1
|
Andersen RE, Alkuraya IF, Ajeesh A, Sakamoto T, Mena EL, Amr SS, Romi H, Kenna MA, Robson CD, Wilch ES, Nalbandian K, Piña-Aguilar R, Walsh CA, Morton CC. Chromosomal structural rearrangements implicate long non-coding RNAs in rare germline disorders. Hum Genet 2024; 143:921-938. [PMID: 39060644 PMCID: PMC11294402 DOI: 10.1007/s00439-024-02693-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
In recent years, there has been increased focus on exploring the role the non-protein-coding genome plays in Mendelian disorders. One class of particular interest is long non-coding RNAs (lncRNAs), which has recently been implicated in the regulation of diverse molecular processes. However, because lncRNAs do not encode protein, there is uncertainty regarding what constitutes a pathogenic lncRNA variant, and thus annotating such elements is challenging. The Developmental Genome Anatomy Project (DGAP) and similar projects recruit individuals with apparently balanced chromosomal abnormalities (BCAs) that disrupt or dysregulate genes in order to annotate the human genome. We hypothesized that rearrangements disrupting lncRNAs could be the underlying genetic etiology for the phenotypes of a subset of these individuals. Thus, we assessed 279 cases with BCAs and selected 191 cases with simple BCAs (breakpoints at only two genomic locations) for further analysis of lncRNA disruptions. From these, we identified 66 cases in which the chromosomal rearrangements directly disrupt lncRNAs. In 30 cases, no genes of any other class aside from lncRNAs are directly disrupted, consistent with the hypothesis that lncRNA disruptions could underly the phenotypes of these individuals. Strikingly, the lncRNAs MEF2C-AS1 and ENSG00000257522 are each disrupted in two unrelated cases. Furthermore, we experimentally tested the lncRNAs TBX2-AS1 and MEF2C-AS1 and found that knockdown of these lncRNAs resulted in decreased expression of the neighboring transcription factors TBX2 and MEF2C, respectively. To showcase the power of this genomic approach for annotating lncRNAs, here we focus on clinical reports and genetic analysis of seven individuals with likely developmental etiologies due to lncRNA disruptions.
Collapse
Affiliation(s)
- Rebecca E Andersen
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ibrahim F Alkuraya
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
- Harvard College, Cambridge, MA, USA
| | - Abna Ajeesh
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Tyler Sakamoto
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children's Hospital, Boston, MA, USA
- Harvard College, Cambridge, MA, USA
| | - Elijah L Mena
- Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Sami S Amr
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Hila Romi
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Margaret A Kenna
- Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA, USA
| | - Caroline D Robson
- Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA, USA
- Department of Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Ellen S Wilch
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Katarena Nalbandian
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Raul Piña-Aguilar
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Cynthia C Morton
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- University of Manchester, Manchester Center for Audiology and Deafness, Manchester, UK.
| |
Collapse
|
2
|
Andersen RE, Alkuraya IF, Ajeesh A, Sakamoto T, Mena EL, Amr SS, Romi H, Kenna MA, Robson CD, Wilch ES, Nalbandian K, Piña-Aguilar R, Walsh CA, Morton CC. Rare germline disorders implicate long non-coding RNAs disrupted by chromosomal structural rearrangements. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.16.24307499. [PMID: 38946951 PMCID: PMC11213069 DOI: 10.1101/2024.06.16.24307499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
In recent years, there has been increased focus on exploring the role the non-protein-coding genome plays in Mendelian disorders. One class of particular interest is long non-coding RNAs (lncRNAs), which has recently been implicated in the regulation of diverse molecular processes. However, because lncRNAs do not encode protein, there is uncertainty regarding what constitutes a pathogenic lncRNA variant, and thus annotating such elements is challenging. The Developmental Genome Anatomy Project (DGAP) and similar projects recruit individuals with apparently balanced chromosomal abnormalities (BCAs) that disrupt or dysregulate genes in order to annotate the human genome. We hypothesized that rearrangements disrupting lncRNAs could be the underlying genetic etiology for the phenotypes of a subset of these individuals. Thus, we assessed 279 cases with BCAs and selected 191 cases with simple BCAs (breakpoints at only two genomic locations) for further analysis of lncRNA disruptions. From these, we identified 66 cases in which the chromosomal rearrangements directly disrupt lncRNAs. Strikingly, the lncRNAs MEF2C-AS1 and ENSG00000257522 are each disrupted in two unrelated cases. Furthermore, in 30 cases, no genes of any other class aside from lncRNAs are directly disrupted, consistent with the hypothesis that lncRNA disruptions could underly the phenotypes of these individuals. To showcase the power of this genomic approach for annotating lncRNAs, here we focus on clinical reports and genetic analysis of two individuals with BCAs and additionally highlight six individuals with likely developmental etiologies due to lncRNA disruptions.
