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Molecular Mechanisms Contributing to the Etiology of Congenital Diaphragmatic Hernia: A Review and Novel Cases. J Pediatr 2022; 246:251-265.e2. [PMID: 35314152 DOI: 10.1016/j.jpeds.2022.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 12/25/2022]
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2
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Effects of the NF-κB Signaling Pathway Inhibitor BAY11-7082 in the Replication of ASFV. Viruses 2022; 14:v14020297. [PMID: 35215890 PMCID: PMC8877168 DOI: 10.3390/v14020297] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 02/01/2023] Open
Abstract
African swine fever virus (ASFV) mainly infects the monocyte/macrophage lineage of pigs and regulates the production of cytokines that influence host immune responses. Several studies have reported changes in cytokine production after infection with ASFV, but the regulatory mechanisms have not yet been elucidated. Therefore, the aim of this study was to examine the immune response mechanism of ASFV using transcriptomic and proteomic analyses. Through multi-omics joint analysis, it was found that ASFV infection regulates the expression of the host NF-B signal pathway and related cytokines. Additionally, changes in the NF-κB signaling pathway and IL-1β and IL-8 expression in porcine alveolar macrophages (PAMs) infected with ASFV were examined. Results show that ASFV infection activates the NF-κB signaling pathway and up-regulates the expression of IL-1β and IL-8. The NF-κB inhibitor BAY11-7082 inhibited the expression profiles of phospho-NF-κB p65, p-IκB, and MyD88 proteins, and inhibited ASFV-induced NF-κB signaling pathway activation. Additionally, the results show that the NF-κB inhibitor BAY11-7082 can inhibit the replication of ASFV and can inhibit IL-1β and, IL-8 expression. Overall, the findings of this study indicate that ASFV infection activates the NF-κB signaling pathway and up-regulates the expression of IL-1β and IL-8, and inhibits the replication of ASFV by inhibiting the NF-κB signaling pathway and interleukin-1 beta and interleukin-8 production. These findings not only provide new insights into the molecular mechanism of the association between the NF-κB signaling pathway and ASFV infection, but also indicate that the NF-κB signaling pathway is a potential immunomodulatory pathway that controls ASF.
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Brosens E, Brouwer RWW, Douben H, van Bever Y, Brooks AS, Wijnen RMH, van IJcken WFJ, Tibboel D, Rottier RJ, de Klein A. Heritability and De Novo Mutations in Oesophageal Atresia and Tracheoesophageal Fistula Aetiology. Genes (Basel) 2021; 12:genes12101595. [PMID: 34680991 PMCID: PMC8535313 DOI: 10.3390/genes12101595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 01/12/2023] Open
Abstract
Tracheoesophageal Fistula (TOF) is a congenital anomaly for which the cause is unknown in the majority of patients. OA/TOF is a variable feature in many (often mono-) genetic syndromes. Research using animal models targeting genes involved in candidate pathways often result in tracheoesophageal phenotypes. However, there is limited overlap in the genes implicated by animal models and those found in OA/TOF-related syndromic anomalies. Knowledge on affected pathways in animal models is accumulating, but our understanding on these pathways in patients lags behind. If an affected pathway is associated with both animals and patients, the mechanisms linking the genetic mutation, affected cell types or cellular defect, and the phenotype are often not well understood. The locus heterogeneity and the uncertainty of the exact heritability of OA/TOF results in a relative low diagnostic yield. OA/TOF is a sporadic finding with a low familial recurrence rate. As parents are usually unaffected, de novo dominant mutations seems to be a plausible explanation. The survival rates of patients born with OA/TOF have increased substantially and these patients start families; thus, the detection and a proper interpretation of these dominant inherited pathogenic variants are of great importance for these patients and for our understanding of OA/TOF aetiology.
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Affiliation(s)
- Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
- Correspondence:
| | - Rutger W. W. Brouwer
- Department of Cell Biology, Center for Biomics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (R.W.W.B.); (W.F.J.v.I.)
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Alice S. Brooks
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Rene M. H. Wijnen
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (R.M.H.W.); (D.T.)
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Center for Biomics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (R.W.W.B.); (W.F.J.v.I.)
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (R.M.H.W.); (D.T.)
| | - Robbert J. Rottier
- Departments of Pediatric Surgery & Cell Biology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
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Imany-Shakibai H, Yin O, Russell MR, Sklansky M, Satou G, Afshar Y. Discordant congenital heart defects in monochorionic twins: Risk factors and proposed pathophysiology. PLoS One 2021; 16:e0251160. [PMID: 33956871 PMCID: PMC8101911 DOI: 10.1371/journal.pone.0251160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
A six-fold increase in congenital heart defects (CHD) exists among monochorionic (MC) twins compared to singleton or dichorionic twin pregnancies. Though MC twins share an identical genotype, discordant phenotypes related to CHD and other malformations have been described, with reported rates of concordance for various congenital anomalies at less than 20%. Our objective was to characterize the frequency and spectrum of CHD in a contemporary cohort of MC twins, coupled with genetic and clinical variables to provide insight into risk factors and pathophysiology of discordant CHD in MC twins. Retrospective analysis of all twins receiving prenatal fetal echocardiography at a single institution from January 2010 –March 2020 (N = 163) yielded 23 MC twin pairs (46 neonates) with CHD (n = 5 concordant CHD, n = 18 discordant CHD). The most common lesions were septal defects (60% and 45.5% in concordant and discordant cohorts, respectively) and right heart lesions (40% and 18.2% in concordant and discordant cohorts, respectively). Diagnostic genetic testing was abnormal for 20% of the concordant and 5.6% of the discordant pairs, with no difference in rate of abnormal genetic results between the groups (p = 0.395). No significant association was found between clinical risk factors and development of discordant CHD (p>0.05). This data demonstrates the possibility of environmental and epigenetic influences versus genotypic factors in the development of discordant CHD in monochorionic twins.
