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Gong X, Liu Y, Zhang Q, Liang K, Wei J, Du H. LHFPL2 Serves as a Potential Biomarker for M2 Polarization of Macrophages in Renal Cell Carcinoma. Int J Mol Sci 2024; 25:6707. [PMID: 38928412 PMCID: PMC11204190 DOI: 10.3390/ijms25126707] [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: 05/19/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Renal cell carcinoma (RCC) is one of the most common malignant tumors of the kidney, presenting significant challenges for clinical diagnosis and treatment. Macrophages play crucial roles in RCC, promoting tumor progression and warranting further investigation. Previous studies have identified LHFPL2 as a transmembrane protein associated with reproduction, but its relationship with tumors or macrophages has not been discussed. This study utilized transcriptomic sequencing data from 609 KIRC patients in the TCGA database and single-cell sequencing data from 34,326 renal carcinoma cells for subsequent analysis. We comprehensively evaluated the expression of LHFPL2 and its relationship with clinical features, tumor prognosis, immune infiltration, and mutations. Additionally, we further assessed the correlation between LHFPL2 and macrophage M2 polarization using single-cell data and explored its potential as a cancer therapeutic target through molecular docking. The results demonstrated that LHFPL2 is upregulated in RCC and associated with poor survival rates. In clinical staging, the proportion of malignant and high-metastasis patients was higher in the high-LHFPL2 group than in the low-LHFPL2 group. Furthermore, we found that LHFPL2 influences RCC immune infiltration, with its expression positively correlated with various immune checkpoint and M2-related gene expressions, positively associated with M2 macrophage infiltration, and negatively correlated with activated NK cells. Moreover, LHFPL2 showed specific expression in macrophages, with the high-expression subgroup exhibiting higher M2 polarization, hypoxia, immune evasion, and angiogenesis scores, promoting tumor progression. Finally, we predicted several potential drugs targeting LHFPL2, such as conivaptan and nilotinib. Our analysis elaborately delineates the immune characteristics of LHFPL2 in the tumor microenvironment and its positive correlation with macrophage M2 polarization, providing new insights into tumor immunotherapy. We also propose potential FDA-approved drugs targeting this gene, which should be tested for their binding effects with LHFPL2 in future studies.
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Affiliation(s)
| | | | | | | | | | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (X.G.); (Y.L.); (Q.Z.); (K.L.); (J.W.)
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Giffen KP, Liu H, Yamane KL, Li Y, Chen L, Kramer KL, Zallocchi M, He DZ. Molecular Specializations Underlying Phenotypic Differences in Inner Ear Hair Cells of Zebrafish and Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595729. [PMID: 38826418 PMCID: PMC11142236 DOI: 10.1101/2024.05.24.595729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Hair cells (HCs) are the sensory receptors of the auditory and vestibular systems in the inner ears of vertebrates that selectively transduce mechanical stimuli into electrical activity. Although all HCs have the hallmark stereocilia bundle for mechanotransduction, HCs in non-mammals and mammals differ in their molecular specialization in the apical, basolateral and synaptic membranes. HCs of non-mammals, such as zebrafish (zHCs), are electrically tuned to specific frequencies and possess an active process in the stereocilia bundle to amplify sound signals. Mammalian cochlear HCs, in contrast, are not electrically tuned and achieve amplification by somatic motility of outer HCs (OHCs). To understand the genetic mechanisms underlying differences among adult zebrafish and mammalian cochlear HCs, we compared their RNA-seq-characterized transcriptomes, focusing on protein-coding orthologous genes related to HC specialization. There was considerable shared expression of gene orthologs among the HCs, including those genes associated with mechanotransduction, ion transport/channels, and synaptic signaling. For example, both zebrafish and mouse HCs express Tmc1, Lhfpl5, Tmie, Cib2, Cacna1d, Cacnb2, Otof, Pclo and Slc17a8. However, there were some notable differences in expression among zHCs, OHCs, and inner HCs (IHCs), which likely underlie the distinctive physiological properties of each cell type. Tmc2 and Cib3 were not detected in adult mouse HCs but tmc2a and b and cib3 were highly expressed in zHCs. Mouse HCs express Kcna10, Kcnj13, Kcnj16, and Kcnq4, which were not detected in zHCs. Chrna9 and Chrna10 were expressed in mouse HCs. In contrast, chrna10 was not detected in zHCs. OHCs highly express Slc26a5 which encodes the motor protein prestin that contributes to OHC electromotility. However, zHCs have only weak expression of slc26a5, and subsequently showed no voltage dependent electromotility when measured. Notably, the zHCs expressed more paralogous genes including those associated with HC-specific functions and transcriptional activity, though it is unknown whether they have functions similar to their mammalian counterparts. There was overlap in the expressed genes associated with a known hearing phenotype. Our analyses unveil substantial differences in gene expression patterns that may explain phenotypic specialization of zebrafish and mouse HCs. This dataset also includes several protein-coding genes to further the functional characterization of HCs and study of HC evolution from non-mammals to mammals.