Collapse
Affiliation(s)
- Rebecca E. Andersen
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ibrahim F. Alkuraya
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard College, Cambridge, MA, USA
| | - Abna Ajeesh
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Tyler Sakamoto
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Harvard College, Cambridge, MA, USA
| | - Elijah L. Mena
- Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
| | - Sami S. Amr
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Hila Romi
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Margaret A. Kenna
- Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology, Boston Children’s Hospital, Boston, MA, USA
| | - Caroline D. Robson
- Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology, Boston Children’s Hospital, Boston, MA, USA
- Department of Radiology, Boston Children’s Hospital, Boston, MA, USA
| | - Ellen S. Wilch
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Katarena Nalbandian
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Raul Piña-Aguilar
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Christopher A. Walsh
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Cynthia C. Morton
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
- University of Manchester, Manchester Center for Audiology and Deafness, UK
| |
Collapse
|
3
|
Sánchez-Gaya V, Rada-Iglesias A. POSTRE: a tool to predict the pathological effects of human structural variants. Nucleic Acids Res 2023; 51:e54. [PMID: 36999617 PMCID: PMC10201441 DOI: 10.1093/nar/gkad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Understanding the pathological impact of non-coding genetic variation is a major challenge in medical genetics. Accumulating evidences indicate that a significant fraction of genetic alterations, including structural variants (SVs), can cause human disease by altering the function of non-coding regulatory elements, such as enhancers. In the case of SVs, described pathomechanisms include changes in enhancer dosage and long-range enhancer-gene communication. However, there is still a clear gap between the need to predict and interpret the medical impact of non-coding variants, and the existence of tools to properly perform these tasks. To reduce this gap, we have developed POSTRE (Prediction Of STRuctural variant Effects), a computational tool to predict the pathogenicity of SVs implicated in a broad range of human congenital disorders. By considering disease-relevant cellular contexts, POSTRE identifies SVs with either coding or long-range pathological consequences with high specificity and sensitivity. Furthermore, POSTRE not only identifies pathogenic SVs, but also predicts the disease-causative genes and the underlying pathological mechanism (e.g, gene deletion, enhancer disconnection, enhancer adoption, etc.). POSTRE is available at https://github.com/vicsanga/Postre.
Collapse
Affiliation(s)
- Víctor Sánchez-Gaya
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Albert Einstein 22, 39011 Santander, Spain
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Albert Einstein 22, 39011 Santander, Spain
| |
Collapse
|
4
|
Davidson C, Wordsworth BP, Cohen CJ, Knight JC, Vecellio M. Chromosome conformation capture approaches to investigate 3D genome architecture in Ankylosing Spondylitis. Front Genet 2023; 14:1129207. [PMID: 36760998 PMCID: PMC9905691 DOI: 10.3389/fgene.2023.1129207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Ankylosing Spondylitis (AS) is a chronic inflammatory arthritis of the spine exhibiting a strong genetic background. The mechanistic and functional understanding of the AS-associated genomic loci, identified with Genome Wide Association Studies (GWAS), remains challenging. Chromosome conformation capture (3C) and derivatives are recent techniques which are of great help in elucidating the spatial genome organization and of enormous support in uncover a mechanistic explanation for disease-associated genetic variants. The perturbation of three-dimensional (3D) genome hierarchy may lead to a plethora of human diseases, including rheumatological disorders. Here we illustrate the latest approaches and related findings on the field of genome organization, highlighting how the instability of 3D genome conformation may be among the causes of rheumatological disease phenotypes. We suggest a new perspective on the inclusive potential of a 3C approach to inform GWAS results in rheumatic diseases. 3D genome organization may ultimately lead to a more precise and comprehensive functional interpretation of AS association, which is the starting point for emerging and more specific therapies.
