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Dugo E, Piva F, Giulietti M, Giannella L, Ciavattini A. Copy number variations in endometrial cancer: from biological significance to clinical utility. Int J Gynecol Cancer 2024; 34:1089-1097. [PMID: 38677776 DOI: 10.1136/ijgc-2024-005295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024] Open
Abstract
The molecular basis of endometrial cancer, which is the most common malignancy of the female reproductive organs, relies not only on onset of mutations but also on copy number variations, the latter consisting of gene gains or losses. In this review, we introduce copy number variations and discuss their involvement in endometrial cancer to determine the perspectives of clinical applicability. We performed a literature analysis on PubMed of publications over the past 30 years and annotated clinical information, including histological and molecular subtypes, adopted molecular techniques for identification of copy number variations, their locations, and the genes involved. We highlight correlations between the presence of some specific copy number variations and myometrial invasion, lymph node metastasis, advanced International Federation of Gynecology and Obstetrics (FIGO) stage, high grade, drug response, and cancer progression. In particular, type I endometrial cancer cells have few copy number variations and are mainly located in 8q and 1q, while type II, high grade, and advanced FIGO stage endometrial cancer cells are aneuploid and have a greater number of copy number variations. As expected, the higher the number of copy number variations the worse the prognosis, especially if they amplify CCNE1, ERBB2, KRAS, MYC, and PIK3CA oncogenes. Great variability in copy number and location among patients with the same endometrial cancer histological or molecular subtype emerged, making them interesting candidates to be explored for the improvement of patient stratification. Copy number variations have a role in endometrial cancer progression, and therefore their detection may be useful for more accurate prediction of prognosis. Unfortunately, only a few studies have been carried out on the role of copy number variations according to the molecular classification of endometrial cancer, and even fewer have explored the correlation with drugs. For these reasons, further studies, also using single cell RNA sequencing, are needed before reaching a clinical application.
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Affiliation(s)
- Erica Dugo
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luca Giannella
- Woman's Health Sciences Department, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Ciavattini
- Woman's Health Sciences Department, Polytechnic University of Marche, Ancona, Italy
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2
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Zeng K, Du J, Chen YZ, Wang DY, Sun ML, Li YZ, Wang DY, Liu SH, Zhu XM, Lv P, Du Z, Liu K, Yao J. Metabolomics efficiently discriminates monozygotic twins in peripheral blood. Int J Legal Med 2024:10.1007/s00414-024-03269-1. [PMID: 38858273 DOI: 10.1007/s00414-024-03269-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
Monozygotic (MZ) twins cannot be distinguished using conventional forensic STR typing because they present identical STR genotypings. However, MZ twins do not always live in the same environment and often have different dietary and other lifestyle habits. Metabolic profiles are deyermined by individual characteristics and are also influenced by the environment in which they live. Therefore, they are potential markers capable of identifying MZ twins. Moreover, the production of proteins varies from organism to organism and is influenced by both the physiological state of the body and the external environment. Hence, we used metabolomics and proteomics to identify metabolites and proteins in peripheral blood to discriminate MZ twins. We identified 1749 known metabolites and 622 proteins in proteomic analysis. The metabolic profiles of four pairs of MZ twins revealed minor differences in intra-MZ twins and major differences in inter-MZ twins. Each pair of MZ twins exhibited distinct characteristics, and four metabolites-methyl picolinate, acesulfame, paraxanthine, and phenylbenzimidazole sulfonic acid-were observed in all four MZ twin pairs. These four differential exogenous metabolites conincidently show that the different external environments and life styles can be well distinguished by metabolites, considering that twins do not all have the same eating habits and living environments. Moreover, MZ twins showed different protein profiles in serum but not in whole blood. Thus, our results indicate that differential metabolites provide potential biomarkers for the personal identification of MZ twins in forensic medicine.
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Affiliation(s)
- Kuo Zeng
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Jiang Du
- Department of Pathology, School of Basic Medicine, China Medical University, Shenyang, P.R. China
| | - Yun-Zhou Chen
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Dan-Yang Wang
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Mao-Ling Sun
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Yu-Zhang Li
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Dong-Yi Wang
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Shu-Han Liu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Xiu-Mei Zhu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Peng Lv
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Zhe Du
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Kun Liu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, P.R. China.
| | - Jun Yao
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China.
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China.
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China.
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3
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Sun W, Wang Z, Wen S, Huang A, Li H, Jiang L, Feng Q, Fan D, Tian Q, Han D, Liu X. Technical strategy for monozygotic twin discrimination by single-nucleotide variants. Int J Legal Med 2024; 138:767-779. [PMID: 38197923 DOI: 10.1007/s00414-023-03150-7] [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] [Received: 03/08/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Monozygotic (MZ) twins are theoretically genetically identical. Although they are revealed to accumulate mutations after the zygote splits, discriminating between twin genomes remains a formidable challenge in the field of forensic genetics. Single-nucleotide variants (SNVs) are responsible for a substantial portion of genetic variation, thus potentially serving as promising biomarkers for the identification of MZ twins. In this study, we sequenced the whole genome of a pair of female MZ twins when they were 27 and 33 years old to approximately 30 × coverage using peripheral blood on an Illumina NovaSeq 6000 Sequencing System. Potentially discordant SNVs supported by whole-genome sequencing were validated extensively by amplicon-based targeted deep sequencing and Sanger sequencing. In total, we found nine bona fide post-twinning SNVs, all of which were identified in the younger genomes and found in the older genomes. None of the SNVs occurred within coding exons, three of which were observed in introns, supported by whole-exome sequencing results. A double-blind test was employed, and the reliability of MZ twin discrimination by discordant SNVs was endorsed. All SNVs were successfully detected when input DNA amounts decreased to 0.25 ng, and reliable detection was limited to seven SNVs below 0.075 ng input. This comprehensive analysis confirms that SNVs could serve as cost-effective biomarkers for MZ twin discrimination.
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Affiliation(s)
- Weifen Sun
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ziwei Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Shubo Wen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Ao Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Hui Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Lei Jiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Danlin Fan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qilin Tian
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Dingding Han
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China.
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Jenkins D. How do stochastic processes and genetic threshold effects explain incomplete penetrance and inform causal disease mechanisms? Philos Trans R Soc Lond B Biol Sci 2024; 379:20230045. [PMID: 38432317 PMCID: PMC10909503 DOI: 10.1098/rstb.2023.0045] [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] [Received: 10/04/2023] [Accepted: 01/16/2024] [Indexed: 03/05/2024] Open
Abstract
Incomplete penetrance is the rule rather than the exception in Mendelian disease. In syndromic monogenic disorders, phenotypic variability can be viewed as the combination of incomplete penetrance for each of multiple independent clinical features. Within genetically identical individuals, such as isogenic model organisms, stochastic variation at molecular and cellular levels is the primary cause of incomplete penetrance according to a genetic threshold model. By defining specific probability distributions of causal biological readouts and genetic liability values, stochasticity and incomplete penetrance provide information about threshold values in biological systems. Ascertainment of threshold values has been achieved by simultaneous scoring of relatively simple phenotypes and quantitation of molecular readouts at the level of single cells. However, this is much more challenging for complex morphological phenotypes using experimental and reductionist approaches alone, where cause and effect are separated temporally and across multiple biological modes and scales. Here I consider how causal inference, which integrates observational data with high confidence causal models, might be used to quantify the relative contribution of different sources of stochastic variation to phenotypic diversity. Collectively, these approaches could inform disease mechanisms, improve predictions of clinical outcomes and prioritize gene therapy targets across modes and scales of gene function. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Dagan Jenkins
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
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Hwa HL, Lin CY, Yu YJ, Linacre A, Lee JCI. DNA identification of monozygotic twins. Forensic Sci Int Genet 2024; 69:102998. [PMID: 38100853 DOI: 10.1016/j.fsigen.2023.102998] [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: 08/23/2023] [Revised: 11/14/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
This study details the differentiation of identical twins based on single mutational base differences. There were three pairs of male monozygotic (MZ) twins in this study. DNA samples from blood, a buccal swab or saliva from each individual were all initially genotyped using 22 autosomal STR and 27 Y-STR loci. Preliminary screening confirmed there were no differences in the STR data between each pair of MZ twins. Whole Genome Sequence (WGS) data were generated from DNA extracted from the three body fluids from each individual. Kinship coefficients with 0.4254, 0.4557 and 0.4543 from 3 twins were generated based on WGS data to further confirm that their relationship was that of MZ twins. The fastq data generated by the Illumina Hiseq 2000 between MZ twins were then treated as "normal" as opposed to "tumor" using commercially available software tools to identify mutational single base changes. Sanger DNA sequencing confirmed there were 1, 5 and 9 single base changes found in WGS data from each of the three MZ twin sets. There was individual variation in the mutational base changes when comparing data from the three body fluids. The methods used in this study to differentiate MZ twins based on WGS data can readily be performed in many operational forensic DNA laboratories using user friendly software.
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Affiliation(s)
- Hsiao-Lin Hwa
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan
| | - Chun-Yen Lin
- Institute of Forensic Medicine, Ministry of Justice, New Taipei City 23016, Taiwan
| | - Yu-Jen Yu
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide 5001, Australia
| | - James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan.
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6
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Saniasiaya J, van der Meer G, Toll EC, McCaffer C, Barber C, Neeff M. Familial congenital laryngotracheal stenosis: A systematic review. Int J Pediatr Otorhinolaryngol 2024; 177:111841. [PMID: 38181460 DOI: 10.1016/j.ijporl.2023.111841] [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] [Received: 11/17/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Congenital laryngotracheal stenosis (CLS) is a rare cause of stridor among newborns. Evidence has shown that several family members can be affected by CLS. Knowledge of the pathophysiology of familial congenital laryngotracheal stenosis (FCLS) will enable more effective therapeutic strategies. OBJECTIVE To determine the clinical course and outcome of familial congenital laryngotracheal stenosis (FCLS). METHODS A literature search was conducted over a period of one month (September 2023) by searching several databases to identify studies published from inception to 31st August 2023. RESULTS Of 256 papers identified, five articles met the inclusion criteria. A total of 17 patients with slight female predominance (59 %) were identified. Familial congenital tracheal stenosis was reported in female twins (100 %). A variety of clinical presentations were listed. An endoscopic airway study was performed on all patients. 64.8 % of the included children were managed surgically. Genetic studies performed on 41 % of children could not locate genetic abnormalities. CONCLUSION Consanguinity, twin births, and female gender could be predisposing factors for FCLS, although the quality of evidence is low due to the rarity of the condition.
