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Atique Tacla M, de Mello Copelli M, Pairet E, Monlleó IL, Ribeiro EM, Lustosa Mendes E, Helaers R, Vieira TP, Vikkula M, Gil-da-Silva-Lopes VL. Molecular investigation in individuals with orofacial clefts and microphthalmia-anophthalmia-coloboma spectrum. Eur J Hum Genet 2023:10.1038/s41431-023-01488-5. [PMID: 37932364 DOI: 10.1038/s41431-023-01488-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 09/29/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023] Open
Abstract
This study describes genomic findings among individuals with both orofacial clefts (OC) and microphthalmia/anophthalmia/coloboma (MAC) recorded in the Brazilian Database on Craniofacial Anomalies (BDCA). Chromosomal microarray analysis (CMA) and Whole Exome Sequencing (WES) were performed in 17 individuals with OC-MAC. Clinical interpretation of molecular findings was based on data available at the BDCA and on re-examination. No copy number variants (CNVs) classified as likely pathogenic or pathogenic were detected by CMA. WES allowed a conclusive diagnosis in six individuals (35.29%), two of them with variants in the CHD7 gene, and the others with variants in the TFAP2A, POMT1, PTPN11, and TP63 genes with the following syndromes: CHARGE, CHD7-spectrum, Branchiooculofacial, POMT1-spectrum, LEOPARD, and ADULT. Variants of uncertain significance (VUS) possibly associated to the phenotypes were found in six other individuals. Among the individuals with VUSes, three individuals presented variants in genes associated to defects of cilia structure and/or function, including DYNC2H1, KIAA0586, WDR34, INTU, RPGRIP1L, KIF7, and LMNA. These results show that WES was the most effective molecular approach for OC-MAC in this cohort. This study also reinforces the genetic heterogeneity of OC-MAC, and the importance of genes related to ciliopathies in this phenotype.
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Affiliation(s)
- Milena Atique Tacla
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Matheus de Mello Copelli
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Eleonore Pairet
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Isabella Lopes Monlleó
- Clinical Genetics Service, University Hospital, Medical Genetics Sector, Faculty of Medicine, Federal University of Alagoas - UFAL, Maceió, AL, Brazil
| | | | | | - Raphaël Helaers
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Tarsis Paiva Vieira
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas, SP, Brazil.
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Günay Ç, Aykol D, Özsoy Ö, Sönmezler E, Hanci YS, Kara B, Akkoyunlu Sünnetçi D, Cine N, Deniz A, Özer T, Ölçülü CB, Yilmaz Ö, Kanmaz S, Yilmaz S, Tekgül H, Yildiz N, Acar Arslan E, Cansu A, Olgaç Dündar N, Kusgoz F, Didinmez E, Gençpinar P, Aksu Uzunhan T, Ertürk B, Gezdirici A, Ayaz A, Ölmez A, Ayanoğlu M, Tosun A, Topçu Y, Kiliç B, Aydin K, Çağlar E, Ersoy Kosvali Ö, Okuyaz Ç, Besen Ş, Tekin Orgun L, Erol İ, Yüksel D, Sezer A, Atasoy E, Toprak Ü, Güngör S, Ozgor B, Karadağ M, Dilber C, Şahinoğlu B, Uyur Yalçin E, Eldes Hacifazlioglu N, Yaramiş A, Edem P, Gezici Tekin H, Yilmaz Ü, Ünalp A, Turay S, Biçer D, Gül Mert G, Dokurel Çetin İ, Kirik S, Öztürk G, Karal Y, Sanri A, Aksoy A, Polat M, Özgün N, Soydemir D, Sarikaya Uzan G, Ülker Üstebay D, Gök A, Yeşilmen MC, Yiş U, Karakülah G, Bursali A, Oktay Y, Hiz Kurul S. Shared Biological Pathways and Processes in Patients with Intellectual Disability: A Multicenter Study. Neuropediatrics 2023. [PMID: 36787800 DOI: 10.1055/a-2034-8528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
BACKGROUND Although the underlying genetic causes of intellectual disability (ID) continue to be rapidly identified, the biological pathways and processes that could be targets for a potential molecular therapy are not yet known. This study aimed to identify ID-related shared pathways and processes utilizing enrichment analyses. METHOD In this multicenter study, causative genes of patients with ID were used as input for Disease Ontology (DO), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. RESULTS Genetic test results of 720 patients from 27 centers were obtained. Patients with chromosomal deletion/duplication, non-ID genes, novel genes, and results with changes in more than one gene were excluded. A total of 558 patients with 341 different causative genes were included in the study. Pathway-based enrichment analysis of the ID-related genes via ClusterProfiler revealed 18 shared pathways, with lysine degradation and nicotine addiction being the most common. The most common of the 25 overrepresented DO terms was ID. The most frequently overrepresented GO biological process, cellular component, and molecular function terms were regulation of membrane potential, ion channel complex, and voltage-gated ion channel activity/voltage-gated channel activity, respectively. CONCLUSION Lysine degradation, nicotine addiction, and thyroid hormone signaling pathways are well-suited to be research areas for the discovery of new targeted therapies in ID patients.