Collapse
Affiliation(s)
- Connor Davidson
- Wellcome Centre of Human Genetics, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - B. Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Carla J. Cohen
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Julian C. Knight
- Wellcome Centre of Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
- Centro Ricerche Fondazione Italiana Ricerca Sull’Artrite (FIRA), Fondazione Pisana x la Scienza ONLUS, San Giuliano Terme, Italy
| |
Collapse
|
5
|
Davis O. Abnormal Chromatin Folding in the Molecular Pathogenesis of Epilepsy and Autism Spectrum Disorder: a Meta-synthesis with Systematic Searching. Mol Neurobiol 2023; 60:768-779. [PMID: 36367658 PMCID: PMC9849311 DOI: 10.1007/s12035-022-03106-9] [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: 07/25/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022]
Abstract
How DNA is folded and packaged in nucleosomes is an essential regulator of gene expression. Abnormal patterns of chromatin folding are implicated in a wide range of diseases and disorders, including epilepsy and autism spectrum disorder (ASD). These disorders are thought to have a shared pathogenesis involving an imbalance in the number of excitatory-inhibitory neurons formed during neurodevelopment; however, the underlying pathological mechanism behind this imbalance is poorly understood. Studies are increasingly implicating abnormal chromatin folding in neural stem cells as one of the candidate pathological mechanisms, but no review has yet attempted to summarise the knowledge in this field. This meta-synthesis is a systematic search of all the articles on epilepsy, ASD, and chromatin folding. Its two main objectives were to determine to what extent abnormal chromatin folding is implicated in the pathogenesis of epilepsy and ASD, and secondly how abnormal chromatin folding leads to pathological disease processes. This search produced 22 relevant articles, which together strongly implicate abnormal chromatin folding in the pathogenesis of epilepsy and ASD. A range of mutations and chromosomal structural abnormalities lead to this effect, including single nucleotide polymorphisms, copy number variants, translocations and mutations in chromatin modifying. However, knowledge is much more limited into how abnormal chromatin organisation subsequently causes pathological disease processes, not yet showing, for example, whether it leads to abnormal excitation-inhibitory neuron imbalance in human brain organoids.
Collapse
Affiliation(s)
- Oliver Davis
- grid.5335.00000000121885934Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| |
Collapse
|
6
|
Lu G, Zhang Y, Xia H, He X, Xu P, Wu L, Li D, Ma L, Wu J, Peng Q. Identification of a de novo mutation of the FOXG1 gene and comprehensive analysis for molecular factors in Chinese FOXG1-related encephalopathies. Front Mol Neurosci 2022; 15:1039990. [PMID: 36568277 PMCID: PMC9768341 DOI: 10.3389/fnmol.2022.1039990] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Background FOXG1-related encephalopathy, also known as FOXG1 syndrome or FOXG1-related disorder, affects most aspects of development and causes microcephaly and brain malformations. This syndrome was previously considered to be the congenital variant of Rett syndrome. The abnormal function or expression of FOXG1, caused by intragenic mutations, microdeletions or microduplications, was considered to be crucial pathological factor for this disorder. Currently, most of the FOXG1-related encephalopathies have been identified in Europeans and North Americans, and relatively few Chinese cases were reported. Methods Array-Comparative Genomic Hybridization (Array-CGH) and whole-exome sequencing (WES) were carried out for the proband and her parent to detect pathogenic variants. Results A de novo nonsense mutation (c.385G>T, p.Glu129Ter) of FOXG1 was identified in a female child in a cohort of 73 Chinese children with neurodevelopmental disorders/intellectual disorders (NDDs/IDs). In order to have a comprehensive view of FOXG1-related encephalopathy in China, relevant published reports were browsed and twelve cases with mutations in FOXG1 or copy number variants (CNVs) involving FOXG1 gene were involved in the analysis eventually. Feeding difficulties, seizures, delayed speech, corpus callosum hypoplasia and underdevelopment of frontal and temporal lobes occurred in almost all cases. Out of the 12 cases, eight patients (66.67%) had single-nucleotide mutations of FOXG1 gene and four patients (33.33%) had CNVs involving FOXG1 (3 microdeletions and 1 microduplication). The expression of FOXG1 could also be potentially disturbed by deletions of several brain-active regulatory elements located in intergenic FOXG1-PRKD1 region. Further analysis indicated that PRKD1 might be a cooperating factor to regulate the expression of FOXG1, MECP2 and CDKL5 to contribute the RTT/RTT-like disorders. Discussion This re-analysis would broaden the existed knowledge about the molecular etiology and be helpful for diagnosis, treatment, and gene therapy of FOXG1-related disorders in the future.
