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Torroglosa A, Villalba-Benito L, Fernández RM, Luzón-Toro B, Moya-Jiménez MJ, Antiñolo G, Borrego S. Identification of New Potential LncRNA Biomarkers in Hirschsprung Disease. Int J Mol Sci 2020; 21:ijms21155534. [PMID: 32748823 PMCID: PMC7432910 DOI: 10.3390/ijms21155534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Hirschsprung disease (HSCR) is a neurocristopathy defined by intestinal aganglionosis due to alterations during the development of the Enteric Nervous System (ENS). A wide spectrum of molecules involved in different signaling pathways and mechanisms have been described in HSCR onset. Among them, epigenetic mechanisms are gaining increasing relevance. In an effort to better understand the epigenetic basis of HSCR, we have performed an analysis for the identification of long non-coding RNAs (lncRNAs) by qRT-PCR in enteric precursor cells (EPCs) from controls and HSCR patients. We aimed to test the presence of a set lncRNAs among 84 lncRNAs in human EPCs, which were previously related with crucial cellular processes for ENS development, as well as to identify the possible differences between HSCR patients and controls. As a result, we have determined a set of lncRNAs with positive expression in human EPCs that were screened for mutations using the exome data from our cohort of HSCR patients to identify possible variants related to this pathology. Interestingly, we identified three lncRNAs with different levels of their transcripts (SOCS2-AS, MEG3 and NEAT1) between HSCR patients and controls. We propose such lncRNAs as possible regulatory elements implicated in the onset of HSCR as well as potential biomarkers of this pathology.
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Affiliation(s)
- Ana Torroglosa
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Leticia Villalba-Benito
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Raquel María Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Berta Luzón-Toro
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - María José Moya-Jiménez
- Department of Pediatric Surgery, University Hospital Virgen del Rocío, 41013 Seville, Spain;
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
- Correspondence:
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Chen L, Dong Y, Chen J, Huang Y, Zhu H. Epigenetics Predicts Serum 25-Hydroxyvitamin D Response to Vitamin D 3 Supplementation in African Americans. Mol Nutr Food Res 2019; 64:e1900738. [PMID: 31667917 DOI: 10.1002/mnfr.201900738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/10/2019] [Indexed: 12/13/2022]
Abstract
SCOPE The effects of vitamin D3 supplementations on circulating 25-hydroxyvitamin D [25(OH)D] are varied. The hypothesis that the baseline DNA methylation plays a role in the serum 25(OH)D response to vitamin D3 supplementation is tested. METHODS AND RESULTS A randomized clinical trial is first conducted among 64 African Americans, who are randomly assigned to a placebo or a 16-week treatment of 600, 2000, and 4000 IU d-1 of vitamin D3 supplements. Expected serum 25(OH)D concentrations at posttest are estimated by intervention, age, gender, body mass index, baseline 25(OH)D concentrations, and seasonal variations. The 25(OH)D response is categorized into a high-response group when the actual 25(OH)D concentrations at posttest are higher than expected, and a low-response group otherwise. The 25(OH)D response is associated with baseline methylation levels of CYP family and VDR genes (raw p < 0.05). At a genome-wide level, the baseline methylation level of cg07873128 (OSBPL5) that regulates cholesterol balance and calcium homeostasis is higher in the low-response group (false discovery rate = 0.028). CONCLUSIONS The baseline methylation levels of CYP family and VDR modulate 25(OH)D response. In addition, the hypermethylation of cg07873128 at the baseline, which is located in the imprinted gene OSBPL5, may reduce the serum 25(OH)D response to vitamin D3 supplementation.