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Affiliation(s)
- Kimberlee P. Giffen
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA
- Augusta University/University of Georgia Medical Partnership, Athens, GA, USA
| | - Huizhan Liu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Kacey L. Yamane
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Yi Li
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
- Department of Otorhinolaryngology, Beijing Tongren Hospital, Beijing Capital Medical University, Beijing, China
| | - Lei Chen
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Ken L. Kramer
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Marisa Zallocchi
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - David Z.Z. He
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
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Sun L, Yang X, Khan A, Yu X, Zhang H, Han S, Habulieti X, Sun Y, Wang R, Zhang X. Panoramic variation analysis of a family with neurodevelopmental disorders caused by biallelic loss-of-function variants in TMEM141, DDHD2, and LHFPL5. Front Med 2024; 18:81-97. [PMID: 37837560 DOI: 10.1007/s11684-023-1006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/27/2023] [Indexed: 10/16/2023]
Abstract
Highly clinical and genetic heterogeneity of neurodevelopmental disorders presents a major challenge in clinical genetics and medicine. Panoramic variation analysis is imperative to analyze the disease phenotypes resulting from multilocus genomic variation. Here, a Pakistani family with parental consanguinity was presented, characterized with severe intellectual disability (ID), spastic paraplegia, and deafness. Homozygosity mapping, integrated single nucleotide polymorphism (SNP) array, whole-exome sequencing, and whole-genome sequencing were performed, and homozygous variants in TMEM141 (c.270G>A, p.Trp90*), DDHD2 (c.411+767_c.1249-327del), and LHFPL5 (c.250delC, p.Leu84*) were identified. A Tmem141p.Trp90*/p.Trp90* mouse model was generated. Behavioral studies showed impairments in learning ability and motor coordination. Brain slice electrophysiology and Golgi staining demonstrated deficient synaptic plasticity in hippocampal neurons and abnormal dendritic branching in cerebellar Purkinje cells. Transmission electron microscopy showed abnormal mitochondrial morphology. Furthermore, studies on a human in vitro neuronal model (SH-SY5Y cells) with stable shRNA-mediated knockdown of TMEM141 showed deleterious effect on bioenergetic function, possibly explaining the pathogenesis of replicated phenotypes in the cross-species mouse model. Conclusively, panoramic variation analysis revealed that multilocus genomic variations of TMEM141, DDHD2, and LHFPL5 together caused variable phenotypes in patient. Notably, the biallelic loss-of-function variants of TMEM141 were responsible for syndromic ID.
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Affiliation(s)
- Liwei Sun
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, National Key Clinical Speciality Construction Project (Obstetrics and Gynecology), Chongqing Health Center for Women and Children, Chongqing, 400013, China
- Chongqing Clinical Research Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, 400013, China
| | - Xueting Yang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Amjad Khan
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
- Faculty of Biological Sciences, Department of Zoology, University of Lakki Marwat, Khyber Pakhtunkhwa, 28420, Pakistan.
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany.
