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Neal SJ, Rajasekaran A, Jusić N, Taylor L, Read M, Alfandari D, Pignoni F, Moody SA. Using Xenopus to discover new candidate genes involved in BOR and other congenital hearing loss syndromes. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:212-240. [PMID: 37830236 PMCID: PMC11014897 DOI: 10.1002/jez.b.23222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/15/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Hearing in infants is essential for brain development, acquisition of verbal language skills, and development of social interactions. Therefore, it is important to diagnose hearing loss soon after birth so that interventions can be provided as early as possible. Most newborns in the United States are screened for hearing deficits and commercially available next-generation sequencing hearing loss panels often can identify the causative gene, which may also identify congenital defects in other organs. One of the most prevalent autosomal dominant congenital hearing loss syndromes is branchio-oto-renal syndrome (BOR), which also presents with defects in craniofacial structures and the kidney. Currently, mutations in three genes, SIX1, SIX5, and EYA1, are known to be causative in about half of the BOR patients that have been tested. To uncover new candidate genes that could be added to congenital hearing loss genetic screens, we have combined the power of Drosophila mutants and protein biochemical assays with the embryological advantages of Xenopus, a key aquatic animal model with a high level of genomic similarity to human, to identify potential Six1 transcriptional targets and interacting proteins that play a role during otic development. We review our transcriptomic, yeast 2-hybrid, and proteomic approaches that have revealed a large number of new candidates. We also discuss how we have begun to identify how Six1 and co-factors interact to direct developmental events necessary for normal otic development.
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Affiliation(s)
- Scott J. Neal
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Anindita Rajasekaran
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Nisveta Jusić
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Louis Taylor
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Mai Read
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Dominique Alfandari
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Francesca Pignoni
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Sally A. Moody
- Department of Anatomy and Cell Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
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Greenberg D, Rosenblum ND, Tonelli M. The multifaceted links between hearing loss and chronic kidney disease. Nat Rev Nephrol 2024; 20:295-312. [PMID: 38287134 DOI: 10.1038/s41581-024-00808-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 01/31/2024]
Abstract
Hearing loss affects nearly 1.6 billion people and is the third-leading cause of disability worldwide. Chronic kidney disease (CKD) is also a common condition that is associated with adverse clinical outcomes and high health-care costs. From a developmental perspective, the structures responsible for hearing have a common morphogenetic origin with the kidney, and genetic abnormalities that cause familial forms of hearing loss can also lead to kidney disease. On a cellular level, normal kidney and cochlea function both depend on cilial activities at the apical surface, and kidney tubular cells and sensory epithelial cells of the inner ear use similar transport mechanisms to modify luminal fluid. The two organs also share the same collagen IV basement membrane network. Thus, strong developmental and physiological links exist between hearing and kidney function. These theoretical considerations are supported by epidemiological data demonstrating that CKD is associated with a graded and independent excess risk of sensorineural hearing loss. In addition to developmental and physiological links between kidney and cochlear function, hearing loss in patients with CKD may be driven by specific medications or treatments, including haemodialysis. The associations between these two common conditions are not commonly appreciated, yet have important implications for research and clinical practice.
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Affiliation(s)
- Dina Greenberg
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Norman D Rosenblum
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, Toronto, Ontario, Canada
- Department of Paediatrics, Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Marcello Tonelli
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada.
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Wang SX, Streit A. Shared features in ear and kidney development - implications for oto-renal syndromes. Dis Model Mech 2024; 17:dmm050447. [PMID: 38353121 PMCID: PMC10886756 DOI: 10.1242/dmm.050447] [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] [Indexed: 02/16/2024] Open
Abstract
The association between ear and kidney anomalies has long been recognized. However, little is known about the underlying mechanisms. In the last two decades, embryonic development of the inner ear and kidney has been studied extensively. Here, we describe the developmental pathways shared between both organs with particular emphasis on the genes that regulate signalling cross talk and the specification of progenitor cells and specialised cell types. We relate this to the clinical features of oto-renal syndromes and explore links to developmental mechanisms.
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Affiliation(s)
- Scarlet Xiaoyan Wang
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Andrea Streit
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
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Baxi A, Jourdeuil K, Cox TC, Clouthier DE, Tavares ALP. Transcriptomic analysis reveals the role of SIX1 in mouse cranial neural crest patterning and bone development. Dev Dyn 2023; 252:1303-1315. [PMID: 37183792 PMCID: PMC10592572 DOI: 10.1002/dvdy.597] [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: 03/09/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND Genetic variants of the transcription factor SIX1 and its co-factor EYA1 underlie 50% of Branchio-oto-renal syndrome (BOR) cases. BOR is characterized by craniofacial defects, including malformed middle ear ossicles leading to conductive hearing loss. In this work, we expand our knowledge of the Six1 gene regulatory network by using a Six1-null mouse line to assess gene expression profiles of E10.5 mandibular arches, which give rise to the neural crest (NC)-derived middle ear ossicles and lower jaw, via bulk RNA sequencing. RESULTS Our transcriptomic analysis led to the identification of 808 differentially expressed genes that are related to translation, NC cell differentiation, osteogenesis, and chondrogenesis including components of the WNT signaling pathway. As WNT signaling is a known contributor to bone development, we demonstrated that SIX1 is required for expression of the WNT antagonist Frzb in the mandibular arch, and determined that SIX1 expression results in repression of WNT signaling. CONCLUSION Our results clarify the mechanisms by which SIX1 regulates the development of NC-derived craniofacial elements that are altered in SIX1-associated disorders. In addition, this work identifies novel genes that could be causative to this birth defect and establishes a link between SIX1 and WNT signaling during patterning of NC cells.