Collapse
Affiliation(s)
- Guanting Lu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Yan Zhang
- Department of Obstetrics and Gynecology, Strategic Support Force Medical Center, Beijing, China
| | - Huiyun Xia
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Xiaoyan He
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Pei Xu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Lianying Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Ding Li
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Liya Ma
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Jin Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People's Hospital, Deyang, China
- Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China
| | - Qiongling Peng
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| |
Collapse
|
7
|
Yang H, Ryu J, Lim C, Choi JW, Park YJ, Jang SW, Shim S. SOXE group transcription factors regulates the expression of FoxG1 during inner ear development. Biochem Biophys Res Commun 2022; 623:96-103. [PMID: 35878429 DOI: 10.1016/j.bbrc.2022.07.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 11/24/2022]
Abstract
The transcription factor FOXG1 plays an important role in inner ear development; however, the cis-regulatory mechanisms controlling the inner-ear-specific expression of FOXG1 are poorly understood. In this study, we aimed to identify the element that specifically regulates FoxG1 expression in the otic vesicle, which develops into the inner ear, through comparative genome analysis between vertebrate species and chromatin immunoprecipitation. The cis-regulatory element (E2) identified showed high evolutionary conservation among vertebrates in the genomic DNA of FoxG1 spanning approximately 3 Mbp. We identified core sequences important for the activity of the otic-vesicle-specific enhancer through in vitro and in vivo reporter assays for various E2 enhancer mutants and determined the consensus sequence for SOX DNA binding. In addition, SoxE, a subfamily of the Sox family, was simultaneously expressed in the otic vesicles of developing embryos and showed a similar protein expression pattern as that of FoxG1. Furthermore, SOXE transcription factors induced specific transcriptional activity through the FoxG1 Otic enhancer (E2b). These findings suggest that the interaction between the otic enhancer of FoxG1 and SOXE transcription factor, in which the otic expression of FoxG1 is evolutionarily well-conserved, is important during early development of the inner ear, a sensory organ important for survival in nature.
Collapse
Affiliation(s)
- Hayoung Yang
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jiho Ryu
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Chungun Lim
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Jae-Won Choi
- Division of BT Convergence, Cheongju University, Cheongju, 28503, Republic of Korea
| | - Young-Jun Park
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
| | - Sung-Wuk Jang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea; Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 138-736, Republic of Korea.
| | - Sungbo Shim
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| |
Collapse
|
8
|
Poszewiecka B, Pienkowski VM, Nowosad K, Robin JD, Gogolewski K, Gambin A. TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure. Nucleic Acids Res 2022; 50:W744-W752. [PMID: 35524567 PMCID: PMC9252839 DOI: 10.1093/nar/gkac318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 01/01/2023] Open
Abstract
In recent years great progress has been made in identification of structural variants (SV) in the human genome. However, the interpretation of SVs, especially located in non-coding DNA, remains challenging. One of the reasons stems in the lack of tools exclusively designed for clinical SVs evaluation acknowledging the 3D chromatin architecture. Therefore, we present TADeus2 a web server dedicated for a quick investigation of chromatin conformation changes, providing a visual framework for the interpretation of SVs affecting topologically associating domains (TADs). This tool provides a convenient visual inspection of SVs, both in a continuous genome view as well as from a rearrangement’s breakpoint perspective. Additionally, TADeus2 allows the user to assess the influence of analyzed SVs within flaking coding/non-coding regions based on the Hi-C matrix. Importantly, the SVs pathogenicity is quantified and ranked using TADA, ClassifyCNV tools and sampling-based P-value. TADeus2 is publicly available at https://tadeus2.mimuw.edu.pl.