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Affiliation(s)
- Li Chen
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Yanbin Dong
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Jie Chen
- Biostatistics and Data Science, Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Ying Huang
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Haidong Zhu
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
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Genome imprinting in stem cells: A mini-review. Gene Expr Patterns 2019; 34:119063. [PMID: 31279979 DOI: 10.1016/j.gep.2019.119063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/21/2019] [Accepted: 06/30/2019] [Indexed: 12/19/2022]
Abstract
Genomic imprinting is an epigenetic process result in silencing of one of the two alleles (maternal or paternal) based on the parent of origin. Dysregulation of imprinted genes results in detectable developmental and differential abnormalities. Epigenetics erasure is required for resetting the cell identity to a ground state during the production of induced pluripotent stem (iPS) cells from somatic cells. There are some contradictory reports regarding the status of the imprinting marks in the genome of iPS cells. Additionally, many studies highlighted the existence of subtle differences in the imprinting loci between different types of iPS cells and embryonic stem (ES) cells. These observations could ultimately undermine the use of patient-derived iPS cells for regenerative medicine.
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Wu D, Gong C, Su C. Genome-wide analysis of differential DNA methylation in Silver-Russell syndrome. SCIENCE CHINA-LIFE SCIENCES 2017. [PMID: 28624953 DOI: 10.1007/s11427-017-9079-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Silver-Russell Syndrome (SRS) is clinically heterogeneous disorder characterized by low birth weight, postnatal growth restriction, and variable dysmorphic features. Current evidence strongly implicates imprinted genes as an important etiology of SRS. Although almost half of the patients showed DNA hypomethylation at the H19/IGF2 imprinted domain, and approximately 7%-10% of SRS patients have maternal uniparental disomy of chromosome 7 (UPD (7) mat); the rest of the SRS patients shows unknown etiology. In this study, we investigate whether there are further DNA methylation defects in SRS patients. We measured DNA methylation in seven SRS patients and five controls at more than 485,000 CpG sites using DNA methylation microarrays. We analyzed methylation changes genome-wide and identified the differentially methylated regions (DMRs) using bisulfite sequencing and digital PCR. Our analysis identifies epimutations at the previously characterized domains of H19/IGF2, providing proof of principle that our methodology can detect the changes in DNA methylation at imprinted loci. In addition, our results showed a novel SRS associated imprinted gene OSBPL5 located on chromosome 11p14 with the probe cg25963939, which is hypomethylated in 4/7 patients (P=0.023, β=-0.243). We also report DMRs in other genes including TGFβ3, HSF1, GAP43, NOTCH4 and MYH14. These DMRs were found to be associated with SRS using GO pathway analysis. In this study, we identified the probe cg25963939, located at the 5'UTR of imprinted gene OSBPL5, as a novel DMR that is associated with SRS. This finding provides new insights into the mechanism of SRS etiology and aid the further stratification of SRS patients by molecular phenotypes.
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Affiliation(s)
- Di Wu
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, MOE Key Laboratory of Major Diseases in Children, Beijing, 100045, China
| | - Chunxiu Gong
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, MOE Key Laboratory of Major Diseases in Children, Beijing, 100045, China.
| | - Chang Su
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, MOE Key Laboratory of Major Diseases in Children, Beijing, 100045, China
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Apáti Á, Szebényi K, Erdei Z, Várady G, Orbán TI, Sarkadi B. The importance of drug transporters in human pluripotent stem cells and in early tissue differentiation. Expert Opin Drug Metab Toxicol 2015; 12:77-92. [DOI: 10.1517/17425255.2016.1121382] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Im I, Jang MJ, Park SJ, Lee SH, Choi JH, Yoo HW, Kim S, Han YM. Mitochondrial Respiratory Defect Causes Dysfunctional Lactate Turnover via AMP-activated Protein Kinase Activation in Human-induced Pluripotent Stem Cell-derived Hepatocytes. J Biol Chem 2015; 290:29493-505. [PMID: 26491018 DOI: 10.1074/jbc.m115.670364] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Indexed: 01/19/2023] Open
Abstract
A defective mitochondrial respiratory chain complex (DMRC) causes various metabolic disorders in humans. However, the pathophysiology of DMRC in the liver remains unclear. To understand DMRC pathophysiology in vitro, DMRC-induced pluripotent stem cells were generated from dermal fibroblasts of a DMRC patient who had a homoplasmic mutation (m.3398T→C) in the mitochondrion-encoded NADH dehydrogenase 1 (MTND1) gene and that differentiated into hepatocytes (DMRC hepatocytes) in vitro. DMRC hepatocytes showed abnormalities in mitochondrial characteristics, the NAD(+)/NADH ratio, the glycogen storage level, the lactate turnover rate, and AMPK activity. Intriguingly, low glycogen storage and transcription of lactate turnover-related genes in DMRC hepatocytes were recovered by inhibition of AMPK activity. Thus, AMPK activation led to metabolic changes in terms of glycogen storage and lactate turnover in DMRC hepatocytes. These data demonstrate for the first time that energy depletion may lead to lactic acidosis in the DMRC patient by reduction of lactate uptake via AMPK in liver.
