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Alhendi ASN, Gazdagh G, Lim D, McMullan D, Wright M, Temple IK, Davies JH, Mackay DJG. A case of mosaic deletion of paternally-inherited PLAGL1 and two cases of upd(6)mat add to evidence for PLAGL1 under-expression as a cause of growth restriction. Am J Med Genet A 2024; 194:383-388. [PMID: 37850521 DOI: 10.1002/ajmg.a.63448] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/18/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
PLAGL1 is one of a group of imprinted genes, whose altered expression causes imprinting disorders impacting growth, development, metabolism, and behavior. PLAGL1 over-expression causes transient neonatal diabetes mellitus (TNDM type 1) and, based on murine models, under-expression would be expected to cause growth restriction. However, only some reported individuals with upd(6)mat have growth restriction, giving rise to uncertainty about the role of PLAGL1 in human growth. Here we report three individuals investigated for growth restriction, two with upd(6)mat and one with a mosaic deletion of the paternally-inherited allele of PLAGL1. These cases add to evidence of its involvement in pre- and early post-natal human growth.
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Affiliation(s)
| | - Gabriella Gazdagh
- Faculty of Medicine, University of Southampton, UK
- University Hospital Southampton, UK
| | - Derek Lim
- Birmingham Women's and Children's Foundation Trust, UK
| | | | | | - I Karen Temple
- Faculty of Medicine, University of Southampton, UK
- University Hospital Southampton, UK
| | - Justin H Davies
- Faculty of Medicine, University of Southampton, UK
- University Hospital Southampton, UK
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2
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Seral-Cortes M, Sabroso-Lasa S, Gonzalez-Gross M, Quesada-Gonzalez C, Stehle P, Gottrand F, Marcos A, Esperanza-Diaz L, Manios Y, Androutsos O, Widhalm K, Molnar D, Huybrechts I, Muntaner M, Meirhaeghe A, Salazar-Tortosa D, Ruiz JR, Esteban LM, Labayen I, Moreno LA. The body mass index increases the genetic risk scores' ability to predict risk of hepatic damage in European adolescents: The HELENA study. Eur J Clin Invest 2023; 53:e14081. [PMID: 37608495 DOI: 10.1111/eci.14081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/24/2023]
Abstract
BACKGROUND Hepatic disorders are often complex and multifactorial, modulated by genetic and environmental determinants. During the last years, the hepatic disease has been progressively established from early stages in life. The use of genetic risk scores (GRS) to predict the genetic susceptibility to a particular phenotype among youth has gained interest in recent years. Moreover, the alanine aminotransferase (ALT) blood biomarker is often considered as hepatic screening tool, in combination with imaging techniques. The aim of the present study was to develop an ALT-specific GRS to help in the evaluation of hepatic damage risk in European adolescents. METHODS A total of 972 adolescents (51.3% females), aged 12.5-17.5 years, from the Healthy Lifestyle in Europe by Nutrition in Adolescence study were included in the analyses. The sample incorporated adolescents in all body mass index (BMI) categories and was divided considering healthy/unhealthy ALT levels, using sex-specific cut-off points. From 1212 a priori ALT-related single nucleotide polymorphisms (SNPs) extracted from candidate gene selection, a first screening of 234 SNPs univariately associated was established, selecting seven significant SNPs (p < .05) in the multivariate model. An unweighted GRS (uGRS) was developed by summing the number of reference alleles, and a weighted GRS (wGRS), by multiplying each allele to its estimated coefficient. RESULTS The uGRS and wGRS were significantly associated with ALT (p < .001). The area under curve was obtained integrating BMI as clinical factor, improving the predictive ability for uGRS (.7039) and wGRS (.7035), using 10-fold internal cross-validation. CONCLUSIONS Considering BMI status, both GRSs could contribute as complementary tools to help in the early diagnosis of hepatic damage risk in European adolescents.
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Affiliation(s)
- Miguel Seral-Cortes
- Growth, Exercise, Nutrition and Development (GENUD) Research Group, Faculty of Health Sciences, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria Aragón (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Sergio Sabroso-Lasa
- Genetic and Molecular Epidemiology Group (GMEG), Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marcela Gonzalez-Gross
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- ImFine Research Group, Department of Health and Human Performance, Facultad de Ciencias de la Actividad Física y del Deporte-INEF, Universidad Politécnica de Madrid, Madrid, Spain
- Institute of Nutritional and Food Sciences, Nutritional Physiology, University of Bonn, Bonn, Germany
| | - Carlos Quesada-Gonzalez
- ImFine Research Group, Department of Health and Human Performance, Facultad de Ciencias de la Actividad Física y del Deporte-INEF, Universidad Politécnica de Madrid, Madrid, Spain
- Department of Applied Mathematics to Information and Communication Technologies, Universidad Politécnica de Madrid, Madrid, Spain
| | - Peter Stehle
- Institute of Nutritional and Food Sciences, Nutritional Physiology, University of Bonn, Bonn, Germany
| | - Frederic Gottrand
- CHU Lille, Inserm U1286 INFINITE, University of Lille, Lille, France
| | - Ascension Marcos
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Immunonutrition Group, Department of Metabolism and Nutrition, Institute of Food Science, Technology and Nutrition (ICTAN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Ligia Esperanza-Diaz
- Immunonutrition Group, Department of Metabolism and Nutrition, Institute of Food Science, Technology and Nutrition (ICTAN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Yannis Manios
- Department of Nutrition and Dietetics, School of Health Science & Education, Harokopio University, Athens, Greece
- Institute of Agri-food and Life Sciences, Hellenic Mediterranean University Research Centre, Heraklion, Greece
| | - Odysseas Androutsos
- Lab of Clinical Nutrition and Dietetics, Department of Nutrition and Dietetics, School of Physical Education, Sport Science and Dietetics, University of Thessaly, Trikala, Greece
| | - Kurt Widhalm
- Division of Clinical Nutrition and Prevention, Department of Paediatrics, Medical University of Vienna, Vienna, Austria
- Austrian Academic Institute for Clinical Nutrition, Vienna, Austria
| | - Denes Molnar
- Department of Pediatrics, Medical School, University of Pécs, Pécs, Hungary
| | - Inge Huybrechts
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- French Network for Nutrition and Cancer Research (NACRe network), Jouy-en-Josas, France
| | - Manon Muntaner
- UMR1167, RID-AGE, Risk Factors and Molecular Determinants of Aging-Related Diseases, Centre Hosp, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Aline Meirhaeghe
- UMR1167, RID-AGE, Risk Factors and Molecular Determinants of Aging-Related Diseases, Centre Hosp, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Diego Salazar-Tortosa
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Jonatan R Ruiz
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Physical Education and Sports, Faculty of Sports Science, Sport and Health University Research Institute (iMUDS), Granada, Spain
- Instituto de Investigación Biosanitaria, ibs.Granada, Granada, Spain
| | | | - Idoia Labayen
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Health Sciences, Public University of Navarra, Pamplona, Spain
| | - Luis A Moreno
- Growth, Exercise, Nutrition and Development (GENUD) Research Group, Faculty of Health Sciences, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria Aragón (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
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3
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Chisnoiu T, Balasa AL, Mihai L, Lupu A, Frecus CE, Ion I, Andrusca A, Pantazi AC, Nicolae M, Lupu VV, Ionescu C, Mihai CM, Cambrea SC. Continuous Glucose Monitoring in Transient Neonatal Diabetes Mellitus-2 Case Reports and Literature Review. Diagnostics (Basel) 2023; 13:2271. [PMID: 37443665 DOI: 10.3390/diagnostics13132271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/03/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Neonatal diabetes mellitus is a rare genetic disease that affects 1 in 90,000 live births. The start of the disease is often before the baby is 6 months old, with rare cases of onset between 6 months and 1 year. It is characterized by low or absent insulin levels in the blood, leading to severe hyperglycemia in the patient, which requires temporary insulin therapy in around 50% of cases or permanent insulin therapy in other cases. Two major processes involved in diabetes mellitus are a deformed pancreas with altered insulin-secreting cell development and/or survival or faulty functioning of the existing pancreatic beta cell. We will discuss the cases of two preterm girls with neonatal diabetes mellitus in this research. In addition to reviewing the literature on the topic, we examined the different mutations, patient care, and clinical outcomes both before and after insulin treatment.
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Affiliation(s)
- Tatiana Chisnoiu
- Department of Pediatrics, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
- Pediatrics, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Adriana Luminita Balasa
- Department of Pediatrics, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
- Pediatrics, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Larisia Mihai
- Department of Pediatrics, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
- Pediatrics, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Ancuta Lupu
- Pediatrics, "Grigore T. Popa", Department of Mother and Child Medicine, University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Corina Elena Frecus
- Department of Pediatrics, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
- Pediatrics, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Irina Ion
- Department of Pediatrics, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
- Pediatrics, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Antonio Andrusca
- Department of Pediatrics, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
- Pediatrics, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Alexandru Cosmin Pantazi
- Department of Pediatrics, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
- Pediatrics, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Maria Nicolae
- Department of Pediatrics, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
- Pediatrics, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Vasile Valeriu Lupu
- Pediatrics, "Grigore T. Popa", Department of Mother and Child Medicine, University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Constantin Ionescu
- Department 1 Preclinical, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
| | - Cristina Maria Mihai
- Department of Pediatrics, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
- Pediatrics, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Simona Claudia Cambrea
- Department of Infectious Diseases, Faculty of General Medicine, "Ovidius" University, 900470 Constanta, Romania
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Henry S, Kokity L, Pirity MK. Polycomb protein RYBP activates transcription factor Plagl1 during in vitro cardiac differentiation of mouse embryonic stem cells. Open Biol 2023; 13:220305. [PMID: 36751888 PMCID: PMC9905990 DOI: 10.1098/rsob.220305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
RING1 and YY1 binding protein (RYBP) is primarily known to function as a repressor being a core component of the non-canonical polycomb repressive complexes 1 (ncPRC1s). However, several ncPRC1-independent functions of RYBP have also been described. We previously reported that RYBP is essential for mouse embryonic development and that Rybp null mutant embryonic stem cells cannot form contractile cardiomyocytes (CMCs) in vitro. We also showed that PLAGL1, a cardiac transcription factor, which is often mutated in congenital heart diseases (CHDs), is not expressed in Rybp-null mutant CMCs. However, the underlying mechanism of how RYBP regulates Plagl1 expression was not revealed. Here, we demonstrate that RYBP cooperated with NKX2-5 to transcriptionally activate the P1 and P3 promoters of the Plagl1 gene and that this activation is ncPRC1-independent. We also show that two non-coding RNAs residing in the Plagl1 locus can also regulate the Plagl1 promoters. Finally, PLAGL1 was able to activate Tnnt2, a gene important for contractility of CMCs in transfected HEK293 cells. Our study shows that the activation of Plagl1 by RYBP is important for sarcomere development and contractility, and suggests that RYBP, via its regulatory functions, may contribute to the development of CHDs.