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Affiliation(s)
- Jeyasakthy Saniasiaya
- Department of Otorhinolaryngology, Starship Children's Hospital, Te Whatu Ora Te Toka Tumai, Auckland, New Zealand; Department of Otorhinolaryngology, Faculty of Medicine, University of Malaya, Malaysia.
| | - Graeme van der Meer
- Department of Otorhinolaryngology, Starship Children's Hospital, Te Whatu Ora Te Toka Tumai, Auckland, New Zealand
| | - Ed C Toll
- Department of Otorhinolaryngology, Starship Children's Hospital, Te Whatu Ora Te Toka Tumai, Auckland, New Zealand
| | - Craig McCaffer
- Department of Otorhinolaryngology, Starship Children's Hospital, Te Whatu Ora Te Toka Tumai, Auckland, New Zealand
| | - Colin Barber
- Department of Otorhinolaryngology, Starship Children's Hospital, Te Whatu Ora Te Toka Tumai, Auckland, New Zealand
| | - Michel Neeff
- Department of Otorhinolaryngology, Starship Children's Hospital, Te Whatu Ora Te Toka Tumai, Auckland, New Zealand
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Oketch DJA, Giulietti M, Piva F. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int J Mol Sci 2023; 25:391. [PMID: 38203561 PMCID: PMC10779192 DOI: 10.3390/ijms25010391] [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: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, characterized by high tumor heterogeneity and a poor prognosis. Inter- and intra-tumoral heterogeneity in PDAC is a major obstacle to effective PDAC treatment; therefore, it is highly desirable to explore the tumor heterogeneity and underlying mechanisms for the improvement of PDAC prognosis. Gene copy number variations (CNVs) are increasingly recognized as a common and heritable source of inter-individual variation in genomic sequence. In this review, we outline the origin, main characteristics, and pathological aspects of CNVs. We then describe the occurrence of CNVs in PDAC, including those that have been clearly shown to have a pathogenic role, and further highlight some key examples of their involvement in tumor development and progression. The ability to efficiently identify and analyze CNVs in tumor samples is important to support translational research and foster precision oncology, as copy number variants can be utilized to guide clinical decisions. We provide insights into understanding the CNV landscapes and the role of both somatic and germline CNVs in PDAC, which could lead to significant advances in diagnosis, prognosis, and treatment. Although there has been significant progress in this field, understanding the full contribution of CNVs to the genetic basis of PDAC will require further research, with more accurate CNV assays such as single-cell techniques and larger cohorts than have been performed to date.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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8
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Boer LL, Winter E, Gorissen B, Oostra RJ. Phenotypically Discordant Anomalies in Conjoined Twins: Quirks of Nature Governed by Molecular Pathways? Diagnostics (Basel) 2023; 13:3427. [PMID: 37998563 PMCID: PMC10669976 DOI: 10.3390/diagnostics13223427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/24/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
A multitude of additional anomalies can be observed in virtually all types of symmetrical conjoined twins. These concomitant defects can be divided into different dysmorphological patterns. Some of these patterns reveal their etiological origin through their topographical location. The so-called shared anomalies are traceable to embryological adjustments and directly linked to the conjoined-twinning mechanism itself, inherently located within the boundaries of the coalescence area. In contrast, discordant patterns are anomalies present in only one of the twin members, intrinsically distant from the area of union. These dysmorphological entities are much more difficult to place in a developmental perspective, as it is presumed that conjoined twins share identical intra-uterine environments and intra-embryonic molecular and genetic footprints. However, their existence testifies that certain developmental fields and their respective developmental pathways take different routes in members of conjoined twins. This observation remains a poorly understood phenomenon. This article describes 69 cases of external discordant patterns within different types of otherwise symmetrical mono-umbilical conjoined twins and places them in a developmental perspective and a molecular framework. Gaining insights into the phenotypes and underlying (biochemical) mechanisms could potentially pave the way and generate novel etiological visions in the formation of conjoined twins itself.
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Affiliation(s)
- Lucas L. Boer
- Department of Medical Imaging, Section Anatomy and Museum for Anatomy and Pathology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Eduard Winter
- Pathologisch-Anatomische Sammlung im Narrenturm-NHM, 1090 Vienna, Austria
| | - Ben Gorissen
- Department of Medical Imaging, Section Anatomy and Museum for Anatomy and Pathology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Roelof-Jan Oostra
- Department of Medical Biology, Sections Clinical Anatomy & Embryology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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Salehian-Dehkordi H, Huang JH, Pirany N, Mehrban H, Lv XY, Sun W, Esmailizadeh A, Lv FH. Genomic Landscape of Copy Number Variations and Their Associations with Climatic Variables in the World's Sheep. Genes (Basel) 2023; 14:1256. [PMID: 37372436 PMCID: PMC10298528 DOI: 10.3390/genes14061256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Sheep show characteristics of phenotypic diversity and adaptation to diverse climatic regions. Previous studies indicated associations between copy number variations (CNVs) and climate-driven adaptive evolution in humans and other domestic animals. Here, we constructed a genomic landscape of CNVs (n = 39,145) in 47 old autochthonous populations genotyped at a set of high-density (600 K) SNPs to detect environment-driven signatures of CNVs using a multivariate regression model. We found 136 deletions and 52 duplications that were significantly (Padj. < 0.05) associated with climatic variables. These climate-mediated selective CNVs are involved in functional candidate genes for heat stress and cold climate adaptation (e.g., B3GNTL1, UBE2L3, and TRAF2), coat and wool-related traits (e.g., TMEM9, STRA6, RASGRP2, and PLA2G3), repairing damaged DNA (e.g., HTT), GTPase activity (e.g., COPG), fast metabolism (e.g., LMF2 and LPIN3), fertility and reproduction (e.g., SLC19A1 and CCDC155), growth-related traits (e.g., ADRM1 and IGFALS), and immune response (e.g., BEGAIN and RNF121) in sheep. In particular, we identified significant (Padj. < 0.05) associations between probes in deleted/duplicated CNVs and solar radiation. Enrichment analysis of the gene sets among all the CNVs revealed significant (Padj. < 0.05) enriched gene ontology terms and pathways related to functions such as nucleotide, protein complex, and GTPase activity. Additionally, we observed overlapping between the CNVs and 140 known sheep QTLs. Our findings imply that CNVs can serve as genomic markers for the selection of sheep adapted to specific climatic conditions.
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Affiliation(s)
- Hosein Salehian-Dehkordi
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Jia-Hui Huang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
| | - Nasrollah Pirany
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Hossein Mehrban
- Department of Animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran; (N.P.); (H.M.)
| | - Xiao-Yang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.-Y.L.); (W.S.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (X.-Y.L.); (W.S.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 76169-14111, Iran
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.S.-D.); (J.-H.H.)
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Xue J, Tan M, Zhang R, Chen D, Liu G, Zheng Y, Wu Q, Xiao Y, Liao M, Qu S, Liang W. Evaluation of microhaplotype panels for complex kinship analysis using massively parallel sequencing. Forensic Sci Int Genet 2023; 65:102887. [PMID: 37209601 DOI: 10.1016/j.fsigen.2023.102887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/22/2023]
Abstract
In recent years, microhaplotypes (MHs) have become a research hotspot within the field of forensic genetics. Traditional MHs contain only SNPs that are closely linked within short fragments. Herein, we broaden the concept of general MHs to include short InDels. Complex kinship identification plays an important role in disaster victim identification and criminal investigations. For distant relatives (e.g., 3rd-degree), many genetic markers are required to enhance power of kinship testing. We performed genome-wide screening for new MH markers composed of two or more variants (InDel or SNP) within 220 bp based on the Chinese Southern Han from the 1000 Genomes Project. An NGS-based 67plex MH panel (Panel B) was successfully developed, and 124 unrelated individual samples were sequenced to obtain population genetic data, including alleles and allele frequencies. Of the 67 genetic markers, 65 MHs were, as far as we know, newly discovered, and 32 MHs had effective number of allele (Ae) values greater than 5.0. The average Ae and heterozygosity of the panel were 5.34 and 0.7352, respectively. Next, 53 MHs from a previous study were collected as Panel A (average Ae of 7.43), and Panel C with 87 MHs (average Ae of 7.02) was formed by combining Panels A and B. We investigated the utility of these three panels in kinship analysis (parent-child, full siblings, 2nd-degree, 3rd-degree, 4th-degree, and 5th-degree relatives), with Panel C exhibiting better performance than the two other panels. Panel C was able to separate parent-child, full-sibling, and 2nd-degree relative duos from unrelated controls in real pedigree data, with a small false testing level (FTL) of 0.11% in simulated 2nd-degree duos. For more distant relationships, the FTL was much higher: 8.99% for 3rd-degree, 35.46% for 4th-degree, and 61.55% for 5th-degree. When a carefully chosen extra relative was known, this may enhance the testing power for distant kinship analysis. Two twins from the Q family (2-5 and 2-7) and W family (3-18 and 3-19) shared the same genotypes in all tested MHs, which led to the incorrect conclusion that an uncle-nephew duo was classified as a parent-child duo. In addition, Panel C showed great capacity for excluding close relatives (2nd-degree and 3rd-degree relatives) during paternity tests. Among 18,246 real and 10,000 simulated unrelated pairs, none were misinterpreted as a relative within 2nd-degree at a log10(LR) cutoff of 4. The panels presented herein could provide supplementary power for the analysis of complex kinship.
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Affiliation(s)
- Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.
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11
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Liu J, Zhang S, Wen Y, Su Y, Jiang L, Li S, Shen J, Zheng X, Li X, Chen X, Wang Z. Exploring rare differences in mitochondrial genome between MZ twins using Ion Torrent semiconductor sequencing. Forensic Sci Int 2023; 348:111708. [PMID: 37119662 DOI: 10.1016/j.forsciint.2023.111708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
Monozygotic (MZ) twins are considered to be genetically identical in that they have the same genomic DNA sequences in theory, and thus cannot be differentiated using forensic standard STR-based DNA profiling. However, a recent study employed deep sequencing to explore extremely rare mutations in the nuclear genome and reported that the mutation analysis could be applied to differentiate between MZ twins. Compared with the nuclear genome, the mitochondrial DNA (mtDNA) exhibits higher mutation rates due to fewer DNA repair mechanisms in the mitochondrial genome (mtGenome) and the lack of proofreading capability of the mtDNA polymerase. In a previous study, we used Illumina ultra-deep sequencing to describe point heteroplasmy (PHP) and nucleotide variant of the mtGenomes in venous blood samples of MZ twins. In the present study, we characterized minor differences of the mtGenomes in three tissue samples from seven sets of MZ twins using Ion Torrent semiconductor sequencing (Thermo Fisher Ion S5 XL system) and commercialized mtGenome sequencing kit (Precision ID mtDNA Whole Genome Panel). PHP was observed in blood samples from one set of MZ twins and in saliva samples from two sets of twins, but it presented in hair shaft samples from all seven sets of MZ twins. Overall, the coding region of the mtGenome exhibits more PHPs than the control region. The results of this study have further attested the competence of mtGenome sequencing in differentiating between MZ twins, and that among the three kinds of samples tested, hair shaft is more likely to accumulate minor differences in the mtGenomes of MZ twins.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shuyuan Zhang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jian Shen
- Anhui Hopegenerich Biotechnology, Hefei 230031, China
| | - Xinyue Zheng
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xingrui Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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12
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Bac B, Hicheri C, Weiss C, Buell A, Vilcek N, Spaeni C, Geula C, Savas JN, Disterhoft JF. The TgF344-AD rat: behavioral and proteomic changes associated with aging and protein expression in a transgenic rat model of Alzheimer's disease. Neurobiol Aging 2023; 123:98-110. [PMID: 36657371 PMCID: PMC10118906 DOI: 10.1016/j.neurobiolaging.2022.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023]
Abstract
Animal models of Alzheimer's Disease (AD) are attractive tools for preclinical, prodromal drug testing. The TgF344-AD (Tg) rat exhibits cognitive deficits and 5 major hallmarks of AD. Here we show that spatial water maze (WMZ) memory deficits and proteomic differences in dorsal CA1 were present in young Tg rats. Aged learning-unimpaired (AU) and aged learning-impaired (AI) proteome associated changes were identified and differed by sex. Levels of phosphorylated tau, reactive astrocytes and microglia were significantly increased in aged Tg rats and correlated with the WMZ learning index (LI); in contrast, no significant correlation was present between amyloid plaques or insoluble Aβ levels and LI. Neuroinflammatory markers were also significantly correlated with LI and increased in female Tg rats. The anti-inflammatory marker, triggering receptor expressed on myeloid cells-2 (TREM2), was significantly reduced in aged impaired Tg rats and correlated with LI. Identifying and understanding mechanisms that allow for healthy aging by overcoming genetic drivers for AD, and/or promoting drivers for successful aging, are important for developing successful therapeutics against AD.
