Medical Sciences and Public Health, Occupational Health Unit, University of Cagliari, Cagliari, Italy
| | - Maria Grazia Ennas
- Department of Biomedical Sciences, Cytomorphology Unit, University of Cagliari, Cagliari, Italy
| | - Giannina Satta
- Department of Medical Sciences and Public Health, Occupational Health Unit, University of Cagliari, Cagliari, Italy
| | - Mariagrazia Zucca
- Department of Biomedical Sciences, Cytomorphology Unit, University of Cagliari, Cagliari, Italy
| | - Daniele Canzio
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy.
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Murani E, Trakooljul N, Hadlich F, Ponsuksili S, Wimmers K. Transcriptome Responses to Dexamethasone Depending on Dose and Glucocorticoid Receptor Sensitivity in the Liver. Front Genet 2019; 10:559. [PMID: 31249595 PMCID: PMC6582245 DOI: 10.3389/fgene.2019.00559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/28/2019] [Indexed: 11/13/2022] Open
Abstract
Tissue sensitivity to glucocorticoids is a key factor dictating outcome of their homeostatic and therapeutic action, whereby liver represents one of the major peripheral targets. Here, we used pigs carrying a natural gain-of-function glucocorticoid receptor (GR) variant Ala610Val (GRAla610Val) as a model to identify genes and pathways related to differential glucocorticoid sensitivity. Animals with different GRAla610Val genotypes were treated either with saline or two different doses of dexamethasone. Genome-wide transcriptional responses depending on treatment, genotype, and their interaction in the liver were investigated using mRNA sequencing. Dexamethasone induced vast transcriptional responses, with more than 30% of present genes being affected. Functional annotation of genes differentially expressed due to dexamethasone treatment suggested that genes related to inflammation respond more sensitively, despite absence of an immune stimulus. In contrast, genes involved in glucose metabolism and cancer appeared to be less sensitive. Analysis of genotype and genotype × treatment interaction revealed that clustered protocadherins, particularly PCDHB7, are most prominently affected by GRAla610Val, mainly depending on dose. GRAla610Val influenced also expression of a set of glucose metabolism related genes, including PPARGC1A and CEBPB, in the absence of dexamethasone though no differences in basal plasma glucose level were observed. This might represent an adaptive response, keeping balance between receptor sensitivity, and level of circulating endogenous glucocorticoids. Administration of low dexamethasone dose changed their expression pattern and induced higher glucose response in carriers of the hypersensitive Val receptor. Our findings suggest that GRAla610Val modulates tissue responses to glucocorticoids dynamically, depending on their circulating level.
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Affiliation(s)
- Eduard Murani
- Institute for Genome Biology - Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Nares Trakooljul
- Institute for Genome Biology - Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Frieder Hadlich
- Institute for Genome Biology - Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Institute for Genome Biology - Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Klaus Wimmers
- Institute for Genome Biology - Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
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40
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Mountoufaris G, Canzio D, Nwakeze CL, Chen WV, Maniatis T. Writing, Reading, and Translating the Clustered Protocadherin Cell Surface Recognition Code for Neural Circuit Assembly. Annu Rev Cell Dev Biol 2019; 34:471-493. [PMID: 30296392 DOI: 10.1146/annurev-cellbio-100616-060701] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ability of neurites of individual neurons to distinguish between themselves and neurites from other neurons and to avoid self (self-avoidance) plays a key role in neural circuit assembly in both invertebrates and vertebrates. Similarly, when individual neurons of the same type project into receptive fields of the brain, they must avoid each other to maximize target coverage (tiling). Counterintuitively, these processes are driven by highly specific homophilic interactions between cell surface proteins that lead to neurite repulsion rather than adhesion. Among these proteins in vertebrates are the clustered protocadherins (Pcdhs), and key to their function is the generation of enormous cell surface structural diversity. Here we review recent advances in understanding how a Pcdh cell surface code is generated by stochastic promoter choice; how this code is amplified and read by homophilic interactions between Pcdh complexes at the surface of neurons; and, finally, how the Pcdh code is translated to cellular function, which mediates self-avoidance and tiling and thus plays a central role in the development of complex neural circuits. Not surprisingly, Pcdh mutations that diminish homophilic interactions lead to wiring defects and abnormal behavior in mice, and sequence variants in the Pcdh gene cluster are associated with autism spectrum disorders in family-based genetic studies in humans.
