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Carvalho LML, Jorge AADL, Bertola DR, Krepischi ACV, Rosenberg C. A Comprehensive Review of Syndromic Forms of Obesity: Genetic Etiology, Clinical Features and Molecular Diagnosis. Curr Obes Rep 2024; 13:313-337. [PMID: 38277088 DOI: 10.1007/s13679-023-00543-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2023] [Indexed: 01/27/2024]
Abstract
Syndromic obesity refers to obesity occurring with additional clinical findings, such as intellectual disability/developmental delay, dysmorphic features, and congenital malformations. PURPOSE OF REVIEW: To present a narrative review regarding the genetic etiology, clinical description, and molecular diagnosis of syndromic obesity, which is a rare condition with high phenotypic variability and genetic heterogeneity. The following syndromes are presented in this review: Prader-Willi, Bardet-Biedl, Pseudohypoparathyroidism, Alström, Smith-Magenis, Cohen, Temple, 1p36 deletion, 16p11.2 microdeletion, Kleefstra, SIM1-related, Börjeson-Forssman-Lehmann, WAGRO, Carpenter, MORM, and MYT1L-related syndromes. RECENT FINDINGS: There are three main groups of mechanisms for syndromic obesity: imprinting, transcriptional activity regulation, and cellular cilia function. For molecular diagnostic, methods of genome-wide investigation should be prioritized over sequencing of panels of syndromic obesity genes. In addition, we present novel syndromic conditions that need further delineation, but evidences suggest they have a higher frequency of obesity. The etiology of syndromic obesity tends to be linked to disrupted neurodevelopment (central) and is associated with a diversity of genes and biological pathways. In the genetic investigation of individuals with syndromic obesity, the possibility that the etiology of the syndromic condition is independent of obesity should be considered. The accurate genetic diagnosis impacts medical management, treatment, and prognosis, and allows proper genetic counseling.
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Affiliation(s)
- Laura Machado Lara Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Alexander Augusto de Lima Jorge
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory (LIM/25), Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
- Genetics Unit of Instituto da Criança, Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil.
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Li Y, Shi L, Zhao F, Luo Y, Zhang M, Wu X, Zhu J. PIM1 attenuates cisplatin-induced AKI by inhibiting Drp1 activation. Cell Signal 2024; 113:110969. [PMID: 37967691 DOI: 10.1016/j.cellsig.2023.110969] [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] [Received: 04/17/2023] [Revised: 10/23/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
Cisplatin, an effective anti-cancer drug, always causes acute kidney injury (AKI) by inducing mitochondrial damage. PIM1 is a serine/threonine kinase, which has been shown to regulate mitochondrial function. However, the role and mechanisms of PIM1 in cisplatin-induced AKI remain unexplored. This study aimed to investigate the effects of PIM1 in cisplatin-induced AKI and its underlying mechanisms. To established Cisplatin-induced AKI model, mice were given a single intraperitoneal injection(20 mg/kg) and BUMPT cells were treated with cisplatin(20 μM). PIM1 inhibitor AZD1208 was used to inhibit PIM1 and PIM1-experssing adenovirus was used to overexpress PIM1. Drp1 inhibitor P110 and pcDNA3-Drp1K38A were used to inhibit the activation of Drp1 and mitochondrial fission. The indicators of renal function, renal morphology, apoptosis and mitochondrial dysfunction were assessed to evaluate cisplatin-induced nephrotoxicity. We observed that PIM1 was activated in cisplatin-induced AKI in vivo and cisplatin-induced tubular cells injury in vitro. PIM1 inhibition aggravated cisplatin-induced AKI in vivo, while PIM1 overexpression attenuated cisplatin-induced kidney injury in vivo and in vitro. Moreover, inhibiting PIM1 exacerbated mitochondrial damage in mice, but overexpressing PIM1 relieved mitochondrial damage in mice and BUMPT cells. In mice and BUMPT cells, inhibiting PIM1 deregulated the expression of p-Drp1S637, overexpressing PIM1 upregulated the ex-pression of p-Drp1S637. And inhibiting Drp1 activity alleviated cell damage in BUMPT cells with PIM1 knockdown or inhibition. This study demonstrated the protective effect of PIM1 in cisplatin-induced AKI, and regulation of Drp1 activation might be the underlying mechanism. Altogether, PIM1 may be a potential therapeutic target for cisplatin-induced AKI.
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Affiliation(s)
- Yuzhen Li
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Lang Shi
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Fan Zhao
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Yanwen Luo
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Mingjiao Zhang
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Xiongfei Wu
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.
| | - Jiefu Zhu
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.
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Chang L, Fukuoka Y, Aouizerat BE, Zhang L, Flowers E. Prediction Performance of Feature Selectors and Classifiers on Highly Dimensional Transcriptomic Data for Prediction of Weight Loss in Filipino Americans at Risk for Type 2 Diabetes. Biol Res Nurs 2023; 25:393-403. [PMID: 36600204 PMCID: PMC10404908 DOI: 10.1177/10998004221147513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Background: Accurate prediction of risk for chronic diseases like type 2 diabetes (T2D) is challenging due to the complex underlying etiology. Integration of more complex data types from sensors and leveraging technologies for collection of -omics datasets may provide greater insights into the specific risk profile for complex diseases.Methods: We performed a literature review to identify feature selection methods and machine learning models for prediction of weight loss in a previously completed clinical trial (NCT02278939) of a behavioral intervention for weight loss in Filipinos at risk for T2D. Features included demographic and clinical characteristics, dietary factors, physical activity, and transcriptomics.Results: We identified four feature selection methods: Correlation-based Feature Subset Selection (CfsSubsetEval) with BestFirst, Kolmogorov-Smirnov (KS) test with correlation featureselection (CFS), DESeq2, and max-relevance-min-relevance (MRMR) with linear forward search and mutual information (MI) and four machine learning algorithms: support vector machine, decision tree, random forest, and extra trees that are applicable to prediction of weight loss using the specified feature types.Conclusion: More accurate prediction of risk for T2D and other complex conditions may be possible by leveraging complex data types from sensors and -omics datasets. Emerging methods for feature selection and machine learning algorithms make this type of modeling feasible.
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Affiliation(s)
- Lisa Chang
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA, USA
- Keck Graduate Institute, Claremont, CA, USA
| | - Yoshimi Fukuoka
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Bradley E. Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, NY, USA
- Department of Oral and Maxillofacial Surgery, New York University, New York, NY, USA
| | - Li Zhang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elena Flowers
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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Chang L, Fukuoka Y, Aouizerat BE, Zhang L, Flowers E. Prediction of Weight Loss in Filipino Americans to Decrease Risk for Type 2 Diabetes: Using Multi-Dimensional Data (Preprint). JMIR Diabetes 2022; 8:e44018. [PMID: 37040172 PMCID: PMC10131631 DOI: 10.2196/44018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) has an immense disease burden, affecting millions of people worldwide and costing billions of dollars in treatment. As T2D is a multifactorial disease with both genetic and nongenetic influences, accurate risk assessments for patients are difficult to perform. Machine learning has served as a useful tool in T2D risk prediction, as it can analyze and detect patterns in large and complex data sets like that of RNA sequencing. However, before machine learning can be implemented, feature selection is a necessary step to reduce the dimensionality in high-dimensional data and optimize modeling results. Different combinations of feature selection methods and machine learning models have been used in studies reporting disease predictions and classifications with high accuracy. OBJECTIVE The purpose of this study was to assess the use of feature selection and classification approaches that integrate different data types to predict weight loss for the prevention of T2D. METHODS The data of 56 participants (ie, demographic and clinical factors, dietary scores, step counts, and transcriptomics) were obtained from a previously completed randomized clinical trial adaptation of the Diabetes Prevention Program study. Feature selection methods were used to select for subsets of transcripts to be used in the selected classification approaches: support vector machine, logistic regression, decision trees, random forest, and extremely randomized decision trees (extra-trees). Data types were included in different classification approaches in an additive manner to assess model performance for the prediction of weight loss. RESULTS Average waist and hip circumference were found to be different between those who exhibited weight loss and those who did not exhibit weight loss (P=.02 and P=.04, respectively). The incorporation of dietary and step count data did not improve modeling performance compared to classifiers that included only demographic and clinical data. Optimal subsets of transcripts identified through feature selection yielded higher prediction accuracy than when all available transcripts were included. After comparison of different feature selection methods and classifiers, DESeq2 as a feature selection method and an extra-trees classifier with and without ensemble learning provided the most optimal results, as defined by differences in training and testing accuracy, cross-validated area under the curve, and other factors. We identified 5 genes in two or more of the feature selection subsets (ie, CDP-diacylglycerol-inositol 3-phosphatidyltransferase [CDIPT], mannose receptor C type 2 [MRC2], PAT1 homolog 2 [PATL2], regulatory factor X-associated ankyrin containing protein [RFXANK], and small ubiquitin like modifier 3 [SUMO3]). CONCLUSIONS Our results suggest that the inclusion of transcriptomic data in classification approaches for prediction has the potential to improve weight loss prediction models. Identification of which individuals are likely to respond to interventions for weight loss may help to prevent incident T2D. Out of the 5 genes identified as optimal predictors, 3 (ie, CDIPT, MRC2, and SUMO3) have been previously shown to be associated with T2D or obesity. TRIAL REGISTRATION ClinicalTrials.gov NCT02278939; https://clinicaltrials.gov/ct2/show/NCT02278939.
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Affiliation(s)
- Lisa Chang
- Department of Physiological Nursing, University of California, San Francisco, San Francisco, CA, United States
- Keck Graduate Institute, Claremont, CA, United States
| | - Yoshimi Fukuoka
- Department of Physiological Nursing, University of California, San Francisco, San Francisco, CA, United States
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, NY, United States
- Department of Oral and Maxillofacial Surgery, New York University, New York, NY, United States
| | - Li Zhang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
- Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Elena Flowers
- Department of Physiological Nursing, University of California, San Francisco, San Francisco, CA, United States
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States
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Chromosome 2q12.3-q13 copy number variants in patients with neurodevelopmental disorders: genotype-phenotype correlation and new hotspots. Psychiatr Genet 2022; 32:171-177. [PMID: 35837682 DOI: 10.1097/ypg.0000000000000319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION The complex structure of the chromosome 2q12.3-q13 region provides a high chance of recombination events between various low copy repeats (LCRs). Copy number variants (CNV) in this region are present in both healthy populations and individuals affected with developmental delay, autism and congenital anomalies. Variable expressivity, reduced penetrance and limited characterization of the affected genes have complicated the classification of the CNVs clinical significance. METHODS Chromosomal microarray analysis data were reviewed for 10 298 patients with neurodevelopmental disorders referred to the UPMC Medical Genetics and Genomics Laboratories. A genotype-phenotype correlation was performed among the patients harboring the 2q12.3-q13 CNVs with overlapping genomic intervals. RESULTS We identified 17 (1 in ~600) individuals with rare CNVs in the 2q12.3-q13 region, including nine patients with deletions, seven individuals with duplications and one patient who had both a deletion and a duplication. Likely pathogenic CNVs with the breakpoints between LCRs encompassing the potential dosage-sensitive genes BCL2L11, BUB1, FBLN7 and TMEM87B were the most common. CNVs were also observed between LCRs surrounding the RANBP2 and LIMS1 genes. CONCLUSION Our study provides evidence for pathogenic CNV hotspots within the chromosome 2q12.3-q13 region. We suggest CNV classification based on the affected interval and the involvement of potential dosage-sensitive genes in these patients.
