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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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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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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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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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Bhola SL, Nieuwint AWM, Stuurman KE. A prenatal case of partial trisomy 21 (q22.2q22.3), resulting from a paternal insertion translocation ins(16;21) and uncovered by QF-PCR, and characterized by array CGH and FISH. Clin Case Rep 2018; 6:1313-1316. [PMID: 29988599 PMCID: PMC6028365 DOI: 10.1002/ccr3.1563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 01/19/2018] [Accepted: 03/24/2018] [Indexed: 11/30/2022] Open
Abstract
In addition to detecting trisomies of whole chromosomes, QF-PCR can also detect partial trisomies of the chromosomes 13, 18, and 21, which can suggest an unbalanced translocation. Additional testing with other techniques, such as microarray or FISH, is recommended when an unbalanced translocation is suspected.
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Affiliation(s)
- Shama L. Bhola
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Aggie W. M. Nieuwint
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Kyra E. Stuurman
- Department of Clinical GeneticsErasmus Medical CenterRotterdamThe Netherlands
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Genotype-phenotype correlation for congenital heart disease in Down syndrome through analysis of partial trisomy 21 cases. Genomics 2017. [PMID: 28648597 DOI: 10.1016/j.ygeno.2017.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Among Down syndrome (DS) children, 40-50% have congenital heart disease (CHD). Although trisomy 21 is not sufficient to cause CHD, three copies of at least part of chromosome 21 (Hsa21) increases the risk for CHD. In order to establish a genotype-phenotype correlation for CHD in DS, we built an integrated Hsa21 map of all described partial trisomy 21 (PT21) cases with sufficient indications regarding presence or absence of CHD (n=107), focusing on DS PT21 cases. We suggest a DS CHD candidate region on 21q22.2 (0.96Mb), being shared by most PT21 cases with CHD and containing three known protein-coding genes (DSCAM, BACE2, PLAC4) and four known non-coding RNAs (DSCAM-AS1, DSCAM-IT1, LINC00323, MIR3197). The characterization of a DS CHD candidate region provides a useful approach to identify specific genes contributing to the pathology and to orient further investigations and possibly more effective therapy in relation to the multifactorial pathogenesis of CHD.
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Pelleri MC, Cicchini E, Locatelli C, Vitale L, Caracausi M, Piovesan A, Rocca A, Poletti G, Seri M, Strippoli P, Cocchi G. Systematic reanalysis of partial trisomy 21 cases with or without Down syndrome suggests a small region on 21q22.13 as critical to the phenotype. Hum Mol Genet 2016; 25:2525-2538. [PMID: 27106104 PMCID: PMC5181629 DOI: 10.1093/hmg/ddw116] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/12/2016] [Accepted: 04/12/2016] [Indexed: 01/13/2023] Open
Abstract
A 'Down Syndrome critical region' (DSCR) sufficient to induce the most constant phenotypes of Down syndrome (DS) had been identified by studying partial (segmental) trisomy 21 (PT21) as an interval of 0.6-8.3 Mb within human chromosome 21 (Hsa21), although its existence was later questioned. We propose an innovative, systematic reanalysis of all described PT21 cases (from 1973 to 2015). In particular, we built an integrated, comparative map from 125 cases with or without DS fulfilling stringent cytogenetic and clinical criteria. The map allowed to define or exclude as candidates for DS fine Hsa21 sequence intervals, also integrating duplication copy number variants (CNVs) data. A highly restricted DSCR (HR-DSCR) of only 34 kb on distal 21q22.13 has been identified as the minimal region whose duplication is shared by all DS subjects and is absent in all non-DS subjects. Also being spared by any duplication CNV in healthy subjects, HR-DSCR is proposed as a candidate for the typical DS features, the intellectual disability and some facial phenotypes. HR-DSCR contains no known gene and has relevant homology only to the chimpanzee genome. Searching for HR-DSCR functional loci might become a priority for understanding the fundamental genotype-phenotype relationships in DS.
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Affiliation(s)
- 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
| | - 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
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138 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
| | - 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
| | - 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
| | - Alessandro Rocca
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138 Bologna, BO, Italy
| | - Giulia Poletti
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138 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
| | - 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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