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Kim HY, Shin CH, Shin CH, Ko JM. Uncovering the phenotypic consequences of multi-locus imprinting disturbances using genome-wide methylation analysis in genomic imprinting disorders. PLoS One 2023; 18:e0290450. [PMID: 37594968 PMCID: PMC10437897 DOI: 10.1371/journal.pone.0290450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
Imprinted genes are regulated by DNA methylation of imprinted differentially methylated regions (iDMRs). An increasing number of patients with congenital imprinting disorders (IDs) exhibit aberrant methylation at multiple imprinted loci, multi-locus imprinting disturbance (MLID). We examined MLID and its possible impact on clinical features in patients with IDs. Genome-wide DNA methylation analysis (GWMA) using blood leukocyte DNA was performed on 13 patients with Beckwith-Wiedemann syndrome (BWS), two patients with Silver-Russell syndrome (SRS), and four controls. HumanMethylation850 BeadChip analysis for 77 iDMRs (809 CpG sites) identified three patients with BWS and one patient with SRS showing additional hypomethylation, other than the disease-related iDMRs, suggestive of MLID. Two regions were aberrantly methylated in at least two patients with BWS showing MLID: PPIEL locus (chromosome 1: 39559298 to 39559744), and FAM50B locus (chromosome 6: 3849096 to 3849469). All patients with BWS- and SRS-MLID did not show any other clinical characteristics associated with additional involved iDMRs. Exome analysis in three patients with BWS who exhibited multiple hypomethylation did not identify any causative variant related to MLID. This study indicates that a genome-wide approach can unravel MLID in patients with an apparently isolated ID. Patients with MLID showed only clinical features related to the original IDs. Long-term follow-up studies in larger cohorts are warranted to evaluate any possible phenotypic consequences of other disturbed imprinted loci.
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Affiliation(s)
- Hwa Young Kim
- Department of Pediatrics, Division of Pediatric Endocrinology and Metabolism, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Choong Ho Shin
- Department of Pediatrics, Division of Pediatric Endocrinology and Metabolism, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Ho Shin
- Department of Orthopaedics, Division of Pediatric Orthopedics, Seoul National University College of Medicine, Seoul, Korea
| | - Jung Min Ko
- Department of Pediatrics, Division of Clinical Genetics, Seoul National University College of Medicine, Seoul, Korea
- Rare Disease Center, Seoul National University Hospital, Seoul, Korea
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2
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Alsharairi NA. Exploring the Diet-Gut Microbiota-Epigenetics Crosstalk Relevant to Neonatal Diabetes. Genes (Basel) 2023; 14:genes14051017. [PMID: 37239377 DOI: 10.3390/genes14051017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Neonatal diabetes (NDM) is a rare monogenic disorder that presents as hyperglycemia during the first six months of life. The link between early-life gut microbiota dysbiosis and susceptibility to NDM remains uncertain. Experimental studies have demonstrated that gestational diabetes mellitus (GDM) could develop into meconium/gut microbiota dysbiosis in newborns, and thus, it is thought to be a mediator in the pathogenesis of NDM. Epigenetic modifications have been considered as potential mechanisms by which the gut microbiota and susceptibility genes interact with the neonatal immune system. Several epigenome-wide association studies have revealed that GDM is associated with neonatal cord blood and/or placental DNA methylation alterations. However, the mechanisms linking diet in GDM with gut microbiota alterations, which may in turn induce the expression of genes linked to NDM, are yet to be unraveled. Therefore, the focus of this review is to highlight the impacts of diet, gut microbiota, and epigenetic crosstalk on altered gene expression in NDM.
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Affiliation(s)
- Naser A Alsharairi
- Heart, Mind & Body Research Group, Griffith University, Gold Coast, QLD P.O. Box 4222, Australia
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3
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Bilo L, Ochoa E, Lee S, Dey D, Kurth I, Kraft F, Rodger F, Docquier F, Toribio A, Bottolo L, Binder G, Fekete G, Elbracht M, Maher ER, Begemann M, Eggermann T. Molecular characterisation of 36 multilocus imprinting disturbance (MLID) patients: a comprehensive approach. Clin Epigenetics 2023; 15:35. [PMID: 36859312 PMCID: PMC9979536 DOI: 10.1186/s13148-023-01453-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Imprinting disorders (ImpDis) comprise diseases which are caused by aberrant regulation of monoallelically and parent-of-origin-dependent expressed genes. A characteristic molecular change in ImpDis patients is aberrant methylation signatures at disease-specific loci, without an obvious DNA change at the specific differentially methylated region (DMR). However, there is a growing number of reports on multilocus imprinting disturbances (MLIDs), i.e. aberrant methylation at different DMRs in the same patient. These MLIDs account for a significant number of patients with specific ImpDis, and several reports indicate a central role of pathogenic maternal effect variants in their aetiology by affecting the maturation of the oocyte and the early embryo. Though several studies on the prevalence and the molecular causes of MLID have been conducted, homogeneous datasets comprising both genomic and methylation data are still lacking. RESULTS Based on a cohort of 36 MLID patients, we here present both methylation data obtained from next-generation sequencing (NGS, ImprintSeq) approaches and whole-exome sequencing (WES). The compilation of methylation data did not reveal a disease-specific MLID episignature, and a predisposition for the phenotypic modification was not obvious as well. In fact, this lack of epigenotype-phenotype correlation might be related to the mosaic distribution of imprinting defects and their functional relevance in specific tissues. CONCLUSIONS Due to the higher sensitivity of NGS-based approaches, we suggest that ImprintSeq might be offered at reference centres in case of ImpDis patients with unusual phenotypes but MLID negative by conventional tests. By WES, additional MLID causes than the already known maternal effect variants could not be identified, neither in the patients nor in the maternal exomes. In cases with negative WES results, it is currently unclear to what extent either environmental factors or undetected genetic variants contribute to MLID.