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Affiliation(s)
- Birsu Bac
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cheima Hicheri
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Craig Weiss
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Amelia Buell
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Natalia Vilcek
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Claudia Spaeni
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Changiz Geula
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - John F Disterhoft
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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13
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Ralston NVC. Concomitant selenoenzyme inhibitor exposures as etiologic contributors to disease: Implications for preventative medicine. Arch Biochem Biophys 2023; 733:109469. [PMID: 36423662 DOI: 10.1016/j.abb.2022.109469] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
The physiological activities of selenium (Se) occur through enzymes that incorporate selenocysteine (Sec), a rare but important amino acid. The human genome includes 25 genes coding for Sec that employ it to catalyze challenging reactions. Selenoenzymes control thyroid hormones, calcium activities, immune responses, and perform other vital roles, but most are devoted to preventing and reversing oxidative damage. As the most potent intracellular nucleophile (pKa 5.2), Sec is vulnerable to binding by metallic and organic soft electrophiles (E*). These electron poor reactants initially form covalent bonds with nucleophiles such as cysteine (Cys) whose thiol (pKa 8.3) forms adducts which function as suicide substrates for selenoenzymes. These adducts orient E* to interact with Sec and since Se has a higher affinity for E* than sulfur, the E* transfers to Sec and irreversibly inhibits the enzyme's activity. Organic electrophiles have lower Se-binding affinities than metallic E*, but exposure sources are more abundant. Individuals with poor Se status are more vulnerable to the toxic effects of high E* exposures. The relative E*:Se stoichiometries remain undefined, but the aggregate effects of multiple E* exposures are predicted to be additive and possibly synergistic under certain conditions. The potential for the combined Se-binding effects of common pharmaceutical, dietary, or environmental E* require study, but even temporary loss of selenoenzyme activities would accentuate oxidative damage to tissues. As various degenerative diseases are associated with accumulating DNA damage, defining the effects of complementary E* exposures on selenoenzyme activities may enhance the ability of preventative medicine to support healthy aging.
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Affiliation(s)
- Nicholas V C Ralston
- Earth System Science and Policy, University of North Dakota, Grand Forks, ND, USA.
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14
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Ting Y, Ting Z, Fei Z, Chun-Fang L, Zhen H. Prenatal Diagnosis of Structural Anomaly Among Singletons and Twins: Eight-Year Experience in a Chinese Tertiary Center. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2023; 42:185-192. [PMID: 35942928 DOI: 10.1002/jum.16069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/04/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES This study was designed to reveal structural abnormalities in singleton and twin pregnancies in the Chinese population. METHODS This retrospective study spanned 8 years and included 1228 singleton pregnancies (112,919 examinees) and 49 twin pregnancies (1865 examinees) with structural anomalies diagnosed by ultrasound. Detailed descriptions of anomalies, gestational weeks at diagnosis, and maternal age were recorded. The odds ratio was evaluated in twin pregnancies with detectable structural anomalies. RESULTS The annual average "ultrasound prevalence of fetal anomalies" among singleton and twin pregnancies were 1.09 and 3.06%, respectively. Mothers with twin anomalies were older (P < .001), and twin pregnancies were diagnosed with anomalies in earlier gestational weeks than singleton (P = .011). No differences were found in the types of anomalies between singleton and twin pregnancies. Central nervous system anomaly was the most common type in singleton and twin pregnancies. Twin pregnancies had higher rates of major anomalies than singleton (total OR 2.45), especially cardiovascular, central nervous, and gastrointestinal systems and ear/eye/face/neck disorders. CONCLUSIONS Compared with singleton, twin pregnancies had higher odds of detectable structural anomalies. Twin pregnancies with structural anomalies were diagnosed at earlier gestational age and associated with older maternal age. Central nervous system anomaly was the most common type in singleton and twin pregnancies.
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Affiliation(s)
- Yuan Ting
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Zhang Ting
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Zhao Fei
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Li Chun-Fang
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Han Zhen
- Department of Obstetrics & Gynecology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
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15
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Bao B, Hu H, Chen L, Lu S, Tang Q, Liang Z. SNP and DNA methylation analyses of a monozygotic twins discordant for complete endocardial cushion defect: a case report. Am J Transl Res 2022; 14:8271-8278. [PMID: 36505317 PMCID: PMC9730093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/24/2022] [Indexed: 12/15/2022]
Abstract
The exact cause of complete endocardial cushion defect (ECD) is still unknown. This report describes a unique pair of monozygotic twins (MZ twins) discordant for ECD. The chromosome karyotyping analysis revealed normal karyotype of 46, XY, 16qh+ and mat in both MZ twins. A genome-wide analysis of DNA using the Affymetrix SNP 6.0 revealed identical genotyping of single nucleotide polymorphisms (SNPs) and copy number variations (CNVs). An extensive methylation assay was carried out by NimbleGen 3 × 720 K CpG Island Plus RefSeq Promoter Arrays to analyze the potential epigenetic differences. The DNA methylation profiles of the affected twin seemed increased compared with that of the unaffected twin. However, further validation of Notch1 promoter hypermethylation and six top-ranked differentially methylated CpG sites by sodium bisulfate modification and methylation-specific PCR, failed to reveal consistent methylation differences between the twins. Other relevant factors, such as heritability and penetrance of the condition that place the MZ twins near to a threshold for ECD or variations in local epigenetic events in the twins' heart tissues, are probably responsible for the phenotypic discordance.
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Affiliation(s)
- Bihui Bao
- Department of Obstetrics and Gynecology, Qingbaijiang Women’s and Children’s Hospital (Maternal and Child Health Hospital), West China Second University Hospital, Sichuan UniversityChengdu 610300, Sichuan, China
| | - Hua Hu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital (Xinqiao Hospital), Army Medical UniversityChongqing 400037, China
| | - Limei Chen
- Department of Obstetrics and Gynecology, Qingbaijiang Women’s and Children’s Hospital (Maternal and Child Health Hospital), West China Second University Hospital, Sichuan UniversityChengdu 610300, Sichuan, China
| | - Shiyong Lu
- Department of Obstetrics and Gynecology, Qingbaijiang Women’s and Children’s Hospital (Maternal and Child Health Hospital), West China Second University Hospital, Sichuan UniversityChengdu 610300, Sichuan, China
| | - Qifeng Tang
- Department of Anesthesiology, Shanghai Hechuan-Rhine TCM HospitalShanghai 201103, China
| | - Zhiqing Liang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital (Southwest Hospital), Army Medical UniversityChongqing 400038, China
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16
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Heritability of musculoskeletal pain and pain sensitivity phenotypes: two generations of the Raine Study. Pain 2021; 163:e580-e587. [PMID: 34686644 DOI: 10.1097/j.pain.0000000000002411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/12/2021] [Indexed: 11/25/2022]
Abstract
ABSTRACT There is a need to better understand biological factors that increase the risk of persistent musculoskeletal pain and heightened pain sensitivity. Knowing the heritability (how genes account for differences in people's traits) can enhance the understanding of genetic versus environmental influences of pain and pain sensitivity. However, there are gaps in current knowledge, including the need for intergenerational studies to broaden our understanding of the genetic basis of pain. Data from Gen1 and Gen2 of the Raine Study were used to investigate the heritability of musculoskeletal pain, and pressure and cold pain sensitivity. Participants included parents (Gen 1, n=1092) and their offspring (Gen 2, n=688) who underwent a battery of testing and questionnaires including pressure and cold pain threshold testing and assessments of physical activity, sleep, musculoskeletal pain, mental health and adiposity. Heritability estimates were derived using the Sequential Oliogenic Linkage Analysis Routines (SOLAR) software. Heritability estimates for musculoskeletal pain and pressure pain sensitivity were significant, accounting for between 0.190 and 0.289 of the variation in the phenotype. In contrast, heritability of cold pain sensitivity was not significant. This is the largest intergenerational study to date to comprehensively investigate the heritability of both musculoskeletal pain and pain sensitivity, using robust statistical analysis. This study provides support for the heritability of musculoskeletal pain and pain sensitivity to pressure, suggesting the need for further convergence of genetic and environmental factors in models for the development and/or maintenance of these pain disorders.
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17
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Brosens E, Brouwer RWW, Douben H, van Bever Y, Brooks AS, Wijnen RMH, van IJcken WFJ, Tibboel D, Rottier RJ, de Klein A. Heritability and De Novo Mutations in Oesophageal Atresia and Tracheoesophageal Fistula Aetiology. Genes (Basel) 2021; 12:genes12101595. [PMID: 34680991 PMCID: PMC8535313 DOI: 10.3390/genes12101595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 01/12/2023] Open
Abstract
Tracheoesophageal Fistula (TOF) is a congenital anomaly for which the cause is unknown in the majority of patients. OA/TOF is a variable feature in many (often mono-) genetic syndromes. Research using animal models targeting genes involved in candidate pathways often result in tracheoesophageal phenotypes. However, there is limited overlap in the genes implicated by animal models and those found in OA/TOF-related syndromic anomalies. Knowledge on affected pathways in animal models is accumulating, but our understanding on these pathways in patients lags behind. If an affected pathway is associated with both animals and patients, the mechanisms linking the genetic mutation, affected cell types or cellular defect, and the phenotype are often not well understood. The locus heterogeneity and the uncertainty of the exact heritability of OA/TOF results in a relative low diagnostic yield. OA/TOF is a sporadic finding with a low familial recurrence rate. As parents are usually unaffected, de novo dominant mutations seems to be a plausible explanation. The survival rates of patients born with OA/TOF have increased substantially and these patients start families; thus, the detection and a proper interpretation of these dominant inherited pathogenic variants are of great importance for these patients and for our understanding of OA/TOF aetiology.
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Affiliation(s)
- Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
- Correspondence:
| | - Rutger W. W. Brouwer
- Department of Cell Biology, Center for Biomics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (R.W.W.B.); (W.F.J.v.I.)
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Alice S. Brooks
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Rene M. H. Wijnen
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (R.M.H.W.); (D.T.)
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Center for Biomics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (R.W.W.B.); (W.F.J.v.I.)
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (R.M.H.W.); (D.T.)
| | - Robbert J. Rottier
- Departments of Pediatric Surgery & Cell Biology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
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18
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White TL, Gonsalves MA. Dignity neuroscience: universal rights are rooted in human brain science. Ann N Y Acad Sci 2021; 1505:40-54. [PMID: 34350987 PMCID: PMC9291326 DOI: 10.1111/nyas.14670] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/25/2021] [Accepted: 07/08/2021] [Indexed: 01/22/2023]
Abstract
Universal human rights are defined by international agreements, law, foreign policy, and the concept of inherent human dignity. However, rights defined on this basis can be readily subverted by overt and covert disagreements and can be treated as distant geopolitical events rather than bearing on individuals’ everyday lives. A robust case for universal human rights is urgently needed and must meet several disparate requirements: (1) a framework that resolves tautological definitions reached solely by mutual, revocable agreement; (2) a rationale that transcends differences in beliefs, creed, and culture; and (3) a personalization that empowers both individuals and governments to further human rights protections. We propose that human rights in existing agreements comprise five elemental types: (1) agency, autonomy, and self‐determination; (2) freedom from want; (3) freedom from fear; (4) uniqueness; and (5) unconditionality, including protections for vulnerable populations. We further propose these rights and protections are rooted in fundamental properties of the human brain. We provide a robust, empirical foundation for universal rights based on emerging work in human brain science that we term dignity neuroscience. Dignity neuroscience provides an empirical foundation to support and foster human dignity, universal rights, and their active furtherance by individuals, nations, and international law.
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Affiliation(s)
- Tara L White
- Department of Behavioral and Social Sciences, School of Public Health, Brown University, Providence, Rhode Island.,Center for Alcohol and Addiction Studies, Brown University, Providence, Rhode Island.,Carney Institute for Brain Science, Brown University, Providence, Rhode Island.,University of Cambridge, England, Cambridge, UK
| | - Meghan A Gonsalves
- Neuroscience Graduate Program, Brown University, Providence, Rhode Island
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Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol 2021; 22:92. [PMID: 33781308 PMCID: PMC8006362 DOI: 10.1186/s13059-021-02285-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. RESULTS Here, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. CONCLUSIONS This study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.