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Affiliation(s)
- George Mountoufaris
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical School, and Zuckerman Institute, Columbia University, New York, NY 10027, USA; .,Current address: Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical School, and Zuckerman Institute, Columbia University, New York, NY 10027, USA;
| | - Chiamaka L Nwakeze
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical School, and Zuckerman Institute, Columbia University, New York, NY 10027, USA;
| | - Weisheng V Chen
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical School, and Zuckerman Institute, Columbia University, New York, NY 10027, USA; .,Current address: Leveragen, Inc., Cambridge, Massachusetts 02139, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical School, and Zuckerman Institute, Columbia University, New York, NY 10027, USA;
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Curia MC, Fantini F, Lattanzio R, Tavano F, Di Mola F, Piantelli M, Battista P, Di Sebastiano P, Cama A. High methylation levels of PCDH10 predict poor prognosis in patients with pancreatic ductal adenocarcinoma. BMC Cancer 2019; 19:452. [PMID: 31088413 PMCID: PMC6518703 DOI: 10.1186/s12885-019-5616-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 04/15/2019] [Indexed: 01/24/2023] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies and is not a clinically homogeneous disease, but subsets of patients with distinct prognosis and response to therapy can be identified by genome-wide analyses. Mutations in major PDAC driver genes were associated with poor survival. By bioinformatics analysis, we identified protocadherins among the most frequently mutated genes in PDAC suggesting an important role of these genes in the biology of this tumor. Promoter methylation of protocadherins has been suggested as a prognostic marker in different tumors, but in PDAC this epigenetic modification has not been extensively studied. Thus, we evaluated whether promoter methylation of three frequently mutated protocadherins, PCDHAC2, PCDHGC5 and PCDH10 could be used as survival predictors in PDAC patients. Methods DNA extracted from 23 PDACs and adjacent non-neoplastic pancreatic tissues were bisulfite treated. Combined Bisulfite Restriction Analysis (COBRA) coupled to denaturing high-performance liquid chromatography (dHPLC) detection and bisulfite genomic sequencing (BGS) were used to determine the presence of methylated CpG dinucleotides in the promoter amplicons analyzed. Results In an exploratory analysis, two protocadherins showed the same pattern of CpG methylation in PDAC and adjacent non-neoplastic pancreatic tissues: lack of methylation for PCDHAC2, complete methylation for PCDHGC5. Conversely, the third protocadherin analyzed, PCDH10, showed a variable degree of CpG methylation in PDAC and absence of methylation in adjacent non-neoplastic pancreatic tissues. At Kaplan–Meier analysis, high levels of PCDH10 methylation defined according to the receiver operating characteristic (ROC) curve analysis were significantly associated with worse progression-free survival (PFS) rates (P = 0.008), but not with overall survival (OS). High levels of PCDH10 methylation were a prognostic factor influencing PFS (HR = 4.0: 95% CI, 1.3–12.3; P = 0.016), but not the OS. Conclusions In this study, we show for the first time that the methylation status of PCDH10 can predict prognosis in PDAC patients with a significant impact on the outcome in terms of progression-free survival. High levels of PCDH10 promoter methylation could be useful to identify patients at high risk of disease progression, contributing to a more accurate stratification of PDAC patients for personalized clinical management.
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Affiliation(s)
- Maria Cristina Curia
- Department of Medical, Oral and Biotechnological Sciences,'G. d'Annunzio' University, Via dei Vestini n.31, 66100, Chieti, Italy.
| | - Fabiana Fantini
- Department of Medical, Oral and Biotechnological Sciences,'G. d'Annunzio' University, Via dei Vestini n.31, 66100, Chieti, Italy
| | - Rossano Lattanzio
- Department of Medical, Oral and Biotechnological Sciences,'G. d'Annunzio' University, Via dei Vestini n.31, 66100, Chieti, Italy.,Center of Excellence on Aging and Translational Medicine (CeSi-Met), "G. d'Annunzio" University, Chieti, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Francesco Di Mola
- Division of Surgical Oncology "SS Annunziata" Hospital, Chieti, Italy
| | - Mauro Piantelli
- Department of Medical, Oral and Biotechnological Sciences,'G. d'Annunzio' University, Via dei Vestini n.31, 66100, Chieti, Italy
| | - Pasquale Battista
- Department of Medical, Oral and Biotechnological Sciences,'G. d'Annunzio' University, Via dei Vestini n.31, 66100, Chieti, Italy
| | | | - Alessandro Cama
- Department of Pharmacy,'G, d'Annunzio' University, Chieti, Italy
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42
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Kuehner JN, Bruggeman EC, Wen Z, Yao B. Epigenetic Regulations in Neuropsychiatric Disorders. Front Genet 2019; 10:268. [PMID: 31019524 PMCID: PMC6458251 DOI: 10.3389/fgene.2019.00268] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/11/2019] [Indexed: 12/14/2022] Open
Abstract
Precise genetic and epigenetic spatiotemporal regulation of gene expression is critical for proper brain development, function and circuitry formation in the mammalian central nervous system. Neuronal differentiation processes are tightly regulated by epigenetic mechanisms including DNA methylation, histone modifications, chromatin remodelers and non-coding RNAs. Dysregulation of any of these pathways is detrimental to normal neuronal development and functions, which can result in devastating neuropsychiatric disorders, such as depression, schizophrenia and autism spectrum disorders. In this review, we focus on the current understanding of epigenetic regulations in brain development and functions, as well as their implications in neuropsychiatric disorders.