Collapse
Affiliation(s)
- Barbara Poszewiecka
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Victor Murcia Pienkowski
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, MMG, Marseille, France.,Department of Medical Genetics, Medical University of Warsaw, Adolfa Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Karol Nowosad
- Department of Cell Biology, Erasmus Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, Netherlands.,Department of Biomedical Sciences, Laboratory of Molecular Genetics, Medical University of Lublin, Doktora Witolda Chodźki 1, 20-400 Lublin, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, MMG, Marseille, France
| | - Krzysztof Gogolewski
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Anna Gambin
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| |
Collapse
|
9
|
Akol I, Gather F, Vogel T. Paving Therapeutic Avenues for FOXG1 Syndrome: Untangling Genotypes and Phenotypes from a Molecular Perspective. Int J Mol Sci 2022; 23:ijms23020954. [PMID: 35055139 PMCID: PMC8780739 DOI: 10.3390/ijms23020954] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/23/2021] [Accepted: 01/13/2022] [Indexed: 02/01/2023] Open
Abstract
Development of the central nervous system (CNS) depends on accurate spatiotemporal control of signaling pathways and transcriptional programs. Forkhead Box G1 (FOXG1) is one of the master regulators that play fundamental roles in forebrain development; from the timing of neurogenesis, to the patterning of the cerebral cortex. Mutations in the FOXG1 gene cause a rare neurodevelopmental disorder called FOXG1 syndrome, also known as congenital form of Rett syndrome. Patients presenting with FOXG1 syndrome manifest a spectrum of phenotypes, ranging from severe cognitive dysfunction and microcephaly to social withdrawal and communication deficits, with varying severities. To develop and improve therapeutic interventions, there has been considerable progress towards unravelling the multi-faceted functions of FOXG1 in the neurodevelopment and pathogenesis of FOXG1 syndrome. Moreover, recent advances in genome editing and stem cell technologies, as well as the increased yield of information from high throughput omics, have opened promising and important new avenues in FOXG1 research. In this review, we provide a summary of the clinical features and emerging molecular mechanisms underlying FOXG1 syndrome, and explore disease-modelling approaches in animals and human-based systems, to highlight the prospects of research and possible clinical interventions.
Collapse
Affiliation(s)
- Ipek Akol
- Department of Molecular Embryology, Institute for Anatomy and Cell Biology, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany; (I.A.); (F.G.)
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Center for Basics in NeuroModulation (NeuroModul Basics), Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Fabian Gather
- Department of Molecular Embryology, Institute for Anatomy and Cell Biology, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany; (I.A.); (F.G.)
| | - Tanja Vogel
- Department of Molecular Embryology, Institute for Anatomy and Cell Biology, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany; (I.A.); (F.G.)
- Center for Basics in NeuroModulation (NeuroModul Basics), Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Correspondence:
| |
Collapse
|
10
|
Ye XC, Roslin NM, Paterson AD, Lyons CJ, Pegado V, Richmond P, Shyr C, Fornes O, Han X, Higginson M, Ross CJ, Giaschi D, Gregory-Evans C, Patel MS, Wasserman WW. Linkage analysis identifies an isolated strabismus locus at 14q12 overlapping with FOXG1 syndrome region. J Med Genet 2020; 59:46-55. [PMID: 33257509 PMCID: PMC8685624 DOI: 10.1136/jmedgenet-2020-107226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/05/2020] [Accepted: 09/29/2020] [Indexed: 11/21/2022]
Abstract
Strabismus is a common condition, affecting 1%–4% of individuals. Isolated strabismus has been studied in families with Mendelian inheritance patterns. Despite the identification of multiple loci via linkage analyses, no specific genes have been identified from these studies. The current study is based on a seven-generation family with isolated strabismus inherited in an autosomal dominant manner. A total of 13 individuals from a common ancestor have been included for linkage analysis. Among these, nine are affected and four are unaffected. A single linkage signal has been identified at an 8.5 Mb region of chromosome 14q12 with a multipoint LOD (logarithm of the odds) score of 4.69. Disruption of this locus is known to cause FOXG1 syndrome (or congenital Rett syndrome; OMIM #613454 and *164874), in which 84% of affected individuals present with strabismus. With the incorporation of next-generation sequencing and in-depth bioinformatic analyses, a 4 bp non-coding deletion was prioritised as the top candidate for the observed strabismus phenotype. The deletion is predicted to disrupt regulation of FOXG1, which encodes a transcription factor of the Forkhead family. Suggestive of an autoregulation effect, the disrupted sequence matches the consensus FOXG1 and Forkhead family transcription factor binding site and has been observed in previous ChIP-seq studies to be bound by Foxg1 in early mouse brain development. Future study of this specific deletion may shed light on the regulation of FOXG1 expression and may enhance our understanding of the mechanisms contributing to strabismus and FOXG1 syndrome.
