1
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Heim F, Scharff C, Fisher SE, Riebel K, Ten Cate C. Auditory discrimination learning and acoustic cue weighing in female zebra finches with localized FoxP1 knockdowns. J Neurophysiol 2024; 131:950-963. [PMID: 38629163 DOI: 10.1152/jn.00228.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 05/21/2024] Open
Abstract
Rare disruptions of the transcription factor FOXP1 are implicated in a human neurodevelopmental disorder characterized by autism and/or intellectual disability with prominent problems in speech and language abilities. Avian orthologues of this transcription factor are evolutionarily conserved and highly expressed in specific regions of songbird brains, including areas associated with vocal production learning and auditory perception. Here, we investigated possible contributions of FoxP1 to song discrimination and auditory perception in juvenile and adult female zebra finches. They received lentiviral knockdowns of FoxP1 in one of two brain areas involved in auditory stimulus processing, HVC (proper name) or CMM (caudomedial mesopallium). Ninety-six females, distributed over different experimental and control groups were trained to discriminate between two stimulus songs in an operant Go/Nogo paradigm and subsequently tested with an array of stimuli. This made it possible to assess how well they recognized and categorized altered versions of training stimuli and whether localized FoxP1 knockdowns affected the role of different features during discrimination and categorization of song. Although FoxP1 expression was significantly reduced by the knockdowns, neither discrimination of the stimulus songs nor categorization of songs modified in pitch, sequential order of syllables or by reversed playback were affected. Subsequently, we analyzed the full dataset to assess the impact of the different stimulus manipulations for cue weighing in song discrimination. Our findings show that zebra finches rely on multiple parameters for song discrimination, but with relatively more prominent roles for spectral parameters and syllable sequencing as cues for song discrimination.NEW & NOTEWORTHY In humans, mutations of the transcription factor FoxP1 are implicated in speech and language problems. In songbirds, FoxP1 has been linked to male song learning and female preference strength. We found that FoxP1 knockdowns in female HVC and caudomedial mesopallium (CMM) did not alter song discrimination or categorization based on spectral and temporal information. However, this large dataset allowed to validate different cue weights for spectral over temporal information for song recognition.
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Affiliation(s)
- Fabian Heim
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Language and Genetics Department, Max Planck Institute for Psycholinguistics,Nijmegen, The Netherlands
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | | | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics,Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Katharina Riebel
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Carel Ten Cate
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Leiden Institute for Brain and Cognition, Leiden, The Netherlands
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2
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Topa A, Rohlin A, Fehr A, Lovmar L, Stenman G, Tarnow P, Maltese G, Bhatti-Søfteland M, Kölby L. The value of genome-wide analysis in craniosynostosis. Front Genet 2024; 14:1322462. [PMID: 38318288 PMCID: PMC10839781 DOI: 10.3389/fgene.2023.1322462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024] Open
Abstract
Background: This study assessed the diagnostic yield of high-throughput sequencing methods in a cohort of craniosynostosis (CS) patients not presenting causal variants identified through previous targeted analysis. Methods: Whole-genome or whole-exome sequencing (WGS/WES) was performed in a cohort of 59 patients (from 57 families) assessed by retrospective phenotyping as having syndromic or nonsyndromic CS. Results: A syndromic form was identified in 51% of the unrelated cases. A genetic cause was identified in 38% of syndromic cases, with novel variants detected in FGFR2 (a rare Alu insertion), TWIST1, TCF12, KIAA0586, HDAC9, FOXP1, and NSD2. Additionally, we report two patients with rare recurrent variants in KAT6A and YY1 as well as two patients with structural genomic aberrations: one with a 22q13 duplication and one with a complex rearrangement involving chromosome 2 (2p25 duplication including SOX11 and deletion of 2q22). Moreover, we identified potentially relevant variants in 87% of the remaining families with no previously detected causal variants, including novel variants in ADAMTSL4, ASH1L, ATRX, C2CD3, CHD5, ERF, H4C5, IFT122, IFT140, KDM6B, KMT2D, LTBP1, MAP3K7, NOTCH2, NSD1, SOS1, SPRY1, POLR2A, PRRX1, RECQL4, TAB2, TAOK1, TET3, TGFBR1, TCF20, and ZBTB20. Conclusion: These results confirm WGS/WES as a powerful diagnostic tool capable of either targeted in silico or broad genomic analysis depending on phenotypic presentation (e.g., classical or unusual forms of syndromic CS).