- Alexander von Humboldt fellowship Foundation, Berlin, 10117, Germany.
| | - Xue Yu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, China
| | - Han Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
- Department of Laboratory Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China
| | - Shirui Han
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xiaerbati Habulieti
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Yang Sun
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory for Complex Severe and Rare Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
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Beurg M, Schwalbach ET, Fettiplace R. LHFPL5 is a key element in force transmission from the tip link to the hair cell mechanotransducer channel. Proc Natl Acad Sci U S A 2024; 121:e2318270121. [PMID: 38194445 PMCID: PMC10801851 DOI: 10.1073/pnas.2318270121] [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: 10/19/2023] [Accepted: 11/30/2023] [Indexed: 01/11/2024] Open
Abstract
During auditory transduction, sound-evoked vibrations of the hair cell stereociliary bundles open mechanotransducer (MET) ion channels via tip links extending from one stereocilium to its neighbor. How tension in the tip link is delivered to the channel is not fully understood. The MET channel comprises a pore-forming subunit, transmembrane channel-like protein (TMC1 or TMC2), aided by several accessory proteins, including LHFPL5 (lipoma HMGIC fusion partner-like 5). We investigated the role of LHFPL5 in transduction by comparing MET channel activation in outer hair cells of Lhfpl5-/- knockout mice with those in Lhfpl5+/- heterozygotes. The 10 to 90 percent working range of transduction in Tmc1+/+; Lhfpl5+/- was 52 nm, from which the single-channel gating force, Z, was evaluated as 0.34 pN. However, in Tmc1+/+; Lhfpl5-/- mice, the working range increased to 123 nm and Z more than halved to 0.13 pN, indicating reduced sensitivity. Tip link tension is thought to activate the channel via a gating spring, whose stiffness is inferred from the stiffness change on tip link destruction. The gating stiffness was ~40 percent of the total bundle stiffness in wild type but was virtually abolished in Lhfpl5-/-, implicating LHFPL5 as a principal component of the gating spring. The mutation Tmc1 p.D569N reduced the LHFPL5 immunolabeling in the stereocilia and like Lhfpl5-/- doubled the MET working range, but other deafness mutations had no effect on the dynamic range. We conclude that tip-link tension is transmitted to the channel primarily via LHFPL5; residual activation without LHFPL5 may occur by direct interaction between PCDH15 and TMC1.
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Affiliation(s)
- Maryline Beurg
- Department of Neuroscience, University of WisconsinSchool of Medicine and Public Health, Madison, WI53706
| | - Evan Travis Schwalbach
- Department of Neuroscience, University of WisconsinSchool of Medicine and Public Health, Madison, WI53706
| | - Robert Fettiplace
- Department of Neuroscience, University of WisconsinSchool of Medicine and Public Health, Madison, WI53706
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Jung J, Müller U. Mechanoelectrical transduction-related genetic forms of hearing loss. CURRENT OPINION IN PHYSIOLOGY 2023; 32:100632. [PMID: 36936795 PMCID: PMC10022594 DOI: 10.1016/j.cophys.2023.100632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Hair cells of the mammalian cochlea are specialized mechanosensory cells that convert mechanical stimuli into electrical signals to initiate the neuronal responses that lead to the perception of sound. The mechanoelectrical transduction (MET) machinery of cochlear hair cells is a multimeric protein complex that consists of the pore forming subunits of the MET channel and several essential accessory subunits that are crucial to regulate channel function and render the channel mechanically sensitive. Mutations have been discovered in the genes that encode all known components of the MET machinery. These mutations cause hearing loss with or without vestibular dysfunction. Some mutations also affect other tissues such as the retina. In this brief review, we will summarize gene mutations that affect the MET machinery of hair cells and how the study of the affected genes has illuminated our understanding of the physiological role of the encoded proteins.
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Affiliation(s)
- Jinsei Jung
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ulrich Müller
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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6
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Calcium signaling and genetic rare diseases: An auditory perspective. Cell Calcium 2023; 110:102702. [PMID: 36791536 DOI: 10.1016/j.ceca.2023.102702] [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: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
Deafness is a highly heterogeneous disorder which stems, for 50%, from genetic origins. Sensory transduction relies mainly on sensory hair cells of the cochlea, in the inner ear. Calcium is key for the function of these cells and acts as a fundamental signal transduction. Its homeostasis depends on three factors: the calcium influx, through the mechanotransduction channel at the apical pole of the hair cell as well as the voltage-gated calcium channel at the base of the cells; the calcium buffering via Ca2+-binding proteins in the cytoplasm, but also in organelles such as mitochondria and the reticulum endoplasmic mitochondria-associated membranes with specialized proteins; and the calcium extrusion through the Ca-ATPase pump, located all over the plasma membrane. In addition, the synaptic transmission to the central nervous system is also controlled by calcium. Genetic studies of inherited deafness have tremendously helped understand the underlying molecular pathways of calcium signaling. In this review, we discuss these different factors in light of the associated genetic diseases (syndromic and non-syndromic deafness) and the causative genes.