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Affiliation(s)
- Surya Henry
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Lilla Kokity
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Melinda Katalin Pirity
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary
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5
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Lloyd DT, Skinner HG, Maguire R, Murphy SK, Motsinger-Reif AA, Hoyo C, House JS. Clomifene and Assisted Reproductive Technology in Humans Are Associated with Sex-Specific Offspring Epigenetic Alterations in Imprinted Control Regions. Int J Mol Sci 2022; 23:10450. [PMID: 36142363 PMCID: PMC9499479 DOI: 10.3390/ijms231810450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 12/04/2022] Open
Abstract
Children conceived with assisted reproductive technology (ART) have an increased risk of adverse outcomes, including congenital malformations and imprinted gene disorders. In a retrospective North Carolina-based-birth-cohort, we examined the effect of ovulation drugs and ART on CpG methylation in differentially methylated CpGs in known imprint control regions (ICRs). Nine ICRs containing 48 CpGs were assessed for methylation status by pyrosequencing in mixed leukocytes from cord blood. After restricting to non-smoking, college-educated participants who agreed to follow-up, ART-exposed (n = 27), clomifene-only-exposed (n = 22), and non-exposed (n = 516) groups were defined. Associations of clomifene and ART with ICR CpG methylation were assessed with linear regression and stratifying by offspring sex. In males, ART was associated with hypomethylation of the PEG3 ICR [β(95% CI) = -1.46 (-2.81, -0.12)] and hypermethylation of the MEG3 ICR [3.71 (0.01, 7.40)]; clomifene-only was associated with hypomethylation of the NNAT ICR [-5.25 (-10.12, -0.38)]. In female offspring, ART was associated with hypomethylation of the IGF2 ICR [-3.67 (-6.79, -0.55)]. Aberrant methylation of these ICRs has been associated with cardiovascular disease and metabolic and behavioral outcomes in children. The results suggest that the increased risk of adverse outcomes in offspring conceived through ART may be due in part to altered methylation of ICRs. Larger studies utilizing epigenome-wide interrogation are warranted.
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Affiliation(s)
- Dillon T. Lloyd
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
| | - Harlyn G. Skinner
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Rachel Maguire
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Duke University, Durham, NC 27701, USA
| | - Alison A. Motsinger-Reif
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - John S. House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
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6
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Lafontaine S, Sirard MA. IGF2R, KCNQ1, PLAGL1, and SNRPN DNA methylation is completed in bovine by the early antral follicle stage. Mol Reprod Dev 2022; 89:290-297. [PMID: 35698757 DOI: 10.1002/mrd.23621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/03/2022] [Accepted: 06/03/2022] [Indexed: 11/06/2022]
Abstract
Imprinted genes are inherited with different DNA methylation patterns depending on the maternal or paternal origin of the allele. In cattle (Bos taurus), abnormal methylation of these genes is linked to the large offspring syndrome, a neonatal overgrowth phenotype analogous to the human Beckwith-Wiedemann syndrome. We hypothesized that in bovine oocytes, some of the methylation patterns on maternally imprinted genes are acquired in the last phase of folliculogenesis. The pyrosequencing analysis of IGF2R, KCNQ1, PLAGL1, and SNRPN imprinted genes showed no clear progression of methylation in oocytes from follicles 1-2 mm (late pre antral/early antral) and up. Instead, these oocytes displayed complete methylation at the imprinted differentially methylated regions (>80%). Other mechanisms related to imprint maintenance should be investigated to explain the hypomethylation at IGF2R, KCNQ1, PLAGL1, and SNRPN maternally imprinted sites observed in some bovine embryos.
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Affiliation(s)
- Simon Lafontaine
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Département des Sciences Animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Québec, Canada
| | - Marc-André Sirard
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Département des Sciences Animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Québec, Canada
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7
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Vaigauskaitė B, Baušytė R, Valatkaitė E, Skliutė G, Kazėnaitė E, Ramašauskaitė D, Navakauskienė R. Prognostic Gene Predictors of Gestational Diabetes in Endometrium and Follicular Fluid of Women after Infertility. Medicina (B Aires) 2022; 58:medicina58040498. [PMID: 35454338 PMCID: PMC9025034 DOI: 10.3390/medicina58040498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
Background and objectives. Gestational diabetes mellitus is an increasingly diagnosed metabolic disorder during pregnancy with unknown pathological pathways. Taking into account the growing numbers of women who are conceiving after assisted reproductive technologies, they comprise an engaging target group for gestational diabetes mellitus etiopathogenesis research. In terms of metabolism and genetics, as the evidence shows, both unexplained infertility and gestational diabetes mellitus pose challenges for their interpretation due to the complex bodily processes. Materials and Methods. Our study examined the expression of genes (IGF2, GRB10, CRTC2, HMGA2, ESR1, DLK1, SLC6A15, GPT2, PLAGL1) associated with glucose metabolism in unexplained infertility patients who conceived after in vitro fertilization procedure, were diagnosed with GDM and their findings were compared with control population. Results. There were no significant differences in gene expression of endometrium stromal cells between healthy pregnant women and women with gestational diabetes, although the significant downregulation of CRTC2 was observed in the follicular fluid of women with gestational diabetes mellitus. Moreover, expression of HMGA2 and ESR1 was significantly reduced in FF cells when compared to endometrial cells. Conclusions. These findings may indicate about the importance of follicular fluid as an indicator for gestational diabetes and should be explored more by further research.
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Affiliation(s)
- Brigita Vaigauskaitė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (R.B.); (E.V.); (G.S.); (R.N.)
- Centre of Obstetrics and Gynaecology of the Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Santariškių St, LT-08661 Vilnius, Lithuania;
- Correspondence:
| | - Raminta Baušytė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (R.B.); (E.V.); (G.S.); (R.N.)
- Centre of Obstetrics and Gynaecology of the Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Santariškių St, LT-08661 Vilnius, Lithuania;
| | - Elvina Valatkaitė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (R.B.); (E.V.); (G.S.); (R.N.)
| | - Giedrė Skliutė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (R.B.); (E.V.); (G.S.); (R.N.)
| | - Edita Kazėnaitė
- Faculty of Medicine, Vilnius University Hospital Santaros Klinikos, Vilnius University, Santariškių St, LT-08661 Vilnius, Lithuania;
| | - Diana Ramašauskaitė
- Centre of Obstetrics and Gynaecology of the Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Santariškių St, LT-08661 Vilnius, Lithuania;
| | - Rūta Navakauskienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (R.B.); (E.V.); (G.S.); (R.N.)
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8
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Vázquez-Mosquera ME, González-Vioque E, Barbosa-Gouveia S, Bellido-Guerrero D, Tejera-Pérez C, Martinez-Olmos MA, Fernández-Pombo A, Castaño-González LA, Chans-Gerpe R, Couce ML. Transcriptomic analysis of patients with clinical suspicion of maturity-onset diabetes of the young (MODY) with a negative genetic diagnosis. Orphanet J Rare Dis 2022; 17:105. [PMID: 35246208 PMCID: PMC8896342 DOI: 10.1186/s13023-022-02263-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Background Diagnosis of mature-onset diabetes of the young (MODY), a non-autoimmune monogenic form of diabetes mellitus, is confirmed by genetic testing. However, a positive genetic diagnosis is achieved in only around 50% of patients with clinical characteristics of this disease. Results We evaluated the diagnostic utility of transcriptomic analysis in patients with clinical suspicion of MODY but a negative genetic diagnosis. Using Nanostring nCounter technology, we conducted transcriptomic analysis of 19 MODY-associated genes in peripheral blood samples from 19 patients and 8 healthy controls. Normalized gene expression was compared between patients and controls and correlated with each patient’s biochemical and clinical variables. Z-scores were calculated to identify significant changes in gene expression in patients versus controls. Only 7 of the genes analyzed were detected in peripheral blood. HADH expression was significantly lower in patients versus controls. Among patients with suspected MODY, GLIS3 expression was higher in obese versus normal-weight patients, and in patients aged < 25 versus > 25 years at diabetes onset. Significant alteration with respect to controls of any gene was observed in 57.9% of patients. Conclusions Although blood does not seem to be a suitable sample for transcriptomic analysis of patients with suspected MODY, in our study, we detected expression alterations in some of the genes studied in almost 58% of patients. That opens the door for future studies that can clarify the molecular cause of the clinic of these patients and thus be able to maintain a more specific follow-up and treatment in each case. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02263-3.
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Affiliation(s)
- María E Vázquez-Mosquera
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy
| | - Emiliano González-Vioque
- Division of Clinical Biochemistry, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Sofía Barbosa-Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy
| | | | - Cristina Tejera-Pérez
- Division of Endocrinology, Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain
| | - Miguel A Martinez-Olmos
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,Division of Endocrinology and Nutrition, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Antía Fernández-Pombo
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,Division of Endocrinology and Nutrition, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Luis A Castaño-González
- Endocrinology and Diabetes Research Group, Instituto de Investigación Sanitaria BioCruces, Barakaldo, Spain
| | - Roi Chans-Gerpe
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy
| | - María L Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain. .,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. .,Universidad de Santiago de Compostela, Santiago de Compostela, Spain. .,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy.
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9
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Dabi YT, Degechisa ST. Genome Editing and Human Pluripotent Stem Cell Technologies for in vitro Monogenic Diabetes Modeling. Diabetes Metab Syndr Obes 2022; 15:1785-1797. [PMID: 35719247 PMCID: PMC9199525 DOI: 10.2147/dmso.s366967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/08/2022] [Indexed: 12/01/2022] Open
Abstract
Diabetes is a metabolic disease characterized by chronic hyperglycemia. Polygenic diabetes, which encompasses type-1 and type-2 diabetes, is the most prevalent kind of diabetes and is caused by a combination of different genetic and environmental factors, whereas rare phenotype monogenic diabetes is caused by a single gene mutation. Monogenic diabetes includes Neonatal diabetes mellitus and Maturity-onset diabetes of the young. The majority of our current knowledge about the pathogenesis of diabetes stems from studies done on animal models. However, the genetic difference between these creatures and humans makes it difficult to mimic human clinical pathophysiology, limiting their value in modeling key aspects of human disease. Human pluripotent stem cell technologies combined with genome editing techniques have been shown to be better alternatives for creating in vitro models that can provide crucial knowledge about disease etiology. This review paper addresses genome editing and human pluripotent stem cell technologies for in vitro monogenic diabetes modeling.
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Affiliation(s)
- Yosef Tsegaye Dabi
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Medical Laboratory Science, Wollega University, Nekemte, Ethiopia
- Correspondence: Yosef Tsegaye Dabi, Email
| | - Sisay Teka Degechisa
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Arba Minch University, Arba Minch, Ethiopia
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10
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Transient Neonatal Diabetes Mellitus with the Rare Association of Nonsuppurative Sialadenitis and Genetic Defects in 6q24. Case Rep Pediatr 2021; 2021:5901898. [PMID: 34422424 PMCID: PMC8376448 DOI: 10.1155/2021/5901898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/04/2021] [Indexed: 11/17/2022] Open
Abstract
Background Transient neonatal diabetes mellitus (TNDM) is the most common cause of diabetes in the first week of life, with an overall incidence of 1 in 90,000 to 160,000 live births. TNDM occurs soon after birth and undergoes spontaneous remission during infancy; however, it may relapse to a permanent form of diabetes mellitus in childhood or adolescence. We report a case of TNDM due to hypomethylation on chromosome 6q24, associated with a rare clinical finding of nonsuppurative submandibular sialadenitis managed by subcutaneous insulin, and who underwent remission by three months of age. Case Presentation. We report a male neonate of Arab ancestry delivered by caesarean section at 37 weeks of gestation. He had intrauterine growth retardation with a birth weight of 2.099 kg. He presented with hyperglycemia on the first day of life, which was managed with parenteral insulin infusion. Blood glucose control was initially difficult to achieve due to difficulties in preparing such small doses of insulin and the significant variations in blood glucose concentrations, without ketosis. Blood tests revealed low serum insulin and C-peptide levels. Genetic analysis revealed multiple loci hypomethylation of the PLAGL1/HYMAI-DMR in the TNDM region in chromosome 6q24 and two pathogenic heterozygous variants in the ZFP57 gene. Segregation analysis showed that both parents were heterozygous carriers of familial ZFP57 variants. The clinical course was associated with bilateral nonsuppurative sialadenitis, which is extremely rare among newborns. Conclusion Sialadenitis is a well-known phenomenon that is rarely diagnosed in neonates. To the best of our knowledge, this is the first case report to describe the exceedingly rare association of nonsuppurative submandibular sialadenitis in a neonate with TNDM due to multiple loci hypomethylation of the PLAGL1/HYMAI-DMR in the TNDM region in 6q24 and heterozygous pathogenic variants in the ZFP57 gene.
