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Murphy AJ, Wilton SD, Aung-Htut MT, McIntosh CS. Down syndrome and DYRK1A overexpression: relationships and future therapeutic directions. Front Mol Neurosci 2024; 17:1391564. [PMID: 39114642 PMCID: PMC11303307 DOI: 10.3389/fnmol.2024.1391564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/15/2024] [Indexed: 08/10/2024] Open
Abstract
Down syndrome is a genetic-based disorder that results from the triplication of chromosome 21, leading to an overexpression of many triplicated genes, including the gene encoding Dual-Specificity Tyrosine Phosphorylation-Regulated Kinase 1A (DYRK1A). This protein has been observed to regulate numerous cellular processes, including cell proliferation, cell functioning, differentiation, and apoptosis. Consequently, an overexpression of DYRK1A has been reported to result in cognitive impairment, a key phenotype of individuals with Down syndrome. Therefore, downregulating DYRK1A has been explored as a potential therapeutic strategy for Down syndrome, with promising results observed from in vivo mouse models and human clinical trials that administered epigallocatechin gallate. Current DYRK1A inhibitors target the protein function directly, which tends to exhibit low specificity and selectivity, making them unfeasible for clinical or research purposes. On the other hand, antisense oligonucleotides (ASOs) offer a more selective therapeutic strategy to downregulate DYRK1A expression at the gene transcript level. Advances in ASO research have led to the discovery of numerous chemical modifications that increase ASO potency, specificity, and stability. Recently, several ASOs have been approved by the U.S. Food and Drug Administration to address neuromuscular and neurological conditions, laying the foundation for future ASO therapeutics. The limitations of ASOs, including their high production cost and difficulty delivering to target tissues can be overcome by further advances in ASO design. DYRK1A targeted ASOs could be a viable therapeutic approach to improve the quality of life for individuals with Down syndrome and their families.
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Affiliation(s)
- Aidan J. Murphy
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - May T. Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - Craig S. McIntosh
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
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Sarkar S, Patranabis S. Emerging Role of Extracellular Vesicles in Intercellular Communication in the Brain: Implications for Neurodegenerative Diseases and Therapeutics. Cell Biochem Biophys 2024; 82:379-398. [PMID: 38300375 DOI: 10.1007/s12013-024-01221-z] [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: 12/19/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024]
Abstract
Extracellular vesicles (EVs) are minute lipid-bilayer sacs discharged by cells, encompassing a diverse array of proteins, nucleic acids, and lipids. The identification of EVs as pivotal agents in intercellular communication has sparked compelling research pathways in the realms of cell biology and neurodegenerative diseases. Utilizing EVs for medicinal reasons has garnered interest due to the adaptability of EV-mediated communication. EVs can be classified based on their physical characteristics, biochemical composition, or cell of origin following purification. This review delves into the primary sub-types of EVs, providing an overview of the biogenesis of each type. Additionally, it explores the diverse environmental conditions triggering EV release and the originating cells, including stem cells and those from the Central Nervous System. Within the brain, EVs play a pivotal role as essential mediators of intercellular communication, significantly impacting synaptic plasticity, brain development, and the etiology of neurological diseases. Their potential diagnostic and therapeutic applications in various brain-related conditions are underscored, given their ability to carry specific cargo. Specially engineered EVs hold promise for treating diverse diseases, including neurodegenerative disorders. This study primarily emphasizes the diagnostic and potential therapeutic uses of EVs in neurological disorders such as Alzheimer's Disease, Huntington's Disease, Parkinson's Disease, Amyotrophic Lateral Sclerosis, and Prions disease. It also summarizes innovative techniques for detecting EVs in the brain, suggesting that EVs could serve as non-invasive biomarkers for early detection, disease monitoring, and prognosis in neurological disorders.
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Yahia S, Salem NA, El-Hawary A, Salem M, El-Farahaty RM, El-Gilany AEH, Shoaib RMS, Noureldin MA. Serum apelin-12 and obesity-related markers in Egyptian children with Down syndrome. Eur J Pediatr 2024; 183:461-470. [PMID: 37930396 PMCID: PMC10858121 DOI: 10.1007/s00431-023-05315-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
Children with Down syndrome (DS) exhibit higher overweight/obesity rates than their typically developing peers. Apelin-12 is a bioactive adipokine that exerts vital roles in obesity-related cardiometabolic comorbidities. To date, apelin-12 has not been investigated in obese-DS. This study aimed to explore the possible association between serum apelin-12 and obesity-related markers and to evaluate the efficiency of apelin-12 in the prediction of metabolic syndrome (MetS) in obese-DS compared to BMI Z-score matched obese-control. The cross-sectional study included 150 prepubertal children classified into three groups; obese-DS (n = 50), obese-control (n = 50), and normal-weight-control (n = 50). Anthropometric parameters, body adiposity, fasting serum levels of blood glucose (FBG), insulin, lipid profile, and apelin-12 were evaluated. Homeostasis model assessment of insulin resistance (HOMA-IR) was calculated from FBG and insulin. MetS was defined using Adult Treatment Panel III criteria modified for the pediatric age group. ROC curves were analyzed to evaluate the efficiency of apelin-12 in predicting MetS in obesity groups. Obese-DS exhibited higher body adiposity with marked central fat distribution, atherogenic lipid profile, and higher HOMA-IR compared to obese-control. Apelin-12 was significantly higher in obese-DS and obese-DS with MetS compared to obese-control and obese-control with MetS respectively (p < 0.001). The increase in apelin-12 with higher obesity grades was pronounced in obese-DS. Apelin-12 strongly correlated with body adiposity, several MetS risk factors, and HOMA-IR in obese-DS. Significantly higher AUC for apelin-12 in the diagnosis of MetS among obese-DS than obese-control (AUC = 0.948 vs. AUC = 0.807; p = 0.04). CONCLUSIONS The current study supports the crucial role of apelin-12 in obesity-related clinical and biochemical markers and in MetS in obese-DS and obese-control. Serum apelin-12 is a potential diagnostic biomarker for MetS with greater performance in obese-DS than obese-control raising its potential for clinical and therapeutic applications. WHAT IS KNOWN • Obese-DS children displayed excess body adiposity, Pronounced central fat distribution, atherogenic lipid profile, higher HOMA-IR, and higher prevalence of MetS than obese-control. WHAT IS NEW • Higher serum apelin-12 was observed in obese-DS and obese-DS with MetS than obese-control and obese-control with MetS respectively. The increase in apelin-12 level with increasing obesity grades was more pronounced in obese-DS. • Apelin-12 strongly correlated with obesity-related markers and MetS components in obese-DS. Apelin-12 performed better as a diagnostic biomarker for MetS in obese-DS than obese-control.
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Affiliation(s)
- Sohier Yahia
- Department of Pediatrics, Genetics Unit, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Nanees A Salem
- Department of Pediatrics, Endocrinology Unit, Faculty of Medicine, Mansoura University, Mansoura, Egypt.
- Mansoura University Children's Hospital, El-Gomhoria St, Post Office 35516, Box 50, Mansoura, 53355, Egypt.
| | - Amany El-Hawary
- Department of Pediatrics, Endocrinology Unit, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | | | - Reham M El-Farahaty
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | | | - Rasha M S Shoaib
- Food and Dairy Sciences and Technology Department, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
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Perluigi M, Di Domenico F, Butterfield DA. Oxidative damage in neurodegeneration: roles in the pathogenesis and progression of Alzheimer disease. Physiol Rev 2024; 104:103-197. [PMID: 37843394 PMCID: PMC11281823 DOI: 10.1152/physrev.00030.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/30/2023] [Accepted: 05/24/2023] [Indexed: 10/17/2023] Open
Abstract
Alzheimer disease (AD) is associated with multiple etiologies and pathological mechanisms, among which oxidative stress (OS) appears as a major determinant. Intriguingly, OS arises in various pathways regulating brain functions, and it seems to link different hypotheses and mechanisms of AD neuropathology with high fidelity. The brain is particularly vulnerable to oxidative damage, mainly because of its unique lipid composition, resulting in an amplified cascade of redox reactions that target several cellular components/functions ultimately leading to neurodegeneration. The present review highlights the "OS hypothesis of AD," including amyloid beta-peptide-associated mechanisms, the role of lipid and protein oxidation unraveled by redox proteomics, and the antioxidant strategies that have been investigated to modulate the progression of AD. Collected studies from our groups and others have contributed to unraveling the close relationships between perturbation of redox homeostasis in the brain and AD neuropathology by elucidating redox-regulated events potentially involved in both the pathogenesis and progression of AD. However, the complexity of AD pathological mechanisms requires an in-depth understanding of several major intracellular pathways affecting redox homeostasis and relevant for brain functions. This understanding is crucial to developing pharmacological strategies targeting OS-mediated toxicity that may potentially contribute to slow AD progression as well as improve the quality of life of persons with this severe dementing disorder.
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Affiliation(s)
- Marzia Perluigi
- Department of Biochemical Sciences "A. Rossi Fanelli," Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Fabio Di Domenico
- Department of Biochemical Sciences "A. Rossi Fanelli," Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - D Allan Butterfield
- Department of Chemistry and Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States
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Dalton SE, Workalemahu T, Allshouse AA, Page JM, Reddy UM, Saade GR, Pinar H, Goldenberg RL, Dudley DJ, Silver RM. Copy number variants and fetal growth in stillbirths. Am J Obstet Gynecol 2023; 228:579.e1-579.e11. [PMID: 36356697 PMCID: PMC10149588 DOI: 10.1016/j.ajog.2022.11.1274] [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: 04/27/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Fetal growth abnormalities are associated with a higher incidence of stillbirth, with small and large for gestational age infants incurring a 3 to 4- and 2 to 3-fold increased risk, respectively. Although clinical risk factors such as diabetes, hypertension, and placental insufficiency have been associated with fetal growth aberrations and stillbirth, the role of underlying genetic etiologies remains uncertain. OBJECTIVE This study aimed to assess the relationship between abnormal copy number variants and fetal growth abnormalities in stillbirths using chromosomal microarray. STUDY DESIGN A secondary analysis utilizing a cohort study design of stillbirths from the Stillbirth Collaborative Research Network was performed. Exposure was defined as abnormal copy number variants including aneuploidies, pathogenic copy number variants, and variants of unknown clinical significance. The outcomes were small for gestational age and large for gestational age stillbirths, defined as a birthweight <10th percentile and greater than the 90th percentile for gestational age, respectively. RESULTS Among 393 stillbirths with chromosomal microarray and birthweight data, 16% had abnormal copy number variants. The small for gestational age outcome was more common among those with abnormal copy number variants than those with a normal microarray (29.5% vs 16.5%; P=.038). This finding was consistent after adjusting for clinically important variables. In the final model, only abnormal copy number variants and maternal age remained significantly associated with small for gestational age stillbirths, with an adjusted odds ratio of 2.22 (95% confidence interval, 1.12-4.18). Although large for gestational age stillbirths were more likely to have an abnormal microarray: 6.2% vs 3.3% (P=.275), with an odds ratio of 2.35 (95% confidence interval, 0.70-7.90), this finding did not reach statistical significance. CONCLUSION Genetic abnormalities are more common in the setting of small for gestational age stillborn fetuses. Abnormal copy number variants not detectable by traditional karyotype make up approximately 50% of the genetic abnormalities in this population.