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7
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Soler DC, Ballesteros A, Sloan AE, McCormick TS, Stepanyan R. Multiple plasma membrane reporters discern LHFPL5 region that blocks trafficking to the plasma membrane. Sci Rep 2023; 13:2528. [PMID: 36781873 PMCID: PMC9925724 DOI: 10.1038/s41598-023-28045-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/11/2023] [Indexed: 02/15/2023] Open
Abstract
The mechano-electrical transduction (MET) channel of the inner ear receptor cells, termed hair cells, is a protein complex that enables our senses of hearing and balance. Hair cell MET requires an elaborate interplay of multiple proteins that form the MET channel. One of the MET complex components is the transmembrane protein LHFPL5, which is required for hair cell MET and hearing. LHFPL5 is thought to form a multi-protein complex with other MET channel proteins, such as PCDH15, TMIE, and TMC1. Despite localizing to the plasma membrane of stereocilia, the mechanosensing organelles of hair cells, LHFPL5 requires its binding partner within the MET complex, PCDH15, to localize to the stereocilia tips in hair cells and to the plasma membrane in heterologous cells. Using the Aquaporin 3-tGFP reporter (AGR) for plasma membrane localization, we found that a region within extracellular loop 1, which interacts with PCDH15, precludes the trafficking of AGR reporter to the plasma membrane in heterologous cell lines. Our results suggest that the presence of protein partners may mask endoplasmic reticulum retention regions or enable the proper folding and trafficking of the MET complex components, to facilitate expression of the MET complex at the stereocilia membrane.
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Affiliation(s)
- David C Soler
- Department of Neurosurgery, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
- Brain Tumor and Neuro-Oncology Center, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
- University Hospitals-Cleveland Medical Center and the Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - Angela Ballesteros
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Andrew E Sloan
- Department of Neurosurgery, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Brain Tumor and Neuro-Oncology Center, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- University Hospitals-Cleveland Medical Center and the Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Thomas S McCormick
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
- Murdough Family Center for Psoriasis, University Hospitals Case Medical Center, Cleveland, OH, USA
| | - Ruben Stepanyan
- Department of Otolaryngology - HNS, Case Western Reserve University, Cleveland, OH, USA.
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA.
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Mechanotransduction in mammalian sensory hair cells. Mol Cell Neurosci 2022; 120:103706. [PMID: 35218890 PMCID: PMC9177625 DOI: 10.1016/j.mcn.2022.103706] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 11/23/2022] Open
Abstract
In the inner ear, the auditory and vestibular systems detect and translate sensory information regarding sound and balance. The sensory cells that transform mechanical input into an electrical signal in these systems are called hair cells. A specialized organelle on the apical surface of the hair cells called the hair bundle detects the mechanical signals. Displacement of the hair bundle causes mechanotransduction channels to open. The morphology and organization of the hair bundle, as well as the properties and characteristics of the mechanotransduction process, differ between the different hair cell types in the auditory and vestibular systems. These differences likely contribute to maximizing the transduction of specific signals in each system. This review will discuss the molecules essential for mechanotransduction and the properties of the mechanotransduction process, focusing our attention on recent data and differences between the auditory and vestibular systems.
