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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 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.
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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.
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Ermakova GV, Kucheryavyy AV, Mugue NS, Mischenko AV, Zaraisky AG, Bayramov AV. Three foxg1 paralogues in lampreys and gnathostomes-brothers or cousins? Front Cell Dev Biol 2024; 11:1321317. [PMID: 38229883 PMCID: PMC10789856 DOI: 10.3389/fcell.2023.1321317] [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: 10/13/2023] [Accepted: 12/05/2023] [Indexed: 01/18/2024] Open
Abstract
Foxg1 is a key regulator of the early development of the vertebrate forebrain and sensory organs. In this study, we describe for the first time three foxg1 paralogues in lamprey, representative of one of two basally diverged lineages of vertebrates-the agnathans. We also first describe three foxg1 genes in sterlet-representative of one of the evolutionarily ancient clades of gnathostomes. According to the analysis of local genomic synteny, three foxg1 genes of agnathans and gnathostomes have a common origin as a result of two rounds of genomic duplications in the early evolution of vertebrates. At the same time, it is difficult to reliably establish pairwise orthology between foxg1 genes of agnathans and gnathostomes based on the analysis of phylogeny and local genomic synteny, as well as our studies of the spatiotemporal expression of foxg1 genes in the river lamprey Lampetra fluviatilis and the sterlet Acipenser ruthenus. Thus, the appearance of three foxg1 paralogues in agnathans and gnathostomes could have occurred either as a result of two rounds of duplication of the vertebrate common ancestor genome (2R hypothesis) or as a result of the first common round followed by subsequent independent polyploidizations in two evolutionary lineages (1R hypothesis).
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Affiliation(s)
- Galina V. Ermakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Nikolay S. Mugue
- Russian Federal Research Institute of Fisheries and Oceanography (VNIRO), Moscow, Russia
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Aleksandr V. Mischenko
- Branch for the Freshwater Fisheries of the Russian Federal Research Institute of Fisheries and Oceanography, Moscow, Russia
| | - Andrey G. Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Andrey V. Bayramov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Miller C, Gertsen BG, Schroeder AL, Fong CT, Iqbal MA, Zhang B. Allelic and dosage effects of NHS in X-linked cataract and Nance-Horan syndrome: a family study and literature review. Mol Cytogenet 2021; 14:48. [PMID: 34620209 PMCID: PMC8496034 DOI: 10.1186/s13039-021-00566-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/08/2021] [Indexed: 11/21/2022] Open
Abstract
Nance–Horan syndrome (NHS) is a rare X-linked dominant disorder caused by mutation in the NHS gene on chromosome Xp22.13. (OMIM 302350). Classic NHS manifested in males is characterized by congenital cataracts, dental anomalies, dysmorphic facial features and occasionally intellectual disability. Females typically have a milder presentation. The majority of reported cases of NHS are the result of nonsense mutations and small deletions. Isolated X-linked congenital cataract is caused by non-recurrent rearrangement-associated aberrant NHS transcription. Classic NHS in females associated with gene disruption by balanced X-autosome translocation has been infrequently reported. We present a familial NHS associated with translocation t(X;19) (Xp22.13;q13.1). The proband, a 28-year-old female, presented with intellectual disability, dysmorphic features, short stature, primary amenorrhea, cleft palate, and horseshoe kidney, but no NHS phenotype. A karyotype and chromosome microarray analysis (CMA) revealed partial monosomy Xp/partial trisomy 19q with the breakpoint at Xp22.13 disrupting the NHS gene. Family history revealed congenital cataracts and glaucoma in the patient’s mother, and congenital cataracts in maternal half-sister and maternal grandmother. The same balanced translocation t(X;19) was subsequently identified in both the mother and maternal half-sister, and further clinical evaluation of the maternal half-sister made a diagnosis of NHS. This study describes the clinical implication of NHS gene disruption due to balanced X-autosome translocations as a unique mechanism causing Nance–Horan syndrome, refines dose effects of NHS on disease presentation and phenotype expressivity, and justifies consideration of karyotype and fluorescence in situ hybridization (FISH) analysis for female patients with familial NHS if single-gene analysis of NHS is negative.
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Affiliation(s)
- Caroline Miller
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA
| | - Benjamin G Gertsen
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA
| | - Audrey L Schroeder
- Division of Medical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, 14642, USA.,Department of Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - M Anwar Iqbal
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, 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, Rochester, NY, 14642, USA. .,Department of Pathology and Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA.
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