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Rodríguez-López R, Gimeno-Ferrer F, do Santos DA, Ferrer-Bolufer I, Luján CG, Alcalá OZ, García-Banacloy A, Cogollos VB, Juan CS. Reviewed and updated Algorithm for Genetic Characterization of Syndromic Obesity Phenotypes. Curr Genomics 2022; 23:147-162. [PMID: 36777005 PMCID: PMC9878830 DOI: 10.2174/1389202923666220426093436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/30/2021] [Accepted: 02/01/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Individuals with a phenotype of early-onset severe obesity associated with intellectual disability can have molecular diagnoses ranging from monogenic to complex genetic traits. Severe overweight is the major sign of a syndromic physical appearance and predicting the influence of a single gene and/or polygenic risk profile is extremely complicated among the majority of the cases. At present, considering rare monogenic bases as the principal etiology for the majority of obesity cases associated with intellectual disability is scientifically poor. The diversity of the molecular bases responsible for the two entities makes the appliance of the current routinely powerful genomics diagnostic tools essential. Objective: Clinical investigation of these difficult-to-diagnose patients requires pediatricians and neurologists to use optimized descriptions of signs and symptoms to improve genotype correlations. Methods: The use of modern integrated bioinformatics strategies which are conducted by experienced multidisciplinary clinical teams. Evaluation of the phenotype of the patient's family is also of importance. Results: The next step involves discarding the monogenic canonical obesity syndromes and considering infrequent unique molecular cases, and/or then polygenic bases. Adequate management of the application of the new technique and its diagnostic phases is essential for achieving good cost/efficiency balances. Conclusion: With the current clinical management, it is necessary to consider the potential coincidence of risk mutations for obesity in patients with genetic alterations that induce intellectual disability. In this review, we describe an updated algorithm for the molecular characterization and diagnosis of patients with a syndromic obesity phenotype.
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Affiliation(s)
- Raquel Rodríguez-López
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain;,Address correspondence to this author at the Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Avenida de las Tres Cruces no. 2 46014, Valencia, Spain; Tel: 0034 963 131 800 – 437317; Fax: 0034 963 131 979; E-mail:
| | - Fátima Gimeno-Ferrer
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - David Albuquerque do Santos
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Irene Ferrer-Bolufer
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Carola Guzmán Luján
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Otilia Zomeño Alcalá
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Amor García-Banacloy
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | | | - Carlos Sánchez Juan
- Endocrinology Service, General Hospital Consortium of Valencia, Valencia, Spain
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Genetic investigation of syndromic forms of obesity. Int J Obes (Lond) 2022; 46:1582-1586. [PMID: 35597848 DOI: 10.1038/s41366-022-01149-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Syndromic obesity (SO) refers to obesity with additional phenotypes, including intellectual disability (ID)/developmental delay (DD), dysmorphic features, or organ-specific abnormalities. SO is rare, has high phenotypic variability, and frequently follows a monogenic pattern of inheritance. However, the genetic etiology of most cases of SO has not been elucidated. SUBJECTS AND METHODS In this study, we investigated 20 SO patients by whole-exome sequencing (WES) trios to identify causal genetic variants. RESULTS 4/20 patients had negative results for array comparative genomic hybridization (aCGH) analyses. In the remaining 15 patients, in addition to SNVs and indels, CNVs were also evaluated. Pathogenic/likely pathogenic (P/LP) SNVs/indels were detected in 6/20 patients (involving MED13L, AHDC1, EHMT1, MYT1L, GRIA3, and SETD1A), while two patients carried an inherited VUS. In addition, P/LP CNVs were observed in 3/15 patients (involving SATG2, KIAA0442, and MEIS2). CONCLUSIONS All nine detected P/LP variants involved genes already known to lead to syndromic ID/DD; however, for only two genes (EHMT1 and MYT1L) is the link with obesity well established. This is the first study applying a comprehensive genomic investigation of an SO cohort, showing a high diagnostic yield (~47%). Additionally, our findings suggested that several known ID/DD genes may also predispose individuals to SO.
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Madeo SF, Stanghellini I, Predieri B, Ciancia S, Leo F, Bruzzi P, Calabrese O, Iughetti L. Copy Number Variation Analysis Increases the Number of Candidate Loci Associated with Pediatric Obesity. Horm Res Paediatr 2022; 94:251-262. [PMID: 34482307 DOI: 10.1159/000519299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/28/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Obesity is a multifactorial disease caused by the interaction of genetic, environmental, and behavioral factors. Currently, only a small number of obese children undergo genetic analysis, usually when obesity is associated with dysmorphic features. The aim of this study was to identify genomic rearrangement causing obesity. METHODS We analyzed the DNA of children and adolescents by single-nucleotide polymorphism-array (platform CytoScan HD, Affymetrix). Patients included in this study were obese with dysmorphic features and/or intellectual disabilities and/or neuropsychomotor signs. RESULTS Ninety-four children and adolescents with obesity (9.25 ± 4.04 years old, 60 males) were enrolled in the study. Dysmorphic features were found in 64 out of 94 subjects (68.1%), intellectual disability was found in 23 subjects (24.5%), and other neuropsychomotor signs in 31 (32.9%). Copy number variations (CNVs) were identified in 43 out of 94 patients (45.7%): among these 14 subjects showed at least 1 deletion, 22 duplication, whereas 7 patients showed both deletion and duplication. In 20 subjects (13 males), CNVs were linked or possibly related with obesity; in 23 subjects, this correlation cannot be inferred. CONCLUSION A genetic origin of obesity was detected in about half of our obese children and adolescents with associated dysmorphic features and/or intellectual disability and/or neuropsychomotor signs. In these children, array-CGH analysis can be useful to identify causative genetic mutations, with consequent advantage in therapeutic management and follow-up of these patients.
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Affiliation(s)
- Simona Filomena Madeo
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Ilaria Stanghellini
- Medical Genetics Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Barbara Predieri
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvia Ciancia
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Francesco Leo
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Patrizia Bruzzi
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Olga Calabrese
- Medical Genetics Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Lorenzo Iughetti
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
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Loid P, Pekkinen M, Mustila T, Tossavainen P, Viljakainen H, Lindstrand A, Mäkitie O. Targeted Exome Sequencing of Genes Involved in Rare CNVs in Early-Onset Severe Obesity. Front Genet 2022; 13:839349. [PMID: 35330733 PMCID: PMC8940233 DOI: 10.3389/fgene.2022.839349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/07/2022] [Indexed: 11/17/2022] Open
Abstract
Context: Rare copy number variants (CNVs) have been associated with the development of severe obesity. However, the potential disease-causing contribution of individual genes within the region of CNVs is often not known. Objective: Screening of rare variants in genes involved in CNVs in Finnish patients with severe early-onset obesity to find candidate genes linked to severe obesity. Methods: Custom-made targeted exome sequencing panel to search for rare (minor allele frequency <0.1%) variants in genes affected by previously identified CNVs in 92 subjects (median age 14 years) with early-onset severe obesity (median body mass index (BMI) Z-score + 4.0). Results: We identified thirteen rare heterozygous variants of unknown significance in eleven subjects in twelve of the CNV genes. Two rare missense variants (p.Pro405Arg and p.Tyr232Cys) were found in SORCS1, a gene highly expressed in the brain and previously linked to diabetes risk. Four rare variants were in genes in the proximal 16p11.2 region (a frameshift variant in TAOK2 and missense variants in SEZ6L2, ALDOA and KIF22) and three rare missense variants were in genes in the 22q11.21 region (AIFM3, ARVCF and KLHL22). Conclusion: We report several rare variants in CNV genes in subjects with childhood obesity. However, the role of the individual genes in the previously identified rare CNVs to development of obesity remains uncertain. More studies are needed to understand the potential role of the specific genes within obesity associated CNVs.
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Affiliation(s)
- Petra Loid
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Genetics Research Program, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Minna Pekkinen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Genetics Research Program, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Taina Mustila
- City of Turku Wellfare Services, Diabetes Care, Turku, Finland
| | - Päivi Tossavainen
- Department of Pediatrics, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Heli Viljakainen
- Folkhälsan Research Center, Genetics Research Program, Helsinki, Finland.,Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Genetics Research Program, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Konger RL, Derr-Yellin E, Zimmers TA, Katona T, Xuei X, Liu Y, Zhou HM, Simpson ER, Turner MJ. Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin. Int J Mol Sci 2021; 22:ijms22168634. [PMID: 34445339 PMCID: PMC8395473 DOI: 10.3390/ijms22168634] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/10/2023] Open
Abstract
Both agonist studies and loss-of-function models indicate that PPARγ plays an important role in cutaneous biology. Since PPARγ has a high level of basal activity, we hypothesized that epidermal PPARγ would regulate normal homeostatic processes within the epidermis. In this current study, we performed mRNA sequencing and differential expression analysis of epidermal scrapings from knockout mice and wildtype littermates. Pparg-/-epi mice exhibited a 1.5-fold or greater change in the expression of 11.8% of 14,482 identified transcripts. Up-regulated transcripts included those for a large number of cytokines/chemokines and their receptors, as well as genes associated with inflammasome activation and keratinization. Several of the most dramatically up-regulated pro-inflammatory genes in Pparg-/-epi mouse skin included Igfl3, 2610528A11Rik, and Il1f6. RT-PCR was performed from RNA obtained from non-lesional full-thickness skin and verified a marked increase in these transcripts, as well as transcripts for Igflr1, which encodes the receptor for Igfl3, and the 2610528A11Rik receptor (Gpr15). Transcripts for Il4 were detected in Pparg-/-epi mouse skin, but transcripts for Il17 and Il22 were not detected. Down-regulated transcripts included sebaceous gland markers and a number of genes associated with lipid barrier formation. The change in these transcripts correlates with an asebia phenotype, increased transepidermal water loss, alopecia, dandruff, and the appearance of spontaneous inflammatory skin lesions. Histologically, non-lesional skin showed hyperkeratosis, while inflammatory lesions were characterized by dermal inflammation and epidermal acanthosis, spongiosis, and parakeratosis. In conclusion, loss of epidermal Pparg alters a substantial set of genes that are associated with cutaneous inflammation, keratinization, and sebaceous gland function. The data indicate that epidermal PPARγ plays an important role in homeostatic epidermal function, particularly epidermal differentiation, barrier function, sebaceous gland development and function, and inflammatory signaling.
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Affiliation(s)
- Raymond L. Konger
- Department of Pathology & Laboratory Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA; (E.D.-Y.); (T.K.)
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- The Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (T.A.Z.); (Y.L.)
- Correspondence: ; Tel.: +1-317-274-4154
| | - Ethel Derr-Yellin
- Department of Pathology & Laboratory Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA; (E.D.-Y.); (T.K.)
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Teresa A. Zimmers
- The Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (T.A.Z.); (Y.L.)
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Terrence Katona
- Department of Pathology & Laboratory Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA; (E.D.-Y.); (T.K.)
| | - Xiaoling Xuei
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Yunlong Liu
- The Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (T.A.Z.); (Y.L.)
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Hong-Ming Zhou
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (H.-M.Z.); (M.J.T.)
| | - Ed Ronald Simpson
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (H.-M.Z.); (M.J.T.)
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Matthew J. Turner
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (H.-M.Z.); (M.J.T.)
- Department of Dermatology, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA
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11
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A novel MYT1L mutation in a boy with syndromic obesity: Case report and literature review. Obes Res Clin Pract 2021; 15:124-132. [PMID: 33622623 DOI: 10.1016/j.orcp.2021.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/26/2020] [Accepted: 01/01/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Pathogenic variants involving the MYT1L gene lead to an autosomal dominant form of syndromic obesity, characterized by polyphagia, intellectual disability/developmental delay, and behavioral problems, and that a characteristic facial phenotype does not seem to be recognizable. METHODS Trio whole exome sequencing was performed in a 10-year-old Brazilian male presenting polyphagia, severe early-onset obesity, intellectual disability, speech delay, macrocephaly, frontal bossing, telecanthus, strabismus, and hypogenitalism. Additionally, we performed a literature review of patients carrying non-copy number MYT1L variants. RESULTS A de novo genetic variant not previously reported in MYT1L (NM_015025.4:c.2990C>A) was identified in the proband and classified as pathogenic. From a literature search, 22 further patients carrying non-copy number MYT1L variants were identified, evidencing that although the associated phenotype is quite variable, intellectual disability/developmental and speech delays are always present. Further, most patients have obesity or overweight due to polyphagia. Macrocephaly, strabismus, behavioral problems, and hand/feet malformations are also recurrent features. CONCLUSIONS We described the first Brazilian case of MYT1L related syndrome and highlighted clinical characteristics based on the literature. Other syndromic forms of obesity such as Prader-Willi, Bardet-Biedl, Börjeson-Forssman-Lehmann, MORM, Cohen, Alstrom, and Kleefstra type 1 syndromes should be considered in the differential diagnosis. Further, although obesity is frequent, it is not an obligatory feature of all carriers of MYT1L mutations.