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11
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Genomic Imprinting at the Porcine PLAGL1 Locus and the Orthologous Locus in the Human. Genes (Basel) 2021; 12:genes12040541. [PMID: 33918057 PMCID: PMC8069715 DOI: 10.3390/genes12040541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
Implementation of genomic imprinting in mammals often results in cis-acting silencing of a gene cluster and monoallelic expression, which are important for mammalian growth and function. Compared with widely documented imprinting status in humans and mice, current understanding of genomic imprinting in pigs is relatively limited. The objectives of this study were to identify DNA methylation status and allelic expression of alternative spliced isoforms at the porcine PLAGL1 locus and assess the conservation of the locus compared to the orthologous human locus. DNA methylome and transcriptome were constructed using porcine parthenogenetic or biparental control embryos. Using methylome, differentially methylated regions between those embryos were identified. Alternative splicing was identified by differential splicing analysis, and monoallelic expression was examined using single nucleotide polymorphism sites. Moreover, topological boundary regions were identified by analyzing CTCF binding sites and compared with the boundary of human orthologous locus. As a result, it was revealed that the monoallelic expression of the PLAGL1 gene in porcine embryos via genomic imprinting was maintained in the adult stage. The porcine PLAGL1 locus was largely conserved in regard to maternal hypermethylation, tissue distribution of mRNA expression, monoallelic expression, and biallelic CTCF-binding, with exceptions on transcript isoforms produced by alternative splicing instead of alternative promoter usage. These findings laid the groundwork for comparative studies on the imprinted PLAGL1 gene and related regulatory mechanisms across species.
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12
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Scagliotti V, Esse R, Willis TL, Howard M, Carrus I, Lodge E, Andoniadou CL, Charalambous M. Dynamic Expression of Imprinted Genes in the Developing and Postnatal Pituitary Gland. Genes (Basel) 2021; 12:genes12040509. [PMID: 33808370 PMCID: PMC8066104 DOI: 10.3390/genes12040509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/19/2022] Open
Abstract
In mammals, imprinted genes regulate many critical endocrine processes such as growth, the onset of puberty and maternal reproductive behaviour. Human imprinting disorders (IDs) are caused by genetic and epigenetic mechanisms that alter the expression dosage of imprinted genes. Due to improvements in diagnosis, increasing numbers of patients with IDs are now identified and monitored across their lifetimes. Seminal work has revealed that IDs have a strong endocrine component, yet the contribution of imprinted gene products in the development and function of the hypothalamo-pituitary axis are not well defined. Postnatal endocrine processes are dependent upon the production of hormones from the pituitary gland. While the actions of a few imprinted genes in pituitary development and function have been described, to date there has been no attempt to link the expression of these genes as a class to the formation and function of this essential organ. This is important because IDs show considerable overlap, and imprinted genes are known to define a transcriptional network related to organ growth. This knowledge deficit is partly due to technical difficulties in obtaining useful transcriptomic data from the pituitary gland, namely, its small size during development and cellular complexity in maturity. Here we utilise high-sensitivity RNA sequencing at the embryonic stages, and single-cell RNA sequencing data to describe the imprinted transcriptome of the pituitary gland. In concert, we provide a comprehensive literature review of the current knowledge of the role of imprinted genes in pituitary hormonal pathways and how these relate to IDs. We present new data that implicate imprinted gene networks in the development of the gland and in the stem cell compartment. Furthermore, we suggest novel roles for individual imprinted genes in the aetiology of IDs. Finally, we describe the dynamic regulation of imprinted genes in the pituitary gland of the pregnant mother, with implications for the regulation of maternal metabolic adaptations to pregnancy.
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Affiliation(s)
- Valeria Scagliotti
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
| | - Ruben Esse
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
| | - Thea L. Willis
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE19RT, UK; (T.L.W.); (E.L.); (C.L.A.)
| | - Mark Howard
- MRC Centre for Transplantation, Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London SE19RT, UK;
| | - Isabella Carrus
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
| | - Emily Lodge
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE19RT, UK; (T.L.W.); (E.L.); (C.L.A.)
| | - Cynthia L. Andoniadou
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London SE19RT, UK; (T.L.W.); (E.L.); (C.L.A.)
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Marika Charalambous
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK; (V.S.); (R.C.F.E.); (I.C.)
- Correspondence:
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13
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González-Moro I, Santin I. Long non-coding RNA-regulated pathways in pancreatic β cells: Their role in diabetes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 359:325-355. [PMID: 33832652 DOI: 10.1016/bs.ircmb.2021.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts of more than 200 nucleotides that have not coding potential, but act as gene expression regulators through several molecular mechanisms. Several studies have identified tons of lncRNAs that are expressed in pancreatic β cells and many of them have been shown to have β cell-specific expression, suggesting a potential role in the regulation of basal β cell functions. Indeed, accumulating evidence based on numerous studies, has highlighted the implication of lncRNAs in the regulation of pancreatic β cell differentiation and proliferation, insulin synthesis and secretion, and apoptosis. In addition, several lncRNAs have shown to be implicated in pancreatic β cell dysfunction linked to different types of diabetes, including type 1 and type 2 diabetes, and monogenic forms of the disease. Pathogenic conditions linked to diabetes (inflammation or lipoglucotoxicity, for example) dysregulate the expression of several lncRNAs, suggesting that changes in lncRNA may alter potentially important pathways for β cell function, and eventually leading to β cell dysfunction and diabetes development. In this sense, functional characterization of some lncRNAs has demonstrated that these non-coding molecules participate in the regulation of several crucial pathways at the pancreatic β cell level, and dysregulation of these pathways leads to pathogenic phenotypes. In this review, we provide an overview of the action mechanisms of functionally characterized lncRNAs in healthy β cells and describe the contribution of some diabetes-associated lncRNAs to pancreatic β cell failure.
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Affiliation(s)
- Itziar González-Moro
- Department of Biochemistry and Molecular biology, University of the Basque Country, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Izortze Santin
- Department of Biochemistry and Molecular biology, University of the Basque Country, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; CIBER (Centro de Investigación Biomédica en Red) de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
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14
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Baulina N, Kiselev I, Favorova O. Imprinted Genes and Multiple Sclerosis: What Do We Know? Int J Mol Sci 2021; 22:1346. [PMID: 33572862 PMCID: PMC7866243 DOI: 10.3390/ijms22031346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune neurodegenerative disease of the central nervous system that arises from interplay between non-genetic and genetic risk factors. The epigenetics functions as a link between these factors, affecting gene expression in response to external influence, and therefore should be extensively studied to improve the knowledge of MS molecular mechanisms. Among others, the epigenetic mechanisms underlie the establishment of parent-of-origin effects that appear as phenotypic differences depending on whether the allele was inherited from the mother or father. The most well described manifestation of parent-of-origin effects is genomic imprinting that causes monoallelic gene expression. It becomes more obvious that disturbances in imprinted genes at the least affecting their expression do occur in MS and may be involved in its pathogenesis. In this review we will focus on the potential role of imprinted genes in MS pathogenesis.
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Affiliation(s)
- Natalia Baulina
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Ivan Kiselev
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
| | - Olga Favorova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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15
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Chabosseau P, Rutter GA, Millership SJ. Importance of Both Imprinted Genes and Functional Heterogeneity in Pancreatic Beta Cells: Is There a Link? Int J Mol Sci 2021; 22:1000. [PMID: 33498234 PMCID: PMC7863946 DOI: 10.3390/ijms22031000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 02/02/2023] Open
Abstract
Diabetes mellitus now affects more than 400 million individuals worldwide, with significant impacts on the lives of those affected and associated socio-economic costs. Although defects in insulin secretion underlie all forms of the disease, the molecular mechanisms which drive them are still poorly understood. Subsets of specialised beta cells have, in recent years, been suggested to play critical roles in "pacing" overall islet activity. The molecular nature of these cells, the means through which their identity is established and the changes which may contribute to their functional demise and "loss of influence" in both type 1 and type 2 diabetes are largely unknown. Genomic imprinting involves the selective silencing of one of the two parental alleles through DNA methylation and modified imprinted gene expression is involved in a number of diseases. Loss of expression, or loss of imprinting, can be shown in mouse models to lead to defects in beta cell function and abnormal insulin secretion. In the present review we survey the evidence that altered expression of imprinted genes contribute to loss of beta cell function, the importance of beta cell heterogeneity in normal and disease states, and hypothesise whether there is a direct link between the two.
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Affiliation(s)
| | | | - Steven J. Millership
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; (P.C.); (G.A.R.)
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16
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Villanueva-Hayes C, Millership SJ. Imprinted Genes Impact Upon Beta Cell Function in the Current (and Potentially Next) Generation. Front Endocrinol (Lausanne) 2021; 12:660532. [PMID: 33986727 PMCID: PMC8112240 DOI: 10.3389/fendo.2021.660532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/01/2021] [Indexed: 11/23/2022] Open
Abstract
Beta cell failure lies at the centre of the aetiology and pathogenesis of type 2 diabetes and the epigenetic control of the expression of critical beta cell genes appears to play a major role in this decline. One such group of epigenetically-controlled genes, termed 'imprinted' genes, are characterised by transgenerational monoallelic expression due to differential allelic DNA methylation and play key functional roles within beta cells. Here, we review the evidence for this functional importance of imprinted genes in beta cells as well as their nutritional regulation by the diet and their altered methylation and/or expression in rodent models of diabetes and in type 2 diabetic islets. We also discuss imprinted genes in the context of the next generation, where dietary overnutrition in the parents can lead to their deregulation in the offspring, alongside beta cell dysfunction and defective glucose handling. Both the modulation of imprinted gene expression and the likelihood of developing type 2 diabetes in adulthood are susceptible to the impact of nutritional status in early life. Imprinted loci, therefore, represent an excellent opportunity with which to assess epigenomic changes in beta cells due to the diet in both the current and next generation.
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Fauque P, De Mouzon J, Devaux A, Epelboin S, Gervoise-Boyer MJ, Levy R, Valentin M, Viot G, Bergère A, De Vienne C, Jonveaux P, Pessione F. Reproductive technologies, female infertility, and the risk of imprinting-related disorders. Clin Epigenetics 2020; 12:191. [PMID: 33308308 PMCID: PMC7731556 DOI: 10.1186/s13148-020-00986-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/23/2020] [Indexed: 11/14/2022] Open
Abstract
Background Epidemiological studies suggest that singletons born from assisted reproductive technologies (ART) have a high risk of adverse perinatal outcomes, specifically for imprinting disorders. Because ART processes take place at times when epigenetic reprogramming/imprinting are occurring, there is concern that ART can affect genomic imprints. However, little is currently known about the risk of imprinting defects according to the type of ART or the type of underlying female infertility.