Collapse
Affiliation(s)
- Xin Cynthia Ye
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole M Roslin
- The Centre for Applied Genomics, Hospital for Sick Children Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Andrew D Paterson
- The Centre for Applied Genomics, Hospital for Sick Children Research Institute, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Divisions of Epidemiology and Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher J Lyons
- BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Ophthalmology and Visual Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Victor Pegado
- Department of Ophthalmology and Visual Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Phillip Richmond
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Casper Shyr
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - XiaoHua Han
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Higginson
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin J Ross
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Deborah Giaschi
- BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Ophthalmology and Visual Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Cheryl Gregory-Evans
- Department of Ophthalmology and Visual Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Millan S Patel
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada .,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada .,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
11
|
Interpreting the impact of noncoding structural variation in neurodevelopmental disorders. Genet Med 2020; 23:34-46. [PMID: 32973355 PMCID: PMC7790743 DOI: 10.1038/s41436-020-00974-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
The emergence of novel sequencing technologies has greatly improved the identification of structural variation, revealing that a human genome harbors tens of thousands of structural variants (SVs). Since these SVs primarily impact noncoding DNA sequences, the next challenge is one of interpretation, not least to improve our understanding of human disease etiology. However, this task is severely complicated by the intricacy of the gene regulatory landscapes embedded within these noncoding regions, their incomplete annotation, as well as their dependence on the three-dimensional (3D) conformation of the genome. Also in the context of neurodevelopmental disorders (NDDs), reports of putatively causal, noncoding SVs are accumulating and understanding their impact on transcriptional regulation is presenting itself as the next step toward improved genetic diagnosis.
Collapse
|
12
|
Craig CP, Calamaro E, Fong CT, Iqbal AM, Paciorkowski AR, Zhang B. Diagnosis of FOXG1 syndrome caused by recurrent balanced chromosomal rearrangements: case study and literature review. Mol Cytogenet 2020; 13:40. [PMID: 33632291 PMCID: PMC7905679 DOI: 10.1186/s13039-020-00506-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Background The FOXG1 gene plays a vital role in mammalian brain differentiation and development. Intra- and intergenic mutations resulting in loss of function or altered expression of the FOXG1 gene cause FOXG1 syndrome. The hallmarks of this syndrome are severe developmental delay with absent verbal language, post-natal growth restriction, post-natal microcephaly, and a recognizable movement disorder characterized by chorea and dystonia.
Case presentation Here we describe a case of a 7-year-old male patient found to have a de novo balanced translocation between chromosome 3 at band 3q14.1 and chromosome 14 at band 14q12 via G-banding chromosome and Fluorescence In Situ Hybridization (FISH) analyses. This rearrangement disrupts the proximity of FOXG1 to a previously described smallest region of deletion overlap (SRO), likely resulting in haploinsufficiency. Conclusions This case adds to the growing body of literature implicating chromosomal structural variants in the manifestation of this disorder and highlights the vital role of cis-acting regulatory elements in the normal expression of this gene. Finally, we propose a protocol for reflex FISH analysis to improve diagnostic efficiency for patients with suspected FOXG1 syndrome.
Collapse
Affiliation(s)
- Connor P Craig
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA.,School of Medicine and Dentistry, University of Rochester, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Emily Calamaro
- Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Anwar M Iqbal
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA
| | - Alexander R Paciorkowski
- Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.,Department of Neurology, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.,Center for Neural Development and Disease, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.,Departments of Neuroscience and Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Bin Zhang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA. .,Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.
| |
Collapse
|
13
|
Hou PS, hAilín DÓ, Vogel T, Hanashima C. Transcription and Beyond: Delineating FOXG1 Function in Cortical Development and Disorders. Front Cell Neurosci 2020; 14:35. [PMID: 32158381 PMCID: PMC7052011 DOI: 10.3389/fncel.2020.00035] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/04/2020] [Indexed: 11/13/2022] Open
Abstract
Forkhead Box G1 (FOXG1) is a member of the Forkhead family of genes with non-redundant roles in brain development, where alteration of this gene's expression significantly affects the formation and function of the mammalian cerebral cortex. FOXG1 haploinsufficiency in humans is associated with prominent differences in brain size and impaired intellectual development noticeable in early childhood, while homozygous mutations are typically fatal. As such, FOXG1 has been implicated in a wide spectrum of congenital brain disorders, including the congenital variant of Rett syndrome, infantile spasms, microcephaly, autism spectrum disorder (ASD) and schizophrenia. Recent technological advances have yielded greater insight into phenotypic variations observed in FOXG1 syndrome, molecular mechanisms underlying pathogenesis of the disease, and multifaceted roles of FOXG1 expression. In this review, we explore the emerging mechanisms of FOXG1 in a range of transcriptional to posttranscriptional events in order to evolve our current view of how a single transcription factor governs the assembly of an elaborate cortical circuit responsible for higher cognitive functions and neurological disorders.