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Affiliation(s)
- Helia Imany-Shakibai
- David Geffen School of Medicine, UCLA, Los Angeles, California, United States of America
| | - Ophelia Yin
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, UCLA, Los Angeles, California, United States of America
| | - Matthew R. Russell
- Department of Pediatrics, Kaiser Permanente Southern California, Los Angeles, California, United States of America
| | - Mark Sklansky
- David Geffen School of Medicine, UCLA, Los Angeles, California, United States of America
- Division of Pediatric Cardiology, UCLA Mattel Children’s Hospital, Los Angeles, California, United States of America
| | - Gary Satou
- David Geffen School of Medicine, UCLA, Los Angeles, California, United States of America
- Division of Pediatric Cardiology, UCLA Mattel Children’s Hospital, Los Angeles, California, United States of America
| | - Yalda Afshar
- David Geffen School of Medicine, UCLA, Los Angeles, California, United States of America
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, UCLA, Los Angeles, California, United States of America
- * E-mail:
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5
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Grunert M, Appelt S, Grossfeld P, Sperling SR. The Needle in the Haystack-Searching for Genetic and Epigenetic Differences in Monozygotic Twins Discordant for Tetralogy of Fallot. J Cardiovasc Dev Dis 2020; 7:jcdd7040055. [PMID: 33276527 PMCID: PMC7761217 DOI: 10.3390/jcdd7040055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/20/2022] Open
Abstract
Congenital heart defects (CHDs) are the most common birth defect in human with an incidence of almost 1% of all live births. Most cases have a multifactorial origin with both genetics and the environment playing a role in its development and progression. Adding an epigenetic component to this aspect is exemplified by monozygotic twins which share the same genetic background but have a different disease status. As a result, the interplay between the genetic, epigenetic and the environmental conditions might contribute to the etiology and phenotype. To date, the underlying causes of the majority of CHDs remain poorly understood. In this study, we performed genome-wide high-throughput sequencing to examine the genetic, structural genomic and epigenetic differences of two identical twin pairs discordant for Tetralogy of Fallot (TOF), representing the most common cyanotic form of CHDs. Our results show the almost identical genetic and structural genomic identity of the twins. In contrast, several epigenetic alterations could be observed given by DNA methylation changes in regulatory regions of known cardiac-relevant genes. Overall, this study provides first insights into the impact of genetic and especially epigenetic factors underlying monozygotic twins discordant for CHD like TOF.
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Affiliation(s)
- Marcel Grunert
- Cardiovascular Genetics, Charité—Universitätsmedizin Berlin, 13125 Berlin, Germany; (M.G.); (S.A.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10178 Berlin, Germany
| | - Sandra Appelt
- Cardiovascular Genetics, Charité—Universitätsmedizin Berlin, 13125 Berlin, Germany; (M.G.); (S.A.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10178 Berlin, Germany
| | - Paul Grossfeld
- Division of Cardiology, University of California San Diego, Rady’s Hospital MC 5004, San Diego, CA 92123, USA;
| | - Silke R. Sperling
- Cardiovascular Genetics, Charité—Universitätsmedizin Berlin, 13125 Berlin, Germany; (M.G.); (S.A.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10178 Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Correspondence: ; Tel.: +49-30450540123
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Kang M, Gao J. Integration of Multi-omics Data for Expression Quantitative Trait Loci (eQTL) Analysis and eQTL Epistasis. Methods Mol Biol 2020; 2082:157-171. [PMID: 31849014 DOI: 10.1007/978-1-0716-0026-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Expression quantitative trait loci (eQTL) mapping studies identify genetic loci that regulate gene expression. eQTL mapping studies can capture gene regulatory interactions and provide insight into the genetic mechanism of biological systems. Recently, the integration of multi-omics data, such as single-nucleotide polymorphisms (SNPs), copy number variations (CNVs), DNA methylation, and gene expression, plays an important role in elucidating complex biological systems, since biological systems involve a sequence of complex interactions between various biological processes. This chapter introduces multi-omics data that have been used in many eQTL studies and integrative methodologies that incorporate multi-omics data for eQTL studies. Furthermore, we describe a statistical approach that can detect nonlinear causal relationships between eQTLs, called eQTL epistasis, and its importance.
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Affiliation(s)
- Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Jean Gao
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX, USA.
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7
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Copy Number Variants and Exome Sequencing Analysis in Six Pairs of Chinese Monozygotic Twins Discordant for Congenital Heart Disease. Twin Res Hum Genet 2018; 20:521-532. [PMID: 29192580 PMCID: PMC5729853 DOI: 10.1017/thg.2017.57] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Congenital heart disease (CHD) is one of the most common birth defects. More than 200 susceptibility loci have been identified for CHDs, yet a large part of the genetic risk factors remain unexplained. Monozygotic (MZ) twins are thought to be completely genetically identical; however, discordant phenotypes have been found in MZ twins. Recent studies have demonstrated genetic differences between MZ twins. We aimed to test whether copy number variants (CNVs) and/or genetic mutation differences play a role in the etiology of CHDs by using single nucleotide polymorphism (SNP) genotyping arrays and whole exome sequencing of twin pairs discordant for CHDs. Our goal was to identify mutations present only in the affected twins, which could identify novel candidates for CHD susceptibility loci. We present a comprehensive analysis for the CNVs and genetic mutation results of the selected individuals but detected no consistent differences within the twin pairs. Our study confirms that chromosomal structure or genetic mutation differences do not seem to play a role in the MZ twins discordant for CHD.
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Szylberg Ł, Bodnar M, Lebioda A, Krepska P, Kowalewski A, Bręborowicz G, Marszałek A. Differences in the Expression of TLR-2, NOD2, and NF-κB in Placenta Between Twins. Arch Immunol Ther Exp (Warsz) 2018; 66:463-470. [PMID: 29796818 PMCID: PMC6245244 DOI: 10.1007/s00005-018-0514-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 05/08/2018] [Indexed: 12/12/2022]
Abstract
Dizygotic twins share the same type of genetic relationship as non-twin siblings. Whereas monozygotic (MZ) twins are considered to have identical genetic material, they still differ. There is a number of reasons for early MZ twin discordance, including differences in the in utero environment, stochasticity, genetic mosaicism, and epigenetic factors. During gestation, the efficient innate immune system is of utmost importance. Our study was based on immunohistochemical evaluation of the differences in innate immune protein expression (TLR-2, NOD2, and NF-κB) in the 95 placentas between twins. Our study revealed statistical significant differences between diamniotic–dichorionic and monoamniotic–dichorionic twins. Monoamniotic–monochorionic twins exhibited no significant differences in protein expressions. To identify epigenetic factors causing the differences between twins, we made a series of comparisons with clinical data. The study revealed more cases with infections, miscarriages, in vitro fertilization, and premature rupture of membranes within the group with higher differences level of NF-κB, NOD2 and TLR-2 between twins. In case of twin-to-twin transfusion syndrome, there were no significant differences in innate immune protein expressions between twins. These results show that dissimilar genetic material and separate in utero environment promote discordance in innate immune protein expressions between twins. Moreover, additional blood flow between twins may be favorable in life-threatening conditions ensuring similar microenvironment.