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Affiliation(s)
- Susan E Dalton
- University of Utah Health, Salt Lake City, UT; Intermountain Healthcare, Salt Lake City, UT
| | | | | | | | | | - George R Saade
- University of Texas Medical Branch at Galveston, Galveston, TX
| | - Halit Pinar
- Brown University School of Medicine, Providence, RI
| | | | | | - Robert M Silver
- University of Utah Health, Salt Lake City, UT; Intermountain Healthcare, Salt Lake City, UT.
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Liu Y, Zhang Y, Ren Z, Zeng F, Yan J. RUNX1 Upregulation Causes Mitochondrial Dysfunction via Regulating the PI3K-Akt Pathway in iPSC from Patients with Down Syndrome. Mol Cells 2023; 46:219-230. [PMID: 36625318 PMCID: PMC10086551 DOI: 10.14348/molcells.2023.2095] [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: 06/06/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 01/11/2023] Open
Abstract
Down syndrome (DS) is the most common autosomal aneuploidy caused by trisomy of chromosome 21. Previous studies demonstrated that DS affected mitochondrial functions, which may be associated with the abnormal development of the nervous system in patients with DS. Runt-related transcription factor 1 (RUNX1) is an encoding gene located on chromosome 21. It has been reported that RUNX1 may affect cell apoptosis via the mitochondrial pathway. The present study investigated whether RUNX1 plays a critical role in mitochondrial dysfunction in DS and explored the mechanism by which RUNX1 affects mitochondrial functions. Expression of RUNX1 was detected in induced pluripotent stem cells of patients with DS (DS-iPSCs) and normal iPSCs (N-iPSCs), and the mitochondrial functions were investigated in the current study. Subsequently, RUNX1 was overexpressed in N-iPSCs and inhibited in DS-iPSCs. The mitochondrial functions were investigated thoroughly, including reactive oxygen species levels, mitochondrial membrane potential, ATP content and lysosomal activity. Finally, RNA-sequencing was used to explore the global expression pattern. It was observed that the expression levels of RUNX1 in DS-iPSCs were significantly higher than those in normal controls. Impaired mitochondrial functions were observed in DS-iPSCs. Of note, overexpression of RUNX1 in N-iPSCs resulted in mitochondrial dysfunction, while inhibition of RUNX1 expression could improve the mitochondrial function in DS-iPSCs. Global gene expression analysis indicated that overexpression of RUNX1 may promote the induction of apoptosis in DS-iPSCs by activating the PI3K/Akt signaling pathway. The present findings indicate that abnormal expression of RUNX1 may play a critical role in mitochondrial dysfunction in DS-iPSCs.
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Affiliation(s)
- Yanna Liu
- Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
| | - Yuehua Zhang
- Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
| | - Zhaorui Ren
- Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Fanyi Zeng
- Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
- Department of Histoembryology, Genetics & Development, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingbin Yan
- Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
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Hu H, Geng Z, Zhang S, Xu Y, Wang Q, Chen S, Zhang B, Sun K, Lu Y. Rare copy number variation analysis identifies disease-related variants in atrioventricular septal defect patients. Front Genet 2023; 14:1075349. [PMID: 36816019 PMCID: PMC9936062 DOI: 10.3389/fgene.2023.1075349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Atrioventricular septal defect (AVSD) is a deleterious subtype of congenital heart diseases (CHD) characterized by atrioventricular canal defect. The pathogenic genetic changes of AVSD remain elusive, particularly for copy number variation (CNV), a large segment variation of the genome, which is one of the major forms of genetic variants resulting in congenital heart diseases. In the present study, we recruited 150 AVSD cases and 100 healthy subjects as controls for whole exome sequencing (WES). We identified total 4255 rare CNVs using exon Hidden Markov model (XHMM) and screened rare CNVs by eliminating common CNVs based on controls and Database of Genomic Variants (DGV). Each patient contained at least 9 CNVs, and the CNV burden was prominently presented in chromosomes 19,22,21&16. Small CNVs (<500 kb) were frequently observed. By leveraging gene-based burden test, we further identified 20 candidate AVSD-risk genes. Among them, DYRK1A, OBSCN and TTN were presented in the core disease network of CHD and highly and dynamically expressed in the heart during the development, which indicated they possessed the high potency to be AVSD-susceptible genes. These findings not only provided a roadmap for finally unveiling the genetic cause of AVSD, but also provided more resources and proofs for clinical genetics.
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Affiliation(s)
- Huan Hu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zilong Geng
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shasha Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuejuan Xu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qingjie Wang
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Sun Chen
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bing Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Bing Zhang, ; Kun Sun, ; Yanan Lu,
| | - Kun Sun
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Bing Zhang, ; Kun Sun, ; Yanan Lu,
| | - Yanan Lu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Bing Zhang, ; Kun Sun, ; Yanan Lu,
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Vione B, Ramacieri G, Zavaroni G, Piano A, La Rocca G, Caracausi M, Vitale L, Piovesan A, Gori C, Pirazzoli GL, Strippoli P, Cocchi G, Corvaglia L, Locatelli C, Pelleri MC, Antonaros F. One-carbon pathway metabolites are altered in the plasma of subjects with Down syndrome: Relation to chromosomal dosage. Front Med (Lausanne) 2022; 9:1006891. [PMID: 36530924 PMCID: PMC9751312 DOI: 10.3389/fmed.2022.1006891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/09/2022] [Indexed: 09/19/2023] Open
Abstract
Introduction Down syndrome (DS) is the most common chromosomal disorder and it is caused by trisomy of chromosome 21 (Hsa21). Subjects with DS show a large heterogeneity of phenotypes and the most constant clinical features present are typical facies and intellectual disability (ID). Several studies demonstrated that trisomy 21 causes an alteration in the metabolic profile, involving among all the one-carbon cycle. Methods We performed enzyme-linked immunosorbent assays (ELISAs) to identify the concentration of 5 different intermediates of the one-carbon cycle in plasma samples obtained from a total of 164 subjects with DS compared to 54 euploid subjects. We investigated: tetrahydrofolate (THF; DS n = 108, control n = 41), 5-methyltetrahydrofolate (5-methyl-THF; DS n = 140, control n = 34), 5-formyltetrahydrofolate (5-formyl-THF; DS n = 80, control n = 21), S-adenosyl-homocysteine (SAH; DS n = 94, control n = 20) and S-adenosyl-methionine (SAM; DS n = 24, control n = 15). Results Results highlight specific alterations of THF with a median concentration ratio DS/control of 2:3, a decrease of a necessary molecule perfectly consistent with a chromosomal dosage effect. Moreover, SAM and SAH show a ratio DS/control of 1.82:1 and 3.6:1, respectively. Discussion The relevance of these results for the biology of intelligence and its impairment in trisomy 21 is discussed, leading to the final proposal of 5-methyl-THF as the best candidate for a clinical trial aimed at restoring the dysregulation of one-carbon cycle in trisomy 21, possibly improving cognitive skills of subjects with DS.
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Affiliation(s)
- Beatrice Vione
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Giuseppe Ramacieri
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Giacomo Zavaroni
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Angela Piano
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Giorgia La Rocca
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Caterina Gori
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | | | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Guido Cocchi
- Neonatology Unit, IRCCS Sant’Orsola-Malpighi University Hospital, Bologna, Italy
| | - Luigi Corvaglia
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Neonatology Unit, IRCCS Sant’Orsola-Malpighi University Hospital, Bologna, Italy
| | - Chiara Locatelli
- Neonatology Unit, IRCCS Sant’Orsola-Malpighi University Hospital, Bologna, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
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Kleschevnikov AM. Enhanced GIRK2 channel signaling in Down syndrome: A feasible role in the development of abnormal nascent neural circuits. Front Genet 2022; 13:1006068. [PMID: 36171878 PMCID: PMC9510977 DOI: 10.3389/fgene.2022.1006068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
The most distinctive feature of Down syndrome (DS) is moderate to severe cognitive impairment. Genetic, molecular, and neuronal mechanisms of this complex DS phenotype are currently under intensive investigation. It is becoming increasingly clear that the abnormalities arise from a combination of initial changes caused by triplication of genes on human chromosome 21 (HSA21) and later compensatory adaptations affecting multiple brain systems. Consequently, relatively mild initial cognitive deficits become pronounced with age. This pattern of changes suggests that one approach to improving cognitive function in DS is to target the earliest critical changes, the prevention of which can change the ‘trajectory’ of the brain development and reduce the destructive effects of the secondary alterations. Here, we review the experimental data on the role of KCNJ6 in DS-specific brain abnormalities, focusing on a putative role of this gene in the development of abnormal neural circuits in the hippocampus of genetic mouse models of DS. It is suggested that the prevention of these early abnormalities with pharmacological or genetic means can ameliorate cognitive impairment in DS.
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Drug-Targeted Genomes: Mutability of Ion Channels and GPCRs. Biomedicines 2022; 10:biomedicines10030594. [PMID: 35327396 PMCID: PMC8945769 DOI: 10.3390/biomedicines10030594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
Mutations of ion channels and G-protein-coupled receptors (GPCRs) are not uncommon and can lead to cardiovascular diseases. Given previously reported multiple factors associated with high mutation rates, we sorted the relative mutability of multiple human genes by (i) proximity to telomeres and/or (ii) high adenine and thymine (A+T) content. We extracted genomic information using the genome data viewer and examined the mutability of 118 ion channel and 143 GPCR genes based on their association with factors (i) and (ii). We then assessed these two factors with 31 genes encoding ion channels or GPCRs that are targeted by the United States Food and Drug Administration (FDA)-approved drugs. Out of the 118 ion channel genes studied, 80 met either factor (i) or (ii), resulting in a 68% match. In contrast, a 78% match was found for the 143 GPCR genes. We also found that the GPCR genes (n = 20) targeted by FDA-approved drugs have a relatively lower mutability than those genes encoding ion channels (n = 11), where targeted genes encoding GPCRs were shorter in length. The result of this study suggests that the use of matching rate analysis on factor-druggable genome is feasible to systematically compare the relative mutability of GPCRs and ion channels. The analysis on chromosomes by two factors identified a unique characteristic of GPCRs, which have a significant relationship between their nucleotide sizes and proximity to telomeres, unlike most genetic loci susceptible to human diseases.