Collapse
Affiliation(s)
- Pei-Shan Hou
- Laboratory for Developmental Biology, Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan.,Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Darren Ó hAilín
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Tanja Vogel
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Medical Faculty, University of Freiburg, Freiburg, Germany.,Center for Basics in NeuroModulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carina Hanashima
- Laboratory for Developmental Biology, Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan.,Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Advanced Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, Tokyo, Japan
| |
Collapse
|
14
|
Middelkamp S, Vlaar JM, Giltay J, Korzelius J, Besselink N, Boymans S, Janssen R, de la Fonteijne L, van Binsbergen E, van Roosmalen MJ, Hochstenbach R, Giachino D, Talkowski ME, Kloosterman WP, Cuppen E. Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants. Genome Med 2019; 11:79. [PMID: 31801603 PMCID: PMC6894143 DOI: 10.1186/s13073-019-0692-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients carrying de novo SVs are frequently unknown. METHODS We applied a combination of systematic experimental and bioinformatic methods to improve the molecular diagnosis of 39 patients with multiple congenital abnormalities and/or intellectual disability harboring apparent de novo SVs, most with an inconclusive diagnosis after regular genetic testing. RESULTS In 7 of these cases (18%), whole-genome sequencing analysis revealed disease-relevant complexities of the SVs missed in routine microarray-based analyses. We developed a computational tool to predict the effects on genes directly affected by SVs and on genes indirectly affected likely due to the changes in chromatin organization and impact on regulatory mechanisms. By combining these functional predictions with extensive phenotype information, candidate driver genes were identified in 16/39 (41%) patients. In 8 cases, evidence was found for the involvement of multiple candidate drivers contributing to different parts of the phenotypes. Subsequently, we applied this computational method to two cohorts containing a total of 379 patients with previously detected and classified de novo SVs and identified candidate driver genes in 189 cases (50%), including 40 cases whose SVs were previously not classified as pathogenic. Pathogenic position effects were predicted in 28% of all studied cases with balanced SVs and in 11% of the cases with copy number variants. CONCLUSIONS These results demonstrate an integrated computational and experimental approach to predict driver genes based on analyses of WGS data with phenotype association and chromatin organization datasets. These analyses nominate new pathogenic loci and have strong potential to improve the molecular diagnosis of patients with de novo SVs.
Collapse
Affiliation(s)
- Sjors Middelkamp
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Judith M Vlaar
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Jacques Giltay
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Jerome Korzelius
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Lisanne de la Fonteijne
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Markus J van Roosmalen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Ron Hochstenbach
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, 10043, Orbassano, Italy
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wigard P Kloosterman
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands.
| |
Collapse
|
15
|
Perenthaler E, Yousefi S, Niggl E, Barakat TS. Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development. Front Cell Neurosci 2019; 13:352. [PMID: 31417368 PMCID: PMC6685065 DOI: 10.3389/fncel.2019.00352] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/16/2019] [Indexed: 12/22/2022] Open
Abstract
The development of the human cerebral cortex is a complex and dynamic process, in which neural stem cell proliferation, neuronal migration, and post-migratory neuronal organization need to occur in a well-organized fashion. Alterations at any of these crucial stages can result in malformations of cortical development (MCDs), a group of genetically heterogeneous neurodevelopmental disorders that present with developmental delay, intellectual disability and epilepsy. Recent progress in genetic technologies, such as next generation sequencing, most often focusing on all protein-coding exons (e.g., whole exome sequencing), allowed the discovery of more than a 100 genes associated with various types of MCDs. Although this has considerably increased the diagnostic yield, most MCD cases remain unexplained. As Whole Exome Sequencing investigates only a minor part of the human genome (1-2%), it is likely that patients, in which no disease-causing mutation has been identified, could harbor mutations in genomic regions beyond the exome. Even though functional annotation of non-coding regions is still lagging behind that of protein-coding genes, tremendous progress has been made in the field of gene regulation. One group of non-coding regulatory regions are enhancers, which can be distantly located upstream or downstream of genes and which can mediate temporal and tissue-specific transcriptional control via long-distance interactions with promoter regions. Although some examples exist in literature that link alterations of enhancers to genetic disorders, a widespread appreciation of the putative roles of these sequences in MCDs is still lacking. Here, we summarize the current state of knowledge on cis-regulatory regions and discuss novel technologies such as massively-parallel reporter assay systems, CRISPR-Cas9-based screens and computational approaches that help to further elucidate the emerging role of the non-coding genome in disease. Moreover, we discuss existing literature on mutations or copy number alterations of regulatory regions involved in brain development. We foresee that the future implementation of the knowledge obtained through ongoing gene regulation studies will benefit patients and will provide an explanation to part of the missing heritability of MCDs and other genetic disorders.