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Affiliation(s)
- Larissa Bilo
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Eguzkine Ochoa
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Sunwoo Lee
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniela Dey
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Ingo Kurth
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Florian Kraft
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Fay Rodger
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - France Docquier
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Ana Toribio
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, London, UK
| | - Gerhard Binder
- Pediatric Endocrinology, University Children's Hospital, Universiy of Tuebingen, Tuebingen, Germany
| | - György Fekete
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Miriam Elbracht
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Matthias Begemann
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Thomas Eggermann
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.
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4
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Di Risi T, Cuomo M, Vinciguerra R, Ferraro S, Della Monica R, Costabile D, Buonaiuto M, Trio F, Capoluongo E, Visconti R, Riccio E, Pisani A, Chiariotti L. Methylome Profiling in Fabry Disease in Clinical Practice: A Proof of Concept. Int J Mol Sci 2022; 23:ijms232012110. [PMID: 36292965 PMCID: PMC9602470 DOI: 10.3390/ijms232012110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Anderson−Fabry disease (FD) is an X-linked disease caused by a functional deficit of the α-galactosidase A enzyme. FD diagnosis relies on the clinical manifestations and research of GLA gene mutations. However, because of the lack of a clear genotype/phenotype correlation, FD diagnosis can be challenging. Recently, several studies have highlighted the importance of investigating DNA methylation patterns for confirming the correct diagnosis of different rare Mendelian diseases, but to date, no such studies have been reported for FD. Thus, in the present investigation, we analyzed for the first time the genome-wide methylation profile of a well-characterized cohort of patients with Fabry disease. We profiled the methylation status of about 850,000 CpG sites in 5 FD patients, all carrying the same mutation in the GLA gene (exon 6 c.901C>G) and presenting comparable low levels of α-Gal A activity. We found that, although the whole methylome profile did not discriminate the FD group from the unaffected one, several genes were significantly differentially methylated in Fabry patients. Thus, we provide here a proof of concept, to be tested in patients with different mutations and in a larger cohort, that the methylation state of specific genes can potentially identify Fabry patients and possibly predict organ involvement and disease evolution.
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Affiliation(s)
- Teodolinda Di Risi
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Public Health, University Federico II, 80131 Naples, Italy
| | - Mariella Cuomo
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
| | | | - Sara Ferraro
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
| | - Rosa Della Monica
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
| | - Davide Costabile
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- SEMM-European School of Molecular Medicine, University Federico II, 80145 Naples, Italy
| | - Michela Buonaiuto
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
| | - Federica Trio
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
| | - Ettore Capoluongo
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
- Department of Clinical Pathology and Genomics, Azienda Ospedaliera per L’Emergenza Cannizzaro, 95126 Catania, Italy
| | - Roberta Visconti
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Institute for the Experimental Endocrinology and Oncology, Italian National Council of Research, 80131 Naples, Italy
| | - Eleonora Riccio
- Institute for Biomedical Research and Innovation, Italian National Research Council, 90146 Palermo, Italy
| | - Antonio Pisani
- Department of Public Health, University Federico II, 80131 Naples, Italy
| | - Lorenzo Chiariotti
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
- Correspondence:
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5
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Akbari V, Garant JM, O'Neill K, Pandoh P, Moore R, Marra MA, Hirst M, Jones SJM. Genome-wide detection of imprinted differentially methylated regions using nanopore sequencing. eLife 2022; 11:77898. [PMID: 35787786 PMCID: PMC9255983 DOI: 10.7554/elife.77898] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/16/2022] [Indexed: 01/02/2023] Open
Abstract
Imprinting is a critical part of normal embryonic development in mammals, controlled by defined parent-of-origin (PofO) differentially methylated regions (DMRs) known as imprinting control regions. Direct nanopore sequencing of DNA provides a means to detect allelic methylation and to overcome the drawbacks of methylation array and short-read technologies. Here, we used publicly available nanopore sequencing data for 12 standard B-lymphocyte cell lines to acquire the genome-wide mapping of imprinted intervals in humans. Using the sequencing data, we were able to phase 95% of the human methylome and detect 94% of the previously well-characterized, imprinted DMRs. In addition, we found 42 novel imprinted DMRs (16 germline and 26 somatic), which were confirmed using whole-genome bisulfite sequencing (WGBS) data. Analysis of WGBS data in mouse (Mus musculus), rhesus monkey (Macaca mulatta), and chimpanzee (Pan troglodytes) suggested that 17 of these imprinted DMRs are conserved. Some of the novel imprinted intervals are within or close to imprinted genes without a known DMR. We also detected subtle parental methylation bias, spanning several kilobases at seven known imprinted clusters. At these blocks, hypermethylation occurs at the gene body of expressed allele(s) with mutually exclusive H3K36me3 and H3K27me3 allelic histone marks. These results expand upon our current knowledge of imprinting and the potential of nanopore sequencing to identify imprinting regions using only parent-offspring trios, as opposed to the large multi-generational pedigrees that have previously been required.