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Kleschevnikov A. GIRK2 Channels in Down Syndrome and Alzheimer's Disease. Curr Alzheimer Res 2022; 19:819-829. [PMID: 36567290 DOI: 10.2174/1567205020666221223122110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/27/2022]
Abstract
Cognitive impairment in Down syndrome (DS) results from the abnormal expression of hundreds of genes. However, the impact of KCNJ6, a gene located in the middle of the 'Down syndrome critical region' of chromosome 21, seems to stand out. KCNJ6 encodes GIRK2 (KIR3.2) subunits of G protein-gated inwardly rectifying potassium channels, which serve as effectors for GABAB, m2, 5HT1A, A1, and many other postsynaptic metabotropic receptors. GIRK2 subunits are heavily expressed in neocortex, cerebellum, and hippocampus. By controlling resting membrane potential and neuronal excitability, GIRK2 channels may thus affect both synaptic plasticity and stability of neural circuits in the brain regions important for learning and memory. Here, we discuss recent experimental data regarding the role of KCNJ6/GIRK2 in neuronal abnormalities and cognitive impairment in models of DS and Alzheimer's disease (AD). The results compellingly show that signaling through GIRK2 channels is abnormally enhanced in mouse genetic models of Down syndrome and that partial suppression of GIRK2 channels with pharmacological or genetic means can restore synaptic plasticity and improve impaired cognitive functions. On the other hand, signaling through GIRK2 channels is downregulated in AD models, such as models of early amyloidopathy. In these models, reduced GIRK2 channel signaling promotes neuronal hyperactivity, causing excitatory-inhibitory imbalance and neuronal death. Accordingly, activation of GABAB/GIRK2 signaling by GIRK channel activators or GABAB receptor agonists may reduce Aβ-induced hyperactivity and subsequent neuronal death, thereby exerting a neuroprotective effect in models of AD.
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12
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Antonaros F, Pitocco M, Abete D, Vione B, Piovesan A, Vitale L, Strippoli P, Caracausi M, Pelleri MC. Structural Characterization of the Highly Restricted Down Syndrome Critical Region on 21q22.13: New KCNJ6 and DSCR4 Transcript Isoforms. Front Genet 2021; 12:770359. [PMID: 34956324 PMCID: PMC8692863 DOI: 10.3389/fgene.2021.770359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022] Open
Abstract
Down syndrome (DS) is caused by trisomy of chromosome 21 and it is the most common genetic cause of intellectual disability (ID) in humans. Subjects with DS show a typical phenotype marked by facial dysmorphisms and ID. Partial trisomy 21 (PT21) is a rare genotype characterized by the duplication of a delimited chromosome 21 (Hsa21) portion and it may or may not be associated with DS diagnosis. The highly restricted Down syndrome critical region (HR-DSCR) is a region of Hsa21 present in three copies in all individuals with PT21 and a diagnosis of DS. This region, located on distal 21q22.13, is 34 kbp long and does not include characterized genes. The HR-DSCR is annotated as an intergenic region between KCNJ6-201 transcript encoding for potassium inwardly rectifying channel subfamily J member 6 and DSCR4-201 transcript encoding Down syndrome critical region 4. Two transcripts recently identified by massive RNA-sequencing (RNA-Seq) and automatically annotated on Ensembl database reveal that the HR-DSCR seems to be partially crossed by KCNJ6-202 and DSCR4-202 isoforms. KCNJ6-202 shares the coding sequence with KCNJ6-201 which is involved in many physiological processes, including heart rate in cardiac cells and circuit activity in neuronal cells. DSCR4-202 transcript has the first two exons in common with DSCR4-201, the only experimentally verified gene uniquely present in Hominidae. In this study, we performed in silico and in vitro analyses of the HR-DSCR. Bioinformatic data, obtained using Sequence Read Archive (SRA) and SRA-BLAST software, were confirmed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and Sanger sequencing on a panel of human tissues. Our data demonstrate that the HR-DSCR cannot be defined as an intergenic region. Further studies are needed to investigate the functional role of the new transcripts, likely involved in DS phenotypes.
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Affiliation(s)
- Francesca Antonaros
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Margherita Pitocco
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Domenico Abete
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Beatrice Vione
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Allison Piovesan
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Lorenza Vitale
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Pierluigi Strippoli
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Caracausi
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Chiara Pelleri
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
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13
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Zhang X, Wang B, You G, Xiang Y, Fu Q, Yu Y, Zhang X. Copy number variation analysis in Chinese children with complete atrioventricular canal and single ventricle. BMC Med Genomics 2021; 14:243. [PMID: 34627233 PMCID: PMC8502261 DOI: 10.1186/s12920-021-01090-y] [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] [Received: 12/14/2020] [Accepted: 09/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is one of the most common birth defects. Copy number variations (CNVs) have been proved to be important genetic factors that contribute to CHD. Here we screened genome-wide CNVs in Chinese children with complete atrioventricular canal (CAVC) and single ventricle (SV), since there were scarce researches dedicated to these two types of CHD. METHODS We screened CNVs in 262 sporadic CAVC cases and 259 sporadic SV cases respectively, using a customized SNP array. The detected CNVs were annotated and filtered using available databases. RESULTS Among 262 CAVC patients, we identified 6 potentially-causative CNVs in 43 individuals (16.41%, 43/262), including 2 syndrome-related CNVs (7q11.23 and 8q24.3 deletion). Surprisingly, 90.70% CAVC patients with detected CNVs (39/43) were found to carry duplications of 21q11.2-21q22.3, which were recognized as trisomy 21 (Down syndrome, DS). In CAVC with DS patients, the female to male ratio was 1.6:1.0 (24:15), and the rate of pulmonary hypertension (PH) was 41.03% (16/39). Additionally, 6 potentially-causative CNVs were identified in the SV patients (2.32%, 6/259), and none of them was trisomy 21. Most CNVs identified in our cohort were classified as rare (< 1%), occurring just once among CAVC or SV individuals except the 21q11.2-21q22.3 duplication (14.89%) in CAVC cohort. CONCLUSIONS Our study identified 12 potentially-causative CNVs in 262 CAVC and 259 SV patients, representing the largest cohort of these two CHD types in Chinese population. The results provided strong correlation between CAVC and DS, which also showed sex difference and high incidence of PH. The presence of potentially-causative CNVs suggests the etiology of complex CHD is incredibly diverse, and CHD candidate genes remain to be discovered.
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Affiliation(s)
- Xingyu Zhang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guoling You
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Xiang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qihua Fu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaoqing Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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14
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Illouz T, Biragyn A, Iulita MF, Flores-Aguilar L, Dierssen M, De Toma I, Antonarakis SE, Yu E, Herault Y, Potier MC, Botté A, Roper R, Sredni B, London J, Mobley W, Strydom A, Okun E. Immune Dysregulation and the Increased Risk of Complications and Mortality Following Respiratory Tract Infections in Adults With Down Syndrome. Front Immunol 2021; 12:621440. [PMID: 34248930 PMCID: PMC8267813 DOI: 10.3389/fimmu.2021.621440] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
The risk of severe outcomes following respiratory tract infections is significantly increased in individuals over 60 years, especially in those with chronic medical conditions, i.e., hypertension, diabetes, cardiovascular disease, dementia, chronic respiratory disease, and cancer. Down Syndrome (DS), the most prevalent intellectual disability, is caused by trisomy-21 in ~1:750 live births worldwide. Over the past few decades, a substantial body of evidence has accumulated, pointing at the occurrence of alterations, impairments, and subsequently dysfunction of the various components of the immune system in individuals with DS. This associates with increased vulnerability to respiratory tract infections in this population, such as the influenza virus, respiratory syncytial virus, SARS-CoV-2 (COVID-19), and bacterial pneumonias. To emphasize this link, here we comprehensively review the immunobiology of DS and its contribution to higher susceptibility to severe illness and mortality from respiratory tract infections.
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Affiliation(s)
- Tomer Illouz
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
- The Paul Feder Laboratory on Alzheimer’s Disease Research, Bar-Ilan University, Ramat Gan, Israel
| | - Arya Biragyn
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institute of Health, Baltimore, MD, United States
| | - Maria Florencia Iulita
- Sant Pau Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Biomedical Research Institute Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Center of Biomedical Investigation Network for Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Lisi Flores-Aguilar
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Mara Dierssen
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain
- University Pompeu Fabra, Barcelona, Spain
- Biomedical Research Networking Center for Rare Diseases (CIBERER), Barcelona, Spain
| | - Ilario De Toma
- Center for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain
- University Pompeu Fabra, Barcelona, Spain
- Biomedical Research Networking Center for Rare Diseases (CIBERER), Barcelona, Spain
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
- iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Eugene Yu
- The Children’s Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
- Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, United States
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique Biologie Moléculaire et Cellulaire, IGBMC - UMR 7104 - Inserm U1258, Illkirch, France
| | - Marie-Claude Potier
- Paris Brain Institute (ICM), CNRS UMR7225, INSERM U1127, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Alexandra Botté
- Paris Brain Institute (ICM), CNRS UMR7225, INSERM U1127, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Randall Roper
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Benjamin Sredni
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - William Mobley
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Andre Strydom
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry Psychology and Neuroscience, King’s College London, London, United Kingdom
- South London and Maudsley NHS Foundation Trust, London, United Kingdom
| | - Eitan Okun
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
- The Paul Feder Laboratory on Alzheimer’s Disease Research, Bar-Ilan University, Ramat Gan, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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15
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Jin C, Gu Z, Jiang X, Yu P, Xu T. A prenatal diagnosis case of partial duplication 21q21.1-q21.2 with normal phenotype maternally inherited. BMC Med Genomics 2021; 14:164. [PMID: 34147104 PMCID: PMC8214785 DOI: 10.1186/s12920-021-01013-x] [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: 11/28/2020] [Accepted: 06/11/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Down syndrome is characterized by trisomy 21 or partial duplication of chromosome 21. Extensive studies have focused on the identification of the Down Syndrome Critical Region (DSCR). We aim to provide evidence that duplication of 21q21.1-q21.2 should not be included in the DSCR and it has no clinical consequences on the phenotype. CASE PRESENTATION Because serological screening was not performed at the appropriate gestational age, noninvasive prenatal testing (NIPT) analysis was performed for a pregnant woman with normal prenatal examinations at 22 weeks of gestation. The NIPT results revealed a 5.8 Mb maternally inherited duplication of 21q21.1-q21.2. To assess whether the fetus also carried this duplication, ultrasound-guided amniocentesis was conducted, and the result of chromosomal microarray analysis (CMA) with amniotic fluid showed a 6.7 Mb duplication of 21q21.1-q21.2 (ranging from position 18,981,715 to 25,707,009). This partial duplication of 21q21.1-q21.2 in the fetus was maternally inherited. After genetic counseling, the pregnant woman and her family decided to continue the pregnancy. CONCLUSION Our case clearly indicates that 21q21.1-q21.2 duplication is not included in the DSCR and most likely has no clinical consequences on phenotype.