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Affiliation(s)
- Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Taejeong Bae
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jeremy Thorpe
- Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Maxwell A Sherman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- MIT Department of Electrical Engineering and Computer Science, Cambridge, MA, USA
| | - Attila G Jones
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sean Cho
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Present Address: Arcus Biosciences, Hayward, CA, 94545, USA
| | | | - Yanmei Dou
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alon Galor
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Irene Lobon
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chaggai Rosenbluh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Simone Tomasi
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Livia Tomasini
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ryan Doan
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Yeongjun Jang
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - David Juan
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B Moldovan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Rujuta Narurkar
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
| | - Matthew T Oetjens
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shobana Sekar
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eduardo Soriano
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
- Vall d'Hebron Institut de Recerca, 08035, Barcelona, Spain
- Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain
- ICREA Academia, 08010 Barcelona, Spain
| | - Richard E Straub
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Andrew Chess
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Tomas Marquès-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel R Weinberger
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, 06520, USA
- Department of Neuroscience, Yale University, New Haven, 06520, CT, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Tashia and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Stanford, CA, 94305, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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20
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Amico S, Smith P, Tobi S, Perry M, Wallace A, Evans DG. Neurofibromatosis type 2 discordance in monozygous twins. Fam Cancer 2021; 19:37-40. [PMID: 31965447 DOI: 10.1007/s10689-019-00148-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Neurofibromatosis type 2 (NF2) is an autosomal dominant condition caused by pathogenic variants in the NF2 gene. The pathogenic variant is either inherited or obtained by de novo mutation, characterised by the presence of schwannomas, meningiomas and ependymomas. Here we report the presence of NF2 in one twin, with bilateral vestibular schwannomas and a pathogenic variant of the NF2 gene identified in both tumour and lymphocytes, while his monozygous brother remains asymptomatic. Imaging of the unaffected twin showed no tumour load and genetic testing via Sanger sequencing and Amplification Refractory Mutation System assay demonstrated low levels of expression of the NF2 variant in lymphocytes. Further testing on non-haemopoietic tissue showed little expression or absence of the pathogenic variant. Given there is no family history and the low level of the variant, we assume the pathogenic variant is a de novo mutation during embryogenesis. De novo mutations have been described as occurring at three possible time points in the creation of monozygous twins with different genetic make-up; prior to the twinning event, as a cause of the event, or after the twinning event. Of these options, we hypothesise that the discordance in the expression of the NF2 variant between these twins is likely due to a mutational event that occurred as a result of either of the latter two possibilities, between which we cannot determine. The pathogenic variant in lymphocytes was likely transferred between the twins through a shared blood supply in utero, and the non-haemopoietic samples that showed low levels of expression, were likely due to the presence of lymphocytic cells. Therefore, we have a discordance between monozygous twins at the NF2 gene.
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Affiliation(s)
- S Amico
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK.
| | - P Smith
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK
| | - S Tobi
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK
| | - M Perry
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK
| | - A Wallace
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK
| | - D G Evans
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK
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21
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Rydzanicz M, Olszewski P, Kedra D, Davies H, Filipowicz N, Bruhn-Olszewska B, Cavalli M, Szczałuba K, Młynek M, Machnicki MM, Stawiński P, Kostrzewa G, Krajewski P, Śladowski D, Chrzanowska K, Dumanski JP, Płoski R. Variable degree of mosaicism for tetrasomy 18p in phenotypically discordant monozygotic twins-Diagnostic implications. Mol Genet Genomic Med 2020; 9:e1526. [PMID: 33319479 PMCID: PMC7963419 DOI: 10.1002/mgg3.1526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 11/23/2022] Open
Abstract
Background Phenotypically discordant monozygotic twins (PDMZTs) offer a unique opportunity to study post‐zygotic genetic variation and provide insights into the linkage between genotype and phenotype. We report a comprehensive analysis of a pair of PDMZTs. Methods Dysmorphic features and delayed neuro‐motor development were observed in the proband, whereas her twin sister was phenotypically normal. Four tissues (blood, skin, hair follicles, and buccal mucosa) from both twins were studied using four complementary methods, including whole‐exome sequencing, karyotyping, array CGH, and SNP array. Results In the proband, tetrasomy 18p affecting all studied tissues except for blood was identified. Karyotyping of fibroblasts revealed isochromosome 18p [i(18p)] in all metaphases. The corresponding analysis of the phenotypically normal sister surprisingly revealed low‐level mosaicism (5.4%) for i(18p) in fibroblasts. Conclusion We emphasize that when mosaicism is suspected, multiple tissues should be studied and we highlight the usefulness of non‐invasive sampling of hair follicles and buccal mucosa as a convenient source of non‐mesoderm‐derived DNA, which complements the analysis of mesoderm using blood. Moreover, low‐level mosaic tetrasomy 18p is well tolerated and such low‐level mosaicism, readily detected by karyotyping, can be missed by other methods. Finally, mosaicism for low‐level tetrasomy 18p might be more common in the general population than it is currently recognized, due to detection limitations.
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Affiliation(s)
| | - Pawel Olszewski
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Darek Kedra
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Natalia Filipowicz
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Bozena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marco Cavalli
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Marlena Młynek
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marcin M Machnicki
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Grażyna Kostrzewa
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Paweł Krajewski
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Dariusz Śladowski
- Department of Transplantology and Central Tissue Bank, Centre for Biostructure, Medical University of Warsaw, Warsaw, Poland
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Jan P Dumanski
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland.,Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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22
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Jimenez-Antolinez YV, Gonzalez-Lopez EE, Ruiz IYV, Cantu-Moreno M, Gomez-Almaguer D, Gonzalez-Llano O. Concordant acute myeloblastic leukemia in identical twins treated with allogeneic transplantation from a younger HLA-identical sibling following a single apheresis procedure. Int J Hematol Oncol 2020; 10:IJH32. [PMID: 34136123 PMCID: PMC8191650 DOI: 10.2217/ijh-2020-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A concordant leukemia is that which occurs in a pair of monozygotic twins; a similar genetic background suggests an in utero monoclonal origin. We present the case of a pair of monozygotic infants with concordant acute myeloid leukemia who underwent a peripheral blood hematopoietic stem-cell transplant (HSCT) from a single, younger human leukocyte antigen-identical sibling donor, using a fractioned graft collected during only one apheresis procedure. Twin A relapsed at +456 and received a second haploidentical HSCT from his father, twin B has been in complete remission since the first HSCT. Both children are in complete remission and with negative minimal residual disease at +900 (after second transplant) and +1488, respectively.
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Affiliation(s)
| | - Elias Eugenio Gonzalez-Lopez
- Hematology Service, Hospital Universitario 'Dr. Jose E. Gonzalez', Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Ileana Yazmín Velasco Ruiz
- Hematology Service, Hospital Universitario 'Dr. Jose E. Gonzalez', Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Marcela Cantu-Moreno
- Hematology Service, Hospital Universitario 'Dr. Jose E. Gonzalez', Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - David Gomez-Almaguer
- Hematology Service, Hospital Universitario 'Dr. Jose E. Gonzalez', Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Oscar Gonzalez-Llano
- Hematology Service, Hospital Universitario 'Dr. Jose E. Gonzalez', Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
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23
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Fan X, Ping L, Sun H, Chen Y, Wang P, Liu T, Jiang R, Zhang X, Chen X. Whole-Exome Sequencing of Discordant Monozygotic Twin Families for Identification of Candidate Genes for Microtia-Atresia. Front Genet 2020; 11:568052. [PMID: 33193662 PMCID: PMC7642525 DOI: 10.3389/fgene.2020.568052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/01/2020] [Indexed: 11/13/2022] Open
Abstract
Objective We used data from twins and their families to probe the genetic factors contributing to microtia-atresia, in particular, early post-twinning variations that potentially account for the discordant phenotypes of monozygotic twin pairs. Methods Six families of monozygotic twins discordant for congenital microtia-atresia were recruited for study. The six patients shared a consistent clinical phenotype of unilateral microtia-atresia. Whole-exome sequencing (WES) was performed for all six twin pairs and their parents. Family segregation and multiple bioinformatics methods were applied to identify suspicious mutations in all families. Recurring mutations commonly detected in at least two families were highlighted. All variants were validated via Sanger sequencing. Gene Ontology (GO) analysis was performed to identify candidate gene sets and related pathways. Copy number variation (CNV), linkage analysis, association analysis and machine learning methods were additionally applied to isolate candidate mutations, and comparative genomics and structural modeling tools used to evaluate their potential roles in onset of microtia-atresia. Results Our analyses revealed 61 genes with suspected mutations associated with microtia-atresia. Five (HOXA4, MUC6, CHST15, TBX10, and AMER1) contained 7 de novo mutations that appeared in at least two families, which have been previously reported as pathogenic for other diseases. Among these, HOXA4 (c.920A>C, p.H307P) was determined as the most likely pathogenic variant for microtia-atresia. GO analysis revealed four gene sets involving 11 pathways potentially related to underlying pathogenesis of the disease. CNVs in three genes (UGT2B17, OVOS, and KATNAL2) were detected in at least two families. Linkage analysis disclosed 13 extra markers for the disease, of which two (FGFR1 and EYA1) were validated via machine learning analysis as plausible candidate genes for the disease. Conclusion Based on comprehensive genetic and bioinformatic analyses of WES data from six families of discordant monozygotic twins with microtia-atresia, we identified multiple candidate genes that may function in post-twinning onset of the disease. The collective findings provide novel insights into the pathogenesis of congenital microtia-atresia.
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Affiliation(s)
- Xinmiao Fan
- Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, China
| | - Lu Ping
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Sun
- Bioinformatics Division, BNRIST and MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Beijing, China
| | - Yushan Chen
- Department of Otolaryngology, The Ohio State University, Columbus, OH, United States
| | - Pu Wang
- Department of Otolaryngology Head and Neck Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing, China
| | - Rui Jiang
- Bioinformatics Division, BNRIST and MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Beijing, China
| | - Xuegong Zhang
- Bioinformatics Division, BNRIST and MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Beijing, China
| | - Xiaowei Chen
- Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, China
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24
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Rolf B, Krawczak M. The germlines of male monozygotic (MZ) twins: Very similar, but not identical. Forensic Sci Int Genet 2020; 50:102408. [PMID: 33157386 DOI: 10.1016/j.fsigen.2020.102408] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 11/19/2022]
Abstract
In 2012, a thought experiment in this journal suggested that paternity cases involving monozygotic (MZ) twins as putative fathers could be solved by means of whole genome sequencing (WGS). Although arising from a single fertilization event, MZ twins nevertheless continue to acquire somatic mutations during their development, including those that occur in the germline. Provided that paternity had been narrowed down to the twin pair beforehand by classical DNA analysis, one post-zygotic mutation would suffice to assign the paternal compartment of an offspring genome unambiguously to either twin if that mutation is found in the offspring and one twin, but not in the other twin. Since the publication of a proof-of-principle report in 2014, we have worked up five additional cases of MZ twin germline discrimination in real life, four paternity disputes and one criminal case requiring the identification of a sperm trace donor among a pair of MZ twin brothers. In this opinion paper, we report on the experiences made in the course of our work and take a look at possibilities for further development of the approach.
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Affiliation(s)
- Burkhard Rolf
- Eurofins Medigenomix Forensik GmbH, Anzinger Str. 7a, 85560, Ebersberg, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Brunswiker Strasse 10, 24105, Kiel, Germany.