From the French national health database, a cohort of 3,501,495 singletons born over a 5-year period (2013–2017) following fresh embryo or frozen embryo transfers (fresh-ET or FET from in vitro fertilization), intrauterine insemination, or natural conception was followed up to early childhood. Based on clinical features, several syndromes/diseases involving imprinted genes were monitored. The effects of ART conception and the underlying cause of female infertility were assessed. Results Compared with infants conceived naturally, children born after fresh-ET had a higher prevalence of imprinting-related diseases, with an aOR of 1.43 [95% CI 1.13–1.81, p = 0.003]. Namely, we observed an increased risk of neonatal diabetes mellitus (1.96 aOR [95% CI 1.43–2.70], p < 0.001). There was an overall independent increase in risk of imprinting diseases for children with mothers diagnosed with endometriosis (1.38 aOR [95% CI 1.06–1.80], p = 0.02). Young and advanced maternal age, primiparity, obesity, smoking, and history of high blood pressure or diabetes were also associated with high global risk. Conclusions This prospective epidemiological study showed that the risk of clinically diagnosed imprinting-related diseases is increased in children conceived after fresh embryo transfers or from mothers with endometriosis. The increased perturbations in genomic imprinting could be caused by controlled ovarian hyperstimulation and potentially endometriosis through the impairment of endometrial receptivity and placentation, leading to epigenetic feto-placental changes. Further studies are now needed to improve understanding of the underlying molecular mechanisms (i.e. genetic or epigenetic causes).
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Affiliation(s)
- Patricia Fauque
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction - CECOS - Université Bourgogne Franche-Comté - INSERM UMR1231, Dijon, France.
| | | | - Aviva Devaux
- Centre d'assistance medicale à la procreation, biologie de la reproduction, CHU Amiens, Amiens, France
| | - Sylvie Epelboin
- Centre d'assistance medicale à la procreation, gynécologie obstétrique, médecine de la reproduction, Université Paris 7 Diderot, groupe hospitalier Bichat Claude-Bernard, AP-HP, Paris, France
| | | | - Rachel Levy
- Sorbonne Université, Saint Antoine Research Center, INSERM équipe Lipodystrophies genetiques et acquises, Service de biologie de la reproduction-CECOS, Hôpital Tenon, AP-HP, 75012, Paris, France
| | - Morgane Valentin
- Diagnostic antenatal, gynécologie obstétrique, Université Paris 7 Diderot, groupe hospitalier Bichat Claude-Bernard, AP-HP, Paris, France
| | - Géraldine Viot
- Unité de Génétique Clinique de La Muette, 50 rue Nicolo, 75116, Paris, France
| | - Arianne Bergère
- Agence de la Biomédecine, 1 avenue du stade de France, 93212, La Plaine Saint Denis, France
| | - Claire De Vienne
- Agence de la Biomédecine, 1 avenue du stade de France, 93212, La Plaine Saint Denis, France
| | - Philippe Jonveaux
- Agence de la Biomédecine, 1 avenue du stade de France, 93212, La Plaine Saint Denis, France
| | - Fabienne Pessione
- Agence de la Biomédecine, 1 avenue du stade de France, 93212, La Plaine Saint Denis, France
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18
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Starks RR, Abu Alhasan R, Kaur H, Pennington KA, Schulz LC, Tuteja G. Transcription Factor PLAGL1 Is Associated with Angiogenic Gene Expression in the Placenta. Int J Mol Sci 2020; 21:ijms21218317. [PMID: 33171905 PMCID: PMC7664191 DOI: 10.3390/ijms21218317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
During pregnancy, the placenta is important for transporting nutrients and waste between the maternal and fetal blood supply, secreting hormones, and serving as a protective barrier. To better understand placental development, we must understand how placental gene expression is regulated. We used RNA-seq data and ChIP-seq data for the enhancer associated mark, H3k27ac, to study gene regulation in the mouse placenta at embryonic day (e) 9.5, when the placenta is developing a complex network of blood vessels. We identified several upregulated transcription factors with enriched binding sites in e9.5-specific enhancers. The most enriched transcription factor, PLAGL1 had a predicted motif in 233 regions that were significantly associated with vasculature development and response to insulin stimulus genes. We then performed several experiments using mouse placenta and a human trophoblast cell line to understand the role of PLAGL1 in placental development. In the mouse placenta, Plagl1 is expressed in endothelial cells of the labyrinth layer and is differentially expressed in placentas from mice with gestational diabetes compared to placentas from control mice in a sex-specific manner. In human trophoblast cells, siRNA knockdown significantly decreased expression of genes associated with placental vasculature development terms. In a tube assay, decreased PLAGL1 expression led to reduced cord formation. These results suggest that Plagl1 regulates overlapping gene networks in placental trophoblast and endothelial cells, and may play a critical role in placental development in normal and complicated pregnancies.
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Affiliation(s)
- Rebekah R. Starks
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA; (R.R.S.); (R.A.A.); (H.K.)
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Rabab Abu Alhasan
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA; (R.R.S.); (R.A.A.); (H.K.)
| | - Haninder Kaur
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA; (R.R.S.); (R.A.A.); (H.K.)
| | | | - Laura C. Schulz
- Obstetrics, Gynecology and Women’s Health, University of Missouri, Columba, MO 65212, USA;
| | - Geetu Tuteja
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA; (R.R.S.); (R.A.A.); (H.K.)
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
- Correspondence:
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19
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Nicolaides NC, Kanaka-Gantenbein C, Papadopoulou-Marketou N, Sertedaki A, Chrousos GP, Papassotiriou I. Emerging technologies in pediatrics: the paradigm of neonatal diabetes mellitus. Crit Rev Clin Lab Sci 2020; 57:522-531. [PMID: 32356495 DOI: 10.1080/10408363.2020.1752141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In the era of precision medicine, the tremendous progress in next-generation sequencing technologies has allowed the identification of an ever-increasing number of genes associated with known Mendelian disorders. Neonatal diabetes mellitus is a rare, genetically heterogeneous endocrine disorder diagnosed before 6 months of age. It may occur alone or in the context of genetic syndromes. Neonatal diabetes mellitus has been linked with genetic defects in at least 26 genes to date. Novel mutations in these disease-causing genes are being reported, giving us a better knowledge of the molecular events that occur upon insulin biosynthesis and secretion from the pancreatic β-cell. Of great importance, some of the identified genes encode proteins that can be therapeutically targeted by drugs per os, leading to transitioning from insulin to sulfonylureas. In this review, we provide an overview of pancreatic β-cell physiology, present the clinical manifestations and the genetic causes of the different forms of neonatal diabetes, and discuss the application of next-generation sequencing methods in the diagnosis and therapeutic management of neonatal diabetes and on research in this area.
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Affiliation(s)
- Nicolas C Nicolaides
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece.,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Christina Kanaka-Gantenbein
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Nektaria Papadopoulou-Marketou
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Amalia Sertedaki
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece.,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Ioannis Papassotiriou
- Department of Clinical Biochemistry, "Aghia Sophia" Children's Hospital, Athens, Greece.,IFCC Emerging Technologies Division, Emerging Technologies in Pediatric Laboratory Medicine (C-ETPLM), Milano, Italy
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20
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Syding LA, Nickl P, Kasparek P, Sedlacek R. CRISPR/Cas9 Epigenome Editing Potential for Rare Imprinting Diseases: A Review. Cells 2020; 9:cells9040993. [PMID: 32316223 PMCID: PMC7226972 DOI: 10.3390/cells9040993] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022] Open
Abstract
Imprinting diseases (IDs) are rare congenital disorders caused by aberrant dosages of imprinted genes. Rare IDs are comprised by a group of several distinct disorders that share a great deal of homology in terms of genetic etiologies and symptoms. Disruption of genetic or epigenetic mechanisms can cause issues with regulating the expression of imprinted genes, thus leading to disease. Genetic mutations affect the imprinted genes, duplications, deletions, and uniparental disomy (UPD) are reoccurring phenomena causing imprinting diseases. Epigenetic alterations on methylation marks in imprinting control centers (ICRs) also alters the expression patterns and the majority of patients with rare IDs carries intact but either silenced or overexpressed imprinted genes. Canonical CRISPR/Cas9 editing relying on double-stranded DNA break repair has little to offer in terms of therapeutics for rare IDs. Instead CRISPR/Cas9 can be used in a more sophisticated way by targeting the epigenome. Catalytically dead Cas9 (dCas9) tethered with effector enzymes such as DNA de- and methyltransferases and histone code editors in addition to systems such as CRISPRa and CRISPRi have been shown to have high epigenome editing efficiency in eukaryotic cells. This new era of CRISPR epigenome editors could arguably be a game-changer for curing and treating rare IDs by refined activation and silencing of disturbed imprinted gene expression. This review describes major CRISPR-based epigenome editors and points out their potential use in research and therapy of rare imprinting diseases.
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Affiliation(s)
- Linn Amanda Syding
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Petr Nickl
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Petr Kasparek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Correspondence: ; Tel.: +420-325-873-243
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21
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Abstract
Neonatal diabetes mellitus (DM) is defined by the onset of persistent hyperglycemia within the first six months of life but may present up to 12 months of life. A gene mutation affecting pancreatic beta cells or synthesis/secretion of insulin is present in more than 80% of the children with neonatal diabetes. Neonatal DM can be transient, permanent, or be a component of a syndrome. Genetic testing is important as a specific genetic mutation can significantly alter the treatment and outcome. Patients with mutations of either KCNJ11 or ABCC8 that encode subunits of the KATP channel gene mutation can be managed with sulfonylurea oral therapy while patients with other genetic mutations require insulin treatment.
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Affiliation(s)
- Amanda Dahl
- Division of Pediatric Endocrinology and Metabolism, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Seema Kumar
- Division of Pediatric Endocrinology and Metabolism, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
- Correspondence: Seema Kumar Division of Pediatric Endocrinology and Metabolism, Department of Pediatric and Adolescent Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN55590, USATel +1 507-284-3300Fax +1 507-284-0727 Email
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22
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Xie J, Ji T, Ferreira MAR, Li Y, Patel BN, Rivera RM. Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model. BMC Bioinformatics 2019; 20:530. [PMID: 31660858 PMCID: PMC6819473 DOI: 10.1186/s12859-019-3141-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/09/2019] [Indexed: 12/29/2022] Open
Abstract
Background High-throughput sequencing experiments, which can determine allele origins, have been used to assess genome-wide allele-specific expression. Despite the amount of data generated from high-throughput experiments, statistical methods are often too simplistic to understand the complexity of gene expression. Specifically, existing methods do not test allele-specific expression (ASE) of a gene as a whole and variation in ASE within a gene across exons separately and simultaneously. Results We propose a generalized linear mixed model to close these gaps, incorporating variations due to genes, single nucleotide polymorphisms (SNPs), and biological replicates. To improve reliability of statistical inferences, we assign priors on each effect in the model so that information is shared across genes in the entire genome. We utilize Bayesian model selection to test the hypothesis of ASE for each gene and variations across SNPs within a gene. We apply our method to four tissue types in a bovine study to de novo detect ASE genes in the bovine genome, and uncover intriguing predictions of regulatory ASEs across gene exons and across tissue types. We compared our method to competing approaches through simulation studies that mimicked the real datasets. The R package, BLMRM, that implements our proposed algorithm, is publicly available for download at https://github.com/JingXieMIZZOU/BLMRM. Conclusions We will show that the proposed method exhibits improved control of the false discovery rate and improved power over existing methods when SNP variation and biological variation are present. Besides, our method also maintains low computational requirements that allows for whole genome analysis.