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Affiliation(s)
- Łukasz Szylberg
- Chair and Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland. .,Chair and Department of Oncologic Pathology and Prophylactics, Greater Poland Cancer Center, Poznań University of Medical Sciences and Department of Oncologic Pathology, Poznan, Poland. .,Department of Pathomorphology, Military Clinical Hospital, Bydgoszcz, Poland.
| | - Magdalena Bodnar
- Chair and Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Anna Lebioda
- Department and Clinic of Perinatology and Gynecology, Poznań University of Medical Sciences, Poznan, Poland
| | - Patrycja Krepska
- Department of Obstetrics and Gynecology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Adam Kowalewski
- Chair and Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Grzegorz Bręborowicz
- Department and Clinic of Perinatology and Gynecology, Poznań University of Medical Sciences, Poznan, Poland
| | - Andrzej Marszałek
- Chair and Department of Oncologic Pathology and Prophylactics, Greater Poland Cancer Center, Poznań University of Medical Sciences and Department of Oncologic Pathology, Poznan, Poland
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Castellani CA, Melka MG, Gui JL, Gallo AJ, O'Reilly RL, Singh SM. Post-zygotic genomic changes in glutamate and dopamine pathway genes may explain discordance of monozygotic twins for schizophrenia. Clin Transl Med 2017; 6:43. [PMID: 29181591 PMCID: PMC5704032 DOI: 10.1186/s40169-017-0174-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/05/2017] [Indexed: 01/06/2023] Open
Abstract
Background Monozygotic twins are valuable in assessing the genetic vs environmental contribution to diseases. In the era of complete genome sequences, they allow identification of mutational mechanisms and specific genes and pathways that offer predisposition to the development of complex diseases including schizophrenia. Methods We sequenced the complete genomes of two pairs of monozygotic twins discordant for schizophrenia (MZD), including one representing a family tetrad. The family specific complete sequences have allowed identification of post zygotic mutations between MZD genomes. It allows identification of affected genes including relevant network and pathways that may account for the diseased state in pair specific patient. Results We found multiple twin specific sequence differences between co-twins that included small nucleotides [single nucleotide variants (SNV), small indels and block substitutions], copy number variations (CNVs) and structural variations. The genes affected by these changes belonged to a number of canonical pathways, the most prominent ones are implicated in schizophrenia and related disorders. Although these changes were found in both twins, they were more frequent in the affected twin in both pairs. Two specific pathway defects, glutamate receptor signaling and dopamine feedback in cAMP signaling pathways, were uniquely affected in the two patients representing two unrelated families. Conclusions We have identified genome-wide post zygotic mutations in two MZD pairs affected with schizophrenia. It has allowed us to use the threshold model and propose the most likely cause of this disease in the two patients studied. The results support the proposition that each schizophrenia patient may be unique and heterogeneous somatic de novo events may contribute to schizophrenia threshold and discordance of the disease in monozygotic twins. Electronic supplementary material The online version of this article (10.1186/s40169-017-0174-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C A Castellani
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - M G Melka
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - J L Gui
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - A J Gallo
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - R L O'Reilly
- Department of Psychiatry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - S M Singh
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada.,Department of Psychiatry, The University of Western Ontario, London, ON, N6A 5B7, Canada
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Kang M, Park J, Kim DC, Biswas AK, Liu C, Gao J. Multi-Block Bipartite Graph for Integrative Genomic Analysis. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:1350-1358. [PMID: 27429442 DOI: 10.1109/tcbb.2016.2591521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Human diseases involve a sequence of complex interactions between multiple biological processes. In particular, multiple genomic data such as Single Nucleotide Polymorphism (SNP), Copy Number Variation (CNV), DNA Methylation (DM), and their interactions simultaneously play an important role in human diseases. However, despite the widely known complex multi-layer biological processes and increased availability of the heterogeneous genomic data, most research has considered only a single type of genomic data. Furthermore, recent integrative genomic studies for the multiple genomic data have also been facing difficulties due to the high-dimensionality and complexity, especially when considering their intra- and inter-block interactions. In this paper, we introduce a novel multi-block bipartite graph and its inference methods, MB2I and sMB2I, for the integrative genomic study. The proposed methods not only integrate multiple genomic data but also incorporate intra/inter-block interactions by using a multi-block bipartite graph. In addition, the methods can be used to predict quantitative traits (e.g., gene expression, survival time) from the multi-block genomic data. The performance was assessed by simulation experiments that implement practical situations. We also applied the method to the human brain data of psychiatric disorders. The experimental results were analyzed by maximum edge biclique and biclustering, and biological findings were discussed.
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Zarayeneh N, Ko E, Oh JH, Suh S, Liu C, Gao J, Kim D, Kang M. Integration of multi-omics data for integrative gene regulatory network inference. INT J DATA MIN BIOIN 2017; 18:223-239. [PMID: 29354189 DOI: 10.1504/ijdmb.2017.10008266] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gene regulatory networks provide comprehensive insights and indepth understanding of complex biological processes. The molecular interactions of gene regulatory networks are inferred from a single type of genomic data, e.g., gene expression data in most research. However, gene expression is a product of sequential interactions of multiple biological processes, such as DNA sequence variations, copy number variations, histone modifications, transcription factors, and DNA methylations. The recent rapid advances of high-throughput omics technologies enable one to measure multiple types of omics data, called 'multi-omics data', that represent the various biological processes. In this paper, we propose an Integrative Gene Regulatory Network inference method (iGRN) that incorporates multi-omics data and their interactions in gene regulatory networks. In addition to gene expressions, copy number variations and DNA methylations were considered for multi-omics data in this paper. The intensive experiments were carried out with simulation data, where iGRN's capability that infers the integrative gene regulatory network is assessed. Through the experiments, iGRN shows its better performance on model representation and interpretation than other integrative methods in gene regulatory network inference. iGRN was also applied to a human brain dataset of psychiatric disorders, and the biological network of psychiatric disorders was analysed.