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12
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Conditional and unconditional genome-wide association study reveal complicate genetic architecture of human body weight and impacts of smoking. Sci Rep 2020; 10:12136. [PMID: 32699216 PMCID: PMC7376032 DOI: 10.1038/s41598-020-68935-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
To reveal the impacts of smoking on genetic architecture of human body weight, we conducted a genome-wide association study on 5,336 subjects in four ethnic populations from MESA (The Multi-Ethnic Study of Atherosclerosis) data. A full genetic model was applied to association mapping for analyzing genetic effects of additive, dominance, epistasis, and their ethnicity-specific effects. Both the unconditional model (base) and conditional model including smoking as a cofactor were investigated. There were 10 SNPs involved in 96 significant genetic effects detected by the base model, which accounted for a high heritability (61.78%). Gene ontology analysis revealed that a number of genetic factors are related to the metabolic pathway of benzopyrene, a main compound in cigarettes. Smoking may play important roles in genetic effects of dominance, dominance-related epistasis, and gene-ethnicity interactions on human body weight. Gene effect prediction shows that the genetic effects of smoking cessation on body weight vary from different populations.
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13
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Cheng W, Ramachandran S, Crawford L. Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits. PLoS Genet 2020; 16:e1008855. [PMID: 32542026 PMCID: PMC7316356 DOI: 10.1371/journal.pgen.1008855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/25/2020] [Accepted: 05/13/2020] [Indexed: 12/22/2022] Open
Abstract
Traditional univariate genome-wide association studies generate false positives and negatives due to difficulties distinguishing associated variants from variants with spurious nonzero effects that do not directly influence the trait. Recent efforts have been directed at identifying genes or signaling pathways enriched for mutations in quantitative traits or case-control studies, but these can be computationally costly and hampered by strict model assumptions. Here, we present gene-ε, a new approach for identifying statistical associations between sets of variants and quantitative traits. Our key insight is that enrichment studies on the gene-level are improved when we reformulate the genome-wide SNP-level null hypothesis to identify spurious small-to-intermediate SNP effects and classify them as non-causal. gene-ε efficiently identifies enriched genes under a variety of simulated genetic architectures, achieving greater than a 90% true positive rate at 1% false positive rate for polygenic traits. Lastly, we apply gene-ε to summary statistics derived from six quantitative traits using European-ancestry individuals in the UK Biobank, and identify enriched genes that are in biologically relevant pathways.
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Affiliation(s)
- Wei Cheng
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SR); (LC)
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Department of Biostatistics, Brown University, Providence, Rhode Island, United States of America
- Center for Statistical Sciences, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SR); (LC)
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14
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González JR, Ruiz-Arenas C, Cáceres A, Morán I, López-Sánchez M, Alonso L, Tolosana I, Guindo-Martínez M, Mercader JM, Esko T, Torrents D, González J, Pérez-Jurado LA. Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases. Am J Hum Genet 2020; 106:846-858. [PMID: 32470372 DOI: 10.1016/j.ajhg.2020.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/28/2020] [Indexed: 11/25/2022] Open
Abstract
The burden of several common diseases including obesity, diabetes, hypertension, asthma, and depression is increasing in most world populations. However, the mechanisms underlying the numerous epidemiological and genetic correlations among these disorders remain largely unknown. We investigated whether common polymorphic inversions underlie the shared genetic influence of these disorders. We performed an inversion association analysis including 21 inversions and 25 obesity-related traits on a total of 408,898 Europeans and validated the results in 67,299 independent individuals. Seven inversions were associated with multiple diseases while inversions at 8p23.1, 16p11.2, and 11q13.2 were strongly associated with the co-occurrence of obesity with other common diseases. Transcriptome analysis across numerous tissues revealed strong candidate genes for obesity-related traits. Analyses in human pancreatic islets indicated the potential mechanism of inversions in the susceptibility of diabetes by disrupting the cis-regulatory effect of SNPs from their target genes. Our data underscore the role of inversions as major genetic contributors to the joint susceptibility to common complex diseases.
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15
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Tian F, Tang P, Sun Z, Zhang R, Zhu D, He J, Liao J, Wan Q, Shen J. miR-210 in Exosomes Derived from Macrophages under High Glucose Promotes Mouse Diabetic Obesity Pathogenesis by Suppressing NDUFA4 Expression. J Diabetes Res 2020; 2020:6894684. [PMID: 32258168 PMCID: PMC7106924 DOI: 10.1155/2020/6894684] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Type 2 diabetes mellitus (T2DM) is featured by insulin resistance and lipid metabolism dysregulation. A large number of miRNAs were identified in exosomes derived from adipose tissue macrophages associated with T2DM pathogenesis, but its pathogenic roles remain unknown. This study is aimed at investigating the function of miR-210 in diabetic obesity. METHODS Exosomes from mouse macrophage RAW264.7 cells were characterized by electron microscopy, combined with biomarker expression by western blot. Expression of miR-210 was determined by quantitative RT-PCR. Glucose uptake was measured by a fluorometric method, and the mitochondrial respiratory chain activity was evaluated by ELISA. The target gene of miR-210 was validated by dual-luciferase reporter and pull-down assays. A mouse obese diabetic model was established by a high-fat diet and streptozocin treatment. RESULTS miR-210 was highly expressed in exosomes derived from high glucose-induced macrophage RAW264.7 cells. Macrophage-derived exosomes impaired glucose uptake and mitochondrial CIV complex activity and suppressed NADH dehydrogenase ubiquinone 1 alpha subcomplex 4 (NDUFA4) expression in 3T3-L1 adipocytes. miR-210 directly bind with mRNA sequences of NDUFA4 gene. Inhibition of miR-210 mitigated the effects of macrophage-derived exosomes on the glucose uptake and complex IV (CIV) activity in 3T3-L1 adipocytes, and NDUFA4 overexpression offset the inhibition of glucose uptake and CIV activity by macrophage-derived exosomes. Furthermore, mice with miR-210 knockout showed greatly repressed diabetic obesity development. CONCLUSION miR-210 derived from adipose tissue macrophages promotes mouse obese diabetes pathogenesis by regulating glucose uptake and mitochondrial CIV activity through targeting NDUFA4 gene expression.
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Affiliation(s)
- Feng Tian
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Ping Tang
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Zhilian Sun
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Ruifen Zhang
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Danhua Zhu
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Junying He
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Jixing Liao
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Qinghua Wan
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Jie Shen
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, China
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16
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Kaelberer MM, Caceres AI, Jordt SE. Activation of a nerve injury transcriptional signature in airway-innervating sensory neurons after lipopolysaccharide-induced lung inflammation. Am J Physiol Lung Cell Mol Physiol 2020; 318:L953-L964. [PMID: 32159971 DOI: 10.1152/ajplung.00403.2019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The lungs and the immune and nervous systems functionally interact to respond to respiratory environmental exposures and infections. The lungs are innervated by vagal sensory neurons of the jugular and nodose ganglia, fused together in smaller mammals as the jugular-nodose complex (JNC). Whereas the JNC shares properties with the other sensory ganglia, the trigeminal (TG) and dorsal root ganglia (DRG), these sensory structures express differential sets of genes that reflect their unique functionalities. Here, we used RNA sequencing (RNA-seq) in mice to identify the differential transcriptomes of the three sensory ganglia types. Using a fluorescent retrograde tracer and fluorescence-activated cell sorting, we isolated a defined population of airway-innervating JNC neurons and determined their differential transcriptional map after pulmonary exposure to lipopolysaccharide (LPS), a major mediator of acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) after infection with gram-negative bacteria or inhalation of organic dust. JNC neurons activated an injury response program, leading to increased expression of gene products such as the G protein-coupled receptor Cckbr, inducing functional changes in neuronal sensitivity to peptides, and Gpr151, also rapidly induced upon neuropathic nerve injury in pain models. Unique JNC-specific transcripts, present at only minimal levels in TG, DRG, and other organs, were identified. These included TMC3, encoding for a putative mechanosensor, and urotensin 2B, a hypertensive peptide. These findings highlight the unique properties of the JNC and reveal that ALI/ARDS rapidly induces a nerve injury-related state, changing vagal excitability.
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Affiliation(s)
| | - Ana Isabel Caceres
- Department of Anesthesiology, Duke University School of Medicine, Durham, North Carolina
| | - Sven-Eric Jordt
- Department of Anesthesiology, Duke University School of Medicine, Durham, North Carolina.,Department of Pharmacology and Cancer Biology, Duke University School of Medicine. Durham, North Carolina.,Integrated Toxicology and Environmental Health Program (ITEHP), Duke University, Durham, North Carolina
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17
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Neurodevelopmental phenotype associated with CHD8-SUPT16H duplication. Neurogenetics 2019; 21:67-72. [PMID: 31823155 DOI: 10.1007/s10048-019-00599-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/27/2019] [Indexed: 12/31/2022]
Abstract
Microdeletions encompassing 14q11.2 locus, involving SUPT16H and CHD8, were shown to cause developmental delay, intellectual disability, autism spectrum disorders and macrocephaly. Variations leading to CHD8 haploinsufficiency or loss of function were also shown to lead to a similar phenotype. Recently, a 14q11.2 microduplication syndrome, encompassing CHD8 and SUPT16H, has been described, highlighting the importance of a tight control of at least CHD8 gene-dosage for a normal development. There have been only a few reports of 14q11.2 microduplications. Patients showed variable neurodevelopmental issues of variable severity. Breakpoints of the microduplications were non-recurrent, making interpretation of the CNV and determination of their clinical relevance difficult. Here, we report on two patients with 14q11.2 microduplication encompassing CHD8 and SUPT16H, one of whom had normal intelligence. Review of previous reports describing patients with comparable microduplications allowed for a more precise delineation of the condition and widening of the phenotypic spectrum.
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18
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Scudiero O, Pero R, Ranieri A, Terracciano D, Fimiani F, Cesaro A, Gentile L, Leggiero E, Laneri S, Moscarella E, Mazzaccara C, Frisso G, D'Alicandro G, Limongelli G, Pastore L, Calabrò P, Lombardo B. Childhood obesity: an overview of laboratory medicine, exercise and microbiome. Clin Chem Lab Med 2019; 58:1385-1406. [PMID: 31821163 DOI: 10.1515/cclm-2019-0789] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022]
Abstract
In the last few years, a significant increase of childhood obesity incidence unequally distributed within countries and population groups has been observed, thus representing an important public health problem associated with several health and social consequences. Obese children have more than a 50% probability of becoming obese adults, and to develop pathologies typical of obese adults, that include type 2-diabetes, dyslipidemia and hypertension. Also environmental factors, such as reduced physical activity and increased sedentary activities, may also result in increased caloric intake and/or decreased caloric expenditure. In the present review, we aimed to identify and describe a specific panel of parameters in order to evaluate and characterize the childhood obesity status useful in setting up a preventive diagnostic approach directed at improving health-related behaviors and identifying predisposing risk factors. An early identification of risk factors for childhood obesity could definitely help in setting up adequate and specific clinical treatments.