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25
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Shi X, Radhakrishnan S, Wen J, Chen JY, Chen J, Lam BA, Mills RE, Stranger BE, Lee C, Setlur SR. Association of CNVs with methylation variation. NPJ Genom Med 2020; 5:41. [PMID: 33062306 PMCID: PMC7519119 DOI: 10.1038/s41525-020-00145-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 08/04/2020] [Indexed: 12/03/2022] Open
Abstract
Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated, the effects of CNVs is relatively less understood. To better characterize mechanisms by which CNVs affect cellular phenotype, we tested their association with variable CpG methylation in a genome-wide manner. Using paired CNV and methylation data from the 1000 genomes and HapMap projects, we identified genome-wide associations by methylation quantitative trait locus (mQTL) analysis. We found individual CNVs being associated with methylation of multiple CpGs and vice versa. CNV-associated methylation changes were correlated with gene expression. CNV-mQTLs were enriched for regulatory regions, transcription factor-binding sites (TFBSs), and were involved in long-range physical interactions with associated CpGs. Some CNV-mQTLs were associated with methylation of imprinted genes. Several CNV-mQTLs and/or associated genes were among those previously reported by genome-wide association studies (GWASs). We demonstrate that germline CNVs in the genome are associated with CpG methylation. Our findings suggest that structural variation together with methylation may affect cellular phenotype.
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Affiliation(s)
- Xinghua Shi
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA.,Present Address: Department of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122 USA
| | - Saranya Radhakrishnan
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115 USA
| | - Jia Wen
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA
| | - Jin Yun Chen
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115 USA
| | - Junjie Chen
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA.,Present Address: Department of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122 USA
| | - Brianna Ashlyn Lam
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, North Carolina 28223 USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109 USA
| | - Barbara E Stranger
- Department of Pharmacology, Northwestern University, Chicago, Illinois 60611 USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032 USA.,Department of Life Sciences, Ewha Womans University, Seoul, 03760 South Korea.,Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061 Shaanxi China
| | - Sunita R Setlur
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115 USA
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26
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Abstract
Mosaicism refers to the occurrence of two or more genomes in an individual derived from a single zygote. Germline mosaicism is a mutation that is limited to the gonads and can be transmitted to offspring. Somatic mosaicism is a postzygotic mutation that occurs in the soma, and it may occur at any developmental stage or in adult tissues. Mosaic variation may be classified in six ways: (a) germline or somatic origin, (b) class of DNA mutation (ranging in scale from single base pairs to multiple chromosomes), (c) developmental context, (d) body location(s), (e) functional consequence (including deleterious, neutral, or advantageous), and (f) additional sources of mosaicism, including mitochondrial heteroplasmy, exogenous DNA sources such as vectors, and epigenetic changes such as imprinting and X-chromosome inactivation. Technological advances, including single-cell and other next-generation sequencing, have facilitated improved sensitivity and specificity to detect mosaicism in a variety of biological contexts.
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Affiliation(s)
- Jeremy Thorpe
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Biochemistry, Cellular, and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA;
| | - Ikeoluwa A Osei-Owusu
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
| | | | - Rossella Tupler
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Biochemistry, Cellular, and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA; .,Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA; .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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27
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Lodewijk GA, Fernandes DP, Vretzakis I, Savage JE, Jacobs FMJ. Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels. Mol Biol Evol 2020; 37:2531-2548. [PMID: 32330268 PMCID: PMC7475042 DOI: 10.1093/molbev/msaa104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ever since the availability of genomes from Neanderthals, Denisovans, and ancient humans, the field of evolutionary genomics has been searching for protein-coding variants that may hold clues to how our species evolved over the last ∼600,000 years. In this study, we identify such variants in the human-specific NOTCH2NL gene family, which were recently identified as possible contributors to the evolutionary expansion of the human brain. We find evidence for the existence of unique protein-coding NOTCH2NL variants in Neanderthals and Denisovans which could affect their ability to activate Notch signaling. Furthermore, in the Neanderthal and Denisovan genomes, we find unusual NOTCH2NL configurations, not found in any of the modern human genomes analyzed. Finally, genetic analysis of archaic and modern humans reveals ongoing adaptive evolution of modern human NOTCH2NL genes, identifying three structural variants acting complementary to drive our genome to produce a lower dosage of NOTCH2NL protein. Because copy-number variations of the 1q21.1 locus, encompassing NOTCH2NL genes, are associated with severe neurological disorders, this seemingly contradicting drive toward low levels of NOTCH2NL protein indicates that the optimal dosage of NOTCH2NL may have not yet been settled in the human population.
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Affiliation(s)
- Gerrald A Lodewijk
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Diana P Fernandes
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Iraklis Vretzakis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics
| | - Frank M J Jacobs
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics
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Abstract
PURPOSE Biliary atresia (BA) in twins is extremely rare reported in the literature, but twin studies are useful methods of examining the associated factors of a complex disease. The objective of this study was to analyze the characteristics and patterns of biliary atresia in twins from reviewing available articles. METHODS PubMed and EMBASE databases were reviewed for related articles using the keywords ''biliary atresia'', ''twins'', ''monozygotic (MZ)'', and ''dizygotic (DZ)'', including relevant papers in the reference lists. RESULTS This analysis was extracted from 12 articles, with a total of 35 twin pairs included. BA was found in 36 out of 70 twin subjects (51.4%), of which had an even gender split. 97.1% twins were discordant, among 55.9% of which were monozygotic twin sets, indicating that BA may be related to genetic phenotype or penetrance. Isolated BA was the largest group with 27 (75%) affected twins. Only one pair of dizygotic twins (2.9%) demonstrate concordance for BA, and have one affected family member. CONCLUSION BA was found in nearly half of twin subjects with an even gender split. Isolated BA was the largest group, in which the number of monozygotic twins was similar with dizygotic twins, so the onset of the disease may not associate with the zygosity of twins. Most of twin sets had discordant disease presentation, especially monozygotic twins therein, emphasizing the role of epigenetic factor in the pathogenesis of BA. Future studies should take genetic testing among any twin sets in BA, especially the disease-associated mutations, thus be useful to investigate the etiology of disease.
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Gou Q, Chen Y, Yu C, Jia J, Feng J, Gao W, Zhu Z, Tang W, Tou J, Bian H, Wang B, Li Y, Li L, Ren H, Wu Y, Zhan J. Biliary atresia in twins'population: a retrospective multicenter study in mainland China. Pediatr Surg Int 2020; 36:711-718. [PMID: 32367198 DOI: 10.1007/s00383-020-04662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2020] [Indexed: 11/29/2022]
Abstract
AIM We evaluated the demographic of biliary atresia (BA) children from twins family and aimed to investigated what it can add to the twins' literature and our understanding of the disease. METHODS This study contains 11 medical centers in mainland China and the medical record of twins with BA was retrospectively analyzed from January 2012 to December 2018. Follow-up was carried out by out-patient review and questionnaire. RESULTS The study included 19 twin pairs in whom there was discordance for BA. Sixteen (84.2%) affected twin underwent Kasai Procedure (KP); median age at KP was 78 (49-168) days. There were ten affected twins that became jaundice-free at 3 months post-KP, and eight occurred with different degrees of cholangitis post-KP. Six affected twins received Liver Transplantation (LT) successfully. The 2 year native liver survival rate and the 2 year overall survival rate of affected twins were 61.1 and 94.4%, respectively. There were three affected monozygotic (MZ) twins and one healthy co-twin with BA-associated congenital malformations, all of which were cardiac malformations. The number of virus infection of affected MZ twins was significantly more (p = 0.04) than affected dizygotic (DZ) twin. CONCLUSIONS Discordance for BA in 19 pairs of twins supported that BA may be related to genetic phenotype or penetrance. The difference in genetic background between MZ and DZ affects the susceptibility of the host to virus infection. High acceptance of KP (84.2%) in our study implied a high motivation for treatment for twins with BA. Delays of KP (78 days) in affected twin may be related to the postnatal gradual onset and the late diagnosis.
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Affiliation(s)
- Qingyun Gou
- Graduate College, Tianjin Medical University, Tianjin, 300070, China.,Department of General Surgery, Tianjin Children's Hospital, LongYan Road 238, Beichen District, Tianjin, 300134, China
| | - Yang Chen
- Department of Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital of Jilin University, Changchun, 130021, China
| | - Chen Yu
- Department of Neonatal Surgery, Anhui Province Children's Hospital, Hefei, 230000, China
| | - Jinfu Jia
- Graduate College, Tianjin Medical University, Tianjin, 300070, China.,Department of General Surgery, Tianjin Children's Hospital, LongYan Road 238, Beichen District, Tianjin, 300134, China
| | - Jiexiong Feng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Gao
- Department of General Surgery, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Zhijun Zhu
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Weibing Tang
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Jinfa Tou
- Department of Neonatal Surgery, Children's Hospital, School of Medicine, Zhejiang University, Zhejiang, 310003, China
| | - Hongqiang Bian
- Department General of Surgery, Wuhan Children's Hospital, Wuhan, 430030, China
| | - Bin Wang
- Department of Surgery, Shenzhen Children's Hospital, Shenzhen, 518026, China
| | - Yingchao Li
- Department of Surgery, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Le Li
- Department of Surgery, Guangzhou Women and Children's Medical Center, Guangzhou, 511440, China
| | - Hongxia Ren
- Department of Neonatal Surgery, Children's Hospital of Shanxi, Taiyuan, 030013, China
| | - Yurui Wu
- Department of Thoracic and Oncological Surgery, Qilu Children's Hospital of Shandong University, Jinan, 250022, China
| | - Jianghua Zhan
- Department of General Surgery, Tianjin Children's Hospital, LongYan Road 238, Beichen District, Tianjin, 300134, China.
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30
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Twin Research in the Post-Genomic Era: Dissecting the Pathophysiological Effects of Adversity and the Social Environment. Int J Mol Sci 2020; 21:ijms21093142. [PMID: 32365612 PMCID: PMC7247668 DOI: 10.3390/ijms21093142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 11/29/2022] Open
Abstract
The role of twins in research is evolving as we move further into the post-genomic era. With the re-definition of what a gene is, it is becoming clear that biological family members who share a specific genetic variant may well not have a similar risk for future disease. This has somewhat invalidated the prior rationale for twin studies. Case co-twin study designs, however, are slowly emerging as the ideal tool to identify both environmentally induced epigenetic marks and epigenetic disease-associated processes. Here, we propose that twin lives are not as identical as commonly assumed and that the case co-twin study design can be used to investigate the effects of the adult social environment. We present the elements in the (social) environment that are likely to affect the epigenome and measures in which twins may diverge. Using data from the German TwinLife registry, we confirm divergence in both the events that occur and the salience for the individual start as early as age 11. Case co-twin studies allow for the exploitation of these divergences, permitting the investigation of the role of not only the adult social environment, but also the salience of an event or environment for the individual, in determining lifelong health trajectories. In cases like social adversity where it is clearly not possible to perform a randomised-controlled trial, we propose that the case co-twin study design is the most rigorous manner with which to investigate epigenetic mechanisms encoding environmental exposure. The role of the case co-twin design will continue to evolve, as we argue that it will permit causal inference from observational data.