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Affiliation(s)
- Ilkyun Im
- From the Department of Biological Sciences, Center for Stem Cell Differentiation, and
| | - Mi-Jin Jang
- From the Department of Biological Sciences, Center for Stem Cell Differentiation, and
| | | | - Sang-Hee Lee
- BioMedical Research Center, Korea Advanced Institute of Science and Technology, Daejeon 34141 and
| | - Jin-Ho Choi
- the Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Han-Wook Yoo
- the Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Seyun Kim
- From the Department of Biological Sciences
| | - Yong-Mahn Han
- From the Department of Biological Sciences, Center for Stem Cell Differentiation, and
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Park SW, Do HS, Kim D, Ko JY, Lee SH, Han YM. Transcriptional Profiles of Imprinted Genes in Human Embryonic Stem Cells During In vitro Differentiation. Int J Stem Cells 2014; 7:108-17. [PMID: 25473448 PMCID: PMC4249893 DOI: 10.15283/ijsc.2014.7.2.108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2014] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Genomic imprinting is an inheritance phenomenon by which a subset of genes are expressed from one allele of two homologous chromosomes in a parent of origin-specific manner. Even though fine-tuned regulation of genomic imprinting process is essential for normal development, no other means are available to study genomic imprinting in human during embryonic development. In relation with this bottleneck, differentiation of human embryonic stem cells (hESCs) into specialized lineages may be considered as an alternative to mimic human development. METHODS AND RESULTS In this study, hESCs were differentiated into three lineage cell types to analyze temporal and spatial expression of imprinted genes. Of 19 imprinted genes examined, 15 imprinted genes showed similar transcriptional level among two hESC lines and two human induced pluripotent stem cell (hiPSC) lines. Expressional patterns of most imprinted genes were varied in progenitors and fully differentiated cells which were derived from hESCs. Also, no consistence was observed in the expression pattern of imprinted genes within an imprinting domain during in vitro differentiation of hESCs into three lineage cell types. CONCLUSIONS Transcriptional expression of imprinted genes is regulated in a cell type- specific manner in hESCs during in vitro differentiation.
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Affiliation(s)
- Sang-Wook Park
- Department of Biological Sciences and Center for Stem Cell Differentiation, Korea Advanced Institute of Science and Technology (KAIST), Daejeon
| | - Hyo-Sang Do
- Department of Biological Sciences and Center for Stem Cell Differentiation, Korea Advanced Institute of Science and Technology (KAIST), Daejeon
| | - Dongkyu Kim
- Department of Biological Sciences and Center for Stem Cell Differentiation, Korea Advanced Institute of Science and Technology (KAIST), Daejeon
| | - Ji-Yun Ko
- Department of Biochemistry and Molecular Biology, College of Medicine, Hanyang University, Seoul, Korea
| | - Sang-Hun Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, Hanyang University, Seoul, Korea
| | - Yong-Mahn Han
- Department of Biological Sciences and Center for Stem Cell Differentiation, Korea Advanced Institute of Science and Technology (KAIST), Daejeon
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