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Liu S, Wang S, Zou L, Xiong W. Mechanisms in cochlear hair cell mechano-electrical transduction for acquisition of sound frequency and intensity. Cell Mol Life Sci 2021; 78:5083-5094. [PMID: 33871677 PMCID: PMC11072359 DOI: 10.1007/s00018-021-03840-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/30/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022]
Abstract
Sound signals are acquired and digitized in the cochlea by the hair cells that further transmit the coded information to the central auditory pathways. Any defect in hair cell function may induce problems in the auditory system and hearing-based brain function. In the past 2 decades, our understanding of auditory transduction has been substantially deepened because of advances in molecular, structural, and functional studies. Results from these experiments can be perfectly embedded in the previously established profile from anatomical, histological, genetic, and biophysical research. This review aims to summarize the progress on the molecular and cellular mechanisms of the mechano-electrical transduction (MET) channel in the cochlear hair cells, which is involved in the acquisition of sound frequency and intensity-the two major parameters of an acoustic cue. We also discuss recent studies on TMC1, the molecule likely to form the MET channel pore.
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Affiliation(s)
- Shuang Liu
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
| | - Shufeng Wang
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
| | - Linzhi Zou
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
| | - Wei Xiong
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China.
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China.
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Farhadi M, Razmara E, Balali M, Hajabbas Farshchi Y, Falah M. How Transmembrane Inner Ear (TMIE) plays role in the auditory system: A mystery to us. J Cell Mol Med 2021; 25:5869-5883. [PMID: 33987950 PMCID: PMC8256367 DOI: 10.1111/jcmm.16610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/26/2021] [Indexed: 01/19/2023] Open
Abstract
Different cellular mechanisms contribute to the hearing sense, so it is obvious that any disruption in such processes leads to hearing impairment that greatly influences the global economy and quality of life of the patients and their relatives. In the past two decades, transmembrane inner ear (TMIE) protein has received a great deal of research interest because its impairments cause hereditary deafness in humans. This evolutionarily conserved membrane protein contributes to a fundamental complex that plays role in the maintenance and function of the sensory hair cells. Although the critical roles of the TMIE in mechanoelectrical transduction or hearing procedures have been discussed, there are little to no review papers summarizing the roles of the TMIE in the auditory system. In order to fill this gap, herein, we discuss the important roles of this protein in the auditory system including its role in mechanotransduction, olivocochlear synapse, morphology and different signalling pathways; we also review the genotype-phenotype correlation that can per se show the possible roles of this protein in the auditory system.
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Affiliation(s)
- Mohammad Farhadi
- ENT and Head and Neck Research Center and DepartmentThe Five Senses Health InstituteHazrat Rasoul Akram HospitalIran University of Medical SciencesTehranIran
| | - Ehsan Razmara
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVICAustralia
| | - Maryam Balali
- ENT and Head and Neck Research Center and DepartmentThe Five Senses Health InstituteHazrat Rasoul Akram HospitalIran University of Medical SciencesTehranIran
| | - Yeganeh Hajabbas Farshchi
- Department of Cellular and Molecular BiologyTehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Masoumeh Falah
- ENT and Head and Neck Research Center and DepartmentThe Five Senses Health InstituteHazrat Rasoul Akram HospitalIran University of Medical SciencesTehranIran
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11
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Abstract
Sound-induced mechanical stimuli are detected by elaborate mechanosensory transduction (MT) machinery in highly specialized hair cells of the inner ear. Genetic studies of inherited deafness in the past decades have uncovered several molecular constituents of the MT complex, and intense debate has surrounded the molecular identity of the pore-forming subunits. How the MT components function in concert in response to physical stimulation is not fully understood. In this review, we summarize and discuss multiple lines of evidence supporting the hypothesis that transmembrane channel-like 1 is a long-sought MT channel subunit. We also review specific roles of other components of the MT complex, including protocadherin 15, cadherin 23, lipoma HMGIC fusion partner-like 5, transmembrane inner ear, calcium and integrin-binding family member 2, and ankyrins. Based on these recent advances, we propose a unifying theory of hair cell MT that may reconcile most of the functional discoveries obtained to date. Finally, we discuss key questions that need to be addressed for a comprehensive understanding of hair cell MT at molecular and atomic levels.