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31
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Kushima I, Aleksic B, Nakatochi M, Shimamura T, Okada T, Uno Y, Morikawa M, Ishizuka K, Shiino T, Kimura H, Arioka Y, Yoshimi A, Takasaki Y, Yu Y, Nakamura Y, Yamamoto M, Iidaka T, Iritani S, Inada T, Ogawa N, Shishido E, Torii Y, Kawano N, Omura Y, Yoshikawa T, Uchiyama T, Yamamoto T, Ikeda M, Hashimoto R, Yamamori H, Yasuda Y, Someya T, Watanabe Y, Egawa J, Nunokawa A, Itokawa M, Arai M, Miyashita M, Kobori A, Suzuki M, Takahashi T, Usami M, Kodaira M, Watanabe K, Sasaki T, Kuwabara H, Tochigi M, Nishimura F, Yamasue H, Eriguchi Y, Benner S, Kojima M, Yassin W, Munesue T, Yokoyama S, Kimura R, Funabiki Y, Kosaka H, Ishitobi M, Ohmori T, Numata S, Yoshikawa T, Toyota T, Yamakawa K, Suzuki T, Inoue Y, Nakaoka K, Goto YI, Inagaki M, Hashimoto N, Kusumi I, Son S, Murai T, Ikegame T, Okada N, Kasai K, Kunimoto S, Mori D, Iwata N, Ozaki N. Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights. Cell Rep 2019; 24:2838-2856. [PMID: 30208311 DOI: 10.1016/j.celrep.2018.08.022] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/24/2018] [Accepted: 08/08/2018] [Indexed: 01/06/2023] Open
Abstract
Compelling evidence in Caucasian populations suggests a role for copy-number variations (CNVs) in autism spectrum disorder (ASD) and schizophrenia (SCZ). We analyzed 1,108 ASD cases, 2,458 SCZ cases, and 2,095 controls in a Japanese population and confirmed an increased burden of rare exonic CNVs in both disorders. Clinically significant (or pathogenic) CNVs, including those at 29 loci common to both disorders, were found in about 8% of ASD and SCZ cases, which was significantly higher than in controls. Phenotypic analysis revealed an association between clinically significant CNVs and intellectual disability. Gene set analysis showed significant overlap of biological pathways in both disorders including oxidative stress response, lipid metabolism/modification, and genomic integrity. Finally, based on bioinformatics analysis, we identified multiple disease-relevant genes in eight well-known ASD/SCZ-associated CNV loci (e.g., 22q11.2, 3q29). Our findings suggest an etiological overlap of ASD and SCZ and provide biological insights into these disorders.
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Affiliation(s)
- Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Masahiro Nakatochi
- Division of Data Science, Data Coordinating Center, Department of Advanced Medicine, Nagoya University Hospital, Nagoya, Aichi 466-8560, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Takashi Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yota Uno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Laboratory for Psychiatric and Molecular Neuroscience, McLean Hospital, Belmont, MA 02478, USA
| | - Mako Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Kanako Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Tomoko Shiino
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8553, Japan
| | - Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yuko Arioka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan; Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Aichi 466-8560, Japan
| | - Akira Yoshimi
- Division of Clinical Sciences and Neuropsychopharmacology, Faculty and Graduate School of Pharmacy, Meijo University, Nagoya, Aichi 468-8503, Japan
| | - Yuto Takasaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yanjie Yu
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yukako Nakamura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Maeri Yamamoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Tetsuya Iidaka
- Department of Physical and Occupational Therapy, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
| | - Shuji Iritani
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Toshiya Inada
- Department of Psychiatry and Psychobiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Nanayo Ogawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Emiko Shishido
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Youta Torii
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Center for Postgraduate Clinical Training and Career Development, Nagoya University Hospital, Nagoya, Aichi 466-8560, Japan
| | - Naoko Kawano
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Institutes of Innovation for Future Society, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yutaka Omura
- Aichi Psychiatric Medical Center, Nagoya, Aichi 464-0031, Japan
| | - Toru Yoshikawa
- Department of Child Psychiatry, Aichi Prefectural Colony Central Hospital, Kasugai, Aichi 480-0392, Japan
| | - Tokio Uchiyama
- Department of Clinical Psychology, Taisho University, Tokyo 170-8470, Japan
| | - Toshimichi Yamamoto
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Ryota Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Suita, Osaka 565-0871, Japan; Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8553, Japan
| | - Hidenaga Yamamori
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yuka Yasuda
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yuichiro Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Jun Egawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Ayako Nunokawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Masanari Itokawa
- Center for Medical Cooperation, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Makoto Arai
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Mitsuhiro Miyashita
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Akiko Kobori
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Michio Suzuki
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama 930-0194, Japan
| | - Tsutomu Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama 930-0194, Japan
| | - Masahide Usami
- Department of Child and Adolescent Psychiatry, Kohnodai Hospital, National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan
| | - Masaki Kodaira
- Department of Child and Adolescent Psychiatry, Kohnodai Hospital, National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan
| | - Kyota Watanabe
- Department of Child and Adolescent Psychiatry, Kohnodai Hospital, National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan
| | - Tsukasa Sasaki
- Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hitoshi Kuwabara
- Research Center for Child Mental Development, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Mamoru Tochigi
- Department of Neuropsychiatry, Teikyo University School of Medicine, Tokyo 173-8605, Japan
| | - Fumichika Nishimura
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Hidenori Yamasue
- Department of Psychiatry, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Yosuke Eriguchi
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Seico Benner
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Masaki Kojima
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Walid Yassin
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Toshio Munesue
- Research Center for Child Mental Development, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Shigeru Yokoyama
- Research Center for Child Mental Development, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yasuko Funabiki
- Department of Cognitive and Behavioral Science, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hirotaka Kosaka
- Research Center for Child Mental Development University of Fukui, Eiheiji, Fukui 910-1193, Japan; Department of Neuropsychiatry, Faculty of Medical Sciences, University of Fukui, Eiheiji, Fukui 910-1193, Japan
| | - Makoto Ishitobi
- Department of Neuropsychiatry, Faculty of Medical Sciences, University of Fukui, Eiheiji, Fukui 910-1193, Japan; Department of Child and Adolescent Mental Health, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Tetsuro Ohmori
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Shusuke Numata
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Tomoko Toyota
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Kazuhiro Yamakawa
- Laboratory for Neurogenetics, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Toshimitsu Suzuki
- Laboratory for Neurogenetics, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Yushi Inoue
- National Epilepsy Center, Shizuoka Institute of Epilepsy and Neurological Disorder, Shizuoka 420-8688, Japan
| | - Kentaro Nakaoka
- Aichi Psychiatric Medical Center, Nagoya, Aichi 464-0031, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Masumi Inagaki
- Department of Developmental Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8553, Japan
| | - Naoki Hashimoto
- Department of Psychiatry, Hokkaido University Graduate School of Medicine, Hokkaido, Sapporo 060-8638, Japan
| | - Ichiro Kusumi
- Department of Psychiatry, Hokkaido University Graduate School of Medicine, Hokkaido, Sapporo 060-8638, Japan
| | - Shuraku Son
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Tempei Ikegame
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Naohiro Okada
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; The International Research Center for Neurointelligence (WPI-IRCN) at The University of Tokyo Institutes for Advanced Study (UTIAS), Tokyo 113-0033, Japan
| | - Shohko Kunimoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Brain and Mind Research Center, Nagoya University, Nagoya, Aichi 466-8550, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan.
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32
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The Face of Early Cognitive Decline? Shape and Asymmetry Predict Choice Reaction Time Independent of Age, Diet or Exercise. Symmetry (Basel) 2019. [DOI: 10.3390/sym11111364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Slower reaction time is a measure of cognitive decline and can occur as early as 24 years of age. We are interested if developmental stability predicts cognitive performance independent of age and lifestyle (e.g., diet and exercise). Developmental stability is the latent capacity to buffer ontogenetic stressors and is measured by low fluctuating asymmetry (FA). FA is random—with respect to the largest side—departures from perfect morphological symmetry. The degree of asymmetry has been associated with physical fitness, morbidity, and mortality in many species, including humans. We expected that low FA (independent of age, diet and exercise) will predict faster choice reaction time (i.e., correct keyboard responses to stimuli appearing in a random location on a computer monitor). Eighty-eight university students self-reported their fish product consumption, exercise, had their faces 3D scanned and cognitive performance measured. Unexpectedly, increased fish product consumption was associated with worsened choice reaction time. Facial asymmetry and multiple face shape variation parameters predicted slower choice reaction time independent of sex, age, diet or exercise. Future work should develop longitudinal interventions to minimize early cognitive decline among vulnerable people (e.g., those who have experienced ontogenetic stressors affecting optimal neurocognitive development).
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33
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Scapoli L, Carinci F, Palmieri A, Cura F, Baj A, Beltramini G, Docimo R, Martinelli M. Copy number variation analysis of twin pairs discordant for cleft lip with or without cleft palate. Int J Immunopathol Pharmacol 2019; 33:2058738419855873. [PMID: 31663445 PMCID: PMC6822181 DOI: 10.1177/2058738419855873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a frequent orofacial malformation. The comparison of concordance rate observed in monozygotic and dizygotic twins supports high level of heritability and a strong genetic component. However, phenotype concordance for orofacial cleft in monozygotic twins is about 50%. The aim of the present investigation was to detect postzygotic events that may account for discordance in monozygotic twins. High-density SNP microarrays hybridization was used to genotype two pairs of monozygotic twins discordant for nsCL/P. Discordant SNP genotypes and copy number variants were analyzed to identify genetic differences responsible of phenotype discrepancy. A number of differences were observed, none involving known nsCL/P candidate genes or genomic regions. Considering the limitation of the study, related to the small sample size and to the large-scale investigation method, the results suggest that the detection of discordant events in other monozygotic twin pairs would be remarkable and warrant further investigations.
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Affiliation(s)
- Luca Scapoli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Francesco Carinci
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Annalisa Palmieri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Francesca Cura
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alessandro Baj
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy.,Maxillofacial and Dental Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giada Beltramini
- Maxillofacial and Dental Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Raffaella Docimo
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata," Rome, Italy
| | - Marcella Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
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Rylaarsdam L, Guemez-Gamboa A. Genetic Causes and Modifiers of Autism Spectrum Disorder. Front Cell Neurosci 2019; 13:385. [PMID: 31481879 PMCID: PMC6710438 DOI: 10.3389/fncel.2019.00385] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/06/2019] [Indexed: 12/18/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is one of the most prevalent neurodevelopmental disorders, affecting an estimated 1 in 59 children. ASD is highly genetically heterogeneous and may be caused by both inheritable and de novo gene variations. In the past decade, hundreds of genes have been identified that contribute to the serious deficits in communication, social cognition, and behavior that patients often experience. However, these only account for 10-20% of ASD cases, and patients with similar pathogenic variants may be diagnosed on very different levels of the spectrum. In this review, we will describe the genetic landscape of ASD and discuss how genetic modifiers such as copy number variation, single nucleotide polymorphisms, and epigenetic alterations likely play a key role in modulating the phenotypic spectrum of ASD patients. We also consider how genetic modifiers can alter convergent signaling pathways and lead to impaired neural circuitry formation. Lastly, we review sex-linked modifiers and clinical implications. Further understanding of these mechanisms is crucial for both comprehending ASD and for developing novel therapies.
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Affiliation(s)
| | - Alicia Guemez-Gamboa
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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35
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Abstract
Causal inference is essential across the biomedical, behavioural and social sciences.By progressing from confounded statistical associations to evidence of causal relationships, causal inference can reveal complex pathways underlying traits and diseases and help to prioritize targets for intervention. Recent progress in genetic epidemiology - including statistical innovation, massive genotyped data sets and novel computational tools for deep data mining - has fostered the intense development of methods exploiting genetic data and relatedness to strengthen causal inference in observational research. In this Review, we describe how such genetically informed methods differ in their rationale, applicability and inherent limitations and outline how they should be integrated in the future to offer a rich causal inference toolbox.