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Affiliation(s)
- Alexandra Topa
- Department of Laboratory Medicine, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Rohlin
- Department of Laboratory Medicine, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - André Fehr
- Department of Laboratory Medicine, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lovisa Lovmar
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Göran Stenman
- Department of Laboratory Medicine, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Peter Tarnow
- Department of Plastic Surgery, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Giovanni Maltese
- Department of Plastic Surgery, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Madiha Bhatti-Søfteland
- Department of Plastic Surgery, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Lars Kölby
- Department of Plastic Surgery, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
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3
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Park SHE, Kulkarni A, Konopka G. FOXP1 orchestrates neurogenesis in human cortical basal radial glial cells. PLoS Biol 2023; 21:e3001852. [PMID: 37540706 PMCID: PMC10431666 DOI: 10.1371/journal.pbio.3001852] [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: 09/19/2022] [Revised: 08/16/2023] [Accepted: 06/21/2023] [Indexed: 08/06/2023] Open
Abstract
During cortical development, human basal radial glial cells (bRGCs) are highly capable of sustained self-renewal and neurogenesis. Selective pressures on this cell type may have contributed to the evolution of the human neocortex, leading to an increase in cortical size. bRGCs have enriched expression for Forkhead Box P1 (FOXP1), a transcription factor implicated in neurodevelopmental disorders (NDDs) such as autism spectrum disorder. However, the cell type-specific roles of FOXP1 in bRGCs during cortical development remain unexplored. Here, we examine the requirement for FOXP1 gene expression regulation underlying the production of bRGCs using human brain organoids. We examine a developmental time point when FOXP1 expression is highest in the cortical progenitors, and the bRGCs, in particular, begin to actively produce neurons. With the loss of FOXP1, we show a reduction in the number of bRGCs, as well as reduced proliferation and differentiation of the remaining bRGCs, all of which lead to reduced numbers of excitatory cortical neurons over time. Using single-nuclei RNA sequencing and cell trajectory analysis, we uncover a role for FOXP1 in directing cortical progenitor proliferation and differentiation by regulating key signaling pathways related to neurogenesis and NDDs. Together, these results demonstrate that FOXP1 regulates human-specific features in early cortical development.
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Affiliation(s)
- Seon Hye E. Park
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ashwinikumar Kulkarni
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, Texas, United States of America
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4
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Cesaroni CA, Pollazzon M, Mancini C, Rizzi S, Cappelletti C, Pizzi S, Frattini D, Spagnoli C, Caraffi SG, Zuntini R, Trimarchi G, Niceta M, Radio FC, Tartaglia M, Garavelli L, Fusco C. Case report: Expanding the phenotype of FOXP1-related intellectual disability syndrome and hyperkinetic movement disorder in differential diagnosis with epileptic seizures. Front Neurol 2023; 14:1207176. [PMID: 37521304 PMCID: PMC10382204 DOI: 10.3389/fneur.2023.1207176] [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: 04/17/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023] Open
Abstract
Objective We aimed to report on previously unappreciated clinical features associated with FOXP1-related intellectual disability (ID) syndrome, a rare neurodevelopmental disorder characterized by global developmental delay, intellectual disability, and language delay, with or without autistic features. Methods We performed whole-exome sequencing (WES) to molecularly characterize an individual presenting with ID, epilepsy, autism spectrum disorder, behavioral problems, and facial dysmorphisms as major features. Results WES allowed us to identify a previously unreported de novo splice site variant, c.1429-1G>T (NM_032682.6), in the FOXP1 gene (OMIM*605515) as the causative event underlying the phenotype. Clinical reassessment of the patient and revision of the literature allowed us to refine the phenotype associated with FOXP1 haploinsufficiency, including hyperkinetic movement disorder and flat angiomas as associated features. Interestingly, the patient also has an asymmetric face and choanal atresia and a novel de novo variant of the CHD7 gene. Conclusion We suggest that FOXP1-related ID syndrome may also predispose to the development of hyperkinetic movement disorders and flat angiomas. These features could therefore require specific management of this condition.