Collapse
Affiliation(s)
| | | | | | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC – University Medical Center, Rotterdam, Netherlands
| |
Collapse
|
16
|
Brookes E, Riccio A. Location, location, location: nuclear structure regulates gene expression in neurons. Curr Opin Neurobiol 2019; 59:16-25. [PMID: 31005709 DOI: 10.1016/j.conb.2019.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/27/2019] [Accepted: 03/18/2019] [Indexed: 12/27/2022]
Abstract
Genome architecture plays a critical role in regulating the expression of genes that are essential for nervous system development. During neuronal differentiation, spatially and temporally regulated transcription allows neuronal migration, the growth of dendrites and axons, and at later stages, synaptic formation and the establishment of neuronal circuitry. Genome topology and relocation of gene loci within the nucleus are now regarded as key factors that contribute to transcriptional regulation. Here, we review recent work supporting the hypothesis that the dynamic organization of chromatin within the nucleus impacts gene activation in response to extrinsic signalling and during neuronal differentiation. The consequences of disruption of the genome architecture on neuronal health will be also discussed.
Collapse
Affiliation(s)
- Emily Brookes
- MRC Laboratory of Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Antonella Riccio
- MRC Laboratory of Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
| |
Collapse
|
17
|
Laugsch M, Bartusel M, Rehimi R, Alirzayeva H, Karaolidou A, Crispatzu G, Zentis P, Nikolic M, Bleckwehl T, Kolovos P, van Ijcken WFJ, Šarić T, Koehler K, Frommolt P, Lachlan K, Baptista J, Rada-Iglesias A. Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs. Cell Stem Cell 2019; 24:736-752.e12. [PMID: 30982769 DOI: 10.1016/j.stem.2019.03.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 01/03/2019] [Accepted: 03/06/2019] [Indexed: 11/18/2022]
Abstract
The pathological consequences of structural variants disrupting 3D genome organization can be difficult to elucidate in vivo due to differences in gene dosage sensitivity between mice and humans. This is illustrated by branchiooculofacial syndrome (BOFS), a rare congenital disorder caused by heterozygous mutations within TFAP2A, a neural crest regulator for which humans, but not mice, are haploinsufficient. Here, we present a BOFS patient carrying a heterozygous inversion with one breakpoint located within a topologically associating domain (TAD) containing enhancers essential for TFAP2A expression in human neural crest cells (hNCCs). Using patient-specific hiPSCs, we show that, although the inversion shuffles the TFAP2A hNCC enhancers with novel genes within the same TAD, this does not result in enhancer adoption. Instead, the inversion disconnects one TFAP2A allele from its cognate enhancers, leading to monoallelic and haploinsufficient TFAP2A expression in patient hNCCs. Our work illustrates the power of hiPSC differentiation to unveil long-range pathomechanisms.
Collapse
Affiliation(s)
- Magdalena Laugsch
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Institute of Human Genetics, CMMC, University Hospital Cologne, Cologne, Germany
| | - Michaela Bartusel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hafiza Alirzayeva
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Agathi Karaolidou
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Giuliano Crispatzu
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Peter Zentis
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Milos Nikolic
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Tore Bleckwehl
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Petros Kolovos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Tomo Šarić
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Katrin Koehler
- Department of Pediatrics, University Clinic Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Peter Frommolt
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Katherine Lachlan
- Human Genetics & Genomic Medicine, University of Southampton, Southampton General Hospital, Southampton, UK; Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton, UK
| | - Julia Baptista
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK; Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Cantabria, Spain.
| |
Collapse
|