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36
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Smith‐Ferguson J, Beekman M. Can't see the colony for the bees: behavioural perspectives of biological individuality. Biol Rev Camb Philos Soc 2019; 94:1935-1946. [DOI: 10.1111/brv.12542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Jules Smith‐Ferguson
- School of Life and Environmental SciencesUniversity of Sydney Sydney New South Wales 2006 Australia
| | - Madeleine Beekman
- School of Life and Environmental SciencesUniversity of Sydney Sydney New South Wales 2006 Australia
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37
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Jansweijer JA, van Spaendonck-Zwarts KY, Tanck MWT, van Tintelen JP, Christiaans I, van der Smagt JJ, Vermeer AMC, Bos JM, Moss AJ, Swan H, Priori SG, Rydberg A, Tfelt-Hansen J, Ackerman MJ, Olivotto I, Charron P, Gimeno JR, van den Berg MP, Wilde AAM, Pinto YM. Heritability in genetic heart disease: the role of genetic background. Open Heart 2019; 6:e000929. [PMID: 31245010 PMCID: PMC6546190 DOI: 10.1136/openhrt-2018-000929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/17/2019] [Accepted: 02/03/2019] [Indexed: 11/22/2022] Open
Abstract
Background Mutations in genes encoding ion channels or sarcomeric proteins are an important cause of hereditary cardiac disease. However, the severity of the resultant disease varies considerably even among those with an identical mutation. Such clinical variation is often thought to be explained largely by differences in genetic background or 'modifier genes'. We aimed to test the prediction that identical genetic backgrounds result in largely similar clinical expression of a cardiac disease causing mutation, by studying the clinical expression of mutations causing cardiac disease in monozygotic twins. Methods We compared first available clinical information on 46 monozygotic twin pairs and 59 control pairs that had either a hereditary cardiomyopathy or channelopathy. Results Despite limited power of this study, we found significant heritability for corrected QT interval (QTc) in long QT syndrome (LQTS). We could not detect significant heritability for structural traits, but found a significant environmental effect on thickness of the interventricular septum in hypertrophic cardiomyopathy. Conclusions Our study confirms previously found robust heritability for electrical traits like QTc in LQTS, and adds information on low or lacking heritability for structural traits in heritable cardiomyopathies. This may steer the search for genetic modifiers in heritable cardiac disease.
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Affiliation(s)
- Joeri A Jansweijer
- Heart Center, Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | | | - Michael W T Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - J Peter van Tintelen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Clinical Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Imke Christiaans
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jasper J van der Smagt
- Department of Medical Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Alexa M C Vermeer
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - J Martijn Bos
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Arthur J Moss
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, New York, USA
| | - Heikki Swan
- Heart and Lung Center, Helsinki University Central Hospital, Helsinki, Finland
| | - Sylvia G Priori
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Annika Rydberg
- Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Jacob Tfelt-Hansen
- Department of Cardiology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michael J Ackerman
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Iacopo Olivotto
- Department of Cardiology, Careggi University Hospital, Florence, Italy
| | - Philippe Charron
- Department of Clinical Genetics, Hopital Ambroise-Pare, Boulogne-Billancourt, France
| | - Juan R Gimeno
- Department of Cardiology, Universitary Hospital Virgen Arrixaca, El Palmar, Murcia, Spain
| | | | - Arthur AM Wilde
- Heart Center, Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Centre of Excellence in Research of Hereditary Disorders, Princess Al-Jawhara Al-Brahim, Jeddah, Saudi Arabia
| | - Yigal M Pinto
- Heart Center, Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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Boer LL, Schepens-Franke AN, Oostra RJ. Two is a Crowd: Two is a Crowd: On the Enigmatic Etiopathogenesis of Conjoined Twinning. Clin Anat 2019; 32:722-741. [PMID: 31001856 PMCID: PMC6849862 DOI: 10.1002/ca.23387] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 04/16/2019] [Indexed: 12/31/2022]
Abstract
In this article, we provide a comprehensive overview of multiple facets in the puzzling genesis of symmetrical conjoined twins. The etiopathogenesis of conjoined twins remains matter for ongoing debate and is currently cited-in virtually every paper on conjoined twins-as partial fission or secondary fusion. Both theories could potentially be extrapolated from embryological adjustments exclusively seen in conjoined twins. Adoption of these, seemingly factual, theoretical proposals has (unconsciously) resulted in crystallized patterns of verbal and graphic representations concerning the enigmatic genesis of conjoined twins. Critical evaluation on their plausibility and solidity remains however largely absent. As it appears, both the fission and fusion theories cannot be applied to the full range of conjunction possibilities and thus remain matter for persistent inconclusiveness. We propose that initial duplication of axially located morphogenetic potent primordia could be the initiating factor in the genesis of ventrally, laterally, and caudally conjoined twins. The mutual position of two primordia results in neo-axial orientation and/or interaction aplasia. Both these embryological adjustments result in conjunction patterns that may seemingly appear as being caused by fission or fusion. However, as we will substantiate, neither fission nor fusion are the cause of most conjoined twinning types; rather what is interpreted as fission or fusion is actually the result of the twinning process itself. Furthermore, we will discuss the currently held views on the origin of conjoined twins and its commonly assumed etiological correlation with monozygotic twinning. Finally, considerations are presented which indicate that the dorsal conjunction group is etiologically and pathogenetically different from other symmetric conjoined twins. This leads us to propose that dorsally united twins could actually be caused by secondary fusion of two initially separate monozygotic twins. An additional reason for the ongoing etiopathogenetic debate on the genesis of conjoined twins is because different types of conjoined twins are classically placed in one overarching receptacle, which has hindered the quest for answers. Clin. Anat. 32:722-741, 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Lucas L Boer
- Department of Anatomy and Museum for Anatomy and Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Annelieke N Schepens-Franke
- Department of Anatomy and Museum for Anatomy and Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Roelof Jan Oostra
- Department of Medical Biology, Section Clinical Anatomy & Embryology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Nicolas G, Veltman JA. The role of de novo mutations in adult-onset neurodegenerative disorders. Acta Neuropathol 2019; 137:183-207. [PMID: 30478624 PMCID: PMC6513904 DOI: 10.1007/s00401-018-1939-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022]
Abstract
The genetic underpinnings of the most common adult-onset neurodegenerative disorders (AOND) are complex in majority of the cases. In some families, however, the disease can be inherited in a Mendelian fashion as an autosomal-dominant trait. Next to that, patients carrying mutations in the same disease genes have been reported despite a negative family history. Although challenging to demonstrate due to the late onset of the disease in most cases, the occurrence of de novo mutations can explain this sporadic presentation, as demonstrated for severe neurodevelopmental disorders. Exome or genome sequencing of patient-parent trios allows a hypothesis-free study of the role of de novo mutations in AOND and the discovery of novel disease genes. Another hypothesis that may explain a proportion of sporadic AOND cases is the occurrence of a de novo mutation after the fertilization of the oocyte (post-zygotic mutation) or even as a late-somatic mutation, restricted to the brain. Such somatic mutation hypothesis, that can be tested with the use of novel sequencing technologies, is fully compatible with the seeding and spreading mechanisms of the pathological proteins identified in most of these disorders. We review here the current knowledge and future perspectives on de novo mutations in known and novel candidate genes identified in the most common AONDs such as Alzheimer's disease, Parkinson's disease, the frontotemporal lobar degeneration spectrum and Prion disorders. Also, we review the first lessons learned from recent genomic studies of control and diseased brains and the challenges which remain to be addressed.
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Affiliation(s)
- Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, 22, Boulevard Gambetta, 76000, 76031, Rouen Cedex, France.
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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Nishioka M, Bundo M, Iwamoto K, Kato T. Somatic mutations in the human brain: implications for psychiatric research. Mol Psychiatry 2019; 24:839-856. [PMID: 30087451 PMCID: PMC6756205 DOI: 10.1038/s41380-018-0129-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/27/2018] [Accepted: 05/25/2018] [Indexed: 01/18/2023]
Abstract
Psychiatric disorders such as schizophrenia and bipolar disorder are caused by complex gene-environment interactions. While recent advances in genomic technologies have enabled the identification of several risk variants for psychiatric conditions, including single-nucleotide variants and copy-number variations, these factors can explain only a portion of the liability to these disorders. Although non-inherited factors had previously been attributed to environmental causes, recent genomic analyses have demonstrated that de novo mutations are among the main non-inherited risk factors for several psychiatric conditions. Somatic mutations in the brain may also explain how stochastic developmental events and environmental insults confer risk for a psychiatric disorder following fertilization. Here, we review evidence regarding somatic mutations in the brains of individuals with and without neuropsychiatric diseases. We further discuss the potential biological mechanisms underlying somatic mutations in the brain as well as the technical issues associated with the detection of somatic mutations in psychiatric research.
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Affiliation(s)
- Masaki Nishioka
- 0000 0001 2151 536Xgrid.26999.3dDivision for Counseling and Support, The University of Tokyo, Tokyo, Japan
| | - Miki Bundo
- 0000 0001 0660 6749grid.274841.cDepartment of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan ,0000 0004 1754 9200grid.419082.6PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama, Japan.
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Waller R, Hyde LW, Klump KL, Burt SA. Parenting Is an Environmental Predictor of Callous-Unemotional Traits and Aggression: A Monozygotic Twin Differences Study. J Am Acad Child Adolesc Psychiatry 2018; 57:955-963. [PMID: 30522741 PMCID: PMC6296820 DOI: 10.1016/j.jaac.2018.07.882] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 06/07/2018] [Accepted: 07/06/2018] [Indexed: 11/15/2022]
Abstract
OBJECTIVE Callous-unemotional (CU) traits increase risk for children to develop severe childhood aggression and conduct disorder. CU traits are typically described as highly heritable, and debate continues about whether the parenting environment matters in their etiology. Strong genetically informed designs are needed to test for the presence of environmental links between parenting practices and CU traits. Our objective was to determine whether parental harshness and parental warmth were related to children's aggression or CU traits when accounting for genetically mediated effects. METHOD We examined 227 monozygotic twin pairs (454 children) drawn from population-based and at-risk samples of twin families, leading to oversampling of twins living in poverty. We computed multi-informant difference scores combining mother and father reports of their harshness and warmth toward each twin, and differences in mother reports of each twin's aggression and CU traits. RESULTS Twin differences in parental harshness were related to differences in both aggression and CU traits, such that the twin who received harsher parenting had higher aggression and more CU traits. Differences in parental warmth were uniquely related to differences in CU traits, such that the twin receiving warmer parenting evidenced lower CU traits. These effects were not moderated by child sex, age, or family income, with the exception that the relationship between differential parental harshness and differential child aggression was stronger among low-income families. CONCLUSION Parenting is related to child CU traits and aggression, over and above genetically mediated effects, with low parental warmth being a unique environmental correlate of CU traits.
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Algady W, Louzada S, Carpenter D, Brajer P, Färnert A, Rooth I, Ngasala B, Yang F, Shaw MA, Hollox EJ. The Malaria-Protective Human Glycophorin Structural Variant DUP4 Shows Somatic Mosaicism and Association with Hemoglobin Levels. Am J Hum Genet 2018; 103:769-776. [PMID: 30388403 PMCID: PMC6218809 DOI: 10.1016/j.ajhg.2018.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/04/2018] [Indexed: 01/23/2023] Open
Abstract
Glycophorin A and glycophorin B are red blood cell surface proteins and are both receptors for the parasite Plasmodium falciparum, which is the principal cause of malaria in sub-Saharan Africa. DUP4 is a complex structural genomic variant that carries extra copies of a glycophorin A-glycophorin B fusion gene and has a dramatic effect on malaria risk by reducing the risk of severe malaria by up to 40%. Using fiber-FISH and Illumina sequencing, we validate the structural arrangement of the glycophorin locus in the DUP4 variant and reveal somatic variation in copy number of the glycophorin B-glycophorin A fusion gene. By developing a simple, specific, PCR-based assay for DUP4, we show that the DUP4 variant reaches a frequency of 13% in the population of a malaria-endemic village in south-eastern Tanzania. We genotype a substantial proportion of that village and demonstrate an association of DUP4 genotype with hemoglobin levels, a phenotype related to malaria, using a family-based association test. Taken together, we show that DUP4 is a complex structural variant that may be susceptible to somatic variation and show that DUP4 is associated with a malarial-related phenotype in a longitudinally followed population.