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23
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Abstract
Genomic imprinting in mammals was discovered over 30 years ago through elegant embryological and genetic experiments in mice. Imprinted genes show a monoallelic and parent of origin-specific expression pattern; the development of techniques that can distinguish between expression from maternal and paternal chromosomes in mice, combined with high-throughput strategies, has allowed for identification of many more imprinted genes, most of which are conserved in humans. Undoubtedly, technical progress has greatly promoted progress in the field of genomic imprinting. Here, we summarize the techniques used to discover imprinted genes, identify new imprinted genes, define imprinting regulation mechanisms, and study imprinting functions.
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Affiliation(s)
- Yuanyuan Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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24
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Tanaka S, Honda Y, Takaku S, Koike T, Oe S, Hirahara Y, Yoshida T, Takizawa N, Takamori Y, Kurokawa K, Kodama T, Yamada H. Involvement of PLAGL1/ZAC1 in hypocretin/orexin transcription. Int J Mol Med 2019; 43:2164-2176. [PMID: 30896835 PMCID: PMC6445593 DOI: 10.3892/ijmm.2019.4143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/19/2019] [Indexed: 12/16/2022] Open
Abstract
The hypocretin/orexin neuropeptide system coordinates the regulation of various physiological processes. Our previous study reported that a reduction in the expression of pleomorphic adenoma gene-like 1 (Plagl1), which encodes a C2H2 zinc-finger transcription factor, occurs in hypocretin neuron-ablated transgenic mice, suggesting that PLAGL1 is co-expressed in hypocretin neurons and regulates hypocretin transcription. The present study examined whether canonical prepro-hypocretin transcription is functionally modulated by PLAGL1. Double immunostaining indicated that the majority of hypocretin neurons were positive for PLAGL1 immunore-activity in the nucleus. Notably, PLAGL1 immunoreactivity in hypocretin neurons was altered in response to several conditions affecting hypocretin function. An uneven localization of PLAGL1 was detected in the nuclei of hypocretin neurons following sleep deprivation. Chromatin immunoprecipitation revealed that endogenous PLAGL1 may bind to a putative PLAGL1-binding site in the proximal region of the hypocretin gene, in the murine hypothalamus. In addition, electroporation of the PLAGL1 expression vector into the fetal hypothalamus promoted hypothalamic hypocretin transcription. These results suggested that PLAGL1 may regulate hypothalamic hypocretin transcription.
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Affiliation(s)
- Susumu Tanaka
- Department of Anatomy and Cell Science, Kansai Medical University, Hirakata, Osaka 573‑1010, Japan
| | - Yoshiko Honda
- SLEEP Disorders Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156‑8506, Japan
| | - Shizuka Takaku
- SLEEP Disorders Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156‑8506, Japan
| | - Taro Koike
- Department of Anatomy and Cell Science, Kansai Medical University, Hirakata, Osaka 573‑1010, Japan
| | - Souichi Oe
- Department of Anatomy and Cell Science, Kansai Medical University, Hirakata, Osaka 573‑1010, Japan
| | - Yukie Hirahara
- Department of Anatomy and Cell Science, Kansai Medical University, Hirakata, Osaka 573‑1010, Japan
| | - Takashi Yoshida
- Department of Urology and Andrology, Kansai Medical University, Hirakata, Osaka 573‑1191, Japan
| | - Nae Takizawa
- Department of Anatomy and Cell Science, Kansai Medical University, Hirakata, Osaka 573‑1010, Japan
| | - Yasuharu Takamori
- Department of Anatomy and Cell Science, Kansai Medical University, Hirakata, Osaka 573‑1010, Japan
| | - Kiyoshi Kurokawa
- Department of Anatomy and Cell Science, Kansai Medical University, Hirakata, Osaka 573‑1010, Japan
| | - Tohru Kodama
- SLEEP Disorders Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156‑8506, Japan
| | - Hisao Yamada
- Department of Anatomy and Cell Science, Kansai Medical University, Hirakata, Osaka 573‑1010, Japan
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25
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Zheng Z, Zhang F, Gao D, Wu Y, Wu H. Gene expression profiles of rat MMECs with different glucose levels and fgl2 gene silencing. Diabetes Metab Res Rev 2018; 34:e3058. [PMID: 30098304 PMCID: PMC11035109 DOI: 10.1002/dmrr.3058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 11/11/2022]
Abstract
BACKGROUND Cardiac microvascular endothelial cells (MMECs) is one of the key factors in the process of diabetic cardiomyopathy, a common chronic complication of diabetes. Fibrinogen-like protein 2 (FGL2) is linked to apoptosis, angiogenesis, and inflammatory response, all of which also occur in diabetes. Thus, we investigate the role of FGL 2 and other genes in the pathology of diabetic cardiomyopathy. METHODS In the present study, we used high-throughput microarray to profile gene expression in rat myocardial MMECs with or without silencing the fgl2 gene and in different glucose environments. We use volcanic maps to isolate genes with significantly different expression levels between conditions, using the standard statistical criteria of fold changes ≥1.5 and P-values ≤0.05. From this list, we identified genes with the most signicant changes in RNA levels and confirmed their protein-level changes with Western blot. Furthermore, bioinformatic analysis predicts possible pathophysiology and clinical relevance of these proteins in diabetic cardiomyopathy. RESULTS We identified 17 upregulated and 15 downregulated genes caused by silencing fgl2 gene. Most of them are involved in metabolism, ion transport, cell membrane surface recognition signal modification, inflammatory response, and immune response. Using Western blot, we were able to confirm protein-level expression changes of three genes. Specifically, in both normal and high glucose conditions, silencing fgl2 significantly decreased the expression levels of CCL3 and PLAGL1 while increasing the expression level of CTSC. Significantly, bioinformatic analyses show that CCL3 is related to type 1 diabetes, PLAGL1 to cardiomyocytes, and CTSC to albuminuria in type 2 diabetes. CONCLUSIONS Our study provides clues for further studies on the mechanism of diabetic cardiomyopathy as well as function of FGL2 in this process, potentially offering new therapeutic strategies for treating diabetic cardiomyopathy.
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Affiliation(s)
- Zhenzhong Zheng
- Department of Cardiology, The First Affiliated Hospital of NanchangUniversity, Nanchang, Jiangxi, China
- Jiangxi Hypertension Research Institute, Nanchang, Jiangxi, China
| | - Fan Zhang
- Department of Nephrology, People’s Hospital of Hunan Province, First Affiliated Hospital of Hunan Normal University, Chang sha, Hunan, China
| | - Dengpeng Gao
- Department of Cardiology, The First Affiliated Hospital of NanchangUniversity, Nanchang, Jiangxi, China
- Jiangxi Hypertension Research Institute, Nanchang, Jiangxi, China
| | - Yujing Wu
- Department of Cardiology, The First Affiliated Hospital of NanchangUniversity, Nanchang, Jiangxi, China
- Jiangxi Hypertension Research Institute, Nanchang, Jiangxi, China
| | - Hao Wu
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, USA
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26
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House JS, Mendez M, Maguire RL, Gonzalez-Nahm S, Huang Z, Daniels J, Murphy SK, Fuemmeler BF, Wright FA, Hoyo C. Periconceptional Maternal Mediterranean Diet Is Associated With Favorable Offspring Behaviors and Altered CpG Methylation of Imprinted Genes. Front Cell Dev Biol 2018; 6:107. [PMID: 30246009 PMCID: PMC6137242 DOI: 10.3389/fcell.2018.00107] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/20/2018] [Indexed: 12/28/2022] Open
Abstract
Background: Maternal diet during pregnancy has been shown to influence the child neuro-developmental outcomes. Studies examining effects of dietary patterns on offspring behavior are sparse. Objective: Determine if maternal adherence to a Mediterranean diet is associated with child behavioral outcomes assessed early in life, and to evaluate the role of differentially methylated regions (DMRs) regulating genomically imprinted genes in these associations. Methods: Among 325 mother/infant pairs, we used regression models to evaluate the association between tertiles of maternal periconceptional Mediterranean diet adherence (MDA) scores derived from a Food Frequency Questionnaire, and social and emotional scores derived from the Infant Toddler Social and Emotional Assessment (ITSEA) questionnaire in the second year of life. Methylation of nine genomically imprinted genes was measured to determine if MDA was associated with CpG methylation. Results: Child depression was inversely associated with maternal MDA (Bonferroni-corrected p = 0.041). While controlling for false-discovery, compared to offspring of women with the lowest MDA tertile, those with MDA scores in middle and high MDA tertiles had decreased odds for atypical behaviors [OR (95% CI) = 0.40 (0.20, 0.78) for middle and 0.40 (0.17, 0.92) for highest tertile], for maladaptive behaviors [0.37 (0.18, 0.72) for middle tertile and 0.42 (0.18, 0.95) for highest tertile] and for an index of autism spectrum disorder behaviors [0.46 (0.23, 0.90) for middle and 0.35 (0.15, 0.80) for highest tertile]. Offspring of women with the highest MDA tertile were less likely to exhibit depressive [OR = 0.28 (0.12, 0.64)] and anxiety [0.42 (0.18, 0.97)] behaviors and increased odds of social relatedness [2.31 (1.04, 5.19)] behaviors when compared to low MDA mothers. Some associations varied by sex. Perinatal MDA score was associated with methylation differences for imprinted control regions of PEG10/SGCE [females: Beta (95% CI) = 1.66 (0.52, 2.80) - Bonferroni-corrected p = 0.048; males: -0.56 (-1.13, -0.00)], as well as both MEG3 and IGF2 in males [0.97 (0.00, 1.94)] and -0.92 (-1.65, -0.19) respectively. Conclusion: In this ethnically diverse cohort, maternal adherence to a Mediterranean diet in early pregnancy was associated with favorable neurobehavioral outcomes in early childhood and with sex-dependent methylation differences of MEG3, IGF2, and SGCE/PEG10 DMRs.
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Affiliation(s)
- John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| | - Michelle Mendez
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rachel L Maguire
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Sarah Gonzalez-Nahm
- Department of Health, Behavior and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Julie Daniels
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Bernard F Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, VA, United States
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States.,Department of Statistics, North Carolina State University, Raleigh, NC, United States
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
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27
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Luijk R, Dekkers KF, van Iterson M, Arindrarto W, Claringbould A, Hop P, Boomsma DI, van Duijn CM, van Greevenbroek MMJ, Veldink JH, Wijmenga C, Franke L, 't Hoen PAC, Jansen R, van Meurs J, Mei H, Slagboom PE, Heijmans BT, van Zwet EW. Genome-wide identification of directed gene networks using large-scale population genomics data. Nat Commun 2018; 9:3097. [PMID: 30082726 PMCID: PMC6079029 DOI: 10.1038/s41467-018-05452-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/04/2018] [Indexed: 12/31/2022] Open
Abstract
Identification of causal drivers behind regulatory gene networks is crucial in understanding gene function. Here, we develop a method for the large-scale inference of gene-gene interactions in observational population genomics data that are both directed (using local genetic instruments as causal anchors, akin to Mendelian Randomization) and specific (by controlling for linkage disequilibrium and pleiotropy). Analysis of genotype and whole-blood RNA-sequencing data from 3072 individuals identified 49 genes as drivers of downstream transcriptional changes (Wald P < 7 × 10-10), among which transcription factors were overrepresented (Fisher's P = 3.3 × 10-7). Our analysis suggests new gene functions and targets, including for SENP7 (zinc-finger genes involved in retroviral repression) and BCL2A1 (target genes possibly involved in auditory dysfunction). Our work highlights the utility of population genomics data in deriving directed gene expression networks. A resource of trans-effects for all 6600 genes with a genetic instrument can be explored individually using a web-based browser.