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Affiliation(s)
- Olga Scudiero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Naples "Federico II", Napoli, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Raffaela Pero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Naples "Federico II", Napoli, Italy
| | - Annaluisa Ranieri
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Naples "Federico II", Napoli, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Daniela Terracciano
- Dipartimento di Scienze Mediche Traslazionali, Università degli Studi di Naples "Federico II", Napoli, Italy
| | - Fabio Fimiani
- Divisione di Cardiologia, Dipartimento di Scienze Cardiotoraciche e Respiratorie, Università della Campania "Luigi Vanvitelli", Naples, Italy
| | - Arturo Cesaro
- Divisione di Cardiologia, Dipartimento di Scienze Cardiotoraciche e Respiratorie, Università della Campania "Luigi Vanvitelli", Naples, Italy
| | | | | | - Sonia Laneri
- Dipartimento di Farmacia, Università degli Studi di Naples "Federico II", Napoli, Italy
| | - Elisabetta Moscarella
- Dipartimento di Scienze Mediche Traslazionali, Università della Campania "Luigi Vanvitelli", Caserta, Italy.,Unità di Cardiologia, Ospedale "Sant'Anna e San Sebastiano", Caserta, Italy
| | - Cristina Mazzaccara
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Naples "Federico II", Napoli, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Giulia Frisso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Naples "Federico II", Napoli, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Giovanni D'Alicandro
- Centro di Medicina dello Sport e delle Disabilità, Dipartimento di Neuroscienze e Riabilitazione, AORN, Santobono-Pausillipon, Naples, Italy
| | - Giuseppe Limongelli
- Dipartimento di Scienze Mediche Traslazionali, Università della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Lucio Pastore
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Naples "Federico II", Napoli, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Paolo Calabrò
- Dipartimento di Scienze Mediche Traslazionali, Università della Campania "Luigi Vanvitelli", Caserta, Italy.,Unità di Cardiologia, Ospedale "Sant'Anna e San Sebastiano", Caserta, Italy
| | - Barbara Lombardo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Naples "Federico II", Napoli, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
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19
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Micleaa D, Al-Khzouza C, Osan S, Bucerzan S, Cret V, Popp RA, Puiu M, Chirita-Emandi A, Zimbru C, Ghervan C. Genomic study via chromosomal microarray analysis in a group of Romanian patients with obesity and developmental disability/intellectual disability. J Pediatr Endocrinol Metab 2019; 32:667-674. [PMID: 31150357 DOI: 10.1515/jpem-2018-0439] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/01/2019] [Indexed: 01/29/2023]
Abstract
Background Obesity with developmental disability/intellectual disability (DD/ID) is the most common association in syndromic obesity. Genomic analysis studies have allowed the decipherment of disease aetiology, both in cases of syndromic obesity as well as in cases of isolated or syndromic DD/ID. However, more data are needed to further elucidate the link between the two. The aim of this pangenomic study was to use single nucleotide polymorphism (SNP) array technology to determine the copy number variant (CNV) type and frequency associated with both obesity and DD/ID. Methods Thirty-six patients were recruited from the Clinical Emergency Hospital for Children, in Cluj-Napoca, Romania during the period 2015-2017. The main inclusion criterion was a diagnosis that included both obesity and DD/ID. Genomic analysis via SNP array technology was performed. Results Out of the 36 patients, 12 (33%) presented CNVs with a higher degree of pathogenicity (A group) and 24 (66%) presented benign CNVs (B group). The SNP array results for the A group were as follows: pathogenic CNVs in 8/12 patients (67%); variants of unknown significance (VOUS) in 2/12 patients (16%); and uniparental disomy (UPD) in 2/12 patients (16%). Conclusions Some of these CNVs have already been observed in patients with both obesity and DD/ID, but the others were noticed only in DD/ID patients and have not been described until now in association with obesity.
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Affiliation(s)
- Diana Micleaa
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Clinical Emergency Hospital for Children, Cluj-Napoca, Romania
| | - Camelia Al-Khzouza
- Clinical Emergency Hospital for Children, Cluj-Napoca, Romania.,Department of Pediatrics 1, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Sergiu Osan
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Simona Bucerzan
- Clinical Emergency Hospital for Children, Cluj-Napoca, Romania.,Department of Pediatrics 1, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Victoria Cret
- Clinical Emergency Hospital for Children, Cluj-Napoca, Romania
| | - Radu Anghel Popp
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Maria Puiu
- "Victor Babeş" University of Medicine and Pharmacy, Timişoara, Romania
| | | | - Cristian Zimbru
- "Victor Babeş" University of Medicine and Pharmacy, Timişoara, Romania
| | - Cristina Ghervan
- Department of Endocrinology, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,County Clinical Emergency Hospital, Cluj-Napoca, Romania
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20
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21
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The effect of copy number variations in chromosome 16p on body weight in patients with intellectual disability. J Hum Genet 2018; 64:221-231. [PMID: 30518945 DOI: 10.1038/s10038-018-0545-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/17/2018] [Accepted: 11/08/2018] [Indexed: 12/14/2022]
Abstract
Syndromic monogenic obesity is a rare and severe early-onset form of obesity. It is characterized by intellectual disability, congenital malformations, and/or dysmorphic facies. The diagnosis of patients is challenging due to the genetic heterogenicity of this condition. However, the use of microarray technology in combination with public databases has been successful on genotype-phenotype correlations, especially for body mass index (BMI) alteration. In this study, the relationship between copy number variations (CNVs) detected by microarray mapping on 16p region and BMI alterations in syndromic patients were assessed. In order to achieve this goal, 680 unrelated Spanish children with intellectual disability were included. 16p region was characterized by using microarray platforms. All detected variants were classified as: (I) one previously non-described 10-Mb duplication in 16p13.2p12.3 region considered causal of intellectual disability and severe overweight, and (II) eleven 16p11.2 CNVs of low prevalence but with recurrence in syndromic patients with severe BMI alteration (nine proximal and two distal). Proximal 16p11.2 CNVs have a dose-dependent effect: underweight in carriers of duplication and obesity in carriers of deletion. KCTD13 was identified as a possible candidate gene for BMI alteration on proximal syndromes, whereas SH2B1 gene was identified as candidate for distal syndromes. The results shown in this paper suggest that syndromic patients could constitute a reliable model to evaluate hypothalamic satiety and obesity disorders as well as generate a wide expectation for primary prevention of comorbidities. Furthermore, 16p13.2p12.3 showed to be an important region on the regulation of body fatness.
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22
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Selvanayagam T, Walker S, Gazzellone MJ, Kellam B, Cytrynbaum C, Stavropoulos DJ, Li P, Birken CS, Hamilton J, Weksberg R, Scherer SW. Genome-wide copy number variation analysis identifies novel candidate loci associated with pediatric obesity. Eur J Hum Genet 2018; 26:1588-1596. [PMID: 29976977 PMCID: PMC6189095 DOI: 10.1038/s41431-018-0189-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 04/10/2018] [Accepted: 05/15/2018] [Indexed: 12/23/2022] Open
Abstract
Obesity is a multifactorial condition that is highly heritable. There have been ~60 susceptibility loci identified, but they only account for a fraction of cases. As copy number variations (CNVs) have been implicated in the etiology of a multitude of human disorders including obesity, here, we investigated the contribution of rare (<1% population frequency) CNVs in pediatric cases of obesity. We genotyped 67 such individuals, including 22 with co-morbid developmental delay and prioritized rare CNVs at known obesity-associated loci, as well as, those impacting genes involved in energy homeostasis or related processes. We identified clinically relevant or potentially clinically relevant CNVs in 15% (10/67) of individuals. Of these, 4% (3/67) had 16p11.2 microdeletions encompassing the known obesity risk gene SH2B1. Notably, we identified two unrelated probands harboring different 6p22.2 microduplications encompassing SCGN, a potential novel candidate gene for obesity. Further, we identified other biologically relevant candidate genes for pediatric obesity including ARID5B, GPR39, PTPRN2, and HNF4G. We found previously reported candidate loci for obesity, and new ones, suggesting CNV analysis may assist in the diagnosis of pediatric obesity.
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Affiliation(s)
- Thanuja Selvanayagam
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Susan Walker
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Matthew J Gazzellone
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Barbara Kellam
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Cheryl Cytrynbaum
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Dimitri J Stavropoulos
- Department of Pediatric Laboratory Medicine, Genome Diagnostics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ping Li
- Division of Endocrinology, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Catherine S Birken
- Division of Pediatric Medicine, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Jill Hamilton
- Division of Endocrinology, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada.
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada.
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23
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Tang J, Fang Q, Shao R, Shen J, He J, Niu D, Lu L. Digital gene-expression profiling analysis of the fatty liver of Landes geese fed different supplemental oils. Gene 2018; 673:32-45. [DOI: 10.1016/j.gene.2018.05.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/08/2018] [Accepted: 05/31/2018] [Indexed: 01/18/2023]
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Ceylan AC, Citli S, Erdem HB, Sahin I, Acar Arslan E, Erdogan M. Importance and usage of chromosomal microarray analysis in diagnosing intellectual disability, global developmental delay, and autism; and discovering new loci for these disorders. Mol Cytogenet 2018; 11:54. [PMID: 30258496 PMCID: PMC6154794 DOI: 10.1186/s13039-018-0402-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/17/2018] [Indexed: 02/06/2023] Open
Abstract
Background Chromosomal microarray analysis is a first-stage test that is used for the diagnosis of intellectual disability and global developmental delay. Chromosomal microarray analysis can detect well-known microdeletion syndromes. It also contributes to the identification of genes that are responsible for the phenotypes in the new copy number variations. Results Chromosomal microarray analysis was conducted on 124 patients with intellectual disability and global developmental delay. Multiplex ligation-dependent probe amplification was used for the confirmation of chromosome 22q11.2 deletion/duplication. 26 pathogenic and likely pathogenic copy number variations were detected in 23 patients (18.55%) in a group of 124 Turkish patients with intellectual disability and global developmental delay. Chromosomal microarray analysis revealed pathogenic de novo Copy number variations, such as a novel 2.9-Mb de novo deletion at 18q22 region with intellectual disability and autism spectrum disorder, and a 22q11.2 region homozygote duplication with new clinical features. Conclusion Our data expand the spectrum of 22q11.2 region mutations, reveal new loci responsible from autism spectrum disorder and provide new insights into the genotype–phenotype correlations of intellectual disability and global developmental delay.
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Affiliation(s)
- Ahmet Cevdet Ceylan
- Trabzon Kanuni Training and Research Hospital, Medical Genetics Unit, Trabzon, Turkey.,2Ankara Yıldırım Beyazıt University, Ankara Atatürk Training and Research Hospital, Department of Medical Genetics, Ankara, Turkey
| | - Senol Citli
- Trabzon Kanuni Training and Research Hospital, Medical Genetics Unit, Trabzon, Turkey
| | - Haktan Bagis Erdem
- Ankara Diskapi Yildirim Beyazit Training and Research Hospital, Medical Genetics Unit, Ankara, Turkey
| | - Ibrahim Sahin
- Ankara Diskapi Yildirim Beyazit Training and Research Hospital, Medical Genetics Unit, Ankara, Turkey
| | - Elif Acar Arslan
- 4Karadeniz Technical University, School of Medicine, Department of Child Neurology, Trabzon, Turkey
| | - Murat Erdogan
- 5Kayseri Training and Research Hospital, Department of Medical Genetics, Kayseri, Turkey
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25
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Wolfe K, McQuillin A, Alesi V, Boudry Labis E, Cutajar P, Dallapiccola B, Dentici ML, Dieux‐Coeslier A, Duban‐Bedu B, Duelund Hjortshøj T, Goel H, Loddo S, Morrogh D, Mosca‐Boidron A, Novelli A, Olivier‐Faivre L, Parker J, Parker MJ, Patch C, Pelling AL, Smol T, Tümer Z, Vanakker O, van Haeringen A, Vanlerberghe C, Strydom A, Skuse D, Bass N. Delineating the psychiatric and behavioral phenotype of recurrent 2q13 deletions and duplications. Am J Med Genet B Neuropsychiatr Genet 2018; 177:397-405. [PMID: 29603867 PMCID: PMC6001478 DOI: 10.1002/ajmg.b.32627] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/01/2018] [Indexed: 12/21/2022]
Abstract
Recurrent deletions and duplications at the 2q13 locus have been associated with developmental delay (DD) and dysmorphisms. We aimed to undertake detailed clinical characterization of individuals with 2q13 copy number variations (CNVs), with a focus on behavioral and psychiatric phenotypes. Participants were recruited via the Unique chromosomal disorder support group, U.K. National Health Service Regional Genetics Centres, and the DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources (DECIPHER) database. A review of published 2q13 patient case reports was undertaken to enable combined phenotypic analysis. We present a new case series of 2q13 CNV carriers (21 deletion, 4 duplication) and the largest ever combined analysis with data from published studies, making a total of 54 deletion and 23 duplication carriers. DD/intellectual disabilities was identified in the majority of carriers (79% deletion, 70% duplication), although in the new cases 52% had an IQ in the borderline or normal range. Despite the median age of the new cases being only 9 years, 64% had a clinical psychiatric diagnosis. Combined analysis found attention deficit hyperactivity disorder (ADHD) to be the most frequent diagnosis (48% deletion, 60% duplication), followed by autism spectrum disorders (33% deletion, 17% duplication). Aggressive (33%) and self-injurious behaviors (33%) were also identified in the new cases. CNVs at 2q13 are typically associated with DD with mildly impaired intelligence, and a high rate of childhood psychiatric diagnoses-particularly ADHD. We have further characterized the clinical phenotype related to imbalances of the 2q13 region and identified it as a region of interest for the neurobiological investigation of ADHD.