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Affiliation(s)
- Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Sandra Louzada
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Danielle Carpenter
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Paulina Brajer
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, 17176 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Ingegerd Rooth
- Nyamisati Malaria Research, Rufiji, National Institute for Medical Research, Dar-es-Salaam, Tanzania
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania; Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala Universitet, 75185 Uppsala, Sweden
| | - Fengtang Yang
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marie-Anne Shaw
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds LS9 7TF, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
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Watahiki M, Trewavas A. Systems, variation, individuality and plant hormones. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 146:3-22. [PMID: 30312622 DOI: 10.1016/j.pbiomolbio.2018.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/06/2018] [Indexed: 02/02/2023]
Abstract
Inter-individual variation in plants and particularly in hormone content, figures strongly in evolution and behaviour. Homo sapiens and Arabidopsis exhibit similar and substantial phenotypic and molecular variation. Whereas there is a very substantial degree of hormone variation in mankind, reports of inter-individual variation in plant hormone content are virtually absent but are likely to be as large if not larger than that in mankind. Reasons for this absence are discussed. Using an example of inter-individual variation in ethylene content in ripening, the article shows how biological time is compressed by hormones. It further resolves an old issue of very wide hormone dose response that result directly from negative regulation in hormone (and light) transduction. Negative regulation is used because of inter-individual variability in hormone synthesis, receptors and ancillary proteins, a consequence of substantial genomic and environmental variation. Somatic mosaics have been reported for several plant tissues and these too contribute to tissue variation and wide variation in hormone response. The article concludes by examining what variation exists in gravitropic responses. There are multiple sensing systems of gravity vectors and multiple routes towards curvature. These are an aspect of the need for reliability in both inter-individual variation and unpredictable environments. Plant hormone inter-individuality is a new area for research and is likely to change appreciation of the mechanisms that underpin individual behaviour.
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Affiliation(s)
- Masaaki Watahiki
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Anthony Trewavas
- Institute of Plant Molecular Science, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, EH9 3 JH, Scotland, United Kingdom.
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Abstract
DNA mutations as a consequence of errors during DNA damage repair, replication, or mitosis are the substrate for evolution. In multicellular organisms, mutations can occur in the germline and also in somatic tissues, where they are associated with cancer and other chronic diseases and possibly with aging. Recent advances in high-throughput sequencing have made it relatively easy to study germline de novo mutations, but in somatic cells, the vast majority of mutations are low-abundant and can be detected only in clonal lineages, such as tumors, or single cells. Here we review recent results on somatic mutations in normal human and animal tissues with a focus on their possible functional consequences.
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Affiliation(s)
- Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
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45
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Hiesinger PR, Hassan BA. The Evolution of Variability and Robustness in Neural Development. Trends Neurosci 2018; 41:577-586. [DOI: 10.1016/j.tins.2018.05.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/10/2018] [Accepted: 05/15/2018] [Indexed: 11/26/2022]
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Vucinovic M, Kardum G, Vukovic J, Vucinovic A. Maturational Changes of Delta Waves in Monozygotic and Dizygotic Infant Twins. J Exp Neurosci 2018; 12:1179069518797108. [PMID: 30181687 PMCID: PMC6111399 DOI: 10.1177/1179069518797108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 08/07/2018] [Indexed: 12/20/2022] Open
Abstract
AIMS To compare developmental changes of delta 1 (0.5-2.0 Hz) and delta 2 (2.25-3.75 Hz) power spectra between healthy monozygotic (MZ) and dizygotic (DZ) twin pairs and among MZ and DZ twin groups during active/REM (AS/REM) and quiet/NREM (QS/NREM) sleep stages at 38th, 46th, and 52nd weeks of postmenstrual age (PMA). MATERIALS AND METHODS Electroencephalography (EEG) recordings were analyzed using fast Fourier transforms. Differences in the developmental changes of delta power within twin pairs and between twin groups were estimated by calculating mean absolute differences of relative spectral values in delta 1 (0.5-2 Hz) and delta 2 (2.25-3.75 Hz) frequencies. RESULTS A review of electrodes showed that relative delta 1 power decreased, whereas delta 2 power increased from 38th toward 52nd week of PMA regardless of zygosity, sleep stages, and electrode position. Twin groups did not significantly differ (P > .05) in within-pair MZ and DZ similarity for delta 1 and delta 2 power spectra; similarity between MZ twin partners for delta 1 and delta 2 power spectra was as high as that of DZ twin partners on each electrode position, sleep stage, and period of measurement. CONCLUSIONS Developmental changes of delta 1 and delta 2 power spectra occurred equally in MZ and DZ twin groups during AS and QS sleep stages at 38th, 46th, and 52th PMA. The rhythm of EEG maturation evidenced by the maturation of delta 1 and delta 2 power spectra was not dependent on zygosity.
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Affiliation(s)
- Mirjana Vucinovic
- Neonatal Intensive Care Unit, Department
of Gynecology and Obstetrics, University Hospital Centre Split, Split, Croatia
| | - Goran Kardum
- Department of Psychology, Faculty of
Humanities and Social Sciences, University of Split, Split, Croatia
| | - Jonatan Vukovic
- Department of Internal Medicine,
University Hospital Centre Split, Split, Croatia
| | - Ana Vucinovic
- Department of Ophthalmology, University
Hospital Centre Split, Split, Croatia
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Aguilera JM, Kim BK, Park DJ. Particular Alimentations for Nutrition, Health and Pleasure. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 87:371-408. [PMID: 30678818 DOI: 10.1016/bs.afnr.2018.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
People around the world select their foods and meals according to particular choices based on physiological disorders and diseases, traditions, lifestyles, beliefs, etc. In this chapter, two of these particular alimentations are reviewed: those of the gourmet and the frail elderly. They take place in an environment where food is usually synonymous of body health disregarding its effects on social, cultural and psychological aspects, including emotions. Based on an extensive literature review, it is proposed that the paradigm changes from food equals health to food means well-being, the latter encompassing physical and physiological aspects as well as psychological, emotional and social aspects at the individual and societal levels. The growing food and nutrition requirements of an aging population are reviewed and special nutritious and enjoyable products available for this group are discussed.
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Affiliation(s)
- José Miguel Aguilera
- Department of Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Bum-Keun Kim
- Division of Strategic Food Research, Korea Food Research Institute, Seoul, South Korea
| | - Dong June Park
- Division of Strategic Food Research, Korea Food Research Institute, Seoul, South Korea
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Lacarrubba-Flores MDJ, Carvalho DR, Ribeiro EM, Moreno CA, Esposito AC, Marson FAL, Loureiro T, Cavalcanti DP. Femoral-facial syndrome: A review of the literature and 14 additional patients including a monozygotic discordant twin pair. Am J Med Genet A 2018; 176:1917-1928. [PMID: 30070764 DOI: 10.1002/ajmg.a.40425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 01/31/2023]
Abstract
Femoral-facial syndrome (FFS, OMIM 134780), also known as femoral hypoplasia-unusual face syndrome, is a rare sporadic syndrome associated with maternal diabetes, and comprising femoral hypoplasia/agenesis and a distinct facies characterized by micrognathia, cleft palate, and other minor dysmorphisms. The evaluation of 14 unpublished Brazilian patients, prompted us to make an extensive literature review comparing both sets of data. From 120 previously reported individuals with FFS, 66 were excluded due to: not meeting the inclusion criteria (n = 21); not providing sufficient data to ascertain the diagnosis (n = 29); were better assigned to another diagnosis (n = 3); and, being fetuses of the second trimester (n = 13) due to the obvious difficult to confirm a typical facies. Clinical-radiological and family information from 54 typical patients were collected and compared with the 14 new Brazilian patients. The comparison between the two sets of patients did not show any relevant differences. Femoral involvement was most frequently hypoplasia, observed in 91.2% of patients, and the typical facies was characterized by micrognathia (97%), cleft palate (61.8%), and minor dysmorphisms (frontal bossing 63.6%, short nose 91.7%, long philtrum 94.9%, and thin upper lip 92.3%). Clubfoot (55.9%) was commonly observed. Other observed findings may be part of FFS or may be simply concurrent anomalies since maternal diabetes is a common risk factor. While maternal diabetes was the only common feature observed during pregnancy (50.8%), no evidence for a monogenic basis was found. Moreover, a monozygotic discordant twin pair was described reinforcing the absence of a major genetic factor associated with FFS.
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Affiliation(s)
- Maria Dora Jazmin Lacarrubba-Flores
- Skeletal Dysplasia Group, Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas [Unicamp], Campinas, São Paulo, Brazil.,Perinatal Genetic Program, Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas [Unicamp], Campinas, São Paulo, Brazil
| | - Daniel Rocha Carvalho
- Genetic Unit, SARAH Network of Rehabilitation Hospital, Federal District, Brasilia, Brazil
| | | | - Carolina Araujo Moreno
- Skeletal Dysplasia Group, Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas [Unicamp], Campinas, São Paulo, Brazil.,Perinatal Genetic Program, Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas [Unicamp], Campinas, São Paulo, Brazil
| | - Ana Carolina Esposito
- Pediatric Division, Hospital Municipal Nossa Senhora do Loreto, Rio de Janeiro, Brazil
| | - Fernando Augusto Lima Marson
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas [Unicamp], Campinas, São Paulo, Brazil
| | - Thereza Loureiro
- Unit of Medical Genetics, Department of Genetics, Faculty of Medicine, University of São Paulo, Riberão Preto, São Paulo, Brazil
| | - Denise Pontes Cavalcanti
- Skeletal Dysplasia Group, Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas [Unicamp], Campinas, São Paulo, Brazil.,Perinatal Genetic Program, Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas [Unicamp], Campinas, São Paulo, Brazil
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Unravelling the Roles of Susceptibility Loci for Autoimmune Diseases in the Post-GWAS Era. Genes (Basel) 2018; 9:genes9080377. [PMID: 30060490 PMCID: PMC6115971 DOI: 10.3390/genes9080377] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/06/2018] [Accepted: 07/23/2018] [Indexed: 12/18/2022] Open
Abstract
Although genome-wide association studies (GWAS) have identified several hundred loci associated with autoimmune diseases, their mechanistic insights are still poorly understood. The human genome is more complex than single nucleotide polymorphisms (SNPs) that are interrogated by GWAS arrays. Apart from SNPs, it also comprises genetic variations such as insertions-deletions, copy number variations, and somatic mosaicism. Although previous studies suggest that common copy number variations do not play a major role in autoimmune disease risk, it is possible that certain rare genetic variations with large effect sizes are relevant to autoimmunity. In addition, other layers of regulations such as gene-gene interactions, epigenetic-determinants, gene and environmental interactions also contribute to the heritability of autoimmune diseases. This review focuses on discussing why studying these elements may allow us to gain a more comprehensive understanding of the aetiology of complex autoimmune traits.
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Copy Number Variants and Exome Sequencing Analysis in Six Pairs of Chinese Monozygotic Twins Discordant for Congenital Heart Disease. Twin Res Hum Genet 2018; 20:521-532. [PMID: 29192580 PMCID: PMC5729853 DOI: 10.1017/thg.2017.57] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Congenital heart disease (CHD) is one of the most common birth defects. More than 200 susceptibility loci have been identified for CHDs, yet a large part of the genetic risk factors remain unexplained. Monozygotic (MZ) twins are thought to be completely genetically identical; however, discordant phenotypes have been found in MZ twins. Recent studies have demonstrated genetic differences between MZ twins. We aimed to test whether copy number variants (CNVs) and/or genetic mutation differences play a role in the etiology of CHDs by using single nucleotide polymorphism (SNP) genotyping arrays and whole exome sequencing of twin pairs discordant for CHDs. Our goal was to identify mutations present only in the affected twins, which could identify novel candidates for CHD susceptibility loci. We present a comprehensive analysis for the CNVs and genetic mutation results of the selected individuals but detected no consistent differences within the twin pairs. Our study confirms that chromosomal structure or genetic mutation differences do not seem to play a role in the MZ twins discordant for CHD.
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