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Affiliation(s)
- Janise N Kuehner
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Emily C Bruggeman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States.,Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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43
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Xu ZJ, Ma JC, Zhou JD, Wen XM, Yao DM, Zhang W, Ji RB, Wu DH, Tang LJ, Deng ZQ, Qian J, Lin J. Reduced protocadherin17 expression in leukemia stem cells: the clinical and biological effect in acute myeloid leukemia. J Transl Med 2019; 17:102. [PMID: 30922328 PMCID: PMC6440111 DOI: 10.1186/s12967-019-1851-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 03/18/2019] [Indexed: 02/07/2023] Open
Abstract
Background Leukemia stem cell (LSC)-enriched genes have been shown to be highly prognostic in acute myeloid leukemia (AML). However, the prognostic value of tumor suppressor genes (TSGs) that are repressed early in LSC remains largely unknown. Methods We compared the public available expression/methylation profiling data of LSCs with that of hematopoietic stem cells (HSCs), in order to identify potential tumor suppressor genes in LSC. The prognostic relevance of PCDH17 was analyzed on a cohort of 173 AML patients from The Cancer Genome Atlas (TCGA), and further validated in three independent cohorts (n = 339). Results We identified protocadherin17 (PCDH17) and demonstrated that it was significantly down-regulated and hypermethylated in LSCs compared with HSCs. Our analyses of primary AML patient samples also confirmed these deregulations. Clinically, low PCDH17 expression was associated with female sex (P = 0.01), higher WBC (P < 0.0001), higher percentages of blasts in bone marrow (BM) and peripheral blood (PB) (P = 0.04 and < 0.001, respectively), presence of FLT3-internal tandem duplications (P = 0.002), mutated NPM1 (P = 0.02), and wild-type TP53 (P = 0.005). Moreover, low PCDH17 expression predicted worse overall survival (OS) in four independent cohorts as well as in the molecularly defined subgroups of AML patients. In multivariable analyses, low PCDH17 expression retained independent prognostic value for OS. Biologically, PCDH17 expression-associated gene signatures were characterized by deregulations of EMT- and Wnt pathway-related genes. Conclusions PCDH17 gene was silenced by DNA methylation in AML. Low PCDH17 expression is associated with distinct clinical and biological features and improves risk stratification in patients with AML. Electronic supplementary material The online version of this article (10.1186/s12967-019-1851-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zi-Jun Xu
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Ji-Chun Ma
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Jing-Dong Zhou
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Xiang-Mei Wen
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Dong-Ming Yao
- Department of Clinical Laboratory Medicine, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, People's Republic of China
| | - Wei Zhang
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Run-Bi Ji
- Department of Clinical Laboratory Medicine, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, People's Republic of China
| | - De-Hong Wu
- Department of Hematology, The Third People's Hospital of Kunshan City, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Li-Juan Tang
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Zhao-Qun Deng
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jun Qian
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jiang Lin
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
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Olsvik PA, Whatmore P, Penglase SJ, Skjærven KH, Anglès d'Auriac M, Ellingsen S. Associations Between Behavioral Effects of Bisphenol A and DNA Methylation in Zebrafish Embryos. Front Genet 2019; 10:184. [PMID: 30906313 PMCID: PMC6418038 DOI: 10.3389/fgene.2019.00184] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/19/2019] [Indexed: 12/21/2022] Open
Abstract
Endocrine-disrupting contaminants have been associated with aberrant changes in epigenetic pathways in animals. In this study, zebrafish embryos were exposed bisphenol A (BPA) to search for associations between behavior and epigenetic mechanisms in fish. For concentration-dependent responses, embryos were exposed to a range of BPA concentrations (0.1 nM to 30 μM). Embryos were analyzed for locomotor activity at 3-, 4-, and 5-days post fertilization (dpf) in response to changing light conditions. Based on concentration-dependent effects on behavior and gene expression, 10 μM BPA [from 24 to 96 hours post fertilization (hpf)] was used for a whole-genome bisulfite sequencing (WGBS) study searching for genome-wide impacts on DNA methylation. Over the examined concentration ranges, hyperactivity was demonstrated for exposures to 0.001 μM BPA in comparison to embryos exposed to lower or higher BPA concentrations. Transcriptional analysis showed significant effects at >0.01 μM BPA for two