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Affiliation(s)
- René Luijk
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Zuid-Holland, 2333 ZC, The Netherlands
| | - Koen F Dekkers
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Zuid-Holland, 2333 ZC, The Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Zuid-Holland, 2333 ZC, The Netherlands
| | - Wibowo Arindrarto
- Sequence Analysis Support Core, Leiden University Medical Center, Leiden, Zuid-Holland, 2333 ZC, The Netherlands
| | - Annique Claringbould
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, 9713 AV, The Netherlands
| | - Paul Hop
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Zuid-Holland, 2333 ZC, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, 1081 TB, The Netherlands
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, ErasmusMC, Rotterdam, 3015 GE, The Netherlands
| | - Marleen M J van Greevenbroek
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, 6211 LK, The Netherlands
- School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, 6229 ER, The Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, 9713 AV, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, 9713 AV, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, 2333 ZC, The Netherlands
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Neuroscience Campus Amsterdam, Amsterdam, 1081 HV, The Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, ErasmusMC, Rotterdam, 3015 CE, The Netherlands
| | - Hailiang Mei
- Sequence Analysis Support Core, Leiden University Medical Center, Leiden, Zuid-Holland, 2333 ZC, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Zuid-Holland, 2333 ZC, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Zuid-Holland, 2333 ZC, The Netherlands.
| | - Erik W van Zwet
- Medical Statistics Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Zuid-Holland, 2333 ZC, The Netherlands.
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28
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Provenzi L, Carli PD, Fumagalli M, Giorda R, Casavant S, Beri S, Citterio A, D'Agata A, Morandi F, Mosca F, Borgatti R, Montirosso R. Very preterm birth is associated with PLAGL1 gene hypomethylation at birth and discharge. Epigenomics 2018; 10:1121-1130. [PMID: 30070601 DOI: 10.2217/epi-2017-0123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIM Recent findings show that DNA methylation is susceptible to very preterm (VPT) birth and to the experience of the early stay in the neonatal intensive care unit. The aim of the study was to compare PLAGL1 methylation between VPT and full-term (FT) infants at birth as well as between VPT infants at discharge and FT infants at birth. METHODS DNA was collected from cord blood of 56 VPT and 27 FT infants at birth and from peripheral blood in VPT infants at neonatal intensive care unit discharge. Sociodemographic and neonatal variables were considered. RESULTS PLAGL1 methylation at birth and at discharge were highly correlated in VPT infants. Lower methylation emerged in VPT infants at birth and discharge compared to FT counterparts. CONCLUSION PLAGL1 hypomethylation emerged as a potential epigenetic mark of VPT birth. Future research is warranted to assess the functional consequences of PLAGL1 diminished methylation in VPT infants' development.
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Affiliation(s)
- Livio Provenzi
- 0-3 Center for the at-Risk Infant, Scientific Institute, IRCCS Eugenio Medea, 238422, Bosisio Parini, Italy
| | - Pietro De Carli
- 0-3 Center for the at-Risk Infant, Scientific Institute, IRCCS Eugenio Medea, 238422, Bosisio Parini, Italy
| | - Monica Fumagalli
- NICU, Department of Clinical Sciences & Community Health, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 201223, Milan, Italy
| | - Roberto Giorda
- Molecular Biology Laboratory, Scientific Institute, IRCCS Eugenio Medea, 238424, Bosisio Parini, Italy
| | - Sharon Casavant
- School of Nursing, University of Connecticut, Storrs, CT, 060325, USA
| | - Silvana Beri
- Molecular Biology Laboratory, Scientific Institute, IRCCS Eugenio Medea, 238424, Bosisio Parini, Italy
| | - Andrea Citterio
- Molecular Biology Laboratory, Scientific Institute, IRCCS Eugenio Medea, 238424, Bosisio Parini, Italy
| | - Amy D'Agata
- College of Nursing, University of Rhode Island, Kingston, RI, 028816, USA
| | | | - Fabio Mosca
- NICU, Department of Clinical Sciences & Community Health, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 201223, Milan, Italy
| | - Renato Borgatti
- Neuropsychiatry & Neurorehabilitation Unit, Scientific Institute, IRCCS Eugenio Medea, 238422, Bosisio Parini, Italy
| | - Rosario Montirosso
- 0-3 Center for the at-Risk Infant, Scientific Institute, IRCCS Eugenio Medea, 238422, Bosisio Parini, Italy
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29
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Neonatal Diabetes Mellitus. MEDICAL BULLETIN OF SISLI ETFAL HOSPITAL 2018; 52:71-78. [PMID: 32595377 PMCID: PMC7315067 DOI: 10.14744/semb.2017.51422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 06/07/2017] [Indexed: 11/23/2022]
Abstract
Neonatal diabetes is a rare cause of hyperglycemia in the neonatal period. It is caused by mutations in genes that encode proteins playing critical roles in normal functions of pancreatic beta cells. Neonatal diabetes is divided into temporary and permanent subtypes. Treatment is based on the correction of fluid-electrolyte disturbances and hyperglycemia. Patients respond to insulin or sulfonylurea treatment according to the mutation type. Close glucose monitoring and education of caregivers about diabetes are vital.
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30
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Cowley M, Skaar DA, Jima DD, Maguire RL, Hudson KM, Park SS, Sorrow P, Hoyo C. Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:037003. [PMID: 29529597 PMCID: PMC6071808 DOI: 10.1289/ehp2085] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Imprinted genes are defined by their preferential expression from one of the two parental alleles. This unique mode of gene expression is dependent on allele-specific DNA methylation profiles established at regulatory sequences called imprinting control regions (ICRs). These loci have been used as biosensors to study how environmental exposures affect methylation and transcription. However, a critical unanswered question is whether they are more, less, or equally sensitive to environmental stressors as the rest of the genome. OBJECTIVES Using cadmium exposure in humans as a model, we aimed to determine the relative sensitivity of ICRs to perturbation of methylation compared to similar, nonimprinted loci in the genome. METHODS We assayed DNA methylation genome-wide using bisulfite sequencing of 19 newborn cord blood and 20 maternal blood samples selected on the basis of maternal blood cadmium levels. Differentially methylated regions (DMRs) associated with cadmium exposure were identified. RESULTS In newborn cord blood and maternal blood, 641 and 1,945 cadmium-associated DMRs were identified, respectively. DMRs were more common at the 15 maternally methylated ICRs than at similar nonimprinted loci in newborn cord blood (p=5.64×10-8) and maternal blood (p=6.22×10-14), suggesting a higher sensitivity for ICRs to cadmium. Genome-wide, Enrichr analysis indicated that the top three functional categories for genes that overlapped DMRs in maternal blood were body mass index (BMI) (p=2.0×10-5), blood pressure (p=3.8×10-5), and body weight (p=0.0014). In newborn cord blood, the top three functional categories were BMI, atrial fibrillation, and hypertension, although associations were not significant after correction for multiple testing (p=0.098). These findings suggest that epigenetic changes may contribute to the etiology of cadmium-associated diseases. CONCLUSIONS We analyzed cord blood and maternal blood DNA methylation profiles genome-wide at nucleotide resolution in individuals selected for high and low blood cadmium levels in the first trimester. Our findings suggest that ICRs may be hot spots for perturbation by cadmium, motivating further study of these loci to investigate potential mechanisms of cadmium action. https://doi.org/10.1289/EHP2085.
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Affiliation(s)
- Michael Cowley
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
- W.M. Keck Center for Behavioral Biology , North Carolina State University , Raleigh, North Carolina, USA
| | - David A Skaar
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Dereje D Jima
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University , Raleigh, North Carolina, USA
| | - Rachel L Maguire
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Kathleen M Hudson
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Sarah S Park
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Patricia Sorrow
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
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Varrault A, Dantec C, Le Digarcher A, Chotard L, Bilanges B, Parrinello H, Dubois E, Rialle S, Severac D, Bouschet T, Journot L. Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network. Nucleic Acids Res 2017; 45:10466-10480. [PMID: 28985358 PMCID: PMC5737700 DOI: 10.1093/nar/gkx672] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 06/29/2017] [Accepted: 07/20/2017] [Indexed: 01/05/2023] Open
Abstract
PLAGL1/ZAC1 undergoes parental genomic imprinting, is paternally expressed, and is a member of the imprinted gene network (IGN). It encodes a zinc finger transcription factor with anti-proliferative activity and is a candidate tumor suppressor gene on 6q24 whose expression is frequently lost in various neoplasms. Conversely, gain of PLAGL1 function is responsible for transient neonatal diabetes mellitus, a rare genetic disease that results from defective pancreas development. In the present work, we showed that Plagl1 up-regulation was not associated with DNA damage-induced cell cycle arrest. It was rather associated with physiological cell cycle exit that occurred with contact inhibition, growth factor withdrawal, or cell differentiation. To gain insights into Plagl1 mechanism of action, we identified Plagl1 target genes by combining chromatin immunoprecipitation and genome-wide transcriptomics in transfected cell lines. Plagl1-elicited gene regulation correlated with multiple binding to the proximal promoter region through a GC-rich motif. Plagl1 target genes included numerous genes involved in signaling, cell adhesion, and extracellular matrix composition, including collagens. Plagl1 targets also included 22% of the 409 genes that make up the IGN. Altogether, this work identified Plagl1 as a transcription factor that coordinated the regulation of a subset of IGN genes and controlled extracellular matrix composition.
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Affiliation(s)
- Annie Varrault
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Christelle Dantec
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Laëtitia Chotard
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Benoit Bilanges
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Hugues Parrinello
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Emeric Dubois
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Stéphanie Rialle
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Dany Severac
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
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Smith CEL, Alexandraki A, Cordery SF, Parmar R, Bonthron DT, Valleley EMA. A tissue-specific promoter derived from a SINE retrotransposon drives biallelic expression of PLAGL1 in human lymphocytes. PLoS One 2017; 12:e0185678. [PMID: 28957425 PMCID: PMC5619815 DOI: 10.1371/journal.pone.0185678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 09/18/2017] [Indexed: 12/20/2022] Open
Abstract
The imprinted gene PLAGL1 is an important regulator of apoptosis and cell cycle arrest. Loss of its expression has been implicated in tumorigenesis in a range of different cancers, and overexpression during fetal development causes transient neonatal diabetes mellitus (TNDM). PLAGL1 lies within an imprinted region of chromosome 6q24, and monoallelic expression from the major, differentially methylated promoter (P1) occurs in most human tissues. However, in peripheral blood leukocytes, the active promoter (P2) is non-imprinted and drives biallelic transcription. We report here a novel PLAGL1 promoter (P5) derived from the insertion of a primate-specific, MIR3 SINE retrotransposon. P5 is highly utilized in lymphocytes, particularly in T cells, and like P2, directs biallelic transcription. Our results show that it is important to consider P5 in relation to PLAGL1 function in T cells when investigating the dysregulation of this gene.