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Affiliation(s)
- Neda Zarayeneh
- Department of Computer Science, Texas A&M University Commerce, Commerce, TX, USA
| | - Euiseong Ko
- Department of Computer Science, Kennesaw State University, Marietta, GA, USA
| | - Jung Hun Oh
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sang Suh
- Department of Computer Science, Texas A&M University Commerce, Commerce, TX, USA
| | - Chunyu Liu
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Jean Gao
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX, USA
| | | | - Mingon Kang
- Department of Computer Science, Kennesaw State University, Marietta, GA, USA
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Szczepanek-Parulska E, Zybek-Kocik A, Wartofsky L, Ruchala M. Thyroid Hemiagenesis: Incidence, Clinical Significance, and Genetic Background. J Clin Endocrinol Metab 2017; 102:3124-3137. [PMID: 28666345 DOI: 10.1210/jc.2017-00784] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Abstract
CONTEXT Thyroid hemiagenesis (THA) constitutes a rare, congenital disorder that is characterized by an absence of one thyroid lobe. Because the pathogenesis and clinical significance of this malformation remain undefined, specific clinical recommendations are lacking, especially for asymptomatic cases. EVIDENCE ACQUISITION The PubMed database was searched (years 1970 to 2017), and the following terms were used to retrieve the results: "thyroid hemiagenesis," "thyroid hemiaplasia," "one thyroid lobe agenesis," and "one thyroid lobe aplasia." Subsequently, reference sections of the retrieved articles were searched. EVIDENCE SYNTHESIS There is a noticeable susceptibility of subjects with THA to develop additional thyroid and nonthyroidal pathologies. In pathogenesis of concomitant thyroid pathologies, a chronic elevation in thyroid-stimulating hormone values may play an important role. Thus far, genetic studies failed to find a common genetic background of the anomaly, and the potential underlying cause was identified in a minority of the cases. CONCLUSIONS Patients with THA are prone to develop additional thyroid pathologies and theoretically might benefit from l-thyroxine treatment to lower the thyrotropin levels to those observed in the normal population. However, further research should be done to ascertain whether such intervention early in life would prevent development of associated thyroid conditions. At least, increased vigilance should be maintained to reveal all of the concomitant disorders as soon as possible during follow-up examinations. Application of high-throughput technologies enabling a genome-wide search for novel factors involved in thyroid embryogenesis might be the next step to expand the knowledge on THA pathogenesis.
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Affiliation(s)
- Ewelina Szczepanek-Parulska
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Ariadna Zybek-Kocik
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Leonard Wartofsky
- Department of Medicine, Washington Hospital Center, Washington, District of Columbia 20010
| | - Marek Ruchala
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
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13
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Mauro JA, Yavorski JM, Blanck G. Stratifying melanoma and breast cancer TCGA datasets on the basis of the CNV of transcription factor binding sites common to proliferation- and apoptosis-effector genes. Gene 2017; 614:37-48. [PMID: 28257835 DOI: 10.1016/j.gene.2017.02.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/03/2017] [Accepted: 02/22/2017] [Indexed: 12/01/2022]
Abstract
Transcription factors that activate both proliferation- and apoptosis-effector genes, along with a number of related observations, have led to a proposal for a feed forward mechanism of activating the two gene classes, whereby a certain concentration of a transcription factor activates the proliferation-effector genes and a higher concentration of the transcription factor activates the apoptosis-effector genes. We reasoned that this paradigm of regulation could lead to, in the cancer setting, a selection for relatively reduced copy numbers of apoptosis-effector gene, transcription factor binding sites (TFBS). Thus, the aim of this investigation was to examine the DNA sequencing read depths of TFBS for a set of proliferation- and apoptosis-effector genes, normalized to the read depths found in matching blood samples, as provided by the cancer genome atlas (TCGA); and thereby document copy number differences among these TFBS. We determined that the melanoma and breast cancer, TCGA datasets could be divided into three categories: (i) no detectable copy number variation for the proliferation- and apoptosis-effector, shared TFBS; (ii) a relative increase in the copy number of proliferation-effector gene TFBS, compared with the copy number of the apoptosis-effector gene TFBS; and (iii) a relative decrease in the number of proliferation-effector gene TFBS. Thus, we conclude that changes in the relative copies of the shared TFBS, for proliferation- and apoptosis-effector genes, have the potential of impacting tumor cell proliferative and apoptotic capacities.
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Affiliation(s)
- James A Mauro
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - John M Yavorski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States; Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.
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14
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Peng R, Zhou Y, Xie HN, Zheng J, Xie YJ, Yang JB. MCDA twins with discordant malformations: submicroscopic chromosomal anomalies detected by chromosomal microarray analysis and clinical outcomes. Prenat Diagn 2016; 36:766-74. [PMID: 27315788 DOI: 10.1002/pd.4859] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/03/2016] [Accepted: 06/10/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Ruan Peng
- Department of Ultrasonic Medicine; Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Yi Zhou
- Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Hong-Ning Xie
- Department of Ultrasonic Medicine; Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Ju Zheng
- Department of Ultrasonic Medicine; Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Ying-Jun Xie
- Department of Ultrasonic Medicine; Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Jian-Bo Yang
- Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
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15
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Lyu N, Guan LL, Ma H, Wang XJ, Wu BM, Shang FH, Wang D, Wen H, Yu X. Failure to Identify Somatic Mutations in Monozygotic Twins Discordant for Schizophrenia by Whole Exome Sequencing. Chin Med J (Engl) 2016; 129:690-5. [PMID: 26960372 PMCID: PMC4804415 DOI: 10.4103/0366-6999.178009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Schizophrenia (SCZ) is a severe, debilitating, and complex psychiatric disorder with multiple causative factors. An increasing number of studies have determined that rare variations play an important role in its etiology. A somatic mutation is a rare form of genetic variation that occurs at an early stage of embryonic development and is thought to contribute substantially to the development of SCZ. The aim of the study was to explore the novel pathogenic somatic single nucleotide variations (SNVs) and somatic insertions and deletions (indels) of SCZ. Methods: One Chinese family with a monozygotic (MZ) twin pair discordant for SCZ was included. Whole exome sequencing was performed in the co-twin and their parents. Rigorous filtering processes were conducted to prioritize pathogenic somatic variations, and all identified SNVs and indels were further confirmed by Sanger sequencing. Results: One somatic SNV and two somatic indels were identified after rigorous selection processes. However, none was validated by Sanger sequencing. Conclusions: This study is not alone in the failure to identify pathogenic somatic variations in MZ twins, suggesting that exonic somatic variations are extremely rare. Further efforts are warranted to explore the potential genetic mechanism of SCZ.