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Affiliation(s)
- Vahid Akbari
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jean-Michel Garant
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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6
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Cao C, Kwok D, Edie S, Li Q, Ding B, Kossinna P, Campbell S, Wu J, Greenberg M, Long Q. kTWAS: integrating kernel machine with transcriptome-wide association studies improves statistical power and reveals novel genes. Brief Bioinform 2021; 22:5985285. [PMID: 33200776 DOI: 10.1093/bib/bbaa270] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/31/2022] Open
Abstract
The power of genotype-phenotype association mapping studies increases greatly when contributions from multiple variants in a focal region are meaningfully aggregated. Currently, there are two popular categories of variant aggregation methods. Transcriptome-wide association studies (TWAS) represent a set of emerging methods that select variants based on their effect on gene expressions, providing pretrained linear combinations of variants for downstream association mapping. In contrast to this, kernel methods such as sequence kernel association test (SKAT) model genotypic and phenotypic variance use various kernel functions that capture genetic similarity between subjects, allowing nonlinear effects to be included. From the perspective of machine learning, these two methods cover two complementary aspects of feature engineering: feature selection/pruning and feature aggregation. Thus far, no thorough comparison has been made between these categories, and no methods exist which incorporate the advantages of TWAS- and kernel-based methods. In this work, we developed a novel method called kernel-based TWAS (kTWAS) that applies TWAS-like feature selection to a SKAT-like kernel association test, combining the strengths of both approaches. Through extensive simulations, we demonstrate that kTWAS has higher power than TWAS and multiple SKAT-based protocols, and we identify novel disease-associated genes in Wellcome Trust Case Control Consortium genotyping array data and MSSNG (Autism) sequence data. The source code for kTWAS and our simulations are available in our GitHub repository (https://github.com/theLongLab/kTWAS).
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Affiliation(s)
- Chen Cao
- Department of Biochemistry & Molecular Biology, University of Calgary
| | - Devin Kwok
- Department of Mathematics & Statistics, University of Calgary
| | | | - Qing Li
- Department of Biochemistry & Molecular Biology, University of Calgary
| | - Bowei Ding
- Department of Mathematics & Statistics, University of Calgary
| | - Pathum Kossinna
- Department of Biochemistry & Molecular Biology, University of Calgary
| | | | - Jingjing Wu
- Department of Mathematics & Statistics, University of Calgary
| | | | - Quan Long
- Departments of Biochemistry & Molecular Biology, Medical Genetics and Mathematics & Statistics
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7
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Abstract
Genomic imprinting is the monoallelic expression of a gene based on parent of origin and is a consequence of differential epigenetic marking between the male and female germlines. Canonically, genomic imprinting is mediated by allelic DNA methylation. However, recently it has been shown that maternal H3K27me3 can result in DNA methylation-independent imprinting, termed "noncanonical imprinting." In this review, we compare and contrast what is currently known about the underlying mechanisms, the role of endogenous retroviral elements, and the conservation of canonical and noncanonical genomic imprinting.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
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8
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A patient with Silver-Russell syndrome with multilocus imprinting disturbance, and Schimke immuno-osseous dysplasia unmasked by uniparental isodisomy of chromosome 2. J Hum Genet 2021; 66:1121-1126. [PMID: 34031513 DOI: 10.1038/s10038-021-00937-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 11/08/2022]
Abstract
Silver-Russell syndrome (SRS) is a congenital disorder characterized by prenatal and postnatal growth failure and craniofacial features. Hypomethylation of the H19/IGF2:IG-differential methylated region (H19LOM) is observed in 50% of SRS patients, and 15% of SRS patients with H19LOM had multilocus imprinting disturbance (MLID). Schimke immuno-osseous dysplasia (SIOD), characterized by spondyloepiphyseal dysplasia and nephropathy, is an autosomal recessive disorder caused by mutations in SMARCAL1 on chromosome 2. We report a patient with typical SRS-related features, spondyloepiphyseal dysplasia, and severe nephropathy. Molecular analyses showed H19LOM, paternal uniparental isodisomy of chromosome 2 (iUPD(2)pat), and a paternally inherited homozygous frameshift variant in SMARCAL1. Genome-wide methylation analysis showed MLID in this patient, although it showed no MLID in another patient with SIOD without SRS phenotype. These results suggest that iUPD(2)pat unmasked the recessive mutation in SMARCAL1 and that the SMARCAL1 gene mutation may have no direct effect on the patient's methylation defects.
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9
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Feng H, Gui Q, Wu G, Zhu W, Dong X, Shen M, Fu X, Shi G, Luo H, Yang X, Xue S, Cheng Q. Long noncoding RNA Nespas inhibits apoptosis of epileptiform hippocampal neurons by inhibiting the PI3K/Akt/mTOR pathway. Exp Cell Res 2020; 398:112384. [PMID: 33212147 DOI: 10.1016/j.yexcr.2020.112384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/27/2020] [Accepted: 11/15/2020] [Indexed: 12/19/2022]
Abstract
Epilepsy is one of the most common neurological diseases with spontaneous recurrent seizures. Long noncoding RNAs (lncRNAs) are crucial modulators in numerous diseases, including epilepsy. However, the functional role and potential mechanism of lncRNA Nespas in epilepsy remain unknown. Our study clarified that Nespas was underexpressed in epileptiform hippocampal tissues and neurons. Furthermore, Nespas promoted hippocampal neuron viability and proliferation, and inhibited hippocampal neuron apoptosis. Mechanistically, Nespas interacted with microRNA 615-3p (miR-615-3p) in epileptiform hippocampal neurons. 26S proteasome non-ATPase regulatory subunit 11 (Psmd11) was a downstream target of miR-615-3p, and Nespas elevated Psmd11 expression via competitively binding to miR-615-3p in epileptiform hippocampal neurons. In addition, rescue assays suggested that Nespas promoted hippocampal neuron viability and proliferation, and suppressed hippocampal neuron apoptosis by upregulation of Psmd11. Furthermore, Nespas suppressed the PI3K/Akt/mTOR pathway via upregulating Psmd11 in epileptiform hippocampal neurons. This report explored the function and regulatory mechanism of Nespas in epileptiform hippocampal neurons for the first time. Our findings revealed that Nespas suppressed the apoptosis of epileptiform hippocampal neurons by inhibiting the PI3K/Akt/mTOR pathway via upregulation of Psmd11 at a miR-615-3p dependent way, indicating that Nespas may offer a new direction for the treatment of epilepsy.