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Affiliation(s)
- Carlo Alberto Cesaroni
- Child Neurology and Psychiatry Unit, Pediatric Neurophysiology Laboratory, Mother-Child Department, Azienda USL-IRCCS Di Reggio Emilia, Reggio Emilia, Italy
| | - Marzia Pollazzon
- Medical Genetics Unit, Mother-Child Department, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Cecilia Mancini
- Molecular Genetics and Functional Genomics Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Susanna Rizzi
- Child Neurology and Psychiatry Unit, Pediatric Neurophysiology Laboratory, Mother-Child Department, Azienda USL-IRCCS Di Reggio Emilia, Reggio Emilia, Italy
| | - Camilla Cappelletti
- Molecular Genetics and Functional Genomics Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Daniele Frattini
- Child Neurology and Psychiatry Unit, Pediatric Neurophysiology Laboratory, Mother-Child Department, Azienda USL-IRCCS Di Reggio Emilia, Reggio Emilia, Italy
| | - Carlotta Spagnoli
- Child Neurology and Psychiatry Unit, Pediatric Neurophysiology Laboratory, Mother-Child Department, Azienda USL-IRCCS Di Reggio Emilia, Reggio Emilia, Italy
| | - Stefano Giuseppe Caraffi
- Medical Genetics Unit, Mother-Child Department, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Roberta Zuntini
- Medical Genetics Unit, Mother-Child Department, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Gabriele Trimarchi
- Medical Genetics Unit, Mother-Child Department, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Marcello Niceta
- Molecular Genetics and Functional Genomics Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Marco Tartaglia
- Molecular Genetics and Functional Genomics Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Livia Garavelli
- Medical Genetics Unit, Mother-Child Department, Azienda USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Carlo Fusco
- Child Neurology and Psychiatry Unit, Pediatric Neurophysiology Laboratory, Mother-Child Department, Azienda USL-IRCCS Di Reggio Emilia, Reggio Emilia, Italy
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5
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Chen M, Sun Y, Qian Y, Chen N, Li H, Wang L, Dong M. Case report: FOXP1 syndrome caused by a de novo splicing variant (c.1652+5 G>A) of the FOXP1 gene. Front Genet 2022; 13:926070. [PMID: 35991577 PMCID: PMC9388729 DOI: 10.3389/fgene.2022.926070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022] Open
Abstract
FOXP1 syndrome is a rare neurodevelopmental disorder characterized by global developmental delay, intellectual disability, and language delay, with or without autistic features. Several splicing variants have been reported for this condition, but most of them lack functional evidence, and the actual effects of the sequence changes are still unknown. In this study, a de novo splicing variant (c.1652 + 5 G>A) of the FOXP1 gene was identified in a patient with global developmental delay, mild intellectual disability, speech delay, and autistic features. Assessed by TA-cloning, the variant promoted the skipping of exon 18 and a premature stop codon (p.Asn511*), resulting in a predicted truncated protein. This variant, that is lacking the forkhead-box DNA-binding domain and nuclear localization signal 2, may disrupt the protein function and thus cause FOXP1 syndrome-related symptoms. Our study extends the phenotypic and allelic spectra of the FOXP1 syndrome.
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Affiliation(s)
- Min Chen
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yixi Sun
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yeqing Qian
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Na Chen
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hongge Li
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Liya Wang
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Minyue Dong
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Minyue Dong,
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6
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Lozano R, Gbekie C, Siper PM, Srivastava S, Saland JM, Sethuram S, Tang L, Drapeau E, Frank Y, Buxbaum JD, Kolevzon A. FOXP1 syndrome: a review of the literature and practice parameters for medical assessment and monitoring. J Neurodev Disord 2021; 13:18. [PMID: 33892622 PMCID: PMC8066957 DOI: 10.1186/s11689-021-09358-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/25/2021] [Indexed: 11/14/2022] Open
Abstract
FOXP1 syndrome is a neurodevelopmental disorder caused by mutations or deletions that disrupt the forkhead box protein 1 (FOXP1) gene, which encodes a transcription factor important for the early development of many organ systems, including the brain. Numerous clinical studies have elucidated the role of FOXP1 in neurodevelopment and have characterized a phenotype. FOXP1 syndrome is associated with intellectual disability, language deficits, autism spectrum disorder, hypotonia, and congenital anomalies, including mild dysmorphic features, and brain, cardiac, and urogenital abnormalities. Here, we present a review of human studies summarizing the clinical features of individuals with FOXP1 syndrome and enlist a multidisciplinary group of clinicians (pediatrics, genetics, psychiatry, neurology, cardiology, endocrinology, nephrology, and psychology) to provide recommendations for the assessment of FOXP1 syndrome.