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Affiliation(s)
| | - Li-Li Guan
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing 100191, China
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16
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McNamara HC, Kane SC, Craig JM, Short RV, Umstad MP. A review of the mechanisms and evidence for typical and atypical twinning. Am J Obstet Gynecol 2016; 214:172-191. [PMID: 26548710 DOI: 10.1016/j.ajog.2015.10.930] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 12/11/2022]
Abstract
The mechanisms responsible for twinning and disorders of twin gestations have been the subject of considerable interest by physicians and scientists, and cases of atypical twinning have called for a reexamination of the fundamental theories invoked to explain twin gestations. This article presents a review of the literature focusing on twinning and atypical twinning with an emphasis on the phenomena of chimeric twins, phenotypically discordant monozygotic twins, mirror-image twins, polar body twins, complete hydatidiform mole with a coexistent twin, vanishing twins, fetus papyraceus, fetus in fetu, superfetation, and superfecundation. The traditional models attributing monozygotic twinning to a fission event, and more recent models describing monozygotic twinning as a fusion event, are critically reviewed. Ethical restrictions on scientific experimentation with human embryos and the rarity of cases of atypical twinning have limited opportunities to elucidate the exact mechanisms by which these phenomena occur. Refinements in the modeling of early embryonic development in twin pregnancies may have significant clinical implications. The article includes a series of figures to illustrate the phenomena described.
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Affiliation(s)
- Helen C McNamara
- Department of Maternal-Fetal Medicine, Royal Womens Hospital, Melbourne, Victoria, Australia
| | - Stefan C Kane
- Department of Maternal-Fetal Medicine, Royal Womens Hospital, Melbourne, Victoria, Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jeffrey M Craig
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Roger V Short
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Mark P Umstad
- Department of Maternal-Fetal Medicine, Royal Womens Hospital, Melbourne, Victoria, Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia.
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17
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Yet I, Tsai PC, Castillo-Fernandez JE, Carnero-Montoro E, Bell JT. Genetic and environmental impacts on DNA methylation levels in twins. Epigenomics 2015; 8:105-17. [PMID: 26678685 DOI: 10.2217/epi.15.90] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Epigenetics describes the study of cellular modifications that can modify the expression of genes without changing the DNA sequence. DNA methylation is one of the most stable and prevalent epigenetic mechanisms. Twin studies have been a valuable model for unraveling the genetic and epigenetic epidemiology of complex traits, and now offer a potential to dissect the factors that impact DNA methylation variability and its biomedical significance. The twin design specifically allows for the study of genetic, environmental and lifestyle factors, and their potential interactions, on epigenetic profiles. Furthermore, genetically identical twins offer a unique opportunity to assess nongenetic impacts on epigenetic profiles. Here, we summarize recent findings from twin studies of DNA methylation profiles across tissues, to define current knowledge regarding the genetic and nongenetic factors that influence epigenetic variation.
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Affiliation(s)
- Idil Yet
- Department of Twin Research & Genetic Epidemiology, King's College, London, UK
| | - Pei-Chien Tsai
- Department of Twin Research & Genetic Epidemiology, King's College, London, UK
| | | | | | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College, London, UK
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18
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Abstract
By definition, monozygotic (MZ) twins carry an identical set of genetic information. The observation of early post-twinning mutational events was shown to cause phenotypic discordance among MZ twin pairs. These mutational events comprise genomic alterations at different scales, ranging from single nucleotide changes to larger copy-number variations (CNVs) of varying sizes, as well as epigenetic changes. Here, we performed whole-exome sequencing (WES) in nine discordant MZ twins to identify somatic mutational events in the affected twin that might exert a dominant negative effect. Five of these MZ twin pairs were discordant for congenital heart defects (CHD), two for endocrine disorders, one for omphalocele, and one for congenital diaphragmatic hernia (CDH). Analysis of WES data from all nine MZ twin pairs using the de novo probability tool DeNovoGear detected only one apparent de novo variation in TMPRSS13 in one of the CHD-affected twins. Analysis of WES data from all nine MZ twin pairs by using standard filter criteria without the de novo probability tool DeNovoGear revealed a total of 6,657 variations in which both the twin pairs differed. After filtering for variations only present in the affected twins and absent in in-house controls, 722 variations remained. Visual inspection for read quality decreased this number to 12, present only in the affected twin. However, Sanger sequencing of the overall 13 variations failed to confirm the variation in the affected twin. These results suggest that somatic mutational events in coding regions do not seem to play a major role in the phenotypic expression of MZ discordant twin pairs.
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19
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Incomplete penetrance: The role of stochasticity in developmental cell colonization. J Theor Biol 2015; 380:309-14. [DOI: 10.1016/j.jtbi.2015.05.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 12/23/2022]
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20
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Vaz SO, Pires R, Pires LM, Carreira IM, Anjos R, Maciel P, Mota-Vieira L. A unique phenotype in a patient with a rare triplication of the 22q11.2 region and new clinical insights of the 22q11.2 microduplication syndrome: a report of two cases. BMC Pediatr 2015; 15:95. [PMID: 26297018 PMCID: PMC4546098 DOI: 10.1186/s12887-015-0417-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 08/13/2015] [Indexed: 11/24/2022] Open
Abstract
Background The rearrangements of the 22q11.2 chromosomal region, most frequently deletions and duplications, have been known to be responsible for multiple congenital anomaly disorders. These rearrangements are implicated in syndromes that have some phenotypic resemblances. While the 22q11.2 deletion, also known as DiGeorge/Velocardiofacial syndrome, has common features that include cardiac abnormalities, thymic hypoplasia, characteristic face, hypocalcemia, cognitive delay, palatal defects, velopharyngeal insufficiency, and other malformations, the microduplication syndrome is largely undetected. This is mainly because phenotypic appearance is variable, milder, less characteristic and unpredictable. In this paper, we report the clinical evaluation and follow-up of two patients affected by 22q11.2 rearrangements, emphasizing new phenotypic features associated with duplication and triplication of this genomic region. Case Presentation Patient 1 is a 24 year-old female with 22q11.2 duplication who has a heart defect (ostium secundum atrial septal defect) and supernumerary teeth (hyperdontia), a feature previously not reported in patients with 22q11.2 microduplication syndrome. Her monozygotic twin sister, who died at the age of one month, had a different heart defect (truncus arteriousus). Patient 2 is a 20 year-old female with a 22q11.2 triplication who had a father with 22q11.2 duplication. In comparison to the first case reported in the literature, she has an aggravated phenotype characterized by heart defects (restrictive VSD and membranous subaortic stenosis), and presented other facial dysmorphisms and urogenital malformations (ovarian cyst). Additionally, she has a hemangioma planum on the right side of her face, a feature of Sturge-Weber syndrome. Conclusions In this report, we described hyperdontia as a new feature of 22q11.2 microdeletion syndrome. Moreover, this syndrome was diagnosed in a patient who had a deceased monozygotic twin affected with a different heart defect, which corresponds to a phenotypic discordance never reported in the literature. Case 2 is the second clinical report of 22q11.2 triplication and presents an aggravated phenotype in contrast to the patient previously reported.