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Affiliation(s)
- Hongxuan Feng
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China; Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University (Suzhou Municipal Hospital), Suzhou, 215002, Jiangsu, China
| | - Qian Gui
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University (Suzhou Municipal Hospital), Suzhou, 215002, Jiangsu, China
| | - Guanhui Wu
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University (Suzhou Municipal Hospital), Suzhou, 215002, Jiangsu, China
| | - Wei Zhu
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University (Suzhou Municipal Hospital), Suzhou, 215002, Jiangsu, China
| | - Xiaofeng Dong
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University (Suzhou Municipal Hospital), Suzhou, 215002, Jiangsu, China
| | - Mingqiang Shen
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University (Suzhou Municipal Hospital), Suzhou, 215002, Jiangsu, China
| | - Xuetao Fu
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, 225001, Jiangsu, China
| | - Guomei Shi
- Department of Neurology, Taixing People's Hospital, Taixing, 225400, Jiangsu, China
| | - Hailong Luo
- Department of Neurology, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, 157011, Heilongjiang, China
| | - Xiaoyan Yang
- Department of Neurology, The People's Hospital of SND, Suzhou, 215129, Jiangsu, China
| | - Shouru Xue
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.
| | - Qingzhang Cheng
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University (Suzhou Municipal Hospital), Suzhou, 215002, Jiangsu, China.
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10
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Brück J, Begemann M, Dey D, Elbracht M, Eggermann T. Molecular characterization of temple syndrome families with 14q32 epimutations. Eur J Med Genet 2020; 63:104077. [PMID: 33010492 DOI: 10.1016/j.ejmg.2020.104077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/07/2020] [Accepted: 09/17/2020] [Indexed: 12/17/2022]
Abstract
Temple Syndrome (TS14) is an imprinting disorder caused by molecular disruptions of the imprinted region in 14q32 (MEG3:TSS-DMR). The frequency of the three known TS14 subtypes (deletions, maternal uniparental disomy (upd(14)mat), loss of methylation (LOM)) is currently in discussion, and within the LOM group, the occurrence of Multilocus Imprinting Disturbances (MLID) has been identified. We present 16 TS14 patients with molecular alterations affecting the MEG3:TSS-DMR, comprising seven patients (43.8%) with LOM, six carriers with upd(14)mat (37.5%), and three cases (18.8%) with a deletion affecting the paternal MEG3:TSS-DMR. We did not find any evidence for MLID in the LOM group, including two cases in which different tissues were available. Whole exome sequencing (WES) in the MEG3:TSS-DMR LOM patients and their parents (Trio WES) did not reveal an obvious pathogenic variant which might cause aberrant methylation at imprinted loci. By summarizing our data with those from the literature, we could show that MLID affecting clinically relevant imprinted loci is rare in TS14 and therefore differs markedly from other imprinting disorders associated with MLID, e.g. Silver-Russell syndrome (SRS) and Beckwith-Wiedemann syndrome (BWS). However, consistent with the clinical overlap with TS14, in SRS patients carrying MLID the MEG3:TSS-DMR is frequently affected. Variants in the known candidate genes for maternal effect variants causing MLID and fetal MLID determinants could not be identified in TS14 patients. Thus, 14q32 epimutations probably have other molecular causes than epimutations in BWS or SRS patients.
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Affiliation(s)
- Johanna Brück
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Daniela Dey
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
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11
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Cao L, He Y, Huang Q, Zhang Y, Deng P, Du W, Hua Z, Zhu M, Wei H. Clinical features and partial proportional molecular genetics in neonatal diabetes mellitus: a retrospective analysis in southwestern China. Endocrine 2020; 69:53-62. [PMID: 32279225 DOI: 10.1007/s12020-020-02279-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/23/2020] [Indexed: 01/29/2023]
Abstract
PURPOSE To explore the relationship of phenotype and genotype of neonatal diabetes mellitus (NDM) in southwestern China. METHODS Sixteen cases of NDM admitted to Children's Hospital of Chongqing Medical University from May 2009 to May 2019 were included in this study. The clinical features of the included infants were retrospectively analyzed. Peripheral blood samples of the patients and their parents were collected for mutation detection. RESULTS Among the 16 cases of NDM, 8 cases were permanent neonatal diabetes mellitus (PNDM) (including 3 clinical syndromes), and 3 cases were transient neonatal diabetes mellitus (TNDM). Mutation detection was performed in six cases. The mutation genes and their loci were FOXP3 p.V408M, KCNJ11 p.C166Y, ABCC8 p.S830P, KCNJ11 p.I182T, KCNJ11 p.G334D, and ZFP57 p.R125X,412. ABCC8 p.S830P was the new found pathogenic site of gene mutation. According to the clinical features and follow-up results, one case was diagnosed as IPEX syndrome, two as DEND syndrome, two as simple PNDM, and one as TNDM. All the TNDM could spontaneously alleviate and then insulin was withdrawn. In PNDM, 75% of those with KATP channel gene mutation could be completely or partially converted to oral sulfonylureas treatment, however, the rest cases needed lifelong insulin replacement therapy. CONCLUSION The clinical manifestations and treatment regimens of patients with NDM vary according to the type of gene mutation. Even the same mutant genotype has differences in phenotype and response to treatment.
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Affiliation(s)
- Luying Cao
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Yi He
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Qinrong Huang
- Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Department of Rehabilitation, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Yu Zhang
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Pinglan Deng
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Weixia Du
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Ziyu Hua
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Min Zhu
- Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, PR China
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Hong Wei
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, PR China.
- Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation base of Child development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, PR China.
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Sousa M, Bruges-Armas J. Monogenic Diabetes: Genetics and Relevance on Diabetes Mellitus Personalized Medicine. Curr Diabetes Rev 2020; 16:807-819. [PMID: 31886753 DOI: 10.2174/1573399816666191230114352] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/11/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Diabetes mellitus (DM) is a complex disease with significant impression in today's world. Aside from the most common types recognized over the years, such as type 1 diabetes (T1DM) and type 2 diabetes (T2DM), recent studies have emphasized the crucial role of genetics in DM, allowing the distinction of monogenic diabetes. METHODS Authors did a literature search with the purpose of highlighting and clarifying the subtypes of monogenic diabetes, as well as the accredited genetic entities responsible for such phenotypes. RESULTS The following subtypes were included in this literature review: maturity-onset diabetes of the young (MODY), neonatal diabetes mellitus (NDM) and maternally inherited diabetes and deafness (MIDD). So far, 14 subtypes of MODY have been identified, while three subtypes have been identified in NDM - transient, permanent, and syndromic. DISCUSSION Despite being estimated to affect approximately 2% of all the T2DM patients in Europe, the exact prevalence of MODY is still unknown, accentuating the need for research focused on biomarkers. Consequently, due to its impact in the course of treatment, follow-up of associated complications, and genetic implications for siblings and offspring of affected individuals, it is imperative to diagnose the monogenic forms of DM accurately. CONCLUSION Currently, advances in the genetics field allowed the recognition of new DM subtypes, which until now, were considered slight variations of the typical forms. Thus, it is imperative to act in the close interaction between genetics and clinical manifestations, to facilitate diagnosis and individualize treatment.
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MESH Headings
- Deafness/classification
- Deafness/diagnosis
- Deafness/genetics
- Diabetes Mellitus, Type 1/diagnosis
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 2/classification
- Diabetes Mellitus, Type 2/diagnosis
- Diabetes Mellitus, Type 2/genetics
- Genetic Testing
- Genotype
- Humans
- Infant
- Infant, Newborn
- Infant, Newborn, Diseases/classification
- Infant, Newborn, Diseases/diagnosis
- Infant, Newborn, Diseases/genetics
- Mitochondrial Diseases/classification
- Mitochondrial Diseases/diagnosis
- Mitochondrial Diseases/genetics
- Mutation
- Phenotype
- Precision Medicine
- Syndrome
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Affiliation(s)
- Madalena Sousa
- Serviço Especializado de Epidemiologia e Biologia Molecular (SEEBMO), Hospital de Santo Espírito da Ilha Terceira (HSEIT), Angra do Heroísmo, Azores, Portugal
| | - Jácome Bruges-Armas
- Serviço Especializado de Epidemiologia e Biologia Molecular (SEEBMO), Hospital de Santo Espírito da Ilha Terceira (HSEIT), Angra do Heroísmo, Azores, Portugal
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13
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Farhadova S, Gomez-Velazquez M, Feil R. Stability and Lability of Parental Methylation Imprints in Development and Disease. Genes (Basel) 2019; 10:genes10120999. [PMID: 31810366 PMCID: PMC6947649 DOI: 10.3390/genes10120999] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
DNA methylation plays essential roles in mammals. Of particular interest are parental methylation marks that originate from the oocyte or the sperm, and bring about mono-allelic gene expression at defined chromosomal regions. The remarkable somatic stability of these parental imprints in the pre-implantation embryo—where they resist global waves of DNA demethylation—is not fully understood despite the importance of this phenomenon. After implantation, some methylation imprints persist in the placenta only, a tissue in which many genes are imprinted. Again here, the underlying epigenetic mechanisms are not clear. Mouse studies have pinpointed the involvement of transcription factors, covalent histone modifications, and histone variants. These and other features linked to the stability of methylation imprints are instructive as concerns their conservation in humans, in which different congenital disorders are caused by perturbed parental imprints. Here, we discuss DNA and histone methylation imprints, and why unravelling maintenance mechanisms is important for understanding imprinting disorders in humans.
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14
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Borchiellini M, Ummarino S, Di Ruscio A. The Bright and Dark Side of DNA Methylation: A Matter of Balance. Cells 2019; 8:cells8101243. [PMID: 31614870 PMCID: PMC6830319 DOI: 10.3390/cells8101243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/06/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation controls several cellular processes, from early development to old age, including biological responses to endogenous or exogenous stimuli contributing to disease transition. As a result, minimal DNA methylation changes during developmental stages drive severe phenotypes, as observed in germ-line imprinting disorders, while genome-wide alterations occurring in somatic cells are linked to cancer onset and progression. By summarizing the molecular events governing DNA methylation, we focus on the methods that have facilitated mapping and understanding of this epigenetic mark in healthy conditions and diseases. Overall, we review the bright (health-related) and dark (disease-related) side of DNA methylation changes, outlining how bulk and single-cell genomic analyses are moving toward the identification of new molecular targets and driving the development of more specific and less toxic demethylating agents.
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Affiliation(s)
- Marta Borchiellini
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy.