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Affiliation(s)
- Chunyan Jin
- Department of Medical Genetics and Prenatal Diagnosis, Hospital Affiliated 5 to Nantong University (Taizhou People's Hospital), 399 Hailing South Road, Taizhou, 225300, Jiangsu, China
| | - Zhiping Gu
- Department of Medical Genetics and Prenatal Diagnosis, Hospital Affiliated 5 to Nantong University (Taizhou People's Hospital), 399 Hailing South Road, Taizhou, 225300, Jiangsu, China
| | - Xiaohan Jiang
- Department of Medical Genetics and Prenatal Diagnosis, Hospital Affiliated 5 to Nantong University (Taizhou People's Hospital), 399 Hailing South Road, Taizhou, 225300, Jiangsu, China
| | - Pei Yu
- Department of Medical Genetics and Prenatal Diagnosis, Hospital Affiliated 5 to Nantong University (Taizhou People's Hospital), 399 Hailing South Road, Taizhou, 225300, Jiangsu, China
| | - Tianhui Xu
- Department of Medical Genetics and Prenatal Diagnosis, Hospital Affiliated 5 to Nantong University (Taizhou People's Hospital), 399 Hailing South Road, Taizhou, 225300, Jiangsu, China.
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16
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Locatelli C, Onnivello S, Antonaros F, Feliciello A, Filoni S, Rossi S, Pulina F, Marcolin C, Vianello R, Toffalini E, Ramacieri G, Martelli A, Procaccini G, Sperti G, Caracausi M, Pelleri MC, Vitale L, Pirazzoli GL, Strippoli P, Cocchi G, Piovesan A, Lanfranchi S. Is the Age of Developmental Milestones a Predictor for Future Development in Down Syndrome? Brain Sci 2021; 11:655. [PMID: 34069813 PMCID: PMC8157296 DOI: 10.3390/brainsci11050655] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 01/23/2023] Open
Abstract
Down Syndrome (DS) is the most common genetic alteration responsible for intellectual disability, which refers to deficits in both intellectual and adaptive functioning. According to this, individuals with Down Syndrome (DS) reach developmental milestones (e.g., sitting, walking, and babbling) in the same order as their typically developing peers, but later in life. Since developmental milestones are the first blocks on which development builds, the aims of the current study are to: (i) expand the knowledge of developmental milestone acquisition; and (ii) explore the relationship between developmental milestone acquisition and later development. For this purpose 105 children/adolescents with DS were involved in this study, divided in two groups, Preschoolers (n = 39) and School-age participants (n = 66). Information on the age of acquisition of Sitting, Walking, Babbling, and Sphincter Control was collected, together with cognitive, motor, and adaptive functioning. Sitting predicted later motor development, but, with age, it became less important in predicting motor development in everyday life. Babbling predicted later language development in older children. Finally, Sphincter Control emerged as the strongest predictor of motor, cognitive, language, and adaptive skills, with its role being more evident with increasing age. Our data suggest that the age of reaching the milestones considered in the study has an influence on successive development, a role that can be due to common neural substrates, the environment, and the developmental cascade effect.
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Affiliation(s)
- Chiara Locatelli
- IRCCS, St. Orsola-Malpighi Polyclinic, via Massarenti 11, 40138 Bologna, Italy; (C.L.); (A.F.); (S.F.); (S.R.); (A.M.); (G.P.); (G.S.)
| | - Sara Onnivello
- Department of Developmental Psychology and Socialization, University of Padova, via Venezia 8, 35131 Padova, Italy; (S.O.); (F.P.); (C.M.); (R.V.); (S.L.)
| | - Francesca Antonaros
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via Belmeloro 8, 40126 Bologna, Italy; (F.A.); (G.R.); (M.C.); (M.C.P.); (L.V.); (P.S.)
| | - Agnese Feliciello
- IRCCS, St. Orsola-Malpighi Polyclinic, via Massarenti 11, 40138 Bologna, Italy; (C.L.); (A.F.); (S.F.); (S.R.); (A.M.); (G.P.); (G.S.)
| | - Sonia Filoni
- IRCCS, St. Orsola-Malpighi Polyclinic, via Massarenti 11, 40138 Bologna, Italy; (C.L.); (A.F.); (S.F.); (S.R.); (A.M.); (G.P.); (G.S.)
- Specialisation School in Anesthesia, Intensive Care and Pain Care, University of Modena and Reggio Emilia, Largo del Pozzo, 71, 41125 Modena, Italy
| | - Sara Rossi
- IRCCS, St. Orsola-Malpighi Polyclinic, via Massarenti 11, 40138 Bologna, Italy; (C.L.); (A.F.); (S.F.); (S.R.); (A.M.); (G.P.); (G.S.)
| | - Francesca Pulina
- Department of Developmental Psychology and Socialization, University of Padova, via Venezia 8, 35131 Padova, Italy; (S.O.); (F.P.); (C.M.); (R.V.); (S.L.)
| | - Chiara Marcolin
- Department of Developmental Psychology and Socialization, University of Padova, via Venezia 8, 35131 Padova, Italy; (S.O.); (F.P.); (C.M.); (R.V.); (S.L.)
| | - Renzo Vianello
- Department of Developmental Psychology and Socialization, University of Padova, via Venezia 8, 35131 Padova, Italy; (S.O.); (F.P.); (C.M.); (R.V.); (S.L.)
| | - Enrico Toffalini
- Department of General Psychology, University of Padova, via Venezia 8, 35131 Padova, Italy;
| | - Giuseppe Ramacieri
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via Belmeloro 8, 40126 Bologna, Italy; (F.A.); (G.R.); (M.C.); (M.C.P.); (L.V.); (P.S.)
| | - Anna Martelli
- IRCCS, St. Orsola-Malpighi Polyclinic, via Massarenti 11, 40138 Bologna, Italy; (C.L.); (A.F.); (S.F.); (S.R.); (A.M.); (G.P.); (G.S.)
| | - Giulia Procaccini
- IRCCS, St. Orsola-Malpighi Polyclinic, via Massarenti 11, 40138 Bologna, Italy; (C.L.); (A.F.); (S.F.); (S.R.); (A.M.); (G.P.); (G.S.)
| | - Giacomo Sperti
- IRCCS, St. Orsola-Malpighi Polyclinic, via Massarenti 11, 40138 Bologna, Italy; (C.L.); (A.F.); (S.F.); (S.R.); (A.M.); (G.P.); (G.S.)
| | - Maria Caracausi
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via Belmeloro 8, 40126 Bologna, Italy; (F.A.); (G.R.); (M.C.); (M.C.P.); (L.V.); (P.S.)
| | - Maria Chiara Pelleri
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via Belmeloro 8, 40126 Bologna, Italy; (F.A.); (G.R.); (M.C.); (M.C.P.); (L.V.); (P.S.)
| | - Lorenza Vitale
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via Belmeloro 8, 40126 Bologna, Italy; (F.A.); (G.R.); (M.C.); (M.C.P.); (L.V.); (P.S.)
| | - Gian Luca Pirazzoli
- Medical Department, Maggiore Hospital, Largo Nigrisoli 2, 40133 Bologna, Italy;
| | - Pierluigi Strippoli
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via Belmeloro 8, 40126 Bologna, Italy; (F.A.); (G.R.); (M.C.); (M.C.P.); (L.V.); (P.S.)
| | - Guido Cocchi
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, via Massarenti 9, 40138 Bologna, Italy;
| | - Allison Piovesan
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, via Belmeloro 8, 40126 Bologna, Italy; (F.A.); (G.R.); (M.C.); (M.C.P.); (L.V.); (P.S.)
| | - Silvia Lanfranchi
- Department of Developmental Psychology and Socialization, University of Padova, via Venezia 8, 35131 Padova, Italy; (S.O.); (F.P.); (C.M.); (R.V.); (S.L.)
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17
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Saber MM, Karimiavargani M, Uzawa T, Hettiarachchi N, Hamada M, Ito Y, Saitou N. Possible roles for the hominoid-specific DSCR4 gene in human cells. Genes Genet Syst 2021; 96:1-11. [PMID: 33762515 DOI: 10.1266/ggs.20-00012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Down syndrome in humans is caused by trisomy of chromosome 21. DSCR4 (Down syndrome critical region 4) is a de novo-originated protein-coding gene present only in human chromosome 21 and its homologous chromosomes in apes. Despite being located in a medically critical genomic region and an abundance of evidence indicating its functionality, the roles of DSCR4 in human cells are unknown. We used a bioinformatic approach to infer the biological importance and cellular roles of this gene. Our analysis indicates that DSCR4 is likely involved in the regulation of interconnected biological pathways related to cell migration, coagulation and the immune system. We also showed that these predicted biological functions are consistent with tissue-specific expression of DSCR4 in migratory immune system leukocyte cells and neural crest cells (NCCs) that shape facial morphology in the human embryo. The immune system and NCCs are known to be affected in Down syndrome individuals, who suffer from DSCR4 misregulation, which further supports our findings. Providing evidence for the critical roles of DSCR4 in human cells, our findings establish the basis for further experimental investigations that will be necessary to confirm the roles of DSCR4 in the etiology of Down syndrome.
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Affiliation(s)
- Morteza M Saber
- Population Genetics Laboratory, National Institute of Genetics.,Department of Biological Sciences, Graduate School of Science, University of Tokyo.,Nano Medical Engineering Laboratory, RIKEN.,Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University
| | - Marziyeh Karimiavargani
- Nano Medical Engineering Laboratory, RIKEN.,Graduate School of Science and Engineering, Saitama University
| | | | | | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST)
| | | | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics.,Department of Biological Sciences, Graduate School of Science, University of Tokyo.,Department of Genetics, School of Life Science, Graduate University for Advanced Studies.,Faculty of Medicine, University of the Ryukyus
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18
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Moyer AJ, Gardiner K, Reeves RH. All Creatures Great and Small: New Approaches for Understanding Down Syndrome Genetics. Trends Genet 2020; 37:444-459. [PMID: 33097276 DOI: 10.1016/j.tig.2020.09.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/26/2022]
Abstract
Human chromosome 21 (Hsa21) contains more than 500 genes, making trisomy 21 one of the most complex genetic perturbations compatible with life. The ultimate goal of Down syndrome (DS) research is to design therapies that improve quality of life for individuals with DS by understanding which subsets of Hsa21 genes contribute to DS-associated phenotypes throughout the lifetime. However, the complexity of DS pathogenesis has made developing appropriate animal models an ongoing challenge. Here, we examine lessons learned from a variety of model systems, including yeast, nematode, fruit fly, and zebrafish, and discuss emerging methods for creating murine models that better reflect the genetic basis of trisomy 21.