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Affiliation(s)
- Sara O Vaz
- Department of Pediatrics of Hospital of Divino Espírito Santo of Ponta Delgada, EPE, Av. D. Manuel I, 9500-370, Ponta Delgada, São Miguel Island, Azores, Portugal.
| | - Renato Pires
- Molecular Genetics and Pathology Unit, Hospital of Divino Espírito Santo of Ponta Delgada, EPE, Av. D. Manuel I, 9500-370, Ponta Delgada, São Miguel Island, Azores, Portugal. .,Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal.
| | - Luís M Pires
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354, Coimbra, Portugal.
| | - Isabel M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354, Coimbra, Portugal. .,Centro de Investigação em Meio Ambiente, Genética e Oncobiologia (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-354, Coimbra, Portugal. .,Centre of Neurosciences (CNC), University of Coimbra, 3000-354, Coimbra, Portugal.
| | - Rui Anjos
- Department of Pediatric Cardiology, Hospital of Santa Cruz, Av. Prof. Dr. Reinaldo dos Santos, 2790-134, Carnaxide, Portugal.
| | - Paula Maciel
- Department of Pediatrics of Hospital of Divino Espírito Santo of Ponta Delgada, EPE, Av. D. Manuel I, 9500-370, Ponta Delgada, São Miguel Island, Azores, Portugal.
| | - Luisa Mota-Vieira
- Molecular Genetics and Pathology Unit, Hospital of Divino Espírito Santo of Ponta Delgada, EPE, Av. D. Manuel I, 9500-370, Ponta Delgada, São Miguel Island, Azores, Portugal. .,Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal. .,Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal.
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21
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Ollikainen M, Ismail K, Gervin K, Kyllönen A, Hakkarainen A, Lundbom J, Järvinen EA, Harris JR, Lundbom N, Rissanen A, Lyle R, Pietiläinen KH, Kaprio J. Genome-wide blood DNA methylation alterations at regulatory elements and heterochromatic regions in monozygotic twins discordant for obesity and liver fat. Clin Epigenetics 2015; 7:39. [PMID: 25866590 PMCID: PMC4393626 DOI: 10.1186/s13148-015-0073-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 03/11/2015] [Indexed: 12/16/2022] Open
Abstract
Background The current epidemic of obesity and associated diseases calls for swift actions to better understand the mechanisms by which genetics and environmental factors affect metabolic health in humans. Monozygotic (MZ) twin pairs showing discordance for obesity suggest that epigenetic influences represent one such mechanism. We studied genome-wide leukocyte DNA methylation variation in 30 clinically healthy young adult MZ twin pairs discordant for body mass index (BMI; average within-pair BMI difference: 5.4 ± 2.0 kg/m2). Results There were no differentially methylated cytosine-guanine (CpG) sites between the co-twins discordant for BMI. However, stratification of the twin pairs based on the level of liver fat accumulation revealed two epigenetically highly different groups. Significant DNA methylation differences (n = 1,236 CpG sites (CpGs)) between the co-twins were only observed if the heavier co-twins had excessive liver fat (n = 13 twin pairs). This unhealthy pattern of obesity was coupled with insulin resistance and low-grade inflammation. The differentially methylated CpGs included 23 genes known to be associated with obesity, liver fat, type 2 diabetes mellitus (T2DM) and metabolic syndrome, and potential novel metabolic genes. Differentially methylated CpG sites were overrepresented at promoters, insulators, and heterochromatic and repressed regions. Based on predictions by overlapping histone marks, repressed and weakly transcribed sites were significantly more often hypomethylated, whereas sites with strong enhancers and active promoters were hypermethylated. Further, significant clustering of differentially methylated genes in vitamin, amino acid, fatty acid, sulfur, and renin-angiotensin metabolism pathways was observed. Conclusions The methylome in leukocytes is altered in obesity associated with metabolic disturbances, and our findings indicate several novel candidate genes and pathways in obesity and obesity-related complications. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0073-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miina Ollikainen
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Khadeeja Ismail
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Kristina Gervin
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Anjuska Kyllönen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Antti Hakkarainen
- Department of Radiology, HUS Medical Imaging Center, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Jesper Lundbom
- Department of Radiology, HUS Medical Imaging Center, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Elina A Järvinen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Jennifer R Harris
- Division of Epidemiology, The Norwegian Institute of Public Health, Oslo, Norway
| | - Nina Lundbom
- Department of Radiology, HUS Medical Imaging Center, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Aila Rissanen
- Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland.,Endocrinology, Abdominal Center, Helsinki University Central Hospital, Helsinki, Finland
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,Endocrinology, Abdominal Center, Helsinki University Central Hospital, Helsinki, Finland.,Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland.,Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, Helsinki, Finland
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22
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Abstract
Monozygotic (MZ) twins are genetically identical at conception, making them informative subjects for studies on somatic mutations. Copy number variants (CNVs) are responsible for a substantial part of genetic variation, have relatively high mutation rates, and are likely to be involved in phenotypic variation. We conducted a genome-wide survey for post-twinning de novo CNVs in 1,097 MZ twin pairs. Comparisons between MZ twins were made by CNVs measured in DNA from blood or buccal epithelium with the Affymetrix 6.0 microarray and two calling algorithms. In addition, CNV concordance rates were compared between the different sources of DNA, and gene-enrichment association analyses were conducted for thought problems (TP) and attention problems (AP) using CNVs concordant within MZ pairs. We found a total of 153 putative post-twinning de novo CNVs >100 kb, of which the majority resided in 15q11.2. Based on the discordance of raw intensity signals a selection was made of 20 de novo CNVs for a qPCR validation experiments. Two out of 20 post-twinning de novo CNVs were validated with qPCR in the same twin pair. The 13-year-old MZ twin pair that showed two discordances in CN in 15q11.2 in their buccal DNA did not show large phenotypic differences. From the remaining 18 putative de novo CNVs, 17 were deletions or duplications that were concordant within MZ twin pairs. Concordance rates within twin pairs of CNV calls with CN ≠ 2 were ~80%. Buccal epithelium-derived DNA showed a slightly but significantly higher concordance rate, and blood-derived DNA showed significantly more concordant CNVs per twin pair. The gene-enrichment analyses on concordant CNVs showed no significant associations between CNVs overlapping with genes involved in neuronal processes and TP or AP after accounting for the source of DNA.