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
| | - Simone Ummarino
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Annalisa Di Ruscio
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
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15
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Banerjee P, Bhagavatula S, Sood A, Midha V, Thelma BK, Senapati S. Association study identified biologically relevant receptor genes with synergistic functions in celiac disease. Sci Rep 2019; 9:13811. [PMID: 31554915 PMCID: PMC6761106 DOI: 10.1038/s41598-019-50120-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/02/2019] [Indexed: 11/10/2022] Open
Abstract
Receptors are essential mediators of cellular physiology, which facilitate molecular and cellular cross-talk with the environment. Nearly 20% of the all known celiac disease (CD) genes are receptors by function. We hypothesized that novel biologically relevant susceptibility receptor genes act in synergy in CD pathogenesis. We attempted to identify novel receptor genes in CD by re-analyzing published Illumina Immunochip dense genotype data for a north Indian and a European (Dutch) cohort. North Indian dataset was screened for 269 known receptor genes. Association statistics for SNPs were considered with minor allele frequency >15% and association P ≤ 0.005 to attend desired study power. Identified markers were tested for cross-ethnic replication in a European CD dataset. Markers were analyzed in-silico to explain their functional significance in CD. Six novel SNPs from MOG (rs29231, p = 1.21e-11), GABBR1 (rs3025643, p = 1.60e-7), OR2H2 (rs1233388, p = 0.0002), ABCF1 (rs9262119, p = 0.0005), ADRA1A (rs10102024, p = 0.003), and ACVR2A (rs7560426, p = 0.004) were identified in north Indians, of which three genes namely, GABBR1 (rs3025643, p = 5.38e-8), OR2H2 (rs1233388, p = 3.29e-5) and ABCF1 (rs9262119, p = 0.0002) were replicated in Dutch. Tissue specific functional annotation, potential epigenetic regulation, co-expression, protein-protein interaction and pathway enrichment analyses indicated differential expression and synergistic function of key genes that could alter cellular homeostasis, ubiquitination mediated phagosome pathway and cellular protein processing to contribute for CD. At present multiple therapeutic compounds/drugs are available targeting GABBR1 and ADRA1A, which could be tested for their effectiveness against CD in controlled drug trials.
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Affiliation(s)
- Pratibha Banerjee
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Sandilya Bhagavatula
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College & Hospital, Ludhiana, Punjab, India
| | - Vandana Midha
- Department of Medicine, Dayanand Medical College & Hospital, Ludhiana, Punjab, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Sabyasachi Senapati
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India.
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16
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Kerr K, McAneney H, Flanagan C, Maxwell AP, McKnight AJ. Differential methylation as a diagnostic biomarker of rare renal diseases: a systematic review. BMC Nephrol 2019; 20:320. [PMID: 31419951 PMCID: PMC6697952 DOI: 10.1186/s12882-019-1517-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The challenges in diagnosis of rare renal conditions can negatively impact patient prognosis, quality of life and result in significant healthcare costs. Differential methylation is emerging as an important biomarker for rare diseases and should be evaluated for rare renal conditions. METHODS A comprehensive systematic review of methylation and rare renal disorders was conducted by searching the electronic databases MEDLINE, EMBASE, PubMed, Cochrane Library, alongside grey literature from GreyLit and OpenGrey databases, for publications published before September 2018. Additionally, the reference lists of the included papers were searched. Data was extracted and appraised including the primary focus, measurement and methodological rigour of the source. Eligibility criteria were adapted using the inclusion criteria from 'The 100,000 Genomes Project' and The National Registry of Rare Kidney Diseases, with additional focus on methylation. RESULTS Thirteen full text articles were included in the review. Diseases analysed for differential methylation included glomerular disease, IgA nephropathy, ADPKD, rare causes of proteinuria, congenital renal agenesis, and membranous nephropathy. CONCLUSIONS Differential methylation has been observed for several rare renal diseases, highlighting its potential for improving molecular characterisation of these disorders. Further investigation of methylation following a standardised reporting structure is necessary to improve research quality. Multi-omic data will provide insights for improved diagnosis, prognosis and support for individuals living and working with rare renal diseases.
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Affiliation(s)
- Katie Kerr
- Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, BT9 7AB, Belfast, Northern Ireland
| | - Helen McAneney
- Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, BT9 7AB, Belfast, Northern Ireland
| | - Cheryl Flanagan
- 100,000 Genomes Project Team, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | | | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, BT9 7AB, Belfast, Northern Ireland.
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17
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Jung J, Kim GW, Lee B, Joo JWJ, Jang W. Integrative genomic and transcriptomic analysis of genetic markers in Dupuytren's disease. BMC Med Genomics 2019; 12:98. [PMID: 31296227 PMCID: PMC6624179 DOI: 10.1186/s12920-019-0518-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Dupuytren’s disease (DD) is a fibroproliferative disorder characterized by thickening and contracting palmar fascia. The exact pathogenesis of DD remains unknown. Results In this study, we identified co-expressed gene set (DD signature) consisting of 753 genes via weighted gene co-expression network analysis. To confirm the robustness of DD signature, module enrichment analysis and meta-analysis were performed. Moreover, this signature effectively classified DD disease samples. The DD signature were significantly enriched in unfolded protein response (UPR) related to endoplasmic reticulum (ER) stress. Next, we conducted multiple-phenotype regression analysis to identify trans-regulatory hotspots regulating expression levels of DD signature using Genotype-Tissue Expression data. Finally, 10 trans-regulatory hotspots and 16 eGenes genes that are significantly associated with at least one cis-eQTL were identified. Conclusions Among these eGenes, major histocompatibility complex class II genes and ZFP57 zinc finger protein were closely related to ER stress and UPR, suggesting that these genetic markers might be potential therapeutic targets for DD. Electronic supplementary material The online version of this article (10.1186/s12920-019-0518-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junghyun Jung
- Department of Life science, Dongguk University-Seoul, Seoul, 04620, Republic of Korea
| | - Go Woon Kim
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, 26 Kyungheedae-ro, Seoul, 02447, South Korea
| | - Byungjo Lee
- Department of Life science, Dongguk University-Seoul, Seoul, 04620, Republic of Korea
| | - Jong Wha J Joo
- Department of Computer Science and Engineering, Dongguk University-Seoul, Seoul, 04620, South Korea.
| | - Wonhee Jang
- Department of Life science, Dongguk University-Seoul, Seoul, 04620, Republic of Korea.