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Affiliation(s)
- Çağatay Günay
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Duygu Aykol
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Özlem Özsoy
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Ece Sönmezler
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Yaren Sena Hanci
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Bülent Kara
- Department of Pediatric Neurology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | | | - Naci Cine
- Department of Medical Genetics, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Adnan Deniz
- Department of Pediatric Neurology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Tolgahan Özer
- Department of Medical Genetics, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Cemile Büşra Ölçülü
- Department of Child Neurology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Özlem Yilmaz
- Department of Child Neurology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Seda Kanmaz
- Department of Child Neurology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Sanem Yilmaz
- Department of Child Neurology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Hasan Tekgül
- Department of Child Neurology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Nihal Yildiz
- Department of Pediatric Neurology, Karadeniz Technical University, Faculty of Medicine, Farabi Hospital, Trabzon, Turkey
| | - Elif Acar Arslan
- Department of Pediatric Neurology, Karadeniz Technical University, Faculty of Medicine, Farabi Hospital, Trabzon, Turkey
| | - Ali Cansu
- Department of Pediatric Neurology, Karadeniz Technical University, Faculty of Medicine, Farabi Hospital, Trabzon, Turkey
| | - Nihal Olgaç Dündar
- Department of Pediatric Neurology, İzmir Katip Çelebi University, Izmir, Turkey
| | - Fatma Kusgoz
- Department of Pediatric Neurology, Tepecik Research and Training Hospital, Izmir, Turkey
| | - Elif Didinmez
- Department of Pediatric Neurology, Tepecik Research and Training Hospital, Izmir, Turkey
| | - Pınar Gençpinar
- Department of Pediatric Neurology, İzmir Katip Çelebi University, Izmir, Turkey
| | - Tuğçe Aksu Uzunhan
- Department of Pediatric Neurology, Prof Dr Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Biray Ertürk
- Department of Pediatric Neurology, Prof Dr Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Başakşehir Çam and Sakura City Hospital, Istanbul, Turkey
| | - Akif Ayaz
- Department of Medical Genetics, Istanbul Medipol University School of Medicine, Istanbul, Turkey
| | - Akgün Ölmez
- Denizli Pediatric Neurology Clinic, Denizli, Turkey
| | - Müge Ayanoğlu
- Department of Child Neurology, Adnan Menderes University School of Medicine, Aydın, Turkey
| | - Ayşe Tosun
- Department of Child Neurology, Adnan Menderes University School of Medicine, Aydın, Turkey
| | - Yasemin Topçu
- Department of Pediatric Neurology, Istanbul Medipol University Faculty of Medicine, Istanbul, Turkey
| | - Betül Kiliç
- Department of Pediatric Neurology, Istanbul Medipol University Faculty of Medicine, Istanbul, Turkey
| | - Kürşad Aydin
- Department of Pediatric Neurology, Istanbul Medipol University Faculty of Medicine, Istanbul, Turkey
| | - Ezgi Çağlar
- Departments of Pediatric Neurology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Özlem Ersoy Kosvali
- Departments of Pediatric Neurology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Çetin Okuyaz
- Departments of Pediatric Neurology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Şeyda Besen
- Division of Pediatric Neurology, Başkent University Adana Medical and Research Center Faculty of Medicine, Adana, Turkey
| | - Leman Tekin Orgun
- Division of Pediatric Neurology, Başkent University Adana Medical and Research Center Faculty of Medicine, Adana, Turkey
| | - İlknur Erol
- Division of Pediatric Neurology, Başkent University Adana Medical and Research Center Faculty of Medicine, Adana, Turkey
| | - Deniz Yüksel
- Department of Pediatric Neurology, University of Health Sciences Faculty of Medicine, Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Abdullah Sezer
- Department of Genetics, University of Health Sciences Faculty of Medicine, Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Ergin Atasoy
- Department of Pediatric Neurology, University of Health Sciences Faculty of Medicine, Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Ülkühan Toprak
- Department of Pediatric Neurology, University of Health Sciences Faculty of Medicine, Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Serdal Güngör
- Department of Paediatric Neurology, Inonu University Faculty of Medicine, Turgut Ozal Research Center, Malatya, Turkey
| | - Bilge Ozgor
- Department of Paediatric Neurology, Inonu University Faculty of Medicine, Turgut Ozal Research Center, Malatya, Turkey
| | - Meral Karadağ
- Department of Paediatric Neurology, Inonu University Faculty of Medicine, Turgut Ozal Research Center, Malatya, Turkey
| | - Cengiz Dilber
- Department of Pediatric Neurology, Kahramanmaras Sutcu Imam University Faculty of Medicine, Kahramanmaraş, Turkey
| | - Bahtiyar Şahinoğlu
- Deparment of Genetics, Dr Ersin Arslan Traning and Research Hospital, Gaziantep, Turkey