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Affiliation(s)
- Anna J Moyer
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Katheleen Gardiner
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA (retired)
| | - Roger H Reeves
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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19
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Antonaros F, Ghini V, Pulina F, Ramacieri G, Cicchini E, Mannini E, Martelli A, Feliciello A, Lanfranchi S, Onnivello S, Vianello R, Locatelli C, Cocchi G, Pelleri MC, Vitale L, Strippoli P, Luchinat C, Turano P, Piovesan A, Caracausi M. Plasma metabolome and cognitive skills in Down syndrome. Sci Rep 2020; 10:10491. [PMID: 32591596 PMCID: PMC7319960 DOI: 10.1038/s41598-020-67195-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Trisomy 21 (Down syndrome, DS) is the main human genetic cause of intellectual disability (ID). Lejeune hypothesized that DS could be considered a metabolic disease, and we found that subjects with DS have a specific plasma and urinary metabolomic profile. In this work we confirmed the alteration of mitochondrial metabolism in DS and also investigated if metabolite levels are related to cognitive aspects of DS. We analyzed the metabolomic profiles of plasma samples from 129 subjects with DS and 46 healthy control (CTRL) subjects by 1H Nuclear Magnetic Resonance (NMR). Multivariate analysis of the NMR metabolomic profiles showed a clear discrimination (up to 94% accuracy) between the two groups. The univariate analysis revealed a significant alteration in 7 metabolites out of 28 assigned unambiguously. Correlations among the metabolite levels in DS and CTRL groups were separately investigated and statistically significant relationships appeared. On the contrary, statistically significant correlations among the NMR-detectable part of DS plasma metabolome and the different intelligence quotient ranges obtained by Griffiths-III or WPPSI-III tests were not found. Even if metabolic imbalance provides a clear discrimination between DS and CTRL groups, it appears that the investigated metabolomic profiles cannot be associated with the degree of ID.
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Affiliation(s)
- Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Veronica Ghini
- CIRMMP, Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, FI, Italy
| | - Francesca Pulina
- Department of Developmental Psychology and Socialization, University of Padova, Via Venezia 8, 35131, Padova, PD, Italy
| | - Giuseppe Ramacieri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Elena Cicchini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Elisa Mannini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Anna Martelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Agnese Feliciello
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Silvia Lanfranchi
- Department of Developmental Psychology and Socialization, University of Padova, Via Venezia 8, 35131, Padova, PD, Italy
| | - Sara Onnivello
- Department of Developmental Psychology and Socialization, University of Padova, Via Venezia 8, 35131, Padova, PD, Italy
| | - Renzo Vianello
- Department of Developmental Psychology and Socialization, University of Padova, Via Venezia 8, 35131, Padova, PD, Italy
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Guido Cocchi
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Claudio Luchinat
- CERM, Center of Magnetic Resonance and Department of Chemistry, University of Florence, via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Paola Turano
- CERM, Center of Magnetic Resonance and Department of Chemistry, University of Florence, via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
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Abstract
Experimental work regarding corrective actions on chromosomes and genes, and control of gene products is yielding promising results. It opens the way to advances in dealing with the etiological aspects of Down syndrome and may lead to important changes in the life of individuals affected with this condition. A small number of molecules are being investigated in pharmacological research that may have positive effects on intellectual functioning. Studies of the pathological consequences of the amyloid cascade and the TAU pathology in the etiology of Alzheimer disease (AD), which is more frequent and occuring earlier in life in persons with Down syndrome (DS), are presented. The search for biological markers of AD and ways for constrasting its early manifestations are also discussed.
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Affiliation(s)
- Jean A. Rondal
- University of Liège, Cognitive Sciences, Building 32, Sart Tilman, Liège 4000, Belgium
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21
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Zedníková I, Chylíková B, Šeda O, Korabečná M, Pazourková E, Břešťák M, Krkavcová M, Calda P, Hořínek A. Genome-wide miRNA profiling in plasma of pregnant women with down syndrome fetuses. Mol Biol Rep 2020; 47:4531-4540. [PMID: 32472298 PMCID: PMC7295716 DOI: 10.1007/s11033-020-05545-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/23/2020] [Indexed: 12/14/2022]
Abstract
Down syndrome (DS) is one of the most common causes of intellectual disability and new approaches allowing its rapid and effective prenatal detection are being explored. In this study, we investigated the diagnostic potential of plasma microRNAs (miRNAs). This study builds upon our previous study in DS placentas, where seven miRNAs were found to be significantly up-regulated. A total of 70 first-trimester plasma samples from pregnant women were included in the present study (35 samples with DS fetuses; 35 with euploid fetuses). Genome-wide miRNA profiling was performed in the pilot study using Affymetrix GeneChip™ miRNA 4.1 Array Strips (18 samples). Selected miRNAs were then analysed in the validation study using quantitative reverse transcription PCR (RT-qPCR; 52 samples). Based on the current pilot study results (12 miRNAs), our previous research on chorionic villi samples (7 miRNAs) and the literature (4 miRNAs), a group of 23 miRNAs was selected for the validation study. Although the results of the pilot study were promising, the validation study using the more sensitive RT-qPCR technique and a larger group of samples revealed no significant differences in miRNA profiles between the compared groups. Our results suggest that testing of the first-trimester plasma miRNAs is probably not suitable for non-invasive prenatal testing (NIPT). Different results could be theoretically achieved at later gestational ages; however, such a result probably would have limited use in clinical practice.
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Affiliation(s)
- Iveta Zedníková
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.
| | - Blanka Chylíková
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Ondřej Šeda
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Marie Korabečná
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Eva Pazourková
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Miroslav Břešťák
- Department of Obstetrics and Gynecology of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
- Screening Center ProfiG2, Prague, Czech Republic
| | | | - Pavel Calda
- Department of Obstetrics and Gynecology of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Aleš Hořínek
- Institute of Biology and Medical Genetics of the First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
- 3rd Department of Medicine, Department of Endocrinology and Metabolism, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
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22
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Zhou L, Zheng Z, Wu L, Xu C, Wu H, Xu X, Tang S. Molecular delineation of small supernumerary marker chromosomes using a single nucleotide polymorphism array. Mol Cytogenet 2020; 13:19. [PMID: 32514314 PMCID: PMC7251855 DOI: 10.1186/s13039-020-00486-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/15/2020] [Indexed: 12/18/2022] Open
Abstract
Background Defining the phenotype-genotype correlation of small supernumerary marker chromosomes (sSMCs) remains a challenge in prenatal diagnosis. We karyotyped 20,481 amniotic fluid samples from pregnant women and explored the molecular characteristics of sSMCs using a single nucleotide polymorphism (SNP) array. Results Out of the 20,481 samples, 15 abnormal karyotypes with sSMC were detected (frequency: 0.073%) and the chromosomal origin was successfully identified by SNP array in 14 of them. The origin of sSMCs were mainly acrocentric-derived chromosomes and the Y chromosome. Two cases of sSMC combined with uniparental disomy (UPD) were detected, UPD(1) and UPD(22). More than half of the cases of sSMC involved mosaicism (8/15) and pathogenicity (9/15) in prenatal diagnosis. A higher prevalence of mosaicism for non-acrocentric chromosomes than acrocentric chromosomes was also revealed. One sSMC derived from chromosome 3 with a neocentromere revealed a 24.99-Mb pathogenic gain of the 3q26.31q29 region on the SNP array, which presented as an abnormal ultrasound indicating nasal bone hypoplasia. Conclusion The clinical phenotypes of sSMCs are variable and so further genetic testing and parental karyotype analysis are needed to confirm the characteristics of sSMCs. The SNP array used here allows a detailed characterisation of the sSMC and establishes a stronger genotype-phenotype correlation, thus allowing detailed genetic counselling for prenatal diagnosis.
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Affiliation(s)
- Lili Zhou
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China
| | - Zhaoke Zheng
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China
| | - Lianpeng Wu
- Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325000 People's Republic of China
| | - Chenyang Xu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China
| | - Hao Wu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China
| | - Xueqin Xu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China
| | - Shaohua Tang
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000 People's Republic of China.,Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325000 People's Republic of China
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23
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Yu YE, Xing Z, Do C, Pao A, Lee EJ, Krinsky-McHale S, Silverman W, Schupf N, Tycko B. Genetic and epigenetic pathways in Down syndrome: Insights to the brain and immune system from humans and mouse models. PROGRESS IN BRAIN RESEARCH 2019; 251:1-28. [PMID: 32057305 PMCID: PMC7286740 DOI: 10.1016/bs.pbr.2019.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The presence of an extra copy of human chromosome 21 (Hsa21) leads to a constellation of phenotypic manifestations in Down syndrome (DS), including prominent effects on the brain and immune system. Intensive efforts to unravel the molecular mechanisms underlying these phenotypes may help developing effective therapies, both in DS and in the general population. Here we review recent progress in genetic and epigenetic analysis of trisomy 21 (Ts21). New mouse models of DS based on syntenic conservation of segments of the mouse and human chromosomes are starting to clarify the contributions of chromosomal subregions and orthologous genes to specific phenotypes in DS. The expression of genes on Hsa21 is regulated by epigenetic mechanisms, and with recent findings of highly recurrent gene-specific changes in DNA methylation patterns in brain and immune system cells with Ts21, the epigenomics of DS has become an active research area. Here we highlight the value of combining human studies with mouse models for defining DS critical genes and understanding the trans-acting effects of a simple chromosomal aneuploidy on genome-wide epigenetic patterning. These genetic and epigenetic studies are starting to uncover fundamental biological mechanisms, leading to insights that may soon become therapeutically relevant.
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Affiliation(s)
- Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States; Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, United States.
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Catherine Do
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Eun Joon Lee
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Sharon Krinsky-McHale
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, United States
| | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Pediatrics, University of California at Irvine, Irvine, CA, United States
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Benjamin Tycko
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States.
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24
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Pelleri MC, Cicchini E, Petersen MB, Tranebjærg L, Mattina T, Magini P, Antonaros F, Caracausi M, Vitale L, Locatelli C, Seri M, Strippoli P, Piovesan A, Cocchi G. Partial trisomy 21 map: Ten cases further supporting the highly restricted Down syndrome critical region (HR-DSCR) on human chromosome 21. Mol Genet Genomic Med 2019; 7:e797. [PMID: 31237416 PMCID: PMC6687668 DOI: 10.1002/mgg3.797] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 05/22/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Down syndrome (DS) is characterized by the presence of an extra full or partial human chromosome 21 (Hsa21). An invaluable model to define genotype-phenotype correlations in DS is the study of the extremely rare cases of partial (segmental) trisomy 21 (PT21), the duplication of only a delimited region of Hsa21 associated or not to DS. A systematic retrospective reanalysis of 125 PT21 cases described up to 2015 allowed the creation of the most comprehensive PT21 map and the identification of a 34-kb highly restricted DS critical region (HR-DSCR) as the minimal region whose duplication is shared by all PT21 subjects diagnosed with DS. We reanalyzed at higher resolution three cases previously published and we accurately searched for any new PT21 reports in order to verify whether HR-DSCR limits could prospectively be confirmed and possibly refined. METHODS Hsa21 partial duplications of three PT21 subjects were refined by adding array-based comparative genomic hybridization data. Seven newly described PT21 cases fulfilling stringent cytogenetic and clinical criteria have been incorporated into the PT21 integrated map. RESULTS The PT21 map now integrates fine structure of Hsa21 sequence intervals of 132 subjects onto a common framework fully consistent with the presence of a duplicated HR-DSCR, on distal 21q22.13 sub-band, only in DS subjects and not in non-DS individuals. No documented exception to the HR-DSCR model was found. CONCLUSIONS The findings presented here further support the association of the HR-DSCR with the diagnosis of DS, representing an unbiased validation of the original model. Further studies are needed to identify and characterize genetic determinants presumably located in the HR-DSCR and functionally associated to the critical manifestations of DS.