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Affiliation(s)
- Wang Zheng
- Departments of Otolaryngology and Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Jeffrey R Holt
- Departments of Otolaryngology and Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA;
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12
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Deafness mutation D572N of TMC1 destabilizes TMC1 expression by disrupting LHFPL5 binding. Proc Natl Acad Sci U S A 2020; 117:29894-29903. [PMID: 33168709 DOI: 10.1073/pnas.2011147117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transmembrane channel-like protein 1 (TMC1) and lipoma HMGIC fusion partner-like 5 (LHFPL5) are recognized as two critical components of the mechanotransduction complex in inner-ear hair cells. However, the physical and functional interactions of TMC1 and LHFPL5 remain largely unexplored. We examined the interaction between TMC1 and LHFPL5 by using multiple approaches, including our recently developed ultrasensitive microbead-based single-molecule pulldown (SiMPull) assay. We demonstrate that LHFPL5 physically interacts with and stabilizes TMC1 in both heterologous expression systems and in the soma and hair bundle of hair cells. Moreover, the semidominant deafness mutation D572N in human TMC1 (D569N in mouse TMC1) severely disrupted LHFPL5 binding and destabilized TMC1 expression. Thus, our findings reveal previously unrecognized physical and functional interactions of TMC1 and LHFPL5 and provide insights into the molecular mechanism by which the D572N mutation causes deafness. Notably, these findings identify a missing link in the currently known physical organization of the mechanotransduction macromolecular complex. Furthermore, this study has demonstrated the power of the microbead-based SiMPull assay for biochemical investigation of rare cells such as hair cells.
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13
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Vona B, Doll J, Hofrichter MAH, Haaf T, Varshney GK. Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. Hear Res 2020; 397:107906. [PMID: 32063424 PMCID: PMC7415493 DOI: 10.1016/j.heares.2020.107906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/13/2020] [Accepted: 01/29/2020] [Indexed: 12/16/2022]
Abstract
Over the past decade, advancements in high-throughput sequencing have greatly enhanced our knowledge of the mutational signatures responsible for hereditary hearing loss. In its present state, the field has a largely uncensored view of protein coding changes in a growing number of genes that have been associated with hereditary hearing loss, and many more that have been proposed as candidate genes. Sequencing data can now be generated using methods that have become widespread and affordable. The greatest hurdles facing the field concern functional validation of uncharacterized genes and rapid application to human diseases, including hearing and balance disorders. To date, over 30 hearing-related disease models exist in zebrafish. New genome editing technologies, including CRISPR/Cas9 will accelerate the functional validation of hearing loss genes and variants in zebrafish. Here, we discuss current progress in the field and recent advances in genome editing approaches.
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Affiliation(s)
- Barbara Vona
- Department of Otolaryngology--Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany.
| | - Julia Doll
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.
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14
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Fetal gene therapy and pharmacotherapy to treat congenital hearing loss and vestibular dysfunction. Hear Res 2020; 394:107931. [PMID: 32173115 DOI: 10.1016/j.heares.2020.107931] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 12/23/2022]
Abstract
Disabling hearing loss is expected to affect over 900 million people worldwide by 2050. The World Health Organization estimates that the annual economic impact of hearing loss globally is US$ 750 billion. The inability to hear may complicate effective interpersonal communication and negatively impact personal and professional relationships. Recent advances in the genetic diagnosis of inner ear disease have keenly focused attention on strategies to restore hearing and balance in individuals with defined gene mutations. Mouse models of human hearing loss serve as the primary approach to test gene therapies and pharmacotherapies. The goal of this review is to articulate the rationale for fetal gene therapy and pharmacotherapy to treat congenital hearing loss and vestibular dysfunction. The differential onset of hearing in mice and humans suggests that a prenatal window of therapeutic efficacy in humans may be optimal to restore sensory function. Mouse studies demonstrating the utility of early fetal intervention in the inner ear show promise. We focus on the modulation of gene expression through two strategies that have successfully treated deafness in animal models and have had clinical success for other conditions in humans: gene replacement and antisense oligonucleotide-mediated modulation of gene expression. The recent establishment of effective therapies targeting the juvenile and adult mouse provide informative counterexamples where intervention in the maturing and fully functional mouse inner ear may be effective. Distillation of the current literature leads to the conclusion that novel therapeutic strategies to treat genetic deafness and imbalance will soon translate to clinical trials.