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Affiliation(s)
- Reymundo Lozano
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Catherine Gbekie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paige M Siper
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shubhika Srivastava
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey M Saland
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Children's Heart Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Swathi Sethuram
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lara Tang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elodie Drapeau
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yitzchak Frank
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander Kolevzon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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7
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Co M, Anderson AG, Konopka G. FOXP transcription factors in vertebrate brain development, function, and disorders. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2020; 9:e375. [PMID: 31999079 PMCID: PMC8286808 DOI: 10.1002/wdev.375] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/17/2019] [Accepted: 01/08/2020] [Indexed: 12/22/2022]
Abstract
FOXP transcription factors are an evolutionarily ancient protein subfamily coordinating the development of several organ systems in the vertebrate body. Association of their genes with neurodevelopmental disorders has sparked particular interest in their expression patterns and functions in the brain. Here, FOXP1, FOXP2, and FOXP4 are expressed in distinct cell type-specific spatiotemporal patterns in multiple regions, including the cortex, hippocampus, amygdala, basal ganglia, thalamus, and cerebellum. These varied sites and timepoints of expression have complicated efforts to link FOXP1 and FOXP2 mutations to their respective developmental disorders, the former affecting global neural functions and the latter specifically affecting speech and language. However, the use of animal models, particularly those with brain region- and cell type-specific manipulations, has greatly advanced our understanding of how FOXP expression patterns could underlie disorder-related phenotypes. While many questions remain regarding FOXP expression and function in the brain, studies to date have illuminated the roles of these transcription factors in vertebrate brain development and have greatly informed our understanding of human development and disorders. This article is categorized under: Nervous System Development > Vertebrates: General Principles Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics Nervous System Development > Vertebrates: Regional Development.
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Affiliation(s)
- Marissa Co
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
| | - Ashley G Anderson
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
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8
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Urreizti R, Grinberg D, Balcells S. C syndrome - what do we know and what could the future hold? Expert Opin Orphan Drugs 2019. [DOI: 10.1080/21678707.2019.1589448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Roser Urreizti
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, Institut de Recerca Sant Joan de Déu, CIBERER, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, Institut de Recerca Sant Joan de Déu, CIBERER, Barcelona, Spain
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, Institut de Recerca Sant Joan de Déu, CIBERER, Barcelona, Spain
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9
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Shaffer JR, LeClair J, Carlson JC, Feingold E, Buxó CJ, Christensen K, Deleyiannis FW, Field LL, Hecht JT, Moreno L, Orioli IM, Padilla C, Vieira AR, Wehby GL, Murray JC, Weinberg SM, Marazita ML, Leslie EJ. Association of low-frequency genetic variants in regulatory regions with nonsyndromic orofacial clefts. Am J Med Genet A 2019; 179:467-474. [PMID: 30582786 PMCID: PMC6374160 DOI: 10.1002/ajmg.a.61002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/06/2018] [Accepted: 11/01/2018] [Indexed: 01/24/2023]
Abstract
Genome-wide scans have shown that common risk alleles for orofacial clefts (OFC) tend to be located in noncoding regulatory elements and cumulatively explain only part of the heritability of OFCs. Low-frequency variants may account for some of the "missing" heritability. Therefore, we scanned low-frequency variants located within putative craniofacial enhancers to identify novel OFC risk variants and implicate new regulatory elements in OFC pathogenesis. Analyses were performed in a multiethnic sample of 1,995 cases of cleft lip with or without cleft palate (CL/P), 221 cases with cleft palate (CP) only, and 1,576 unaffected controls. One hundred and nineteen putative craniofacial enhancers identified from ChIP-Seq studies in craniofacial tissues or cell lines contained multiple low-frequency (0.01-1%) variants, which we genotyped in participants using a custom Illumina panel. Two complementary statistical approaches, sequence kernel association test and combined multivariate and collapsing, were used to test association of the aggregated low-frequency variants across each enhancer region with CL/P and CP. We discovered a significant association between CP and a branchial arch enhancer near FOXP1 (mm60; p-value = .0002). Additionally, we observed a suggestive association between CL/P and a forebrain enhancer near FOXE1 (hs1717; p-value = .001). These findings suggest that low-frequency variants in craniofacial enhancer regions contribute to the complex etiology of nonsyndromic OFCs.