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Affiliation(s)
- Kate Wolfe
- Molecular Psychiatry Laboratory, Division of PsychiatryUniversity College LondonLondonUnited Kingdom
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of PsychiatryUniversity College LondonLondonUnited Kingdom
| | - Viola Alesi
- Medical Genetics Unit, Medical Genetics LaboratoryBambino Gesù Pediatric Hospital, IRCCSRomeItaly
| | | | - Peter Cutajar
- Nottinghamshire Healthcare NHS Foundation TrustNottinghamUnited Kingdom
| | - Bruno Dallapiccola
- Medical Genetics Unit, Medical Genetics LaboratoryBambino Gesù Pediatric Hospital, IRCCSRomeItaly
| | - Maria Lisa Dentici
- Medical Genetics Unit, Medical Genetics LaboratoryBambino Gesù Pediatric Hospital, IRCCSRomeItaly
| | - Anne Dieux‐Coeslier
- Service de génétique clinique, CHU LilleLilleFrance
- EA7364, RADEME, Université de LilleLilleFrance
| | | | - Tina Duelund Hjortshøj
- Kennedy Center, Department of Clinical GeneticsCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
| | - Himanshu Goel
- Hunter GeneticsWaratahNew South WalesAustralia
- University of NewcastleCallaghanNew South WalesAustralia
| | - Sara Loddo
- Medical Genetics Unit, Medical Genetics LaboratoryBambino Gesù Pediatric Hospital, IRCCSRomeItaly
| | - Deborah Morrogh
- North East Thames Regional Genetics Service LaboratoryLondonUnited Kingdom
| | | | - Antonio Novelli
- Medical Genetics Unit, Medical Genetics LaboratoryBambino Gesù Pediatric Hospital, IRCCSRomeItaly
| | - Laurence Olivier‐Faivre
- Centre de référence Anomalies du développement et Syndromes malformatifs, FHU TRANSLADCHU DijonFrance
| | - Jennifer Parker
- North East Thames Regional Genetics Service LaboratoryLondonUnited Kingdom
| | - Michael J. Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western BankSheffieldUnited Kingdom
| | - Christine Patch
- King's College London, Florence Nightingale Faculty of Nursing and MidwiferyLondonUnited Kingdom
- Genomics England, Dawson Hall, Charterhouse SquareLondonUnited Kingdom
| | - Anna L. Pelling
- Information Officer, Unique – The Rare Chromosome Disorder Support Group (www.rarechromo.org), The Stables, Station Road WestOxted, SurreyUnited Kingdom
| | - Thomas Smol
- Institut de génétique médicale, CHU LilleLilleFrance
- EA7364, RADEME, Université de LilleLilleFrance
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical GeneticsCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
| | - Olivier Vanakker
- Center for Medical GeneticsGhent University HospitalGhentBelgium
| | - Arie van Haeringen
- Department of Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Clémence Vanlerberghe
- Service de génétique clinique, CHU LilleLilleFrance
- EA7364, RADEME, Université de LilleLilleFrance
| | - Andre Strydom
- Molecular Psychiatry Laboratory, Division of PsychiatryUniversity College LondonLondonUnited Kingdom
- Department of Forensic and Neurodevelopmental ScienceInstitute of Psychiatry, Psychology and Neuroscience, Kings College LondonLondonUnited Kingdom
| | - David Skuse
- Behavioural and Brain Sciences UnitInstitute of Child Health, University College LondonLondonUnited Kingdom
| | - Nick Bass
- Molecular Psychiatry Laboratory, Division of PsychiatryUniversity College LondonLondonUnited Kingdom
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An atypical autistic phenotype associated with a 2q13 microdeletion: a case report. J Med Case Rep 2018; 12:79. [PMID: 29549886 PMCID: PMC5857311 DOI: 10.1186/s13256-018-1620-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/20/2018] [Indexed: 11/19/2022] Open
Abstract
Background Autism spectrum disorders are serious neurodevelopmental disorders that affect approximately 1% of the population. These disorders are substantially influenced by genetics. Several recent linkage analyses have examined copy number variations associated with autism risk. Microdeletion of the 2q13 region is considered a pathogenic copy number variation. This microdeletion is involved in developmental delays, congenital heart defects, dysmorphism, and various psychiatric disorders, including autism spectrum disorders. There are only 34 reported cases with this chromosomal deletion, and five cases of autism spectrum disorders have been identified among them. The autistic phenotype associated with this microdeletion has never been described. Case presentation We describe the case of a 44-month-old Caucasian girl with the 2q13 microdeletion and autism spectrum disorders with global development delay but no associated organ anomalies. We examined the autistic phenotype using different workups and observed an atypical phenotype defined by relatively preserved relational competency and imitation abilities. Conclusions The main contribution of this case report is the precise description of the autistic phenotype in the case of this deletion. We observed some atypical clinical features that could be markers of this genetic anomaly. We have discussed the pathophysiology of autism associated with this microdeletion and its incomplete penetrance and variable expressivity.
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27
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D’Angelo CS, Varela MC, de Castro CIE, Otto PA, Perez ABA, Lourenço CM, Kim CA, Bertola DR, Kok F, Garcia-Alonso L, Koiffmann CP. Chromosomal microarray analysis in the genetic evaluation of 279 patients with syndromic obesity. Mol Cytogenet 2018; 11:14. [PMID: 29441128 PMCID: PMC5800070 DOI: 10.1186/s13039-018-0363-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/22/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Syndromic obesity is an umbrella term used to describe cases where obesity occurs with additional phenotypes. It often arises as part of a distinct genetic syndrome with Prader-Willi syndrome being a classical example. These rare forms of obesity provide a unique source for identifying obesity-related genetic changes. Chromosomal microarray analysis (CMA) has allowed the characterization of new genetic forms of syndromic obesity, which are due to copy number variants (CNVs); however, CMA in large cohorts requires more study. The aim of this study was to characterize the CNVs detected by CMA in 279 patients with a syndromic obesity phenotype. RESULTS Pathogenic CNVs were detected in 61 patients (22%) and, among them, 35 had overlapping/recurrent CNVs. Genomic imbalance disorders known to cause syndromic obesity were found in 8.2% of cases, most commonly deletions of 1p36, 2q37 and 17p11.2 (5.4%), and we also detected deletions at 1p21.3, 2p25.3, 6q16, 9q34, 16p11.2 distal and proximal, as well as an unbalanced translocation resulting in duplication of the GNB3 gene responsible for a syndromic for of childhood obesity. Deletions of 9p terminal and 22q11.2 proximal/distal were found in 1% and 3% of cases, respectively. They thus emerge as being new putative obesity-susceptibility loci. We found additional CNVs in our study that overlapped with CNVs previously reported in cases of syndromic obesity, including a new case of 13q34 deletion (CHAMP1), bringing to 7 the number of patients in whom such defects have been described in association with obesity. Our findings implicate many genes previously associated with obesity (e.g. PTBP2, TMEM18, MYT1L, POU3F2, SIM1, SH2B1), and also identified other potentially relevant candidates including TAS1R3, ALOX5AP, and GAS6. CONCLUSION Understanding the genetics of obesity has proven difficult, and considerable insight has been obtained from the study of genomic disorders with obesity associated as part of the phenotype. In our study, CNVs known to be causal for syndromic obesity were detected in 8.2% of patients, but we provide evidence for a genetic basis of obesity in as many as 14% of cases. Overall, our results underscore the genetic heterogeneity in syndromic forms of obesity, which imposes a substantial challenge for diagnosis.
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Affiliation(s)
- Carla Sustek D’Angelo
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Monica Castro Varela
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Claudia Irene Emílio de Castro
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Paulo Alberto Otto
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
| | - Ana Beatriz Alvarez Perez
- Department of Morphology and Genetics, Paulista School of Medicine, Federal University of Sao Paulo (UNIFESP), Sao Paulo, SP Brazil
| | - Charles Marques Lourenço
- Neurogenetics Unit, Clinics Hospital of Ribeirao Preto, Faculty of Medicine, University of Sao Paulo, FMRP-USP, Ribeirao Preto, SP Brazil
| | - Chong Ae Kim
- Genetic Unit, Children’s Institute, Faculty of Medicine, University of Sao Paulo, FMUSP, Sao Paulo, SP Brazil
| | - Debora Romeo Bertola
- Genetic Unit, Children’s Institute, Faculty of Medicine, University of Sao Paulo, FMUSP, Sao Paulo, SP Brazil
| | - Fernando Kok
- Department of Neurology, Faculty of Medicine, University of Sao Paulo, FMUSP, Sao Paulo, SP Brazil
| | - Luis Garcia-Alonso
- Department of Morphology and Genetics, Paulista School of Medicine, Federal University of Sao Paulo (UNIFESP), Sao Paulo, SP Brazil
| | - Celia Priszkulnik Koiffmann
- Human Genome and Stem Cell Research Center (HUG-CELL), Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Rua do Matao no 277, Cidade Universitaria-Butanta, Sao Paulo, SP 05508-090 Brazil
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28
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Clinical significance of germline copy number variation in susceptibility of human diseases. J Genet Genomics 2018; 45:3-12. [PMID: 29396143 DOI: 10.1016/j.jgg.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 02/06/2023]
Abstract
Germline copy number variation (CNV) is considered to be an important form of human genetic polymorphisms. Previous studies have identified amounts of CNVs in human genome by advanced technologies, such as comparative genomic hybridization, single nucleotide genotyping, and high-throughput sequencing. CNV is speculated to be derived from multiple mechanisms, such as nonallelic homologous recombination (NAHR) and nonhomologous end-joining (NHEJ). CNVs cover a much larger genome scale than single nucleotide polymorphisms (SNPs), and may alter gene expression levels by means of gene dosage, gene fusion, gene disruption, and long-range regulation effects, thus affecting individual phenotypes and playing crucial roles in human pathogenesis. The number of studies linking CNVs with common complex diseases has increased dramatically in recent years. Here, we provide a comprehensive review of the current understanding of germline CNVs, and summarize the association of germline CNVs with the susceptibility to a wide variety of human diseases that were identified in recent years. We also propose potential issues that should be addressed in future studies.
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29
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Wang W, Jiang W, Hou L, Duan H, Wu Y, Xu C, Tan Q, Li S, Zhang D. Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI. BMC Genomics 2017; 18:872. [PMID: 29132311 PMCID: PMC5683603 DOI: 10.1186/s12864-017-4257-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 11/01/2017] [Indexed: 02/08/2023] Open
Abstract
Background The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) to identify significant genes and specific modules related to BMI based on gene expression profile data of 7 discordant monozygotic twins. Results In the differential gene expression analysis, it appeared that 32 differentially expressed genes (DEGs) were with a trend of up-regulation in twins with higher BMI when compared to their siblings. Categories of positive regulation of nitric-oxide synthase biosynthetic process, positive regulation of NF-kappa B import into nucleus, and peroxidase activity were significantly enriched within GO database and NF-kappa B signaling pathway within KEGG database. DEGs of NAMPT, TLR9, PTGS2, HBD, and PCSK1N might be associated with obesity. In the WGCNA, among the total 20 distinct co-expression modules identified, coral1 module (68 genes) had the strongest positive correlation with BMI (r = 0.56, P = 0.04) and disease status (r = 0.56, P = 0.04). Categories of positive regulation of phospholipase activity, high-density lipoprotein particle clearance, chylomicron remnant clearance, reverse cholesterol transport, intermediate-density lipoprotein particle, chylomicron, low-density lipoprotein particle, very-low-density lipoprotein particle, voltage-gated potassium channel complex, cholesterol transporter activity, and neuropeptide hormone activity were significantly enriched within GO database for this module. And alcoholism and cell adhesion molecules pathways were significantly enriched within KEGG database. Several hub genes, such as GAL, ASB9, NPPB, TBX2, IL17C, APOE, ABCG4, and APOC2 were also identified. The module eigengene of saddlebrown module (212 genes) was also significantly correlated with BMI (r = 0.56, P = 0.04), and hub genes of KCNN1 and AQP10 were differentially expressed. Conclusion We identified significant genes and specific modules potentially related to BMI based on the gene expression profile data of monozygotic twins. The findings may help further elucidate the underlying mechanisms of obesity development and provide novel insights to research potential gene biomarkers and signaling pathways for obesity treatment. Further analysis and validation of the findings reported here are important and necessary when more sample size is acquired. Electronic supplementary material The online version of this article (10.1186/s12864-017-4257-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Wenjie Jiang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Lin Hou
- Department of Biochemistry, Medical College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Haiping Duan
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China.,Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Shibei District, Qingdao, 266033, Shandong Province, People's Republic of China
| | - Yili Wu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China
| | - Chunsheng Xu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China.,Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Shibei District, Qingdao, 266033, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Shibei District, Qingdao, 266033, Shandong Province, People's Republic of China
| | - Qihua Tan
- Epidemiology, Biostatistics and Bio-demography, Institute of Public Health, University of Southern Denmark, DK-5000, Odense C, Denmark.,Human Genetics, Institute of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Shuxia Li
- Human Genetics, Institute of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, No. 38 Dengzhou Road, Shibei District, Qingdao, 266021, Shandong Province, People's Republic of China.