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Affiliation(s)
- Aparna Baxi
- Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington DC, DC 20037, USA
| | - Karyn Jourdeuil
- Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington DC, DC 20037, USA
| | - Timothy C. Cox
- Departments of Oral and Craniofacial Sciences and Pediatrics, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - David E. Clouthier
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Andre L. P. Tavares
- Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington DC, DC 20037, USA
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Thiery AP, Buzzi AL, Hamrud E, Cheshire C, Luscombe NM, Briscoe J, Streit A. scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border. eLife 2023; 12:e82717. [PMID: 37530410 PMCID: PMC10425176 DOI: 10.7554/elife.82717] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/01/2023] [Indexed: 08/03/2023] Open
Abstract
The vertebrate 'neural plate border' is a transient territory located at the edge of the neural plate containing precursors for all ectodermal derivatives: the neural plate, neural crest, placodes and epidermis. Elegant functional experiments in a range of vertebrate models have provided an in-depth understanding of gene regulatory interactions within the ectoderm. However, these experiments conducted at tissue level raise seemingly contradictory models for fate allocation of individual cells. Here, we carry out single cell RNA sequencing of chick ectoderm from primitive streak to neurulation stage, to explore cell state diversity and heterogeneity. We characterise the dynamics of gene modules, allowing us to model the order of molecular events which take place as ectodermal fates segregate. Furthermore, we find that genes previously classified as neural plate border 'specifiers' typically exhibit dynamic expression patterns and are enriched in either neural, neural crest or placodal fates, revealing that the neural plate border should be seen as a heterogeneous ectodermal territory and not a discrete transitional transcriptional state. Analysis of neural, neural crest and placodal markers reveals that individual NPB cells co-express competing transcriptional programmes suggesting that their ultimate identify is not yet fixed. This population of 'border located undecided progenitors' (BLUPs) gradually diminishes as cell fate decisions take place. Considering our findings, we propose a probabilistic model for cell fate choice at the neural plate border. Our data suggest that the probability of a progenitor's daughters to contribute to a given ectodermal derivative is related to the balance of competing transcriptional programmes, which in turn are regulated by the spatiotemporal position of a progenitor.
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Affiliation(s)
- Alexandre P Thiery
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College LondonLondonUnited Kingdom
| | - Ailin Leticia Buzzi
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College LondonLondonUnited Kingdom
| | - Eva Hamrud
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College LondonLondonUnited Kingdom
| | - Chris Cheshire
- Bioinformatics and Computational Biology Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - James Briscoe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Andrea Streit
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College LondonLondonUnited Kingdom
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Lee S, Yun Y, Cha JH, Han JH, Lee DH, Song JJ, Park MK, Lee JH, Oh SH, Choi BY, Lee SY. Phenotypic and molecular basis of SIX1 variants linked to non-syndromic deafness and atypical branchio-otic syndrome in South Korea. Sci Rep 2023; 13:11776. [PMID: 37479820 PMCID: PMC10361970 DOI: 10.1038/s41598-023-38909-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Branchio-oto-renal (BOR)/branchio-otic (BO) syndrome is a rare disorder and exhibits clinically heterogenous phenotypes, marked by abnormalities in the ear, branchial arch, and renal system. Sporadic cases of atypical BOR/BO syndrome have been recently reported; however, evidence on genotype-phenotype correlations and molecular mechanisms of those cases is lacking. We herein identified five SIX1 heterozygous variants (c.307dupC:p.Leu103Profs*51, c.373G>A:p.Glu125Lys, c.386_391del:p.Tyr129_Cys130del, c.397_399del:p.Glu133del, and c.501G>C:p.Gln167His), including three novel variants, through whole-exome sequencing in five unrelated Korean families. All eight affected individuals with SIX1 variants displayed non-syndromic hearing loss (DFNA23) or atypical BO syndrome. The prevalence of major and minor criteria for BOR/BO syndrome was significantly reduced among individuals with SIX1 variants, compared to 15 BOR/BO syndrome families with EYA1 variants. All SIX1 variants interacted with the EYA1 wild-type; their complexes were localized in the nucleus except for the p.Leu103Profs*51 variant. All mutants also showed obvious but varying degrees of reduction in DNA binding affinity, leading to a significant decrease in transcriptional activity. This study presents the first report of SIX1 variants in South Korea, expanding the genotypic and phenotypic spectrum of SIX1 variants, characterized by DFNA23 or atypical BO syndrome, and refines the diverse molecular aspects of SIX1 variants according to the EYA1-SIX1-DNA complex theory.