genes related to DNA methylation (dnmt1, cbs). BPA exposure did not significantly affect global DNA methylation, but 20,474 differentially methylated (DM) sites in 4,873 genes were identified by WGBS analysis. Most DM sites were identified within gene bodies. The genes with the most DM sites were all protocadherin 2 gamma subfamily genes, related to axon targeting, synaptic development and neuronal survival. KEGG pathways most significantly affected by BPA exposure were phosphatidylinositol signaling system, followed by VEGF and MAPK signaling pathways. This study shows that BPA can affect zebrafish embryo swimming activity at very low concentrations as well as affecting numerous methylated sites in genes which are overrepresented in functionally relevant metabolic pathways. In conclusion, altered methylation patterns of genes associated with nervous system development might lead to abnormal swimming activity.
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Olsvik PA, Whatmore P, Penglase SJ, Skjærven KH, Anglès d'Auriac M, Ellingsen S. Associations Between Behavioral Effects of Bisphenol A and DNA Methylation in Zebrafish Embryos. Front Genet 2019. [PMID: 30906313 DOI: 10.3389/fgene.2019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Endocrine-disrupting contaminants have been associated with aberrant changes in epigenetic pathways in animals. In this study, zebrafish embryos were exposed bisphenol A (BPA) to search for associations between behavior and epigenetic mechanisms in fish. For concentration-dependent responses, embryos were exposed to a range of BPA concentrations (0.1 nM to 30 μM). Embryos were analyzed for locomotor activity at 3-, 4-, and 5-days post fertilization (dpf) in response to changing light conditions. Based on concentration-dependent effects on behavior and gene expression, 10 μM BPA [from 24 to 96 hours post fertilization (hpf)] was used for a whole-genome bisulfite sequencing (WGBS) study searching for genome-wide impacts on DNA methylation. Over the examined concentration ranges, hyperactivity was demonstrated for exposures to 0.001 μM BPA in comparison to embryos exposed to lower or higher BPA concentrations. Transcriptional analysis showed significant effects at >0.01 μM BPA for two genes related to DNA methylation (dnmt1, cbs). BPA exposure did not significantly affect global DNA methylation, but 20,474 differentially methylated (DM) sites in 4,873 genes were identified by WGBS analysis. Most DM sites were identified within gene bodies. The genes with the most DM sites were all protocadherin 2 gamma subfamily genes, related to axon targeting, synaptic development and neuronal survival. KEGG pathways most significantly affected by BPA exposure were phosphatidylinositol signaling system, followed by VEGF and MAPK signaling pathways. This study shows that BPA can affect zebrafish embryo swimming activity at very low concentrations as well as affecting numerous methylated sites in genes which are overrepresented in functionally relevant metabolic pathways. In conclusion, altered methylation patterns of genes associated with nervous system development might lead to abnormal swimming activity.
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Kim S, Wyckoff J, Morris AT, Succop A, Avery A, Duncan GE, Jazwinski SM. DNA methylation associated with healthy aging of elderly twins. GeroScience 2018; 40:469-484. [PMID: 30136078 PMCID: PMC6294724 DOI: 10.1007/s11357-018-0040-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/09/2018] [Indexed: 12/21/2022] Open
Abstract
Variation in healthy aging and lifespan is ascribed more to various non-genetic factors than to inherited genetic determinants, and a major goal in aging research is to reveal the epigenetic basis of aging. One approach to this goal is to find genomic sites or regions where DNA methylation correlates with biological age. Using health data from 134 elderly twins, we calculated a frailty index as a quantitative indicator of biological age, and by applying the Infinium HumanMethylation450K BeadChip technology to their leukocyte DNA samples, we obtained quantitative DNA methylation data on genome-wide CpG sites. We analyzed the health and epigenome data by taking two independent associative approaches: the parametric regression-based approach and a non-parametric machine learning approach followed by GO ontology analysis. Our results indicate that DNA methylation at CpG sites in the promoter region of PCDHGA3 is associated with biological age. PCDHGA3 belongs to clustered protocadherin genes, which are all located in a single locus on chromosome 5 in human. Previous studies of the clustered protocadherin genes showed that (1) DNA methylation is associated with age or age-related phenotypes; (2) DNA methylation can modulate gene expression; (3) dysregulated gene expression is associated with various pathologies; and (4) DNA methylation patterns at this locus are associated with adverse lifetime experiences. All these observations suggest that DNA methylation at the clustered protocadherin genes, including PCDHGA3, is a key mediator of healthy aging.