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30
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Breckpot J, Vercruyssen M, Weyts E, Vandevoort S, D'Haenens G, Van Buggenhout G, Leempoels L, Brischoux-Boucher E, Van Maldergem L, Renieri A, Mencarelli MA, D'Angelo C, Mericq V, Hoffer MJ, Tauber M, Molinas C, Castiglioni C, Brison N, Vermeesch JR, Danckaerts M, Sienaert P, Devriendt K, Vogels A. Copy number variation analysis in adults with catatonia confirms haploinsufficiency of SHANK3 as a predisposing factor. Eur J Med Genet 2016; 59:436-43. [PMID: 27519580 DOI: 10.1016/j.ejmg.2016.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/22/2016] [Accepted: 08/08/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Catatonia is a motor dysregulation syndrome co-occurring with a variety of psychiatric and medical disorders. Response to treatment with benzodiazepines and electroconvulsive therapy suggests a neurobiological background. The genetic etiology however remains largely unexplored. Copy Number Variants (CNV), known to predispose to neurodevelopmental disorders, may play a role in the etiology of catatonia. METHODS This study is exploring the genetic field of catatonia through CNV analysis in a cohort of psychiatric patients featuring intellectual disability and catatonia. Fifteen adults admitted to a psychiatric inpatient unit and diagnosed with catatonia were selected for array Comparative Genomic Hybridization analysis at 200 kb resolution. We introduced a CNV interpretation algorithm to define detected CNVs as benign, unclassified, likely pathogenic or causal with regard to catatonia. RESULTS Co-morbid psychiatric diagnoses in these patients were autism, psychotic or mood disorders. Eight patients were found to carry rare CNVs, which could not be classified as benign, comprising 6 duplications and 2 deletions. Microdeletions on 22q13.3, considered causal for catatonia, were detected in 2 patients. Duplications on 16p11.2 and 22q11.2 were previously implicated in psychiatric disorders, but not in catatonia, and were therefore considered likely pathogenic. Driven by the identification of a rare 14q11.2 duplication in one catatonic patient, additional patients with overlapping duplications were gathered to delineate a novel susceptibility locus for intellectual disability and psychiatric disorders on 14q11.2, harboring the gene SUPT16H. Three remaining variants respectively on 2q36.1, 16p13.13 and 17p13.3 were considered variants of unknown significance. CONCLUSION The identification of catatonia-related copy number changes in this study, underscores the importance of genetic research in patients with catatonia. We confirmed that 22q13.3 deletions, affecting the gene SHANK3, predispose to catatonia, and we uncover 14q11.2 duplications as a novel susceptibility factor for intellectual and psychiatric disorders.
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Affiliation(s)
- Jeroen Breckpot
- Center for Human Genetics, Catholic University Leuven, Leuven, Belgium
| | - Marieke Vercruyssen
- University Psychiatric Center KU Leuven, Catholic University of Leuven, Belgium
| | - Eddy Weyts
- St-Camillus Psychiatric Hospital, Bierbeek, Belgium
| | | | | | | | - Lore Leempoels
- University Psychiatric Center KU Leuven, Catholic University of Leuven, Belgium
| | | | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Policlinico Le Scotte, Siena, Italy; Medical Genetics, Azienda University Hospital, Siena, Italy
| | | | - Carla D'Angelo
- Human Genome and Stem Cell Center, University of Sao Paulo, Sao Paulo, Brazil
| | - Veronica Mericq
- Institute of Maternal and Child Research, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mariette J Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maithé Tauber
- Endocrinology Unit, Children's Hospital, CHU Toulouse, Reference Center for Prader-Willi Syndrome, INSERM UMR 1043, Paul Sabatier University, Toulouse, France
| | - Catherine Molinas
- Endocrinology Unit, Children's Hospital, CHU Toulouse, Reference Center for Prader-Willi Syndrome, INSERM UMR 1043, Paul Sabatier University, Toulouse, France.
| | - Claudia Castiglioni
- Unit of Neurology, Department of Pediatric Neurology, Clínica las Condes, Santiago, Chile
| | - Nathalie Brison
- Center for Human Genetics, Catholic University Leuven, Leuven, Belgium
| | - Joris R Vermeesch
- Center for Human Genetics, Catholic University Leuven, Leuven, Belgium
| | - Marina Danckaerts
- University Psychiatric Center KU Leuven, Catholic University of Leuven, Belgium
| | - Pascal Sienaert
- University Psychiatric Center KU Leuven, Catholic University of Leuven, Belgium
| | | | - Annick Vogels
- Center for Human Genetics, Catholic University Leuven, Leuven, Belgium.
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31
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Promoter polymorphisms of NDUFA4 gene were associated with prostate enlargement of benign prostatic hyperplasia. Mol Cell Toxicol 2016. [DOI: 10.1007/s13273-015-0042-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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32
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Ellis KL, Zhou Y, Rodriguez-Murillo L, Beshansky JR, Ainehsazan E, Selker HP, Huggins GS, Cupples LA, Peter I. Common variants associated with changes in levels of circulating free fatty acids after administration of glucose–insulin–potassium (GIK) therapy in the IMMEDIATE trial. THE PHARMACOGENOMICS JOURNAL 2015; 17:76-83. [DOI: 10.1038/tpj.2015.84] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/30/2015] [Accepted: 11/02/2015] [Indexed: 12/31/2022]
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Differential Associations between CDH13 Genotypes, Adiponectin Levels, and Circulating Levels of Cellular Adhesive Molecules. Mediators Inflamm 2015; 2015:635751. [PMID: 26600672 PMCID: PMC4639668 DOI: 10.1155/2015/635751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 10/02/2015] [Accepted: 10/04/2015] [Indexed: 12/30/2022] Open
Abstract
CDH13 gene variants with lower adiponectin levels are paradoxically associated with a more favorable metabolic profile. We investigated the statistical association between CDH13 locus variants and adiponectin levels by examining 12 circulating inflammation marker levels and adiposity status in 530 Han Chinese people in Taiwan. After adjustments for clinical covariates, adiponectin levels were positively associated with soluble vascular cell adhesion molecule-1 (sVCAM1) levels and negatively associated with adiposity status and levels of C-reactive protein (CRP), soluble E-selectin (sE-selectin), and soluble intercellular adhesion molecule-1 (sICAM1). In addition, minor alleles of the CDH13 rs12051272 polymorphism were found to have lower adiponectin levels and higher CRP, sE-selectin, sICAM1, and sVCAM1 levels as well as higher body mass indices and waist circumferences in participants (all P < 0.05). In a subgroup analysis stratified by sex, significant associations between CDH13 genotypes and sE-selectin levels occurred only in men (P = 3.9 × 10−4 and interaction P = 0.005). CDH13 locus variants and adiponectin levels are associated with circulating levels of cellular adhesion molecules and adiposity status in a differential manner that interacts with sex. These results provide further evidence for the crucial role of adiponectin levels and CDH13 gene variants in immune-mediated and inflammatory diseases.
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Limoge F, Faivre L, Gautier T, Petit JM, Gautier E, Masson D, Jego G, El Chehadeh-Djebbar S, Marle N, Carmignac V, Deckert V, Brindisi MC, Edery P, Ghoumid J, Blair E, Lagrost L, Thauvin-Robinet C, Duplomb L. Insulin response dysregulation explains abnormal fat storage and increased risk of diabetes mellitus type 2 in Cohen Syndrome. Hum Mol Genet 2015; 24:6603-13. [PMID: 26358774 DOI: 10.1093/hmg/ddv366] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/03/2015] [Indexed: 12/24/2022] Open
Abstract
Cohen Syndrome (CS) is a rare autosomal recessive disorder, with defective glycosylation secondary to mutations in the VPS13B gene, which encodes a protein of the Golgi apparatus. Besides congenital neutropenia, retinopathy and intellectual deficiency, CS patients are faced with truncal obesity. Metabolism investigations showed abnormal glucose tolerance tests and low HDL values in some patients, and these could be risk factors for the development of diabetes mellitus and/or cardiovascular complications. To understand the mechanisms involved in CS fat storage, we used two models of adipogenesis differentiation: (i) SGBS pre-adipocytes with VPS13B invalidation thanks to siRNA delivery and (ii) CS primary fibroblasts. In both models, VPS13B invalidation led to accelerated differentiation into fat cells, which was confirmed by the earlier and increased expression of specific adipogenic genes, consequent to the increased response of cells to insulin stimulation. At the end of the differentiation protocol, these fat cells exhibited decreased AKT2 phosphorylation after insulin stimulation, which suggests insulin resistance. This study, in association with the in-depth analysis of the metabolic status of the patients, thus allowed us to recommend appropriate nutritional education to prevent the occurrence of diabetes mellitus and to put forward recommendations for the follow-up of CS patients, in particular with regard to the development of metabolic syndrome. We also suggest replacing the term obesity by abnormal fat distribution in CS, which should reduce the number of inappropriate diagnoses in patients who are referred only on the basis of intellectual deficiency associated with obesity.
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Affiliation(s)
- Floriane Limoge
- Génétique des Anomalies du Développement GAD EA4271, Univeristé de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Laurence Faivre
- Génétique des Anomalies du Développement GAD EA4271, Univeristé de Bourgogne Franche-Comté, F-21000 Dijon, France, FHU TRANSLAD, Département de Génétique, Hôpital d'enfants, CHU Dijon, F-21000 Dijon, France
| | - Thomas Gautier
- LNC UMR866, INSERM, Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | | | - Elodie Gautier
- Génétique des Anomalies du Développement GAD EA4271, Univeristé de Bourgogne Franche-Comté, F-21000 Dijon, France, FHU TRANSLAD, Département de Génétique, Hôpital d'enfants, CHU Dijon, F-21000 Dijon, France
| | - David Masson
- LNC UMR866, INSERM, Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Gaëtan Jego
- LNC UMR866, INSERM, Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Salima El Chehadeh-Djebbar
- Génétique des Anomalies du Développement GAD EA4271, Univeristé de Bourgogne Franche-Comté, F-21000 Dijon, France, FHU TRANSLAD, Département de Génétique, Hôpital d'enfants, CHU Dijon, F-21000 Dijon, France
| | - Nathalie Marle
- Génétique des Anomalies du Développement GAD EA4271, Univeristé de Bourgogne Franche-Comté, F-21000 Dijon, France, FHU TRANSLAD, Département de Génétique, Hôpital d'enfants, CHU Dijon, F-21000 Dijon, France
| | - Virginie Carmignac
- Génétique des Anomalies du Développement GAD EA4271, Univeristé de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Valérie Deckert
- LNC UMR866, INSERM, Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | | | - Patrick Edery
- Service de Génétique Clinique, Hôpital Femme Mère Enfant, CHU Lyon, HCL, Lyon, France
| | - Jamal Ghoumid
- Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Nord, Hôpital Jeanne de Flandres, CHRU Lille, Lille, France and
| | - Edward Blair
- Department of Clinical Genetics, Oxford Regional Genetics Service, The Churchill Hospital, Oxford, UK
| | - Laurent Lagrost
- LNC UMR866, INSERM, Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Christel Thauvin-Robinet
- Génétique des Anomalies du Développement GAD EA4271, Univeristé de Bourgogne Franche-Comté, F-21000 Dijon, France, FHU TRANSLAD, Département de Génétique, Hôpital d'enfants, CHU Dijon, F-21000 Dijon, France
| | - Laurence Duplomb
- Génétique des Anomalies du Développement GAD EA4271, Univeristé de Bourgogne Franche-Comté, F-21000 Dijon, France, FHU TRANSLAD, Département de Génétique, Hôpital d'enfants, CHU Dijon, F-21000 Dijon, France,
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Hladilkova E, Barøy T, Fannemel M, Vallova V, Misceo D, Bryn V, Slamova I, Prasilova S, Kuglik P, Frengen E. A recurrent deletion on chromosome 2q13 is associated with developmental delay and mild facial dysmorphisms. Mol Cytogenet 2015; 8:57. [PMID: 26236398 PMCID: PMC4521466 DOI: 10.1186/s13039-015-0157-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/05/2015] [Indexed: 11/24/2022] Open
Abstract
We report two unrelated patients with overlapping chromosome 2q13 deletions (patient 1 in chr2:111415137-113194067 bp and patient 2 in chr2:110980342-113007823 bp, hg 19). Patient 1 presents with developmental delay, microcephaly and mild dysmorphic facial features, and patient 2 with autism spectrum disorder, borderline cognitive abilities, deficits in attention and executive functions and mild dysmorphic facial features. The mother and maternal grandmother of patient 1 were healthy carriers of the deletion. Previously, 2q13 deletions were reported in 27 patients, and the interpretation of its clinical significance varied. Our findings support that the 2q13 deletion is associated with a developmental delay syndrome manifesting with variable expressivity and reduced penetrance which poses a challenge for genetic counselling as well as the clinical recognition of 2q13 deletion patients.