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Affiliation(s)
- Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied BiologyUniversity of BolognaBologna (BO)Italy
| | - Elena Cicchini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied BiologyUniversity of BolognaBologna (BO)Italy
| | - Michael B. Petersen
- Department of GeneticsAalborg University HospitalAalborgDenmark
- Department of Clinical GeneticsAalborg UniversityAalborgDenmark
| | - Lisbeth Tranebjærg
- Department of Clinical Genetics/RigshospitaletThe Kennedy CentreGlostrupDenmark
- University of Copenhagen, Institute of Clinical Medicine, The Panum InstituteCopenhagen NDenmark
| | - Teresa Mattina
- Department of PediatricsMedical Genetics University of CataniaItaly
| | - Pamela Magini
- Medical Genetics UnitSt. Orsola‐Malpighi PolyclinicBologna (BO)Italy
| | - Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied BiologyUniversity of BolognaBologna (BO)Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied BiologyUniversity of BolognaBologna (BO)Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied BiologyUniversity of BolognaBologna (BO)Italy
| | | | - Marco Seri
- Medical Genetics Unit, Department of Medical and Surgical Sciences (DIMEC)St. Orsola‐Malpighi Polyclinic, University of BolognaBologna (BO)Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied BiologyUniversity of BolognaBologna (BO)Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied BiologyUniversity of BolognaBologna (BO)Italy
| | - Guido Cocchi
- Neonatology Unit, Department of Medical and Surgical Sciences (DIMEC)St. Orsola‐Malpighi Polyclinic, University of BolognaBologna (BO)Italy
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25
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Orru S, Papoulidis I, Siomou E, Papadimitriou DT, Sotiriou S, Nikolaidis P, Eleftheriades M, Papanikolaou E, Thomaidis L, Manolakos E. Autism spectrum disorder, anxiety and severe depression in a male patient with deletion and duplication in the 21q22.3 region: A case report. Biomed Rep 2019; 1:1-5. [PMID: 31258897 DOI: 10.3892/br.2019.1210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/27/2019] [Indexed: 12/15/2022] Open
Abstract
In this report, a patient carrying a 650 kb deletion and a 759 kb duplication of chromosomal 21q22.3 region was described. Facial dysmorphic features, hypotonia, short stature, learning impairment, autism spectrum disorder, anxiety and depression were observed clinical characteristics. Mentioned copy number variants were the shortest in length reported so far. The current study hypothesized that the presence of a susceptibility locus for autism spectrum disorder associated with depression and anxiety may be located in a 200 kb region between the PCNT and PRMT2 genes. The current study aimed to provide insight into the human genome morbidity map of chromosome 21.
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Affiliation(s)
- Sandro Orru
- Department of Medical Genetics, University of Cagliari, Binaghi Hospital, I-09126 Cagliari, Italy
| | | | - Elisavet Siomou
- ATG P.C., Clinical Laboratory Genetics, Athens 11528, Greece
| | - Dimitrios T Papadimitriou
- Department of Pediatric Endocrinology and Diabetes, Athens Medical Center, Athens 15125, Greece.,Department of Clinical Embryology, Larissa Medical School, University of Thessaly, Larissa 41334, Greece
| | - Sotirios Sotiriou
- Department of Clinical Embryology, Larissa Medical School, University of Thessaly, Larissa 41334, Greece
| | | | - Makarios Eleftheriades
- Second Department of Obstetrics and Gynecology, Aretaieio Hospital, Medical School, National and Kapodistrian University of Athens, Athens 11528, Greece
| | - Evaggelos Papanikolaou
- Third Department in Obstetrics and Gynecology, Ippokratio Hospital, Aristotle University of Thessaloniki, Thessaloniki 54642, Greece
| | - Loretta Thomaidis
- Developmental Assessment Unit, Second Department of Pediatrics, 'P. & A. Kyriakou' Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - Emmanouil Manolakos
- Department of Medical Genetics, University of Cagliari, Binaghi Hospital, I-09126 Cagliari, Italy.,ATG P.C., Clinical Laboratory Genetics, Athens 11528, Greece.,Developmental Assessment Unit, Second Department of Pediatrics, 'P. & A. Kyriakou' Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens 11527, Greece
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26
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Piovesan A, Antonaros F, Vitale L, Strippoli P, Pelleri MC, Caracausi M. Human protein-coding genes and gene feature statistics in 2019. BMC Res Notes 2019; 12:315. [PMID: 31164174 PMCID: PMC6549324 DOI: 10.1186/s13104-019-4343-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/23/2019] [Indexed: 12/11/2022] Open
Abstract
Objective A well-known limit of genome browsers is that the large amount of genome and gene data is not organized in the form of a searchable database, hampering full management of numerical data and free calculations. Due to the continuous increase of data deposited in genomic repositories, their content revision and analysis is recommended. Using GeneBase, a software with a graphical interface able to import and elaborate National Center for Biotechnology Information (NCBI) Gene database entries, we provide tabulated spreadsheets updated to 2019 about human nuclear protein-coding gene data set ready to be used for any type of analysis about genes, transcripts and gene organization. Results Comparison with previous reports reveals substantial change in the number of known nuclear protein-coding genes (now 19,116), the protein-coding non-redundant transcriptome space [now 59,281,518 base pair (bp), 10.1% increase], the number of exons (now 562,164, 36.2% increase) due to a relevant increase of the RNA isoforms recorded. Other parameters such as gene, exon or intron mean and extreme length appear to have reached a stability that is unlikely to be substantially modified by human genome data updates, at least regarding protein-coding genes. Finally, we confirm that there are no human introns shorter than 30 bp.
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Affiliation(s)
- Allison Piovesan
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, BO, Italy
| | - Francesca Antonaros
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, BO, Italy
| | - Lorenza Vitale
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, BO, Italy
| | - Pierluigi Strippoli
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, BO, Italy
| | - Maria Chiara Pelleri
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, BO, Italy.
| | - Maria Caracausi
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, BO, Italy
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27
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Salvi A, Vezzoli M, Busatto S, Paolini L, Faranda T, Abeni E, Caracausi M, Antonaros F, Piovesan A, Locatelli C, Cocchi G, Alvisi G, De Petro G, Ricotta D, Bergese P, Radeghieri A. Analysis of a nanoparticle‑enriched fraction of plasma reveals miRNA candidates for Down syndrome pathogenesis. Int J Mol Med 2019; 43:2303-2318. [PMID: 31017260 PMCID: PMC6488180 DOI: 10.3892/ijmm.2019.4158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/20/2019] [Indexed: 12/12/2022] Open
Abstract
Down syndrome (DS) is caused by the presence of part or all of a third copy of chromosome 21. DS is associated with several phenotypes, including intellectual disability, congenital heart disease, childhood leukemia and immune defects. Specific microRNAs (miRNAs/miR) have been described to be associated with DS, although none of them so far have been unequivocally linked to the pathology. The present study focuses to the best of our knowledge for the first time on the miRNAs contained in nanosized RNA carriers circulating in the blood. Fractions enriched in nanosized RNA-carriers were separated from the plasma of young participants with DS and their non-trisomic siblings and miRNAs were extracted. A microarray-based analysis on a small cohort of samples led to the identification of the three most abundant miRNAs, namely miR-16-5p, miR-99b-5p and miR-144-3p. These miRNAs were then profiled for 15 pairs of DS and non-trisomic sibling couples by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Results identified a clear differential expression trend of these miRNAs in DS with respect to their non-trisomic siblings and gene ontology analysis pointed to their potential role in a number of typical DS features, including 'nervous system development', 'neuronal cell body' and certain forms of 'leukemia'. Finally, these expression levels were associated with certain typical quantitative and qualitative clinical features of DS. These results contribute to the efforts in defining the DS-associated pathogenic mechanisms and emphasize the importance of properly stratifying the miRNA fluid vehicles in order to probe biomolecules that are otherwise hidden and/or not accessible to (standard) analysis.
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Affiliation(s)
- Alessandro Salvi
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Marika Vezzoli
- Unit of Biostatistics, Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Sara Busatto
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Lucia Paolini
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Teresa Faranda
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Edoardo Abeni
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40138 Bologna, Italy
| | - Francesca Antonaros
- CSGI, Research Center for Colloids and Nanoscience, Sesto Fiorentino, I‑50019 Florence, Italy
| | - Allison Piovesan
- CSGI, Research Center for Colloids and Nanoscience, Sesto Fiorentino, I‑50019 Florence, Italy
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola‑Malpighi Polyclinic, I‑40138 Bologna, Italy
| | - Guido Cocchi
- Neonatology Unit, St. Orsola‑Malpighi Polyclinic, I‑40138 Bologna, Italy
| | - Gualtiero Alvisi
- Department of Molecular Medicine, University of Padua, I‑35121 Padua, Italy
| | - Giuseppina De Petro
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Doris Ricotta
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Annalisa Radeghieri
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
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Antonaros F, Olivucci G, Cicchini E, Ramacieri G, Pelleri MC, Vitale L, Strippoli P, Locatelli C, Cocchi G, Piovesan A, Caracausi M. MTHFR C677T polymorphism analysis: A simple, effective restriction enzyme-based method improving previous protocols. Mol Genet Genomic Med 2019; 7:e628. [PMID: 30868767 PMCID: PMC6503068 DOI: 10.1002/mgg3.628] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/04/2019] [Accepted: 02/11/2019] [Indexed: 12/16/2022] Open
Abstract
Background 5,10‐Methylentetrahydrofolate reductase (MTHFR) C677T polymorphism is one of the most studied genetic variations in the human genome. Polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) is one of the most used techniques to characterize the point mutations in genomic sequences because of its suitability and low cost. The most widely used method for the MTHFR C677T polymorphism characterization was developed by Frosst et al. (1995) but appears to have some technical limitations. The aim of this study was to propose a novel PCR‐RFLP method for the detection of this polymorphism. Methods In order to retrieve all published articles possibly describing any PCR‐RFLP methods useful to analyze MTHFR C677T polymorphism, we performed systematic queries on PubMed, using a combination of Boolean operators (AND/OR) and MeSH terms. Amplify software was used in order to design a new primer pair following the optimal standard criteria. Primer‐BLAST software was used to check primer pair's biological specificity. Results The analysis of previous literature showed that PCR‐RFLP method remains the most used technique. None of the 108 primer pairs described was ideal with regard to main accepted primer pair biochemical technical parameters. The new primer pair amplifies a DNA‐fragment of 513 base pair (bp) that, in the presence of the polymorphism, is cut by Hinf I enzyme in two pieces of 146 bp and 367 bp and clearly visible on 2% agarose gel. The level of expertise and the materials required are minimal and the protocol takes one day to carry out. Conclusion Our original PCR‐RFLP strategy, specifically designed to make the analysis optimal with respect to PCR primers and gel analysis, fits the ideal criteria compared to the widely used strategy by Frosst et al (1995) as well as any other PCR‐RFLP strategies proposed for MTHFR C677T polymorphism genotyping to date.