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15
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Noman M, Ishaq R, Bukhari SA, Ahmed ZM, Riazuddin S. Delineation of Homozygous Variants Associated with Prelingual Sensorineural Hearing Loss in Pakistani Families. Genes (Basel) 2019; 10:genes10121031. [PMID: 31835641 PMCID: PMC6947215 DOI: 10.3390/genes10121031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 12/30/2022] Open
Abstract
Hearing loss is a genetically heterogeneous disorder affecting approximately 360 million people worldwide and is among the most common sensorineural disorders. Here, we report a genetic analysis of seven large consanguineous families segregating prelingual sensorineural hearing loss. Whole-exome sequencing (WES) revealed seven different pathogenic variants segregating with hearing loss in these families, three novel variants (c.1204G>A, c.322G>T, and c.5587C>T) in TMPRSS3, ESRRB, and OTOF, and four previously reported variants (c.208C>T, c.6371G>A, c.226G>A, and c.494C>T) in LRTOMT, MYO15A, KCNE1, and LHFPL5, respectively. All identified variants had very low frequencies in the control databases and were predicted to have pathogenic effects on the encoded proteins. In addition to being familial, we also found intersibship locus heterogeneity in the evaluated families. The known pathogenic c.226C>T variant identified in KCNE1 only segregates with the hearing loss phenotype in a subset of affected members of the family GCNF21. This study further highlights the challenges of identifying disease-causing variants for highly heterogeneous disorders and reports the identification of three novel and four previously reported variants in seven known deafness genes.
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Affiliation(s)
- Muhammad Noman
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Rafaqat Ishaq
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- University Institute of Biochemistry & Biotechnology, PMAS-Arid Agriculture University, Rawalpindi 46000, Pakistan
| | - Shazia A. Bukhari
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Zubair M. Ahmed
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Correspondence: (Z.M.A); (S.R.)
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Correspondence: (Z.M.A); (S.R.)
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16
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Momendoust N, Moshtaghian J, Esmaeili F, Dehghanian F, Dumit V. Induction of Tyrosine Hydroxylase Gene Expression in Embryonal Carcinoma Stem Cells Using a Natural Tissue-Specific Inducer. Dev Neurobiol 2019; 79:559-577. [PMID: 31177638 DOI: 10.1002/dneu.22703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 02/02/2023]
Abstract
A large number of studies have focused on the generation of dopaminergic neurons from pluripotent cells. Differentiation of stem cells into distinct cell types is influenced by tissue-specific microenvironment. Since, central nervous system undergoes further development during postnatal life, in the present study neonatal rat brain tissue extract (NRBE) was applied to direct the differentiation of embryonal carcinoma stem cell line, P19 into dopaminergic (DA) phenotypes. Additionally, a neuroprotective drug, deprenyl was used alone or in combination with the extract. Results from morphological, immunofluorescence, and qPCR analyses showed that during a period of one to three weeks, a large percentage of stem cells were differentiated into neural cells. The results also indicated the greater effect of NRBE on the differentiation of the cells into tyrosine hydroxylase-expressing cells. MS analysis of NRBE showed the enrichment of gene ontology terms related to cell differentiation and neurogenesis. Network analysis of the studied genes and some DA markers resulted in the suggestion of potential regulatory candidates such as AVP, ACHE, LHFPL5, and DLK1 genes. In conclusion, NRBE as a natural native inducer was apparently able to simulate the brain microenvironment and support neural differentiation of P19 cells.