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Affiliation(s)
- Eva Hladilkova
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, P.O.Box 1036, Blindern, N-0315 Oslo, Norway.,Department of Medical Genetics, University Hospital, Children Medical Hospital, Brno, Czech Republic
| | - Tuva Barøy
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, P.O.Box 1036, Blindern, N-0315 Oslo, Norway
| | - Madeleine Fannemel
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, P.O.Box 1036, Blindern, N-0315 Oslo, Norway
| | - Vladimira Vallova
- Department of Medical Genetics, University Hospital, Children Medical Hospital, Brno, Czech Republic.,Department of Genetics and Molecular Biology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno - Bohunice, Czech Republic
| | - Doriana Misceo
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, P.O.Box 1036, Blindern, N-0315 Oslo, Norway
| | - Vesna Bryn
- Department of Habilitation, Sykehuset Innlandet HF, Lillehammer, Norway
| | - Iva Slamova
- Department of Genetics and Molecular Biology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno - Bohunice, Czech Republic.,Sanatorium Helios ltd., Laboratory of Medical Genetics, Brno, Czech Republic
| | - Sarka Prasilova
- Department of Medical Genetics, University Hospital, Children Medical Hospital, Brno, Czech Republic
| | - Petr Kuglik
- Department of Medical Genetics, University Hospital, Children Medical Hospital, Brno, Czech Republic.,Department of Genetics and Molecular Biology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno - Bohunice, Czech Republic
| | - Eirik Frengen
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, P.O.Box 1036, Blindern, N-0315 Oslo, Norway
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36
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Desch L, Marle N, Mosca-Boidron AL, Faivre L, Eliade M, Payet M, Ragon C, Thevenon J, Aral B, Ragot S, Ardalan A, Dhouibi N, Bensignor C, Thauvin-Robinet C, El Chehadeh S, Callier P. 6q16.3q23.3 duplication associated with Prader-Willi-like syndrome. Mol Cytogenet 2015; 8:42. [PMID: 26110021 PMCID: PMC4479069 DOI: 10.1186/s13039-015-0151-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prader-Willi syndrome (PWS) is characterized by hypotonia, delayed neuropsychomotor development, overeating, obesity and mental deficiency. This phenotype is encountered in other conditions, defining Prader-Willi-like syndrome (PWLS). CASE PRESENTATION We report a 14-year-old boy with a complex small supernumerary marker chromosome (sSMC) associated with PWLS. The propositus presents clinical features commonly found in patients with PWLS, including growth hormone deficit. Banding karyotype analysis and fluorescence in situ hybridization (FISH) revealed a marker derived from chromosome 6 and a neocentromere as suspected, but array-CGH enabled us to characterize this marker as a der(10)t(6;10)(6qter → 6q23.3::10p11.1 → 10p11.21)dn. As far as we know, this is the first diagnosed case of PWLS associated with a complex sSMC, involving a 30.9 Mb gain in the 6q16.3q23.3 region and a 3.5 Mb gain in the 10p11.21p11.1 region. Several genes have been mapped to the 6q region including the TCBA1 gene, which is associated with developmental delay and recurrent infections, the ENPP1 gene, associated with insulin resistance and susceptibility to obesity and the BMIQ3 gene, associated with body mass index (BMI). No OMIM gene was found in the smallest 10p11.21p11.1 region. CONCLUSIONS We suggest that the duplicated chromosome segment 6q16.3q23.3 may be responsible for the phenotype of our case and may also be a candidate locus of PWLS.
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Affiliation(s)
- Laurent Desch
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Nathalie Marle
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | | | - Laurence Faivre
- />Centre de référence maladies rares « anomalies du développement et syndromes malformatifs » de l’Est, Centre de Génétique, CHU de Dijon, Dijon, France
| | - Marie Eliade
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Muriel Payet
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Clemence Ragon
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Julien Thevenon
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Bernard Aral
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | - Sylviane Ragot
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
| | | | | | | | - Christel Thauvin-Robinet
- />Centre de référence maladies rares « anomalies du développement et syndromes malformatifs » de l’Est, Centre de Génétique, CHU de Dijon, Dijon, France
| | - Salima El Chehadeh
- />Centre de référence maladies rares « anomalies du développement et syndromes malformatifs » de l’Est, Centre de Génétique, CHU de Dijon, Dijon, France
| | - Patrick Callier
- />Laboratoire de Cytogénétique, Plateau Technique de Biologie, CHU de Dijon, Dijon, France
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Yazdi FT, Clee SM, Meyre D. Obesity genetics in mouse and human: back and forth, and back again. PeerJ 2015; 3:e856. [PMID: 25825681 PMCID: PMC4375971 DOI: 10.7717/peerj.856] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 03/05/2015] [Indexed: 12/19/2022] Open
Abstract
Obesity is a major public health concern. This condition results from a constant and complex interplay between predisposing genes and environmental stimuli. Current attempts to manage obesity have been moderately effective and a better understanding of the etiology of obesity is required for the development of more successful and personalized prevention and treatment options. To that effect, mouse models have been an essential tool in expanding our understanding of obesity, due to the availability of their complete genome sequence, genetically identified and defined strains, various tools for genetic manipulation and the accessibility of target tissues for obesity that are not easily attainable from humans. Our knowledge of monogenic obesity in humans greatly benefited from the mouse obesity genetics field. Genes underlying highly penetrant forms of monogenic obesity are part of the leptin-melanocortin pathway in the hypothalamus. Recently, hypothesis-generating genome-wide association studies for polygenic obesity traits in humans have led to the identification of 119 common gene variants with modest effect, most of them having an unknown function. These discoveries have led to novel animal models and have illuminated new biologic pathways. Integrated mouse-human genetic approaches have firmly established new obesity candidate genes. Innovative strategies recently developed by scientists are described in this review to accelerate the identification of causal genes and deepen our understanding of obesity etiology. An exhaustive dissection of the molecular roots of obesity may ultimately help to tackle the growing obesity epidemic worldwide.
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Affiliation(s)
- Fereshteh T. Yazdi
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
| | - Susanne M. Clee
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - David Meyre
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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38
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Anderson D, Cordell HJ, Fakiola M, Francis RW, Syn G, Scaman ESH, Davis E, Miles SJ, McLeay T, Jamieson SE, Blackwell JM. First genome-wide association study in an Australian aboriginal population provides insights into genetic risk factors for body mass index and type 2 diabetes. PLoS One 2015; 10:e0119333. [PMID: 25760438 PMCID: PMC4356593 DOI: 10.1371/journal.pone.0119333] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 01/28/2015] [Indexed: 12/15/2022] Open
Abstract
A body mass index (BMI) >22kg/m2 is a risk factor for type 2 diabetes (T2D) in Aboriginal Australians. To identify loci associated with BMI and T2D we undertook a genome-wide association study using 1,075,436 quality-controlled single nucleotide polymorphisms (SNPs) genotyped (Illumina 2.5M Duo Beadchip) in 402 individuals in extended pedigrees from a Western Australian Aboriginal community. Imputation using the thousand genomes (1000G) reference panel extended the analysis to 6,724,284 post quality-control autosomal SNPs. No associations achieved genome-wide significance, commonly accepted as P<5x10-8. Nevertheless, genes/pathways in common with other ethnicities were identified despite the arrival of Aboriginal people in Australia >45,000 years ago. The top hit (rs10868204 Pgenotyped = 1.50x10-6; rs11140653 Pimputed_1000G = 2.90x10-7) for BMI lies 5’ of NTRK2, the type 2 neurotrophic tyrosine kinase receptor for brain-derived neurotrophic factor (BDNF) that regulates energy balance downstream of melanocortin-4 receptor (MC4R). PIK3C2G (rs12816270 Pgenotyped = 8.06x10-6; rs10841048 Pimputed_1000G = 6.28x10-7) was associated with BMI, but not with T2D as reported elsewhere. BMI also associated with CNTNAP2 (rs6960319 Pgenotyped = 4.65x10-5; rs13225016 Pimputed_1000G = 6.57x10-5), previously identified as the strongest gene-by-environment interaction for BMI in African-Americans. The top hit (rs11240074 Pgenotyped = 5.59x10-6, Pimputed_1000G = 5.73x10-6) for T2D lies 5’ of BCL9 that, along with TCF7L2, promotes beta-catenin’s transcriptional activity in the WNT signaling pathway. Additional hits occurred in genes affecting pancreatic (KCNJ6, KCNA1) and/or GABA (GABRR1, KCNA1) functions. Notable associations observed for genes previously identified at genome-wide significance in other populations included MC4R (Pgenotyped = 4.49x10-4) for BMI and IGF2BP2 Pimputed_1000G = 2.55x10-6) for T2D. Our results may provide novel functional leads in understanding disease pathogenesis in this Australian Aboriginal population.
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Affiliation(s)
- Denise Anderson
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, 6008, Australia
| | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Michaela Fakiola
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, 6008, Australia
- Cambridge Institute for Medical Research, Department of Medicine, and Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Richard W. Francis
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, 6008, Australia
| | - Genevieve Syn
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, 6008, Australia
| | - Elizabeth S. H. Scaman
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, 6008, Australia
| | - Elizabeth Davis
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, 6008, Australia
- Department of Endocrinology and Diabetes, Princess Margaret Hospital for Children, Subiaco, Western Australia, 6008, Australia
| | - Simon J. Miles
- Ngangganawili Aboriginal Health Service, Wiluna, Western Australia, 6646, Australia
| | - Toby McLeay
- Ngangganawili Aboriginal Health Service, Wiluna, Western Australia, 6646, Australia
| | - Sarra E. Jamieson
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, 6008, Australia
| | - Jenefer M. Blackwell
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, 6008, Australia
- Cambridge Institute for Medical Research, Department of Medicine, and Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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Koufaris C, Papagregoriou G, Kousoulidou L, Moutafi M, Tauber M, Jouret B, Kieffer I, Deltas C, Tanteles GA, Anastasiadou V, Patsalis PC, Sismani C. Haploinsufficiency of the miR-873/miR-876 microRNA cluster is associated with craniofacial abnormalities. Gene 2015; 561:95-100. [PMID: 25680557 DOI: 10.1016/j.gene.2015.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/05/2015] [Accepted: 02/08/2015] [Indexed: 11/20/2022]
Abstract
MicroRNA haploinsufficiency has been associated with developmental defects in only a limited number of cases. Here we report a de novo genomic microdeletion that includes the LINGO2 gene as well as two microRNA genes, MIR873 and MIR876, in a patient with craniofacial abnormalities - in particular macrocephaly and hypertelorism - and learning difficulties. Subsequent analysis revealed that the microRNAs affected by this de novo microdeletion form a mammalian-lineage, neuronal tissue-enriched cluster. In addition, bioinformatic analysis and experimental data indicate that miR-873 is involved in the regulation of the Hedgehog signaling, an essential pathway involved in craniofacial patterning and differentiation. Collectively these observations are consistent with a role of the miR-873/miR-876 microRNA cluster in physiological cranial bone development and indicate that mutations affecting these microRNAs could be a rare cause of developmental defect in humans.