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Affiliation(s)
- Somin Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Yejin Yun
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Ju Hyuen Cha
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul, South Korea
| | - Dae Hee Lee
- CTCELLS, Inc., 21, Yuseong-Daero, 1205 Beon-Gil, Yuseong-Gu, Daejeon, Republic of Korea
| | - Jae-Jin Song
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul, South Korea
| | - Moo Kyun Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Seung Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul, South Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea.
- Department of Genomic Medicine, Precision Medicine & Rare Disease Center, Seoul National University Hospital, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea.
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, South Korea.
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Tang P, Li J, Li J, Yang J, Zhu J. Prenatal diagnosis and genetic analysis of a fetus with Branchio-oto-renal syndrome: A case report. Medicine (Baltimore) 2022; 101:e31172. [PMID: 36316881 PMCID: PMC9622624 DOI: 10.1097/md.0000000000031172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Branchio-oto-renal (BOR) syndrome is an autosomal-dominant disorder characterized by branchial arch anomalies, hearing loss, and kidney defects. Mutations in the human EYA1 gene have been reported associated with BOR syndrome. Here we identified that a novel variant, EYA1: NM_000503.4: c.827-1G > C (Intron 8, shear mutation) was associated with BOR in a fetus of a Chinese family. CASE PRESENTATION Prenatal ultrasound examination showed that both kidneys of the fetus were small and the echo of both kidneys was enhanced. The amount of amniotic fluid was normal, and no other structural abnormalities of the fetus were found. Fetal umbilical cord blood puncture was performed. No abnormality was found in karyotyping and chromosomal microarray analysis (CMA) results. Thus, we performed a trio-based whole exome sequencing (WES), and found that the fetus carried a novel homozygous variant, EYA1: NM_000503.4: c.827-1G > C (Intron 8, shear mutation), but the parents do not have this mutation. The variation sites of fetus and parents were verified by Sanger sequencing to clarify the source of pathogenic variation. CONCLUSION Combined with fetal imaging examination, the novel variation of EYA1: NM_000503.4: c.827-1G > C is the cause of fetal renal dysplasia. This case report indicates that the early use of appropriate technology can clarify the etiology of fetal disease and guide prognosis consultation.
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Affiliation(s)
- Ping Tang
- Fetal Medical Center, Jiaxing Maternity and Children Health Care Hospital/The Affiliated Women and Children’s Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Jiarui Li
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Li
- Department of Surgery, Jiaxing Maternity and Children Health Care Hospital/The Affiliated Women and Children’s Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Juan Yang
- Fetal Medical Center, Jiaxing Maternity and Children Health Care Hospital/The Affiliated Women and Children’s Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Jianjun Zhu
- Fetal Medical Center, Jiaxing Maternity and Children Health Care Hospital/The Affiliated Women and Children’s Hospital of Jiaxing University, Jiaxing, Zhejiang, China
- *Correspondence: Jianjun Zhu, Fetal Medical Center, Jiaxing Maternity and Children Health Care Hospital/The Affiliated Women and Children’s Hospital of Jiaxing University, Jiaxing, Zhejiang, China (e-mail: )
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Advances in Understanding the Pathogenesis of Craniofacial Birth Defects. J Dev Biol 2022; 10:jdb10030027. [PMID: 35893122 PMCID: PMC9326658 DOI: 10.3390/jdb10030027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023] Open
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Rafiq A, Aashaq S, Jan I, Beigh MA. SIX1 transcription factor: A review of cellular functions and regulatory dynamics. Int J Biol Macromol 2021; 193:1151-1164. [PMID: 34742853 DOI: 10.1016/j.ijbiomac.2021.10.133] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]
Abstract
Sine Oculis Homeobox 1 (SIX1) is a member of homeobox transcription factor family having pivotal roles in organismal development and differentiation. This protein functionally acts to regulate the expression of different proteins that are involved in organ development during embryogenesis and in disorders like cancer. Aberrant expression of this homeoprotein has therefore been reported in multiple pathological complexities like hearing impairment and renal anomalies during development and tumorigenesis in adult life. Most of the cellular effects mediated by it are mostly due to its role as a transcription factor. This review presents a concise narrative of its structure, interaction partners and cellular functions vis a vis its role in cancer. We thoroughly discuss the reported molecular mechanisms that govern its function in cellular milieu. Its post-translational regulation by phosphorylation and ubiquitination are also discussed with an emphasis on yet to be explored mechanistic insights regulating its molecular dynamics to fully comprehend its role in development and disease.
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Affiliation(s)
- Asma Rafiq
- Department of Nanotechnology, University of Kashmir, Hazratbal Campus, Srinagar JK-190006, India
| | - Sabreena Aashaq
- Department of Immunology and Molecular Medicine, Sher-i-Kashmir Institute of Medical Sciences, Soura, Srinagar JK-190011, India
| | - Iqra Jan
- Department of Nanotechnology, University of Kashmir, Hazratbal Campus, Srinagar JK-190006, India
| | - Mushtaq A Beigh
- Department of Nanotechnology, University of Kashmir, Hazratbal Campus, Srinagar JK-190006, India.
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