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Affiliation(s)
- Claire E. L. Smith
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Alexia Alexandraki
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Sarah F. Cordery
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Rekha Parmar
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - David T. Bonthron
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Elizabeth M. A. Valleley
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
- * E-mail:
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Zammit MA, Agius SM, Calleja-Agius J. Transient Neonatal Diabetes Mellitus: A Challenge and Opportunity for Specialized Nursing Care. Neonatal Netw 2017; 36:196-205. [PMID: 28764822 DOI: 10.1891/0730-0832.36.4.196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Transient neonatal diabetes mellitus (TNDM) is a rare disorder, with a reported incidence of approximately 1 in 450,000 live births. It is characterized by insulin-requiring hyperglycemia in the neonatal period. The disease improves by early childhood, but the patient may relapse in later life. Diagnosis is made after genetic testing following presentation with hyperglycemia not conforming to Type 1 or Type 2 diabetes. Management is based on insulin and possible sulfonylurea administration. Three genetically distinct subtypes of TNDM are recognized. Type 1 TNDM is due to overexpression of genes at the 6q24 locus, whereas the 11p15 locus is involved in Type 2 and 3 TNDM. In this article the clinical presentation, management, and genetics of TNDM are discussed, particularly emphasizing the role of the neonatal nurse.
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Elhamamsy AR. Role of DNA methylation in imprinting disorders: an updated review. J Assist Reprod Genet 2017; 34:549-562. [PMID: 28281142 PMCID: PMC5427654 DOI: 10.1007/s10815-017-0895-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/23/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic imprinting is a complex epigenetic process that contributes substantially to embryogenesis, reproduction, and gametogenesis. Only small fraction of genes within the whole genome undergoes imprinting. Imprinted genes are expressed in a monoallelic parent-of-origin-specific manner, which means that only one of the two inherited alleles is expressed either from the paternal or maternal side. Imprinted genes are typically arranged in clusters controlled by differentially methylated regions or imprinting control regions. Any defect or relaxation in imprinting process can cause loss of imprinting in the key imprinted loci. Loss of imprinting in most cases has a harmful effect on fetal development and can result in neurological, developmental, and metabolic disorders. Since DNA methylation and histone modifications play a key role in the process of imprinting. This review focuses on the role of DNA methylation in imprinting process and describes DNA methylation aberrations in different imprinting disorders.
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Affiliation(s)
- Amr Rafat Elhamamsy
- Department of Clinical Pharmacy, School of Pharmacy, Tanta University, Tanta, 31512, Gharbia, Egypt.
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35
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Schenkel LC, Rodenhiser D, Siu V, McCready E, Ainsworth P, Sadikovic B. Constitutional Epi/Genetic Conditions: Genetic, Epigenetic, and Environmental Factors. J Pediatr Genet 2017; 6:30-41. [PMID: 28180025 PMCID: PMC5288004 DOI: 10.1055/s-0036-1593849] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
There are more than 4,000 phenotypes for which the molecular basis is at least partly known. Though defects in primary DNA structure constitute a major cause of these disorders, epigenetic disruption is emerging as an important alternative mechanism in the etiology of a broad range of congenital and developmental conditions. These include epigenetic defects caused by either localized (in cis) genetic alterations or more distant (in trans) genetic events but can also include environmental effects. Emerging evidence suggests interplay between genetic and environmental factors in the epigenetic etiology of several constitutional "epi/genetic" conditions. This review summarizes our broadening understanding of how epigenetics contributes to pediatric disease by exploring different classes of epigenomic disorders. It further challenges the simplistic dogma of "DNA encodes RNA encodes protein" to best understand the spectrum of factors that can influence genetic traits in a pediatric population.
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Affiliation(s)
- Laila C. Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
| | - David Rodenhiser
- Children's Health Research Institute, London, Ontario, Canada
- Department of Biochemistry, Western University, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Victoria Siu
- Children's Health Research Institute, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- Department of Biochemistry, Western University, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
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Patten MM, Cowley M, Oakey RJ, Feil R. Regulatory links between imprinted genes: evolutionary predictions and consequences. Proc Biol Sci 2017; 283:rspb.2015.2760. [PMID: 26842569 PMCID: PMC4760173 DOI: 10.1098/rspb.2015.2760] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect to cis-acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes acts in trans on the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of these trans-regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.
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Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, 37th and O Streets NW, Washington, DC 20057, USA
| | - Michael Cowley
- Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Rebecca J Oakey
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Robert Feil
- Centre National de Recherche Scientifique (CNRS), Institute of Molecular Genetics (IGMM), 1919 route de Mende, Montpellier 34293, France University of Montpellier, 163 rue Auguste Broussonnet, Montpellier 34090, France Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Vega-Benedetti AF, Saucedo C, Zavattari P, Vanni R, Zugaza JL, Parada LA. PLAGL1: an important player in diverse pathological processes. J Appl Genet 2016; 58:71-78. [PMID: 27311313 DOI: 10.1007/s13353-016-0355-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 05/02/2016] [Accepted: 06/02/2016] [Indexed: 12/23/2022]
Abstract
The PLAGL1 gene encodes a homonymous zinc finger protein that promotes cell cycle arrest and apoptosis through multiple pathways. The protein has been implicated in metabolic, genetic, and neoplastic illnesses, but the molecular mechanisms by which the protein PLAGL1 participates in such diverse processes remains to be elucidated. In this review, we focus mainly on the molecular biology of PLAGL1 and the relevance of its abnormalities to several pathological processes.
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Affiliation(s)
- Ana F Vega-Benedetti
- Institute of Experimental Pathology, UNSa-CONICET, Ave. Bolivia 5150, 4400, Salta, Argentina
| | - Cinthia Saucedo
- Institute of Experimental Pathology, UNSa-CONICET, Ave. Bolivia 5150, 4400, Salta, Argentina
| | - Patrizia Zavattari
- Biochemistry, Biology and Genetics Unit, Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SP 8, Km 0.700, 09042, Monserrato, Cagliari, Italy
| | - Roberta Vanni
- Biochemistry, Biology and Genetics Unit, Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SP 8, Km 0.700, 09042, Monserrato, Cagliari, Italy
| | - José L Zugaza
- IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain.,Achucarro Basque Center for Neuroscience, Bizkaia Science and Technology Park, Building 205, Zamudio, Spain.,Department of Genetics, Physic Anthropology and Animal Physiology, Faculty of Medicine and Dentistry, University of the Basque Country, Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Luis Antonio Parada
- Institute of Experimental Pathology, UNSa-CONICET, Ave. Bolivia 5150, 4400, Salta, Argentina.
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Trim28 Haploinsufficiency Triggers Bi-stable Epigenetic Obesity. Cell 2016; 164:353-64. [PMID: 26824653 PMCID: PMC4735019 DOI: 10.1016/j.cell.2015.12.025] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/12/2015] [Accepted: 12/08/2015] [Indexed: 12/21/2022]
Abstract
More than one-half billion people are obese, and despite progress in genetic research, much of the heritability of obesity remains enigmatic. Here, we identify a Trim28-dependent network capable of triggering obesity in a non-Mendelian, “on/off” manner. Trim28+/D9 mutant mice exhibit a bi-modal body-weight distribution, with isogenic animals randomly emerging as either normal or obese and few intermediates. We find that the obese-“on” state is characterized by reduced expression of an imprinted gene network including Nnat, Peg3, Cdkn1c, and Plagl1 and that independent targeting of these alleles recapitulates the stochastic bi-stable disease phenotype. Adipose tissue transcriptome analyses in children indicate that humans too cluster into distinct sub-populations, stratifying according to Trim28 expression, transcriptome organization, and obesity-associated imprinted gene dysregulation. These data provide evidence of discrete polyphenism in mouse and man and thus carry important implications for complex trait genetics, evolution, and medicine. Video Abstract
Trim28 haploinsufficiency triggers stochastic bi-stable obesity or polyphenism Non-classical imprinted gene dysregulation specifies “on” versus “off” obese states Peg3 and Nnat perturbation trigger stochastic bi-stable obesity Human BMI distributions and transcriptomes suggest Trim28-associated subpopulations
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Alkorta-Aranburu G, Sukhanova M, Carmody D, Hoffman T, Wysinger L, Keller-Ramey J, Li Z, Johnson AK, Kobiernicki F, Botes S, Fitzpatrick C, Das S, Del Gaudio D. Improved molecular diagnosis of patients with neonatal diabetes using a combined next-generation sequencing and MS-MLPA approach. J Pediatr Endocrinol Metab 2016; 29:523-31. [PMID: 26894574 DOI: 10.1515/jpem-2015-0341] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND We evaluated a methylation-specific multiplex-ligation-dependent probe amplification (MS-MLPA) assay for the molecular diagnosis of transient neonatal diabetes mellitus (TNDM) caused by 6q24 abnormalities and assessed the clinical utility of using this assay in combination with next generation sequencing (NGS) analysis for diagnosing patients with neonatal diabetes (NDM). METHODS We performed MS-MLPA in 18 control samples and 42 retrospective NDM cases with normal bi-parental inheritance of chromosome 6. Next, we evaluated 22 prospective patients by combining NGS analysis of 11 NDM genes and the MS-MLPA assay. RESULTS 6q24 aberrations were identified in all controls and in 19% of patients with normal bi-parental inheritance of chromosome 6. The MS-MLPA/NGS combined approach identified a genetic cause in ~64% of patients with NDM of unknown etiology. CONCLUSIONS MS-MLPA is a reliable method to identify all known 6q24 abnormalities and comprehensive testing of all causes reveals a causal mutation in ~64% of patients.
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Gunes S, Arslan MA, Hekim GNT, Asci R. The role of epigenetics in idiopathic male infertility. J Assist Reprod Genet 2016; 33:553-569. [PMID: 26941097 DOI: 10.1007/s10815-016-0682-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/22/2016] [Indexed: 12/17/2022] Open
Abstract
Infertility is a complex disorder with multiple genetic and environmental causes. Although some specific mutations have been identified, other factors responsible for sperm defects remain largely unknown. Despite considerable efforts to identify the pathophysiology of the disease, we cannot explain the underlying mechanisms of approximately half of infertility cases. This study reviews current data on epigenetic regulation and idiopathic male infertility. Recent data have shown an association between epigenetic modifications and idiopathic infertility. In this regard, epigenetics has emerged as one of the promising research areas in understanding male infertility. Many studies have indicated that epigenetic modifications, including DNA methylation in imprinted and developmental genes, histone tail modifications and short non-coding RNAs in spermatozoa may have a role in idiopathic male infertility.
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Affiliation(s)
- Sezgin Gunes
- Faculty of Medicine, Department of Medical Biology, Ondokuz Mayis University, 55139, Samsun, Turkey.
- Health Sciences Institute, Department of Multidisciplinary Molecular Medicine, Ondokuz Mayis University, 55139, Samsun, Turkey.
| | - Mehmet Alper Arslan
- Faculty of Medicine, Department of Medical Biology, Ondokuz Mayis University, 55139, Samsun, Turkey.