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23
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Day E, Kearns PK, Taylor CJ, Bradley JA. Transplantation Between Monozygotic Twins. Transplantation 2014; 98:485-9. [DOI: 10.1097/tp.0000000000000274] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
Chromosome 17q21.31 microdeletion syndrome is a genomic disorder caused by a recurrent 600 kb long deletion. The deletion affects the region of a common inversion present in about 20% of Europeans. The inversion is associated with the H2 haplotype carrying additional low-copy repeats susceptible to non-allelic homologous recombination, and this haplotype is prone to deletion. No instances of 17q21.31 deletions inherited from an affected parent have been reported, and the deletions always affected a parental chromosome with the H2 haplotype. The syndrome is characterized clinically by intellectual disability, hypotonia, friendly behavior and specific facial dysmorphism with long face, large tubular or pear-shaped nose and bulbous nasal tip. We present monozygotic twin sisters showing the typical clinical picture of the syndrome. The phenotype of the sisters was very similar, with a slightly more severe presentation in Twin B. The 17q21.31 microdeletion was confirmed in both patients but in neither of their parents. Potential copy number differences between the genomes of the twins were subsequently searched using high-resolution single nucleotide polymorphism (SNP) and comparative genome hybridisation (CGH) arrays. However, these analyses identified no additional aberrations or genomic differences that could potentially be responsible for the subtle phenotypic differences. These could possibly be related to the more severe perinatal history of Twin B, or to the variable expressivity of the disorder. In accord with the expectations, one of the parents (the mother) was shown to carry the H2 haplotype, and the maternal allele of chromosome 17q21.31 was missing in the twins.
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25
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Copy number variation distribution in six monozygotic twin pairs discordant for schizophrenia. Twin Res Hum Genet 2014; 17:108-20. [PMID: 24556202 DOI: 10.1017/thg.2014.6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have evaluated copy number variants (CNVs) in six monozygotic twin pairs discordant for schizophrenia. The data from Affymetrix® Human SNP 6.0 arrays™ were analyzed using Affymetrix® Genotyping Console™, Partek® Genomics Suite™, PennCNV, and Golden Helix SVS™. This yielded both program-specific and overlapping results. Only CNVs called by Affymetrix Genotyping Console, Partek Genomics Suite, and PennCNV were used in further analysis. This analysis included an assessment of calls in each of the six twin pairs towards identification of unique CNVs in affected and unaffected co-twins. Real time polymerase chain reaction (PCR) experiments confirmed one CNV loss at 7q11.21 that was found in the affected patient but not in the unaffected twin. The results identified CNVs and genes that were previously implicated in mental abnormalities in four of the six twin pairs. It included PYY (twin pairs 1 and 5), EPHA3 (twin pair 3), KIAA1211L (twin pair 4), and GPR139 (twin pair 5). They represent likely candidate genes and CNVs for the discordance of four of the six monozygotic twin pairs for this heterogeneous neurodevelopmental disorder. An explanation for these differences is ontogenetic de novo events that differentiate in the monozygotic twins during development.
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26
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Jung SH, Yim SH, Oh HJ, Park JE, Kim MJ, Kim GA, Kim TM, Kim JS, Lee BC, Chung YJ. De novo copy number variations in cloned dogs from the same nuclear donor. BMC Genomics 2013; 14:863. [PMID: 24313905 PMCID: PMC3878922 DOI: 10.1186/1471-2164-14-863] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 12/03/2013] [Indexed: 11/23/2022] Open
Abstract
Background Somatic mosaicism of copy number variants (CNVs) in human body organs and de novo CNV event in monozygotic twins suggest that de novo CNVs can occur during mitotic recombination. These de novo CNV events are important for understanding genetic background of evolution and diverse phenotypes. In this study, we explored de novo CNV event in cloned dogs with identical genetic background. Results We analyzed CNVs in seven cloned dogs using the nuclear donor genome as reference by array-CGH, and identified five de novo CNVs in two of the seven clones. Genomic qPCR, dye-swap array-CGH analysis and B-allele profile analysis were used for their validation. Two larger de novo CNVs (5.2 Mb and 338 Kb) on chromosomes X and 19 in clone-3 were consistently validated by all three experiments. The other three smaller CNVs (sized from 36.1 to76.4 Kb) on chromosomes 2, 15 and 32 in clone-3 and clone-6 were verified by at least one of the three validations. In addition to the de novo CNVs, we identified a 37 Mb-sized copy neutral de novo loss of heterozygosity event on chromosome 2 in clone-6. Conclusions To our knowledge, this is the first report of de novo CNVs in the cloned dogs which were generated by somatic cell nuclear transfer technology. To study de novo genetic events in cloned animals can help understand formation mechanisms of genetic variants and their biological implications.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Byeong Chun Lee
- Integrated Research Center for Genome Polymorphism, Department of Microbiology, The Catholic University of Korea, College of Medicine, 505 Banpo-dong, Seocho-gu, Seoul 137-701, Korea.