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18
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Khamis A, Canouil M, Siddiq A, Crouch H, Falchi M, Bulow MV, Ehehalt F, Marselli L, Distler M, Richter D, Weitz J, Bokvist K, Xenarios I, Thorens B, Schulte AM, Ibberson M, Bonnefond A, Marchetti P, Solimena M, Froguel P. Laser capture microdissection of human pancreatic islets reveals novel eQTLs associated with type 2 diabetes. Mol Metab 2019; 24:98-107. [PMID: 30956117 PMCID: PMC6531807 DOI: 10.1016/j.molmet.2019.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Genome wide association studies (GWAS) for type 2 diabetes (T2D) have identified genetic loci that often localise in non-coding regions of the genome, suggesting gene regulation effects. We combined genetic and transcriptomic analysis from human islets obtained from brain-dead organ donors or surgical patients to detect expression quantitative trait loci (eQTLs) and shed light into the regulatory mechanisms of these genes. METHODS Pancreatic islets were isolated either by laser capture microdissection (LCM) from surgical specimens of 103 metabolically phenotyped pancreatectomized patients (PPP) or by collagenase digestion of pancreas from 100 brain-dead organ donors (OD). Genotyping (> 8.7 million single nucleotide polymorphisms) and expression (> 47,000 transcripts and splice variants) analyses were combined to generate cis-eQTLs. RESULTS After applying genome-wide false discovery rate significance thresholds, we identified 1,173 and 1,021 eQTLs in samples of OD and PPP, respectively. Among the strongest eQTLs shared between OD and PPP were CHURC1 (OD p-value=1.71 × 10-24; PPP p-value = 3.64 × 10-24) and PSPH (OD p-value = 3.92 × 10-26; PPP p-value = 3.64 × 10-24). We identified eQTLs in linkage-disequilibrium with GWAS loci T2D and associated traits, including TTLL6, MLX and KIF9 loci, which do not implicate the nearest gene. We found in the PPP datasets 11 eQTL genes, which were differentially expressed in T2D and two genes (CYP4V2 and TSEN2) associated with HbA1c but none in the OD samples. CONCLUSIONS eQTL analysis of LCM islets from PPP led us to identify novel genes which had not been previously linked to islet biology and T2D. The understanding gained from eQTL approaches, especially using surgical samples of living patients, provides a more accurate 3-dimensional representation than those from genetic studies alone.
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Affiliation(s)
- Amna Khamis
- Imperial College London, Department of Genomics of Common Disease, London, UK; University of Lille, CNRS, Institute Pasteur de Lille, UMR 8199 - EGID, F-59000, Lille, France
| | - Mickaël Canouil
- University of Lille, CNRS, Institute Pasteur de Lille, UMR 8199 - EGID, F-59000, Lille, France
| | - Afshan Siddiq
- Imperial College London, Department of Genomics of Common Disease, London, UK
| | - Hutokshi Crouch
- Imperial College London, Department of Genomics of Common Disease, London, UK
| | - Mario Falchi
- Imperial College London, Department of Genomics of Common Disease, London, UK
| | - Manon von Bulow
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Frankfurt, Germany
| | - Florian Ehehalt
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
| | - Lorella Marselli
- University of Pisa, Department of Clinical and Experimental Medicine, Pisa, Italy
| | - Marius Distler
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
| | - Daniela Richter
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
| | - Jürgen Weitz
- Department of Visceral-Thoracic-Vascular Surgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
| | - Krister Bokvist
- Lilly Research Laboratories, Eli Lilly, 46285-0001, Indianapolis, IN, USA
| | - Ioannis Xenarios
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Bernard Thorens
- Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, 1015, Switzerland
| | - Anke M Schulte
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Frankfurt, Germany
| | - Mark Ibberson
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Amelie Bonnefond
- University of Lille, CNRS, Institute Pasteur de Lille, UMR 8199 - EGID, F-59000, Lille, France
| | - Piero Marchetti
- University of Pisa, Department of Clinical and Experimental Medicine, Pisa, Italy
| | - Michele Solimena
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764, Neuherberg, Germany
| | - Philippe Froguel
- Imperial College London, Department of Genomics of Common Disease, London, UK; University of Lille, CNRS, Institute Pasteur de Lille, UMR 8199 - EGID, F-59000, Lille, France.
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19
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Germline Epigenetic Testing of Imprinting Disorders in a Diagnostic Setting. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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20
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Takahashi N, Coluccio A, Thorball CW, Planet E, Shi H, Offner S, Turelli P, Imbeault M, Ferguson-Smith AC, Trono D. ZNF445 is a primary regulator of genomic imprinting. Genes Dev 2019; 33:49-54. [PMID: 30602440 PMCID: PMC6317318 DOI: 10.1101/gad.320069.118] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/07/2018] [Indexed: 12/29/2022]
Abstract
Genomic imprinting is an epigenetic process regulated by germline-derived DNA methylation, causing parental origin-specific monoallelic gene expression. Zinc finger protein 57 (ZFP57) is critical for maintenance of this epigenetic memory during post-fertilization reprogramming, yet incomplete penetrance of ZFP57 mutations in humans and mice suggests additional effectors. We reveal that ZNF445/ZFP445, which we trace to the origins of imprinting, binds imprinting control regions (ICRs) in mice and humans. In mice, ZFP445 and ZFP57 act together, maintaining all but one ICR in vivo, whereas earlier embryonic expression of ZNF445 and its intolerance to loss-of-function mutations indicate greater importance in the maintenance of human imprints.