- Health Sciences Institute, Department of Multidisciplinary Molecular Medicine, Ondokuz Mayis University, 55139, Samsun, Turkey.
| | | | - Ramazan Asci
- Health Sciences Institute, Department of Multidisciplinary Molecular Medicine, Ondokuz Mayis University, 55139, Samsun, Turkey
- Faculty of Medicine, Department of Urology, Ondokuz Mayis University, 55139, Samsun, Turkey
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Monk D. Genomic imprinting in the human placenta. Am J Obstet Gynecol 2015; 213:S152-62. [PMID: 26428495 DOI: 10.1016/j.ajog.2015.06.032] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 05/28/2015] [Accepted: 06/15/2015] [Indexed: 12/22/2022]
Abstract
With the launch of the National Institute of Child Health and Human Development/National Institutes of Health Human Placenta Project, the anticipation is that this often-overlooked organ will be the subject of much intense research. Compared with somatic tissues, the cells of the placenta have a unique epigenetic profile that dictates its transcription patterns, which when disturbed may be associated with adverse pregnancy outcomes. One major class of genes that is dependent on strict epigenetic regulation in the placenta is subject to genomic imprinting, the parent-of-origin-dependent monoallelic gene expression. This review discusses the differences in allelic expression and epigenetic profiles of imprinted genes that are identified between different species, which reflect the continuous evolutionary adaption of this form of epigenetic regulation. These observations divulge that placenta-specific imprinted gene that is reliant on repressive histone signatures in mice are unlikely to be imprinted in humans, whereas intense methylation profiling in humans has uncovered numerous maternally methylated regions that are restricted to the placenta that are not conserved in mice. Imprinting has been proposed to be a mechanism that regulates parental resource allocation and ultimately can influence fetal growth, with the placenta being the key in this process. Furthermore, I discuss the developmental dynamics of both classic and transient placenta-specific imprinting and examine the evidence for an involvement of these genes in intrauterine growth restriction and placenta-associated complications. Finally, I focus on examples of genes that are regulated aberrantly in complicated pregnancies, emphasizing their application as pregnancy-related disease biomarkers to aid the diagnosis of at-risk pregnancies early in gestation.
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Affiliation(s)
- David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain.
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Wang K, Li X, Dong S, Liang J, Mao F, Zeng C, Wu H, Wu J, Cai W, Sun ZS. Q-RRBS: a quantitative reduced representation bisulfite sequencing method for single-cell methylome analyses. Epigenetics 2015. [PMID: 26213102 DOI: 10.1080/15592294.2015.1075690] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Reduced representation bisulfite sequencing (RRBS) is a powerful method of DNA methylome profiling that can be applied to single cells. However, no previous report has described how PCR-based duplication-induced artifacts affect the accuracy of this method when measuring DNA methylation levels. For quantifying the effects of duplication-induced artifacts on methylome profiling when using ultra-trace amounts of starting material, we developed a novel method, namely quantitative RRBS (Q-RRBS), in which PCR-induced duplication is excluded through the use of unique molecular identifiers (UMIs). By performing Q-RRBS on varying amounts of starting material, we determined that duplication-induced artifacts were more severe when small quantities of the starting material were used. However, through using the UMIs, we successfully eliminated these artifacts. In addition, Q-RRBS could accurately detect allele-specific methylation in absence of allele-specific genetic variants. Our results demonstrate that Q-RRBS is an optimal strategy for DNA methylation profiling of single cells or samples containing ultra-trace amounts of cells.
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Affiliation(s)
- Kangli Wang
- a Institute of Genomic Medicine; Wenzhou Medical University ; Wenzhou , China
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Cheong CY, Chng K, Ng S, Chew SB, Chan L, Ferguson-Smith AC. Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation. Genome Res 2015; 25:611-23. [PMID: 25862382 PMCID: PMC4417110 DOI: 10.1101/gr.183301.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 03/04/2015] [Indexed: 12/22/2022]
Abstract
Genomic imprinting is an epigenetic mechanism resulting in parental allele-specific gene expression. Defects in normal imprinting are found in cancer, assisted reproductive technologies, and several human syndromes. In mouse models, germline-derived DNA methylation is shown to regulate imprinting. Though imprinting is largely conserved between mammals, species- and tissue-specific domains of imprinted expression exist. Using the cynomolgus macaque (Macaca fascicularis) to assess primate-specific imprinting, we present a comprehensive view of tissue-specific imprinted expression and DNA methylation at established imprinted gene clusters. For example, like mouse and unlike human, macaque IGF2R is consistently imprinted, and the PLAGL1, INPP5F transcript variant 2, and PEG3 imprinting control regions are not methylated in the macaque germline but acquire this post-fertilization. Methylome data from human early embryos appear to support this finding. These suggest fundamental differences in imprinting control mechanisms between primate species and rodents at some imprinted domains, with implications for our understanding of the epigenetic programming process in humans and its influence on disease.
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Affiliation(s)
- Clara Y Cheong
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Keefe Chng
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Shilen Ng
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Siew Boom Chew
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Louiza Chan
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Anne C Ferguson-Smith
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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Guillomot M, Campion E, Prézelin A, Sandra O, Hue I, Le Bourhis D, Richard C, Biase F, Rabel C, Wallace R, Lewin H, Renard JP, Jammes H. Spatial and temporal changes of Decorin, Type I collagen and Fibronectin expression in normal and clone bovine placenta. Placenta 2014; 35:737-47. [DOI: 10.1016/j.placenta.2014.06.366] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/12/2014] [Accepted: 06/13/2014] [Indexed: 01/06/2023]
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Kameswaran V, Kaestner KH. The Missing lnc(RNA) between the pancreatic β-cell and diabetes. Front Genet 2014; 5:200. [PMID: 25071830 PMCID: PMC4077016 DOI: 10.3389/fgene.2014.00200] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 06/15/2014] [Indexed: 01/15/2023] Open
Abstract
Diabetes mellitus represents a group of complex metabolic diseases that result in impaired glucose homeostasis, which includes destruction of β-cells or the failure of these insulin-secreting cells to compensate for increased metabolic demand. Despite a strong interest in characterizing the transcriptome of the different human islet cell types to understand the molecular basis of diabetes, very little attention has been paid to the role of long non-coding RNAs (lncRNAs) and their contribution to this disease. Here we summarize the growing evidence for the potential role of these lncRNAs in β-cell function and dysregulation in diabetes, with a focus on imprinted genomic loci.
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Affiliation(s)
- Vasumathi Kameswaran
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
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Zhou Y, Zhang X, Klibanski A. Genetic and epigenetic mutations of tumor suppressive genes in sporadic pituitary adenoma. Mol Cell Endocrinol 2014; 386:16-33. [PMID: 24035864 PMCID: PMC3943596 DOI: 10.1016/j.mce.2013.09.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 09/03/2013] [Indexed: 12/28/2022]
Abstract
Human pituitary adenomas are the most common intracranial neoplasms. Approximately 5% of them are familial adenomas. Patients with familial tumors carry germline mutations in predisposition genes, including AIP, MEN1 and PRKAR1A. These mutations are extremely rare in sporadic pituitary adenomas, which therefore are caused by different mechanisms. Multiple tumor suppressive genes linked to sporadic tumors have been identified. Their inactivation is caused by epigenetic mechanisms, mainly promoter hypermethylation, and can be placed into two groups based on their functional interaction with tumor suppressors RB or p53. The RB group includes CDKN2A, CDKN2B, CDKN2C, RB1, BMP4, CDH1, CDH13, GADD45B and GADD45G; AIP and MEN1 genes also belong to this group. The p53 group includes MEG3, MGMT, PLAGL1, RASSF1, RASSF3 and SOCS1. We propose that the tumor suppression function of these genes is mainly mediated by the RB and p53 pathways. We also discuss possible tumor suppression mechanisms for individual genes.
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Affiliation(s)
- Yunli Zhou
- Neuroendocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, United States
| | - Xun Zhang
- Neuroendocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, United States
| | - Anne Klibanski
- Neuroendocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, United States.
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Hisanaga-Oishi Y, Nishiwaki-Ueda Y, Nojima K, Ueda H. Analysis of the expression of candidate genes for type 1 diabetes susceptibility in T cells. Endocr J 2014; 61:577-88. [PMID: 24705559 DOI: 10.1507/endocrj.ej14-0002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Type 1 diabetes is characterized by T-cell-mediated autoimmune destruction of pancreatic β-cells. Currently, approximately 50 type 1 diabetes susceptibility genes or chromosomal regions have been identified. However, the functions of type 1 diabetes susceptibility genes in T cells are elusive. In this study, we evaluated the correlation between type 1 diabetes susceptibility genes and T-cell signaling. The expression levels of 22 candidate type 1 diabetes susceptibility genes in T cells from nonobese diabetic (NOD), control C57BL/6 (B6), and NOD-control F1 hybrid mice were analyzed in response to 2 key immunoregulatory cytokines: interleukin-2 (IL-2) and transforming growth factor β (TGF-β). Exogenous gene expression studies were also performed in EL4 and Jurkat E6.1 T-cell lines. Significant differences in the expression of Clec16a, Dlk1, Il2, Ptpn22, Rnls, and Zac1 (also known as Plagl1) were observed in T cells derived from the 3 strains of mice, and TGF-β differentially influenced the expression of Ctla4, Foxp3, Il2, Ptpn22, Sh2b3, and Zac1. We found that TGF-β induced Zac1 expression in both primary T cells and EL4 cells and that exogenous expression of Zac1 and ZAC1 in T-cell lines altered the expression of Il2 and DLK1, respectively. The results of our study indicate the possibility that additional genetic pathways underlying type 1 diabetes susceptibility, including those involving Clec16a, Dlk1, Rnls, Sh2b3, and Zac1 under IL-2 and TGF-β signaling in T cells, may be shared between human and NOD mice.
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Affiliation(s)
- Yuko Hisanaga-Oishi
- Department of Molecular Endocrinology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
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Girardot M, Feil R, Llères D. Epigenetic deregulation of genomic imprinting in humans: causal mechanisms and clinical implications. Epigenomics 2013; 5:715-28. [DOI: 10.2217/epi.13.66] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian genes controlled by genomic imprinting play important roles in development and diverse postnatal processes. A growing number of congenital disorders have been linked to genomic imprinting. Each of these is caused by perturbed gene expression at one principal imprinted domain. Some imprinting disorders, including the Prader–Willi and Angelman syndromes, are caused almost exclusively by genetic mutations. In several others, including the Beckwith–Wiedemann and Silver–Russell growth syndromes, and transient neonatal diabetes mellitus, imprinted expression is perturbed mostly by epigenetic alterations at ‘imprinting control regions’ and at other specific regulatory sequences. In a minority of these patients, DNA methylation is altered at multiple imprinted loci, suggesting that common trans-acting factors are affected. Here, we review the epimutations involved in congenital imprinting disorders and the associated clinical features. Trans-acting factors known to be causally involved are discussed and other trans-acting factors that are potentially implicated are also presented.
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Affiliation(s)
- Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
| | - David Llères
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
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Goi C, Little P, Xie C. Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data. BMC Genomics 2013; 14 Suppl 5:S2. [PMID: 24564528 PMCID: PMC3852067 DOI: 10.1186/1471-2164-14-s5-s2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Cell type and TF specific interactions between Transcription Factors (TFs) and cofactors are essential for transcriptional regulation through recruitment of general transcription machinery to gene promoter regions and their identification heavily reliant on protein interaction assays. Results Using TF targeted chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) data from Encyclopedia of DNA Elements (ENCODE), we report cell type and TF specific TF-cofactor interactions captured in vivo through enrichments of non target cofactor binding site motifs within ChIP-seq peaks. We observe enrichments in both known and novel cofactor motifs. Conclusions Given the regulatory implications which TF and cofactor interactions have on a cell's phenotype, their identification is necessary but challenging. Here we present the findings to our analyses surrounding the investigation of TF-cofactor interactions encoded within TF ChIP-seq peaks. Novel cofactor binding site enrichments observed provides valuable insight into TF and cell type specific interactions driving TF interactions.
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