| | - Emek Uyur Yalçin
- Departments of Pediatrics and Pediatric Neurology, University of Health Sciences, Zeynep Kamil Maternity and Children's Diseases Hospital, Istanbul, Turkey
| | - Nilüfer Eldes Hacifazlioglu
- Departments of Pediatrics and Pediatric Neurology, University of Health Sciences, Zeynep Kamil Maternity and Children's Diseases Hospital, Istanbul, Turkey
| | - Ahmet Yaramiş
- Diyarbakır Pediatric Neurology Clinic, Diyarbakır, Turkey
| | - Pınar Edem
- Department of Pediatric Neurology, Bakırcay University, Cigli District Training Hospital, Izmir, Turkey
| | - Hande Gezici Tekin
- Department of Pediatric Neurology, Bakırcay University, Cigli District Training Hospital, Izmir, Turkey
| | - Ünsal Yilmaz
- Department of Pediatric Neurology, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Aycan Ünalp
- Department of Pediatric Neurology, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Sevim Turay
- Department of Pediatric Neurology, Duzce University Faculty of Medicine, Düzce, Turkey
| | - Didem Biçer
- Department of Pediatric Neurology, Çukurova University Faculty of Medicine, Adana, Turkey
| | - Gülen Gül Mert
- Department of Pediatric Neurology, Çukurova University Faculty of Medicine, Adana, Turkey
| | - İpek Dokurel Çetin
- Department of Pediatric Neurology, Balıkesir Atatürk Training and Research Hospital, Balıkesir, Turkey
| | - Serkan Kirik
- Fırat University School of Medicine, Pediatric Neurology, Elazığ, Turkey
| | - Gülten Öztürk
- Department of Pediatric Neurology, Marmara University School of Medicine, Istanbul, Turkey
| | - Yasemin Karal
- Department of Pediatric Neurology, Trakya University, Faculty of Medicine, Edirne, Turkey
| | - Aslıhan Sanri
- Department of Pediatric Genetics, University of Health Sciences, Samsun Training and Research Hospital, Samsun, Turkey
| | - Ayşe Aksoy
- Department of Pediatric Neurology, Ondokuz Mayıs University, Samsun, Turkey
| | - Muzaffer Polat
- Department of Pediatric Neurology, Celal Bayar University School of Medicine, Manisa, Turkey
| | - Nezir Özgün
- Department of Pediatric Neurology, Mardin Artuklu University, Faculty of Health Sciences, Mardin, Turkey
| | - Didem Soydemir
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Gamze Sarikaya Uzan
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Döndü Ülker Üstebay
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Ayşen Gök
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Mehmet Can Yeşilmen
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Uluç Yiş
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Ahmet Bursali
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Semra Hiz Kurul
- Department of Pediatric Neurology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
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Yu J, Liao PJ, Xu W, Jones JR, Everman DB, Flanagan-Steet H, Keller TH, Virshup DM. Structural model of human PORCN illuminates disease-associated variants and drug-binding sites. J Cell Sci 2021; 134:273795. [PMID: 34817055 DOI: 10.1242/jcs.259383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/11/2021] [Indexed: 12/20/2022] Open
Abstract
Wnt signaling is essential for normal development and is a therapeutic target in cancer. The enzyme PORCN, or porcupine, is a membrane-bound O-acyltransferase (MBOAT) that is required for the post-translational modification of all Wnts, adding an essential mono-unsaturated palmitoleic acid to a serine on the tip of Wnt hairpin 2. Inherited mutations in PORCN cause focal dermal hypoplasia, and therapeutic inhibition of PORCN slows the growth of Wnt-dependent cancers. Based on homology to mammalian MBOAT proteins, we developed and validated a structural model of human PORCN. The model accommodates palmitoleoyl-CoA and Wnt hairpin 2 in two tunnels in the conserved catalytic core, shedding light on the catalytic mechanism. The model predicts how previously uncharacterized human variants of uncertain significance can alter PORCN function. Drugs including ETC-159, IWP-L6 and LGK-974 dock in the PORCN catalytic site, providing insights into PORCN pharmacologic inhibition. This structural model enhances our mechanistic understanding of PORCN substrate recognition and catalysis, as well as the inhibition of its enzymatic activity, and can facilitate the development of improved inhibitors and the understanding of disease-relevant PORCN mutants. This article has an associated First Person interview with the joint first authors of the paper.
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Affiliation(s)
- Jia Yu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
| | - Pei-Ju Liao
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
| | - Weijun Xu
- Discovery Chemistry, Experimental Drug Development Centre, 10 Biopolis Road, Chromos, 138670, Singapore
| | - Julie R Jones
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - David B Everman
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Thomas H Keller
- Discovery Chemistry, Experimental Drug Development Centre, 10 Biopolis Road, Chromos, 138670, Singapore
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
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