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Affiliation(s)
- Nozomi Takahashi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Andrea Coluccio
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Christian W Thorball
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Hui Shi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Michael Imbeault
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | | | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
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21
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Kessler NJ, Waterland RA, Prentice AM, Silver MJ. Establishment of environmentally sensitive DNA methylation states in the very early human embryo. SCIENCE ADVANCES 2018; 4:eaat2624. [PMID: 30009262 PMCID: PMC6040841 DOI: 10.1126/sciadv.aat2624] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/01/2018] [Indexed: 05/04/2023]
Abstract
The molecular mechanisms responsible for the developmental origins of later disease are currently unknown. We previously demonstrated that women's periconceptional nutrition predicts their offspring's DNA methylation at metastable epialleles (MEs). We present a genome-wide screen yielding 687 MEs and track their trajectories across nine developmental stages in human in vitro fertilization embryos. MEs exhibit highly unusual methylation dynamics across the implantation-gastrulation transition, producing a large excess of intermediate methylation states, suggesting the potential for differential programming in response to external signals. Using a natural experiment in rural Gambia, we show that genomic regions sensitive to season of conception are highly enriched for MEs and show similar atypical methylation patterns. MEs are enriched for proximal enhancers and transcription start sites and are influenced by genotype. Together, these observations position MEs as distinctive epigenomic features programmed in the early embryo, sensitive to genetic and periconceptional environment, and with the potential to influence phenotype.
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Affiliation(s)
- Noah J. Kessler
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Robert A. Waterland
- U.S. Department of Agriculture/Agricultural Research Service Children’s Nutrition Research Center, Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Matt J. Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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22
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Fu J, Wei C, Zhang W, Schlondorff D, Wu J, Cai M, He W, Baron MH, Chuang PY, Liu Z, He JC, Lee K. Gene expression profiles of glomerular endothelial cells support their role in the glomerulopathy of diabetic mice. Kidney Int 2018; 94:326-345. [PMID: 29861058 PMCID: PMC6054896 DOI: 10.1016/j.kint.2018.02.028] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 02/06/2018] [Accepted: 02/15/2018] [Indexed: 01/15/2023]
Abstract
Endothelial dysfunction promotes the pathogenesis of diabetic nephropathy (DN), which is considered to be an early event in disease progression. However, the molecular changes associated with glomerular endothelial cell (GEC) injury in early DN are not well defined. Most gene expression studies have relied on the indirect assessment of GEC injury from isolated glomeruli or renal cortices. Here, we present transcriptomic analysis of isolated GECs, using streptozotocin-induced diabetic wildtype (STZ-WT) and diabetic eNOS-null (STZ-eNOS-/-) mice as models of mild and advanced DN, respectively. GECs of both models in comparison to their respective nondiabetic controls showed significant alterations in the regulation of apoptosis, oxidative stress, and proliferation. The extent of these changes was greater in STZ-eNOS-/- than in STZ-WT GECs. Additionally, genes in STZ-eNOS-/- GECs indicated further dysregulation in angiogenesis and epigenetic regulation. Moreover, a biphasic change in the number of GECs, characterized by an initial increase and subsequent decrease over time, was observed only in STZ-eNOS-/- mice. This is consistent with an early compensatory angiogenic process followed by increased apoptosis, leading to an overall decrease in GEC survival in DN progression. From the genes altered in angiogenesis in STZ-eNOS-/- GECs, we identified potential candidate genes, Lrg1 and Gpr56, whose function may augment diabetes-induced angiogenesis. Thus, our results support a role for GEC in DN by providing direct evidence for alterations of GEC gene expression and molecular pathways. Candidate genes of specific pathways, such as Lrg1 and Gpr56, can be further explored for potential therapeutic targeting to mitigate the initiation and progression of DN.
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Affiliation(s)
- Jia Fu
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chengguo Wei
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Weijia Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Detlef Schlondorff
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jinshan Wu
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Minchao Cai
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Wu He
- Flow Cytometry Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Margaret H Baron
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Peter Y Chuang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China.
| | - John Cijiang He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Renal Program, James J. Peters VA Medical Center at Bronx, New York, New York, USA.
| | - Kyung Lee
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
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23
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Letourneau LR, Greeley SAW. Congenital forms of diabetes: the beta-cell and beyond. Curr Opin Genet Dev 2018; 50:25-34. [PMID: 29454299 DOI: 10.1016/j.gde.2018.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 12/11/2022]
Abstract
The majority of patients diagnosed with diabetes less than 6 months of age, and many cases diagnosed between 6 and 12 months of age, have a gene mutation that causes permanent or transient hyperglycemia. Recent research advances have allowed for the discovery of new causes of congenital diabetes, including genes involved in pancreatic development (GATA4, NKX2-2, MNX1) and monogenic causes of autoimmune dysregulation (STAT3, LRBA). Ongoing follow-up of patients with KCNJ11 and ABCC8 mutations has supported the safety and efficacy of sulfonylureas, as well as the use of insulin pumps and continuous glucose monitors in infants with insulin-requiring forms of monogenic diabetes. Future studies are needed to improve clinical care and outcomes for these patients and their families.
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Affiliation(s)
- Lisa R Letourneau
- Department of Medicine, Section of Adult and Pediatric Endocrinology, Diabetes and Metabolism, University of Chicago Medicine, 5841 S. Maryland Ave. MC 1027, Chicago, IL 60637, USA
| | - Siri Atma W Greeley
- Department of Medicine, Section of Adult and Pediatric Endocrinology, Diabetes and Metabolism, University of Chicago Medicine, 5841 S. Maryland Ave. MC 1027, Chicago, IL 60637, USA; Department of Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes and Metabolism, University of Chicago Medicine, 5841 S. Maryland Ave. MC 1027, Chicago, IL 60637, USA.
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24
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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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