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Affiliation(s)
- Sangkyu Kim
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA.
| | - Jennifer Wyckoff
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Anne-T Morris
- Virginia Commonwealth University, Mid-Atlantic Twin Registry, Richmond, VA, USA
| | | | - Ally Avery
- University of Washington Twin Registry, Seattle, WA, USA
- Washington State Twin Registry, Washington State University - Health Sciences Spokane, Spokane, WA, USA
| | - Glen E Duncan
- University of Washington Twin Registry, Seattle, WA, USA
- Washington State Twin Registry, Washington State University - Health Sciences Spokane, Spokane, WA, USA
| | - S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
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Aref-Eshghi E, Schenkel LC, Ainsworth P, Lin H, Rodenhiser DI, Cutz JC, Sadikovic B. Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues. Front Oncol 2018; 8:100. [PMID: 29740534 PMCID: PMC5925605 DOI: 10.3389/fonc.2018.00100] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/21/2018] [Indexed: 01/27/2023] Open
Abstract
Introduction The current methodology involving diagnosis of prostate cancer (PCa) relies on the pathology examination of prostate needle biopsies, a method with high false negative rates partly due to temporospatial, molecular, and morphological heterogeneity of prostate adenocarcinoma. It is postulated that molecular markers have a potential to assign diagnosis to a considerable portion of undetected prostate tumors. This study examines the genome-wide DNA methylation changes in PCa in search of genomic markers for the development of a diagnostic algorithm for PCa screening. Methods Archival PCa and normal tissues were assessed using genomic DNA methylation arrays. Differentially methylated sites and regions (DMRs) were used for functional assessment, gene-set enrichment and protein interaction analyses, and examination of transcription factor-binding patterns. Raw signal intensity data were used for identification of recurrent copy number variations (CNVs). Non-redundant fully differentiating cytosine-phosphate-guanine sites (CpGs), which did not overlap CNV segments, were used in an L1 regularized logistic regression model (LASSO) to train a classification algorithm. Validation of this algorithm was performed using a large external cohort of benign and tumor prostate arrays. Results Approximately 6,000 probes and 600 genomic regions showed significant DNA methylation changes, primarily involving hypermethylation. Gene-set enrichment and protein interaction analyses found an overrepresentation of genes related to cell communications, neurogenesis, and proliferation. Motif enrichment analysis demonstrated enrichment of tumor suppressor-binding sites nearby DMRs. Several of these regions were also found to contain copy number amplifications. Using four non-redundant fully differentiating CpGs, we trained a classification model with 100% accuracy in discriminating tumors from benign samples. Validation of this algorithm using an external cohort of 234 tumors and 92 benign samples yielded 96% sensitivity and 98% specificity. The model was found to be highly sensitive to detect metastatic lesions in bone, lymph node, and soft tissue, while being specific enough to differentiate the benign hyperplasia of prostate from tumor. Conclusion A considerable component of PCa DNA methylation profile represent driver events potentially established/maintained by disruption of tumor suppressor activity. As few as four CpGs from this profile can be used for screening of PCa.