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Affiliation(s)
- Francesca Antonaros
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Giulia Olivucci
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Elena Cicchini
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Giuseppe Ramacieri
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Chiara Pelleri
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Lorenza Vitale
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Pierluigi Strippoli
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Guido Cocchi
- Neonatology Unit, Department of Medical and Surgical Sciences (DIMEC), St. Orsola-Malpighi Polyclinic, University of Bologna, Bologna, Italy
| | - Allison Piovesan
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Caracausi
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
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TAFAZOLI A, BEHJATI F, FARHUD DD, ABBASZADEGAN MR. Combination of Genetics and Nanotechnology for Down Syndrome Modification: A Potential Hypothesis and Review of the Literature. IRANIAN JOURNAL OF PUBLIC HEALTH 2019; 48:371-378. [PMID: 31223563 PMCID: PMC6570805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Down syndrome (DS) is one of the most prevalent genetic disorders in humans. The use of new approaches in genetic engineering and nanotechnology methods in combination with natural cellular phenomenon can modify the disease in affected people. We consider two CRISPR/Cas9 systems to cut a specific region from short arm of the chromosome 21 (Chr21) and replace it with a novel designed DNA construct, containing the essential genes in chromatin remodeling for inactivating of an extra Chr21. This requires mimicking of the natural cellular pattern for inactivation of the extra X chromosome in females. By means of controlled dosage of an appropriate Nano-carrier (a surface engineered Poly D, L-lactide-co-glycolide (PLGA) for integrating the relevant construct in Trisomy21 brain cell culture media and then in DS mouse model, we would be able to evaluate the modification and the reduction of the active extra Chr21 and in turn reduce substantial adverse effects of the disease, like intellectual disabilities. The hypothesis and study seek new insights in Down syndrome modification.
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Affiliation(s)
- Alireza TAFAZOLI
- Department of Analysis and Bioanalysis of Medicine, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, Bialystok, Poland, Department of Endocrinology, Diabetology and Internal Medicine, Clinical Research Center, Medical University of Bialystok, Bialystok, Poland
| | - Farkhondeh BEHJATI
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Dariush D. FARHUD
- School of Public Health, Tehran University of Medical Sciences, Tehran, Iran, Department of Basic Sciences, Iranian Academy of Medical Sciences, Tehran, Iran
| | - Mohammad Reza ABBASZADEGAN
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,Corresponding Author:
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Piovesan A, Pelleri MC, Antonaros F, Strippoli P, Caracausi M, Vitale L. On the length, weight and GC content of the human genome. BMC Res Notes 2019; 12:106. [PMID: 30813969 PMCID: PMC6391780 DOI: 10.1186/s13104-019-4137-z] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/15/2019] [Indexed: 01/08/2023] Open
Abstract
Objective Basic parameters commonly used to describe genomes including length, weight and relative guanine-cytosine (GC) content are widely cited in absence of a primary source. By using updated data and original software we determined these values to the best of our knowledge as standard reference for the whole human nuclear genome, for each chromosome and for mitochondrial DNA. We also devised a method to calculate the relative GC content in the whole messenger RNA sequence set and in transcriptomes by multiplying the GC content of each gene by its mean expression level. Results The male nuclear diploid genome extends for 6.27 Gigabase pairs (Gbp), is 205.00 cm (cm) long and weighs 6.41 picograms (pg). Female values are 6.37 Gbp, 208.23 cm, 6.51 pg. The individual variability and the implication for the DNA informational density in terms of bits/volume were discussed. The genomic GC content is 40.9%. Following analysis in different transcriptomes and species, we showed that the greatest deviation was observed in the pathological condition analysed (trisomy 21 leukaemic cells) and in Caenorhabditis elegans. Our results may represent a solid basis for further investigation on human structural and functional genomics while also providing a framework for other genome comparative analysis. Electronic supplementary material The online version of this article (10.1186/s13104-019-4137-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
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Schnabel F, Smogavec M, Funke R, Pauli S, Burfeind P, Bartels I. Down syndrome phenotype in a boy with a mosaic microduplication of chromosome 21q22. Mol Cytogenet 2018; 11:62. [PMID: 30619508 PMCID: PMC6310980 DOI: 10.1186/s13039-018-0410-4] [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] [Received: 07/26/2018] [Accepted: 12/02/2018] [Indexed: 12/14/2022] Open
Abstract
Background Down syndrome, typically caused by trisomy 21, may also be associated by duplications of the Down syndrome critical region (DSCR) on chromosome 21q22. However, patients with small duplications of DSCR without accompanying deletions have rarely been reported. Case presentation Here we report a 5½-year-old boy with clinical features of Down syndrome including distinct craniofacial dysmorphism and sandal gaps as well as developmental delay. Conventional karyotype was normal, whereas interphase FISH analysis revealed three signals for DSCR in approximately 40% of lymphocytes and 80% of buccal mucosa cells. Array-CGH analysis confirmed a 2.56 Mb duplication of chromosome 21q22.13q22.2 encompassing DYRK1A. Conclusion This presents one of the smallest duplications within DSCR leading to a Down syndrome phenotype. Since the dosage sensitive gene DYRK1A is the only duplicated candidate DSCR gene in our patient, this finding supports the hypothesis that DYRK1A contributes to dysmorphic and intellectual features of Down syndrome even in a mosaic state.
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Affiliation(s)
- Franziska Schnabel
- 1Institute of Human Genetics, University Medical Center, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany
| | - Mateja Smogavec
- 1Institute of Human Genetics, University Medical Center, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany
| | - Rudolf Funke
- Department of Neuropediatrics, Sozialpädiatrisches Zentrum, Mönchebergstr. 41-43, 34125 Kassel, Germany
| | - Silke Pauli
- 1Institute of Human Genetics, University Medical Center, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany
| | - Peter Burfeind
- 1Institute of Human Genetics, University Medical Center, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany
| | - Iris Bartels
- 1Institute of Human Genetics, University Medical Center, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany
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Zhao X, Bhattacharyya A. Human Models Are Needed for Studying Human Neurodevelopmental Disorders. Am J Hum Genet 2018; 103:829-857. [PMID: 30526865 DOI: 10.1016/j.ajhg.2018.10.009] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 10/09/2018] [Indexed: 12/19/2022] Open
Abstract
The analysis of animal models of neurological disease has been instrumental in furthering our understanding of neurodevelopment and brain diseases. However, animal models are limited in revealing some of the most fundamental aspects of development, genetics, pathology, and disease mechanisms that are unique to humans. These shortcomings are exaggerated in disorders that affect the brain, where the most significant differences between humans and animal models exist, and could underscore failures in targeted therapeutic interventions in affected individuals. Human pluripotent stem cells have emerged as a much-needed model system for investigating human-specific biology and disease mechanisms. However, questions remain regarding whether these cell-culture-based models are sufficient or even necessary. In this review, we summarize human-specific features of neurodevelopment and the most common neurodevelopmental disorders, present discrepancies between animal models and human diseases, demonstrate how human stem cell models can provide meaningful information, and discuss the challenges that exist in our pursuit to understand distinctively human aspects of neurodevelopment and brain disease. This information argues for a more thoughtful approach to disease modeling through consideration of the valuable features and limitations of each model system, be they human or animal, to mimic disease characteristics.
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Affiliation(s)
- Xinyu Zhao
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA.
| | - Anita Bhattacharyya
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA.
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Vormittag-Nocito E, Ni H, Schmidt ML, Lindgren V. Thrombocytopenia and Predisposition to Acute Myeloid Leukemia due to Mosaic Ring 21 with Loss of RUNX1: Cytogenetic and Molecular Characterization. Mol Syndromol 2018; 9:306-311. [PMID: 30800047 DOI: 10.1159/000494645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2018] [Indexed: 12/14/2022] Open
Abstract
Familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML) has been well documented in the literature and is a new entity within the latest revised edition of the WHO Classification of Tumors of Hematopoietic and Lymphoid Tissues (OMIM). The disorder arises due to mutations within the RUNX1 gene in chromosome 21; mutations within the Runt-binding domain are the most commonly encountered anomalies that cause decreased platelet count and function. Rare cases of haploinsufficiency have also been shown to cause this disorder. Here, we describe a 12-year-old female with mosaicism for a ring chromosome 21 and monosomy 21 who was born with thrombocytopenia which is now explained by loss of the RUNX1 gene resulting in FPD/AML. We also comment on the structure of the ring and the mechanism of its formation.
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Affiliation(s)
| | | | - Mary L Schmidt
- Department of Pediatrics, University of Illinois at Chicago, Chicago, IL, USA
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Li W, Wang X, Li S. Investigation of copy number variations on chromosome 21 detected by comparative genomic hybridization (CGH) microarray in patients with congenital anomalies. Mol Cytogenet 2018; 11:42. [PMID: 31061677 PMCID: PMC6497326 DOI: 10.1186/s13039-018-0391-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/19/2018] [Indexed: 11/10/2022] Open
Abstract
Background The clinical features of Down syndrome vary among individuals, with those most common being congenital heart disease, intellectual disability, developmental abnormity and dysmorphic features. Complex combination of Down syndrome phenotype could be produced by partially copy number variations (CNVs) on chromosome 21 as well. By comparing individual with partial CNVs of chromosome 21 with other patients of known CNVs and clinical phenotypes, we hope to provide a better understanding of the genotype-phenotype correlation of chromosome 21. Methods A total of 2768 pediatric patients sample collected at the Genetics Laboratory at Oklahoma University Health Science Center were screened using CGH Microarray for CNVs on chromosome 21. Results We report comprehensive clinical and molecular descriptions of six patients with microduplication and seven patients with microdeletion on the long arm of chromosome 21. Patients with microduplication have varied clinical features including developmental delay, microcephaly, facial dysmorphic features, pulmonary stenosis, autism, preauricular skin tag, eye pterygium, speech delay and pain insensitivity. We found that patients with microdeletion presented with developmental delay, microcephaly, intrauterine fetal demise, epilepsia partialis continua, congenital coronary anomaly and seizures. Conclusion Three patients from our study combine with four patients in public database suggests an association between 21q21.1 microduplication of CXADR gene and patients with developmental delay. One patient with 21q22.13 microdeletion of DYRK1A shows association with microcephaly and scoliosis. Our findings helped pinpoint critical genes in the genotype-phenotype association with a high resolution of 0.1 Mb and expanded the clinical features observed in patients with CNVs on the long arm of chromosome 21.