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Affiliation(s)
- Costas Koufaris
- Department of Cytogenetics and Genomics, The Cyprus institute of Neurology and Genetics, Cyprus
| | | | - Ludmila Kousoulidou
- Department of Cytogenetics and Genomics, The Cyprus institute of Neurology and Genetics, Cyprus
| | - Maria Moutafi
- Department of Cytogenetics and Genomics, The Cyprus institute of Neurology and Genetics, Cyprus
| | - Maithé Tauber
- Centre de référence du Syndrome de Prader-Willi, Unité d'endocrinologie, obésité, maladies osseuses, génétique et gynécologiqe médicale, Hôpital des enfants CHU Toulouse, France
| | - Béatrice Jouret
- Centre de référence du Syndrome de Prader-Willi, Unité d'endocrinologie, obésité, maladies osseuses, génétique et gynécologiqe médicale, Hôpital des enfants CHU Toulouse, France
| | - Isabelle Kieffer
- Unité d'endocrinologie, obésité, maladies osseuses, génétique et gynécologiqe médicale, Hôpital des enfants CHU Toulouse, France
| | | | - George A Tanteles
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, Cyprus
| | | | - Philippos C Patsalis
- Translational Genetics Team, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Carolina Sismani
- Department of Cytogenetics and Genomics, The Cyprus institute of Neurology and Genetics, Cyprus.
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40
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D'Angelo CS, Moller Dos Santos MF, Alonso LG, Koiffmann CP. Two New Cases of 1p21.3 Deletions and an Unbalanced Translocation t(8;12) among Individuals with Syndromic Obesity. Mol Syndromol 2015; 6:63-70. [PMID: 26279650 DOI: 10.1159/000371600] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2014] [Indexed: 01/09/2023] Open
Abstract
Obesity is a highly heritable but genetically heterogeneous disorder. Various well-known microdeletion syndromes (e.g. 1p36, 2q37, 6q16, 9q34, 17p11.2) can cause this phenotype along with intellectual disability (ID) and other findings. Chromosomal microarrays have identified 'new' microdeletion/duplication syndromes often associated with obesity. We report on 2 unrelated patients with an overlapping region of deletion at 1p21.3p21.2, and a third patient with a de novo recurrent unbalanced translocation der(8)t(8;12)(p23.1;p13.31), detected by 180K array CGH in a prospective cohort of syndromic obesity patients. Deletion of 1p21.3 is a rare condition, and there have been only 11 cases of the same recurrent translocation between chromosomes 8 and 12 [t(8;12)] reported to date. The former has been associated with ID, autistic spectrum disorder (ASD) and mild dysmorphic features, and in 4 patients who were obese or had a tendency to obesity, a minimal overlapping region of 2 genes, DPYD and MIR137, was detected; t(8;12) has recently been recognized to cause a childhood obesity syndrome due to duplication of the GNB3 gene. Thus, our findings add to the existing literature on the clinical description of these new syndromes, providing additional support that these loci are associated with syndromic obesity. We suggest that heterozygous loss of MIR137 may contribute to obesity as well as ID and ASD.
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Affiliation(s)
- Carla S D'Angelo
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Mauren F Moller Dos Santos
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Luis G Alonso
- Genetics Division, Department of Morphology and Genetics, Federal University of São Paulo, São Paulo, Brazil
| | - Celia P Koiffmann
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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41
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Hasstedt SJ, Xin Y, Mao R, Lewis T, Adams TD, Hunt SC. A Copy Number Variant on Chromosome 20q13.3 Implicated in Thinness and Severe Obesity. J Obes 2015; 2015:623431. [PMID: 26881067 PMCID: PMC4736014 DOI: 10.1155/2015/623431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/20/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND/OBJECTIVES To identify copy number variants (CNVs) which are associated with body mass index (BMI). SUBJECTS/METHODS CNVs were identified using array comparative genomic hybridization (aCGH) on members of pedigrees ascertained through severely obese (BMI ≥ 35 kg/m(2)) sib pairs (86 pedigrees) and thin (BMI ≤ 23 kg/m(2)) probands (3 pedigrees). Association was inferred through pleiotropy of BMI with CNV log2 intensity ratio. RESULTS A 77-kilobase CNV on chromosome 20q13.3, confirmed by real-time qPCR, exhibited deletions in the obese subjects and duplications in the thin subjects (P = 2.2 × 10(-6)). Further support for the presence of a deletion derived from inference by likelihood analysis of null alleles for SNPs residing in the region. CONCLUSIONS One or more of 7 genes residing in a chromosome 20q13.3 CNV region appears to influence BMI. The strongest candidate is ARFRP1, which affects glucose metabolism in mice.
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Affiliation(s)
- Sandra J. Hasstedt
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- *Sandra J. Hasstedt:
| | - Yuanpei Xin
- Cardiovascular Genetics Division, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Rong Mao
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Tracey Lewis
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Ted D. Adams
- Cardiovascular Genetics Division, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Steven C. Hunt
- Cardiovascular Genetics Division, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
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D'Angelo CS, Varela MC, de Castro CI, Kim CA, Bertola DR, Lourenço CM, Perez ABA, Koiffmann CP. Investigation of selected genomic deletions and duplications in a cohort of 338 patients presenting with syndromic obesity by multiplex ligation-dependent probe amplification using synthetic probes. Mol Cytogenet 2014; 7:75. [PMID: 25411582 PMCID: PMC4236449 DOI: 10.1186/s13039-014-0075-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 10/19/2014] [Indexed: 01/02/2023] Open
Abstract
Background Certain rare syndromes with developmental delay or intellectual disability caused by genomic copy number variants (CNVs), either deletions or duplications, are associated with higher rates of obesity. Current strategies to diagnose these syndromes typically rely on phenotype-driven investigation. However, the strong phenotypic overlap between syndromic forms of obesity poses challenges to accurate diagnosis, and many different individual cytogenetic and molecular approaches may be required. Multiplex ligation-dependent probe amplification (MLPA) enables the simultaneous analysis of multiple targeted loci in a single test, and serves as an important screening tool for large cohorts of patients in whom deletions and duplications involving specific loci are suspected. Our aim was to design a synthetic probe set for MLPA analysis to investigate in a cohort of 338 patients with syndromic obesity deletions and duplications in genomic regions that can cause this phenotype. Results We identified 18 patients harboring copy number imbalances; 18 deletions and 5 duplications. The alterations in ten patients were delineated by chromosomal microarrays, and in the remaining cases by additional MLPA probes incorporated into commercial kits. Nine patients showed deletions in regions of known microdeletion syndromes with obesity as a clinical feature: in 2q37 (4 cases), 9q34 (1 case) and 17p11.2 (4 cases). Four patients harbored CNVs in the DiGeorge syndrome locus at 22q11.2. Two other patients had deletions within the 22q11.2 ‘distal’ locus associated with a variable clinical phenotype and obesity in some individuals. The other three patients had a recurrent CNV of one of three susceptibility loci: at 1q21.1 ‘distal’, 16p11.2 ‘distal’, and 16p11.2 ‘proximal’. Conclusions Our study demonstrates the utility of an MLPA-based first line screening test to the evaluation of obese patients presenting with syndromic features. The overall detection rate with the synthetic MLPA probe set was about 5.3% (18 out of 338). Our experience leads us to suggest that MLPA could serve as an effective alternative first line screening test to chromosomal microarrays for diagnosis of syndromic obesity, allowing for a number of loci (e.g., 1p36, 2p25, 2q37, 6q16, 9q34, 11p14, 16p11.2, 17p11.2), known to be clinically relevant for this patient population, to be interrogated simultaneously.
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Affiliation(s)
- Carla S D'Angelo
- Human Genome and Stem Cell Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Monica C Varela
- Human Genome and Stem Cell Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Cláudia Ie de Castro
- Human Genome and Stem Cell Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Chong A Kim
- Genetics Unit, Department of Pediatrics, Children Institute, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Débora R Bertola
- Genetics Unit, Department of Pediatrics, Children Institute, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Charles M Lourenço
- Neurogenetics Unit, Department of Medical Genetics, School of Medicine, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Ana Beatriz A Perez
- Department of Morphology, Medical Genetics Center, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Celia P Koiffmann
- Human Genome and Stem Cell Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
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How Fatty Acids and Common Genetic Variants Together Affect the Inflammation of Adipose Tissue. CURRENT CARDIOVASCULAR RISK REPORTS 2014. [DOI: 10.1007/s12170-014-0411-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Johnson ME, Zhao J, Schug J, Deliard S, Xia Q, Guy VC, Sainz J, Kaestner KH, Wells AD, Grant SFA. Two novel type 2 diabetes loci revealed through integration of TCF7L2 DNA occupancy and SNP association data. BMJ Open Diabetes Res Care 2014; 2:e000052. [PMID: 25469308 PMCID: PMC4250976 DOI: 10.1136/bmjdrc-2014-000052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/04/2014] [Accepted: 10/03/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The transcription factor 7-like 2 (TCF7L2) locus is strongly implicated in the pathogenesis of type 2 diabetes (T2D). We previously mapped the genomic regions bound by TCF7L2 using ChIP (chromatin immunoprecipitation)-seq in the colorectal carcinoma cell line, HCT116, revealing an unexpected highly significant over-representation of genome-wide association studies (GWAS) loci associated primarily with endocrine (in particular T2D) and cardiovascular traits. METHODS In order to further explore if this observed phenomenon occurs in other cell lines, we carried out ChIP-seq in HepG2 cells and leveraged ENCODE data for five additional cell lines. Given that only a minority of the predicted genetic component to most complex traits has been identified to date, plus our GWAS-related observations with respect to TCF7L2 occupancy, we investigated if restricting association analyses to the genes yielded from this approach, in order to reduce the constraints of multiple testing, could reveal novel T2D loci. RESULTS We found strong evidence for the continued enrichment of endocrine and cardiovascular GWAS categories, with additional support for cancer. When investigating all the known GWAS loci bound by TCF7L2 in the shortest gene list, derived from HCT116, the coronary artery disease-associated variant, rs46522 at the UBE2Z-GIP-ATP5G1-SNF8 locus, yielded significant association with T2D within DIAGRAM. Furthermore, when we analyzed tag-SNPs (single nucleotide polymorphisms) in genes not previously implicated by GWAS but bound by TCF7L2 within 5 kb, we observed a significant association of rs4780476 within CPPED1 in DIAGRAM. CONCLUSIONS ChIP-seq data generated with this GWAS-implicated transcription factor provided a biologically plausible method to limit multiple testing in the assessment of genome-wide genotyping data to uncover two novel T2D-associated loci.
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Affiliation(s)
- Matthew E Johnson
- Division of Human Genetics , The Children's Hospital of Philadelphia , Philadelphia, Pennsylvania , USA
| | - Jianhua Zhao
- Division of Human Genetics , The Children's Hospital of Philadelphia , Philadelphia, Pennsylvania , USA
| | - Jonathan Schug
- Department of Genetics and Institute of Diabetes, Obesity and Metabolism , Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania , USA
| | - Sandra Deliard
- Division of Human Genetics , The Children's Hospital of Philadelphia , Philadelphia, Pennsylvania , USA
| | - Qianghua Xia
- Division of Human Genetics , The Children's Hospital of Philadelphia , Philadelphia, Pennsylvania , USA
| | - Vanessa C Guy
- Division of Human Genetics , The Children's Hospital of Philadelphia , Philadelphia, Pennsylvania , USA
| | - Jesus Sainz
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), Spanish National Research Council (CSIC) , Santander , Spain
| | - Klaus H Kaestner
- Department of Genetics and Institute of Diabetes, Obesity and Metabolism , Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania , USA
| | - Andrew D Wells
- Pathology and Laboratory Medicine , Children's Hospital of Philadelphia , Philadelphia, Pennsylvania , USA
| | - Struan F A Grant
- Division of Human Genetics , The Children's Hospital of Philadelphia , Philadelphia, Pennsylvania , USA ; Department of Genetics and Institute of Diabetes, Obesity and Metabolism , Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania , USA ; Department of Pediatrics , Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania , USA
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