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27
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Bouhlal Y, Martinez S, Gong H, Dumas K, Shieh JTC. Twin Mitochondrial Sequence Analysis. Mol Genet Genomic Med 2013; 1:174-186. [PMID: 24040623 PMCID: PMC3768015 DOI: 10.1002/mgg3.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
When applying genome-wide sequencing technologies to disease investigation, it is increasingly important to resolve sequence variation in regions of the genome that may have homologous sequences. The human mitochondrial genome challenges interpretation given the potential for heteroplasmy, somatic variation, and homologous nuclear mitochondrial sequences (numts). Identical twins share the same mitochondrial DNA (mtDNA) from early life, but whether the mitochondrial sequence remains similar is unclear. We compared an adult monozygotic twin pair using high-throughput sequencing and evaluated variants with primer extension and mitochondrial preenrichment. Thirty-seven variants were shared between the twin individuals, and the variants were verified on the original genomic DNA. These studies support highly identical genetic sequence in this case. Certain low-level variant calls were of high quality and homology to the mtDNA, and they were further evaluated. When we assessed calls in preenriched mtDNA templates, we found that these may represent numts, which can be differentiated from mtDNA variation. We conclude that twin identity extends to mtDNA, and it is critical to differentiate between numts and mtDNA in genome sequencing, particularly as significant heteroplasmy could influence genome interpretation. Further studies on mtDNA and numts will aid in understanding how variation occurs and persists.
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Affiliation(s)
- Yosr Bouhlal
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
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28
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Kunio M, Yang C, Minakuchi Y, Ohori K, Soutome M, Hirasawa T, Kazuki Y, Adachi N, Suzuki S, Itoh M, Goto YI, Andoh T, Kurosawa H, Akamatsu W, Ohyama M, Okano H, Oshimura M, Sasaki M, Toyoda A, Kubota T. Comparison of Genomic and Epigenomic Expression in Monozygotic Twins Discordant for Rett Syndrome. PLoS One 2013; 8:e66729. [PMID: 23805272 PMCID: PMC3689680 DOI: 10.1371/journal.pone.0066729] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/10/2013] [Indexed: 12/12/2022] Open
Abstract
Monozygotic (identical) twins have been widely used in genetic studies to determine the relative contributions of heredity and the environment in human diseases. Discordance in disease manifestation between affected monozygotic twins has been attributed to either environmental factors or different patterns of X chromosome inactivation (XCI). However, recent studies have identified genetic and epigenetic differences between monozygotic twins, thereby challenging the accepted experimental model for distinguishing the effects of nature and nurture. Here, we report the genomic and epigenomic sequences in skin fibroblasts of a discordant monozygotic twin pair with Rett syndrome, an X-linked neurodevelopmental disorder characterized by autistic features, epileptic seizures, gait ataxia and stereotypical hand movements. The twins shared the same de novo mutation in exon 4 of the MECP2 gene (G269AfsX288), which was paternal in origin and occurred during spermatogenesis. The XCI patterns in the twins did not differ in lymphocytes, skin fibroblasts, and hair cells (which originate from ectoderm as does neuronal tissue). No reproducible differences were detected between the twins in single nucleotide polymorphisms (SNPs), insertion-deletion polymorphisms (indels), or copy number variations. Differences in DNA methylation between the twins were detected in fibroblasts in the upstream regions of genes involved in brain function and skeletal tissues such as Mohawk Homeobox (MKX), Brain-type Creatine Kinase (CKB), and FYN Tyrosine Kinase Protooncogene (FYN). The level of methylation in these upstream regions was inversely correlated with the level of gene expression. Thus, differences in DNA methylation patterns likely underlie the discordance in Rett phenotypes between the twins.
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Affiliation(s)
- Miyake Kunio
- Department of Epigenetic Medicine, Faculty of Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
| | - Chunshu Yang
- Department of Epigenetic Medicine, Faculty of Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Kenta Ohori
- Department of Epigenetic Medicine, Faculty of Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
| | - Masaki Soutome
- Department of Epigenetic Medicine, Faculty of Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
| | - Takae Hirasawa
- Department of Epigenetic Medicine, Faculty of Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
| | - Yasuhiro Kazuki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
| | - Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
| | - Seiko Suzuki
- Department of Child Neurology, National Center Hospital for Mental, Nervous, and Muscular Disorders, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Masayuki Itoh
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Yu-ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Tomoko Andoh
- Department of Biotechnology, Faculty of Life and Environmental Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | - Hiroshi Kurosawa
- Department of Biotechnology, Faculty of Life and Environmental Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | - Wado Akamatsu
- Department of Physiology, Keio University School of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Manabu Ohyama
- Department of Dermatology, Keio University School of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Mitsuo Oshimura
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center Hospital for Mental, Nervous, and Muscular Disorders, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Takeo Kubota
- Department of Epigenetic Medicine, Faculty of Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
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CNV analysis in monozygotic twin pairs discordant for urorectal malformations. Twin Res Hum Genet 2013; 16:802-7. [PMID: 23659922 DOI: 10.1017/thg.2013.29] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Early post-twinning mutational events can account for discordant phenotypes in monozygotic (MZ) twin pairs. Such mutational events may comprise genomic alterations of different sizes, ranging from single nucleotides to large copy-number variations (CNVs). Anorectal malformations (ARM) and the bladder exstrophy-epispadias complex (BEEC) represent the most severe end of the urorectal malformation spectrum. Recently, CNV studies in patients with sporadic ARM and the BEEC have identified de novo events that occur in specific chromosomal regions. We hypothesized that early arising, post-twinning CNVs might contribute to discordance in MZ twin pairs with ARM or the BEEC; knowledge of such CNVs might help to identify additional chromosomal regions involved in the development of these malformations. We investigated four discordant MZ twin pairs (three ARM and one BEEC) using molecular karyotyping arrays comprising 1,140,419 markers with a median marker spacing of 1.5 kb. Filtering the coding regions for possible disease-causing post-twinning de novo CNVs present only in the affected twin, but not in the unaffected twin or the parents, identified a total of 136 CNVs. These 136 CNVs were then filtered against publicly available databases and finally re-evaluated visually. No potentially causative CNV remained after applying these filter criteria. Our results suggest that post-twinning CNV events that affect coding regions of the genome did not contribute to the discordant phenotypes in MZ twin pairs that we investigated. Possible causes for the discordant phenotypes include changes in regulatory elements or smaller genetic changes within coding regions which may be detectable by whole-exome sequencing.
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30
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