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Affiliation(s)
- Wenfu Li
- Genetics Laboratory, University of Oklahoma Health Sciences Center, 1122 NE 13th Street, Suite 1400, Oklahoma City, OK 73104 USA
| | - Xianfu Wang
- Genetics Laboratory, University of Oklahoma Health Sciences Center, 1122 NE 13th Street, Suite 1400, Oklahoma City, OK 73104 USA
| | - Shibo Li
- Genetics Laboratory, University of Oklahoma Health Sciences Center, 1122 NE 13th Street, Suite 1400, Oklahoma City, OK 73104 USA
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Pelleri MC, Cattani C, Vitale L, Antonaros F, Strippoli P, Locatelli C, Cocchi G, Piovesan A, Caracausi M. Integrated Quantitative Transcriptome Maps of Human Trisomy 21 Tissues and Cells. Front Genet 2018; 9:125. [PMID: 29740474 PMCID: PMC5928158 DOI: 10.3389/fgene.2018.00125] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/27/2018] [Indexed: 12/17/2022] Open
Abstract
Down syndrome (DS) is due to the presence of an extra full or partial chromosome 21 (Hsa21). The identification of genes contributing to DS pathogenesis could be the key to any rational therapy of the associated intellectual disability. We aim at generating quantitative transcriptome maps in DS integrating all gene expression profile datasets available for any cell type or tissue, to obtain a complete model of the transcriptome in terms of both expression values for each gene and segmental trend of gene expression along each chromosome. We used the TRAM (Transcriptome Mapper) software for this meta-analysis, comparing transcript expression levels and profiles between DS and normal brain, lymphoblastoid cell lines, blood cells, fibroblasts, thymus and induced pluripotent stem cells, respectively. TRAM combined, normalized, and integrated datasets from different sources and across diverse experimental platforms. The main output was a linear expression value that may be used as a reference for each of up to 37,181 mapped transcripts analyzed, related to both known genes and expression sequence tag (EST) clusters. An independent example in vitro validation of fibroblast transcriptome map data was performed through “Real-Time” reverse transcription polymerase chain reaction showing an excellent correlation coefficient (r = 0.93, p < 0.0001) with data obtained in silico. The availability of linear expression values for each gene allowed the testing of the gene dosage hypothesis of the expected 3:2 DS/normal ratio for Hsa21 as well as other human genes in DS, in addition to listing genes differentially expressed with statistical significance. Although a fraction of Hsa21 genes escapes dosage effects, Hsa21 genes are selectively over-expressed in DS samples compared to genes from other chromosomes, reflecting a decisive role in the pathogenesis of the syndrome. Finally, the analysis of chromosomal segments reveals a high prevalence of Hsa21 over-expressed segments over the other genomic regions, suggesting, in particular, a specific region on Hsa21 that appears to be frequently over-expressed (21q22). Our complete datasets are released as a new framework to investigate transcription in DS for individual genes as well as chromosomal segments in different cell types and tissues.
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Affiliation(s)
- Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Chiara Cattani
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Chiara Locatelli
- Neonatology Unit, Sant'Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Guido Cocchi
- Neonatology Unit, Sant'Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine, Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy
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Caracausi M, Ghini V, Locatelli C, Mericio M, Piovesan A, Antonaros F, Pelleri MC, Vitale L, Vacca RA, Bedetti F, Mimmi MC, Luchinat C, Turano P, Strippoli P, Cocchi G. Plasma and urinary metabolomic profiles of Down syndrome correlate with alteration of mitochondrial metabolism. Sci Rep 2018; 8:2977. [PMID: 29445163 PMCID: PMC5813015 DOI: 10.1038/s41598-018-20834-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/22/2018] [Indexed: 01/16/2023] Open
Abstract
Down syndrome (DS) is caused by the presence of a supernumerary copy of the human chromosome 21 (Hsa21) and is the most frequent genetic cause of intellectual disability (ID). Key traits of DS are the distinctive facies and cognitive impairment. We conducted for the first time an analysis of the Nuclear Magnetic Resonance (NMR)-detectable part of the metabolome in plasma and urine samples, studying 67 subjects with DS and 29 normal subjects as controls selected among DS siblings. Multivariate analysis of the NMR metabolomic profiles showed a clear discrimination (up to of 80% accuracy) between the DS and the control groups. The univariate analysis of plasma and urine revealed a significant alteration for some interesting metabolites. Remarkably, most of the altered concentrations were consistent with the 3:2 gene dosage model, suggesting effects caused by the presence of three copies of Hsa21 rather than two: DS/normal ratio in plasma was 1.23 (pyruvate), 1.47 (succinate), 1.39 (fumarate), 1.33 (lactate), 1.4 (formate). Several significantly altered metabolites are produced at the beginning or during the Krebs cycle. Accounting for sex, age and fasting state did not significantly affect the main result of both multivariate and univariate analysis.
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Affiliation(s)
- Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Veronica Ghini
- CERM, Center of Magnetic Resonance, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.,CIRMMP, Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Martina Mericio
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Rosa Anna Vacca
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Council of Research, Via Amendola 165/A, I-70126, Bari, Italy
| | - Federica Bedetti
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
| | - Maria Chiara Mimmi
- Department of Medical and Biological Sciences, University of Udine, P.le Massimiliano Kolbe 4, 33100, Udine, Italy
| | - Claudio Luchinat
- CERM, Center of Magnetic Resonance, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy
| | - Paola Turano
- CERM, Center of Magnetic Resonance, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Guido Cocchi
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy
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Vitale L, Piovesan A, Antonaros F, Strippoli P, Pelleri MC, Caracausi M. A molecular view of the normal human thyroid structure and function reconstructed from its reference transcriptome map. BMC Genomics 2017; 18:739. [PMID: 28923001 PMCID: PMC5604164 DOI: 10.1186/s12864-017-4049-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/10/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The thyroid is the earliest endocrine structure to appear during human development, and thyroid hormones are necessary for proper organism development, in particular for the nervous system and heart, normal growth and skeletal maturation. To date a quantitative, validated transcriptional atlas of the whole normal human thyroid does not exist and the availability of a detailed expression map might be an excellent occasion to investigate the many features of the thyroid transcriptome. RESULTS We present a view at the molecular level of the normal human thyroid histology and physiology obtained by a systematic meta-analysis of all the available gene expression profiles for the whole organ. A quantitative transcriptome reference map was generated by using the TRAM (Transcriptome Mapper) software able to combine, normalize and integrate a total of 35 suitable datasets from different sources thus providing a typical reference expression value for each of the 27,275 known, mapped transcripts obtained. The experimental in vitro validation of data was performed by "Real-Time" reverse transcription polymerase chain reaction showing an excellent correlation coefficient (r = 0.93) with data obtained in silico. CONCLUSIONS Our study provides a quantitative global reference portrait of gene expression in the normal human thyroid and highlights differential expression between normal human thyroid and a pool of non-thyroid tissues useful for modeling correlations between thyroidal gene expression and specific thyroid functions and diseases. The experimental in vitro validation supports the possible usefulness of the human thyroid transcriptome map as a reference for molecular studies of the physiology and pathology of this organ.
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Affiliation(s)
- Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine, (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
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Dosier LBM, Vaughn BV, Fan Z. Sleep Disorders in Childhood Neurogenetic Disorders. CHILDREN-BASEL 2017; 4:children4090082. [PMID: 28895939 PMCID: PMC5615272 DOI: 10.3390/children4090082] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/16/2017] [Accepted: 08/21/2017] [Indexed: 01/13/2023]
Abstract
enetic advances in the past three decades have transformed our understanding and treatment of many human diseases including neurogenetic disorders. Most neurogenetic disorders can be classified as "rare disease," but collectively neurogenetic disorders are not rare and are commonly encountered in general pediatric practice. The authors decided to select eight relatively well-known neurogenetic disorders including Down syndrome, Angelman syndrome, Prader-Willi syndrome, Smith-Magenis syndrome, congenital central hypoventilation syndrome, achondroplasia, mucopolysaccharidoses, and Duchenne muscular dystrophy. Each disorder is presented in the following format: overview, clinical characteristics, developmental aspects, associated sleep disorders, management and research/future directions.
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Key Words
- Neurogenetic, Sleep, Neurodevelopmental, Angelman, Down syndrome, Trisomy 21, Smith–Magenis, Muchopolysaccharidosis, Achondroplasia, Duchenne, Congenital Central Hypoventilation
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Affiliation(s)
- Laura Beth Mann Dosier
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Bradley V Vaughn
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Zheng Fan
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Caracausi M, Piovesan A, Antonaros F, Strippoli P, Vitale L, Pelleri MC. Systematic identification of human housekeeping genes possibly useful as references in gene expression studies. Mol Med Rep 2017; 16:2397-2410. [PMID: 28713914 PMCID: PMC5548050 DOI: 10.3892/mmr.2017.6944] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/16/2017] [Indexed: 12/21/2022] Open
Abstract
The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium-high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes. Recent advancements in the quality and completeness of human expression microarray data and in their statistical analysis may provide new clues toward the quantitative standardization of human gene expression studies in biology and medicine, both cross- and within-tissue. The systematic approach used by the present study is based on the Transcriptome Mapper tool and exploits the automated reassignment of probes to corresponding genes, intra- and inter-sample normalization, elaboration and representation of gene expression values in linear form within an indexed and searchable database with a graphical interface recording quantitative levels of expression, expression variability and cross-tissue width of expression for more than 31,000 transcripts. The present study conducted a meta-analysis of a pool of 646 expression profile data sets from 54 different human tissues and identified actin γ 1 as the HK gene that best fits the combination of all the traditional criteria to be used as a reference gene for general use; two ribosomal protein genes, RPS18 and RPS27, and one aquaporin gene, POM121 transmembrane nucleporin C, were also identified. The present study provided a list of tissue- and organ-specific genes that may be most suited for the following individual tissues/organs: Adipose tissue, bone marrow, brain, heart, kidney, liver, lung, ovary, skeletal muscle and testis; and also provides in these cases a representative, quantitative portrait of the relative, typical gene-expression profile in the form of searchable database tables.
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Affiliation(s)
- Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
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Piovesan A, Caracausi M, Antonaros F, Pelleri MC, Vitale L. GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw153. [PMID: 28025344 PMCID: PMC5199132 DOI: 10.1093/database/baw153] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/28/2016] [Accepted: 10/31/2016] [Indexed: 11/25/2022]
Abstract
We release GeneBase 1.1, a local tool with a graphical interface useful for parsing, structuring and indexing data from the National Center for Biotechnology Information (NCBI) Gene data bank. Compared to its predecessor GeneBase (1.0), GeneBase 1.1 now allows dynamic calculation and summarization in terms of median, mean, standard deviation and total for many quantitative parameters associated with genes, gene transcripts and gene features (exons, introns, coding sequences, untranslated regions). GeneBase 1.1 thus offers the opportunity to perform analyses of the main gene structure parameters also following the search for any set of genes with the desired characteristics, allowing unique functionalities not provided by the NCBI Gene itself. In order to show the potential of our tool for local parsing, structuring and dynamic summarizing of publicly available databases for data retrieval, analysis and testing of biological hypotheses, we provide as a sample application a revised set of statistics for human nuclear genes, gene transcripts and gene features. In contrast with previous estimations strongly underestimating the length of human genes, a ‘mean’ human protein-coding gene is 67 kbp long, has eleven 309 bp long exons and ten 6355 bp long introns. Median, mean and extreme values are provided for many other features offering an updated reference source for human genome studies, data useful to set parameters for bioinformatic tools and interesting clues to the biomedical meaning of the gene features themselves. Database URL: http://apollo11.isto.unibo.it/software/
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Affiliation(s)
- Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy
| | - Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy
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