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Affiliation(s)
- John R. Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
| | - Jessica LeClair
- formerly of Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Jenna C. Carlson
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Carmen J. Buxó
- Dental and Craniofacial Genomics Core, School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico, 00936, USA
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, DK-5000, Denmark
| | - Frederic W.B. Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO, 80045, USA
| | - L. Leigh Field
- Department of Medical Genetics, University of British Columbia, Vancouver, V6H 3N1, Canada
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry UT Health at Houston, Houston, TX, 77030, USA
| | - Lina Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Ieda M. Orioli
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro, 21941-617, Brazil
| | - Carmencita Padilla
- Department of Pediatrics, College of Medicine; and Institute of Human Genetics, National Institutes of Health; University of the Philippines Manila, Manila, The Philippines, 1000; and Philippine Genome Center, University of the Philippines System, Manila, The Philippines 1101
| | - Alexandre R. Vieira
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52246, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Department of Anthropology, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA, 30322
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Characterization of a recurrent missense mutation in the forkhead DNA-binding domain of FOXP1. Sci Rep 2018; 8:16161. [PMID: 30385778 PMCID: PMC6212433 DOI: 10.1038/s41598-018-34437-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/12/2018] [Indexed: 12/11/2022] Open
Abstract
Haploinsufficiency of Forkhead box protein P1 (FOXP1), a highly conserved transcription factor, leads to developmental delay, intellectual disability, autism spectrum disorder, speech delay, and dysmorphic features. Most of the reported FOXP1 mutations occur on the C-terminus of the protein and cluster around to the forkhead domain. All reported FOXP1 pathogenic variants result in abnormal cellular localization and loss of transcriptional repression activity of the protein product. Here we present three patients with the same FOXP1 mutation, c.1574G>A (p.R525Q), that results in the characteristic loss of transcription repression activity. This mutation, however, represents the first reported FOXP1 mutation that does not result in cytoplasmic or nuclear aggregation of the protein but maintains normal nuclear localization.
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11
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Vuillaume ML, Cogné B, Jeanne M, Boland A, Ung DC, Quinquis D, Besnard T, Deleuze JF, Redon R, Bézieau S, Laumonnier F, Toutain A. Whole genome sequencing identifies a de novo 2.1 Mb balanced paracentric inversion disrupting FOXP1 and leading to severe intellectual disability. Clin Chim Acta 2018; 485:218-223. [PMID: 29969624 DOI: 10.1016/j.cca.2018.06.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/25/2018] [Accepted: 06/29/2018] [Indexed: 01/08/2023]
Abstract
The FOXP1 gene, located on chromosome 3p13, encodes the Forkhead-box protein P1, one of the four forkhead transcription factors which repress transcription by forming active homo- and heterodimers and regulate distinct patterns of gene expression crucial for embryogenesis and normal development. FOXP1 mutations, mostly truncating, have been described in patients with mild to moderate intellectual disability (ID), autism spectrum disorder (ASD), and speech and language impairment (MIM #613670). Here, we report a small de novo heterozygous balanced inversion of 2.1 Mb located at 3p14.1p13 identified by Whole Genomic Sequencing (WGS) and disrupting the genes FAM19A4 and FOXP1. This inversion was found in a patient with severe ID, ASD, seizures and very unusual vascular anomalies which were never described in the clinical spectrum of FOXP1 mutations. We show that the neurodevelopmental phenotype observed in the patient most likely results from FOXP1 haploinsufficiency as this heterozygous inversion leads to a 60 to 85% decrease of FOXP1 mRNA levels and to the complete absence of FOXP1 full-length protein. These findings, in addition to expanding the molecular spectrum of FOXP1 mutations, emphasize the emerging role of WGS in identifying small balanced chromosomal rearrangements responsible for neurodevelopmental disorders and not detected by conventional cytogenetics.
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Affiliation(s)
- M-L Vuillaume
- Service de Génétique, Centre Hospitalier Universitaire de Tours, France; UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - B Cogné
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Nantes, France; INSERM, CNRS, UNIV Nantes, l'Institut du Thorax, Nantes, France
| | - M Jeanne
- Service de Génétique, Centre Hospitalier Universitaire de Tours, France; UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - A Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Direction de La Recherche Fondamentale, CEA, Evry, France
| | - D-C Ung
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - D Quinquis
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Nantes, France
| | - T Besnard
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Nantes, France
| | - J-F Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Direction de La Recherche Fondamentale, CEA, Evry, France
| | - R Redon
- INSERM, CNRS, UNIV Nantes, l'Institut du Thorax, Nantes, France
| | - S Bézieau
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Nantes, France; INSERM, CNRS, UNIV Nantes, l'Institut du Thorax, Nantes, France
| | - F Laumonnier
- Service de Génétique, Centre Hospitalier Universitaire de Tours, France; UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - A Toutain
- Service de Génétique, Centre Hospitalier Universitaire de Tours, France; UMR 1253, iBrain, Université de Tours, Inserm, Tours, France.
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