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Affiliation(s)
- Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
| | - David I Rodenhiser
- Department of Pediatrics, Western University and Children's Health Research Institute, London, ON, Canada.,Department of Biochemistry, Western University and Children's Health Research Institute, London, ON, Canada.,Department of Oncology, Western University and Children's Health Research Institute, London, ON, Canada
| | - Jean-Claude Cutz
- Department of Pathology and Laboratory Medicine, McMaster University, Hamilton, ON, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences, London, ON, Canada
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Byzia E, Soloch N, Bodnar M, Szaumkessel M, Kiwerska K, Kostrzewska-Poczekaj M, Jarmuz-Szymczak M, Szylberg L, Wierzbicka M, Bartochowska A, Kalinowicz E, Grenman R, Szyfter K, Marszalek A, Giefing M. Recurrent transcriptional loss of the PCDH17 tumor suppressor in laryngeal squamous cell carcinoma is partially mediated by aberrant promoter DNA methylation. Mol Carcinog 2018; 57:878-885. [PMID: 29566279 DOI: 10.1002/mc.22808] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/06/2018] [Accepted: 03/20/2018] [Indexed: 12/18/2022]
Abstract
Protocadherins are cell-cell adhesion molecules encoded by a large family of genes. Recent reports demonstrate recurrent silencing of protocadherin genes in tumors and provide strong arguments for their tumor supresor functionality. Loss of protocadherins may contribute to cancer development not only by altering cell-cell adhesion, that is a hallmark of cancer, but also by enhancing proliferation and epithelial mesenchymal transition of cells via deregulation of the WNT signaling pathway. In this study we have further corroborated our previous findings on the involvement of PCDH17 in laryngeal squamous cell carcinoma (LSCC). We used bisulfite pyrosequencing to analyze a cohort of primary LSCC tumors for alterations in PCDH17 promoter DNA methylation as an alternative gene inactivation mechanism to the homozygous deletions reported earlier. Moreover, we analyzed primary LSCC samples by immunohistochemistry for PCDH17 protein loss. We identified recurrent elevation of PCDH17 promoter DNA methylation in 32/81 (40%) primary tumors (P < 0.001) and therein hypermethylation of 12 (15%) cases in contrast to no tumor controls (n = 24) that were all unmethylated. Importantly, DNA demethylation by decitabine has restored low level PCDH17 expression in LSCC cell lines. In conclusion, we provide a mechanistic explanation of recurrently observed PCDH17 silencing in LSCC by demonstrating the role of promoter methylation in this process. In light of these findings and recent reports showing that PCDH17 methylation is detectable in serum of cancer patients we suggest that testing PCDH17 DNA methylation might serve as a potential biomarker in LSCC.
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Affiliation(s)
- Ewa Byzia
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Natalia Soloch
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Bodnar
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland.,Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Katarzyna Kiwerska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Tumor Pathology, Greater Poland Cancer Center, Poznan, Poland
| | | | - Malgorzata Jarmuz-Szymczak
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Lukasz Szylberg
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Malgorzata Wierzbicka
- Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Bartochowska
- Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | - Ewelina Kalinowicz
- Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | - Reidar Grenman
- Department of Otorhinolaryngology, -Head and Neck Surgery, Turku University Central Hospital and Turku University, Turku, Finland.,Department of Medical Biochemistry, Turku University Central Hospital and Turku University, Turku, Finland
| | - Krzysztof Szyfter
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Andrzej Marszalek
- Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences and Greater Poland Cancer Center, Poznan, Poland
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznan, Poland
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Suzuki-Muromoto S, Wakusawa K, Miyabayashi T, Sato R, Okubo Y, Endo W, Inui T, Togashi N, Kato A, Oba H, Nakashima M, Saitsu H, Matsumoto N, Haginoya K. A case of new PCDH12 gene variants presented as dyskinetic cerebral palsy with epilepsy. J Hum Genet 2018; 63:749-753. [DOI: 10.1038/s10038-018-0432-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 01/29/2023]
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50
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Mah KM, Weiner JA. Regulation of Wnt signaling by protocadherins. Semin Cell Dev Biol 2017; 69:158-171. [PMID: 28774578 PMCID: PMC5586504 DOI: 10.1016/j.semcdb.2017.07.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/21/2017] [Accepted: 07/28/2017] [Indexed: 12/23/2022]
Abstract
The ∼70 protocadherins comprise the largest group within the cadherin superfamily. Their diversity, the complexity of the mechanisms through which their genes are regulated, and their many critical functions in nervous system development have engendered a growing interest in elucidating the intracellular signaling pathways through which they act. Recently, multiple protocadherins across several subfamilies have been implicated as modulators of Wnt signaling pathways, and through this as potential tumor suppressors. Here, we review the extant data on the regulation by protocadherins of Wnt signaling pathways and components, and highlight some key unanswered questions that could shape future research.
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Affiliation(s)
- Kar Men Mah
- Department of Biology, The University of Iowa, Iowa City, IA, USA.
| | - Joshua A Weiner
- Department of Biology, The University of Iowa, Iowa City, IA, USA; Department of Psychiatry, The University of Iowa, Iowa City, IA, USA; Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, USA.
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