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Affiliation(s)
- Nazila Momendoust
- Department of Biology, Faculty of Sciences, University of Isfahan, Hezarjerib Avenue, Isfahan, 8174673441, Iran
| | - Jamal Moshtaghian
- Department of Biology, Faculty of Sciences, University of Isfahan, Hezarjerib Avenue, Isfahan, 8174673441, Iran
| | - Fariba Esmaeili
- Department of Biology, Faculty of Sciences, University of Isfahan, Hezarjerib Avenue, Isfahan, 8174673441, Iran
| | - Fariba Dehghanian
- Department of Biology, Faculty of Sciences, University of Isfahan, Hezarjerib Avenue, Isfahan, 8174673441, Iran
| | - Veronica Dumit
- School of Life Science (LifeNet), Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, 79106, Germany.,Center for Biological Systems Analysis (ZBSA), University Medical Center Freiburg, Freiburg, Germany
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17
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Cunningham CL, Müller U. Molecular Structure of the Hair Cell Mechanoelectrical Transduction Complex. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a033167. [PMID: 30082452 DOI: 10.1101/cshperspect.a033167] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cochlear hair cells employ mechanically gated ion channels located in stereocilia that open in response to sound wave-induced motion of the basilar membrane, converting mechanical stimulation to graded changes in hair cell membrane potential. Membrane potential changes in hair cells cause neurotransmitter release from hair cells that initiate electrical signals in the nerve terminals of afferent fibers from spiral ganglion neurons. These signals are then propagated within the central nervous system (CNS) to mediate the sensation of hearing. Recent studies show that the mechanoelectrical transduction (MET) machinery of hair cells is formed by an ensemble of proteins. Candidate components forming the MET channel have been identified, but none alone fulfills all criteria necessary to define them as pore-forming subunits of the MET channel. We will review here recent findings on the identification and function of proteins that are components of the MET machinery in hair cells and consider remaining open questions.
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Affiliation(s)
- Christopher L Cunningham
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland 21205
| | - Ulrich Müller
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland 21205
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18
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Carpena NT, Lee MY. Genetic Hearing Loss and Gene Therapy. Genomics Inform 2018; 16:e20. [PMID: 30602081 PMCID: PMC6440668 DOI: 10.5808/gi.2018.16.4.e20] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
Genetic hearing loss crosses almost all the categories of hearing loss which includes the following: conductive, sensory, and neural; syndromic and nonsyndromic; congenital, progressive, and adult onset; high-frequency, low-frequency, or mixed frequency; mild or profound; and recessive, dominant, or sex-linked. Genes play a role in almost half of all cases of hearing loss but effective treatment options are very limited. Genetic hearing loss is considered to be extremely genetically heterogeneous. The advancements in genomics have been instrumental to the identification of more than 6,000 causative variants in more than 150 genes causing hearing loss. Identification of genes for hearing impairment provides an increased insight into the normal development and function of cells in the auditory system. These defective genes will ultimately be important therapeutic targets. However, the auditory system is extremely complex which requires tremendous advances in gene therapy including gene vectors, routes of administration, and therapeutic approaches. This review summarizes and discusses recent advances in elucidating the genomics of genetic hearing loss and technologies aimed at developing a gene therapy that may become a treatment option for in the near future.
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Affiliation(s)
- Nathanial T Carpena
- Department of Otolaryngology-Head and Neck Surgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Min Young Lee
- Department of Otolaryngology-Head and Neck Surgery, Dankook University College of Medicine, Cheonan 31116, Korea.,Beckman Laser Institute Korea, Dankook University, Cheonan 31116, Korea
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19
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Al-Amri AH, Al Saegh A, Al-Mamari W, El-Asrag ME, Al-Kindi MN, Al Khabouri M, Al Wardy N, Al Lamki K, Gabr A, Idris A, Inglehearn CF, Clapcote SJ, Ali M. LHFPL5 mutation: A rare cause of non-syndromic autosomal recessive hearing loss. Eur J Med Genet 2018; 62:103592. [PMID: 30476627 DOI: 10.1016/j.ejmg.2018.11.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/30/2018] [Accepted: 11/22/2018] [Indexed: 11/18/2022]
Abstract
Hearing loss is a debilitating disorder that impairs language acquisition, resulting in disability in children and potential isolation in adulthood. Its onset can have a genetic basis, though environmental factors, which are often preventable, can also cause the condition. The genetic forms are highly heterogeneous, and early detection is necessary to arrange appropriate patient support. Here we report the molecular basis of hereditary hearing loss in a consanguineous family with multiple affected members from Oman. Combining homozygosity mapping with whole exome sequencing identified a novel homozygous nucleotide substitution c.575T > C in the lipoma HMGIC fusion partner-like 5 gene (LHFPL5), that converted the 192nd amino acid residue in the protein from a leucine to a proline, p.(Leu192Pro). Sanger sequencing confirmed segregation with the disease phenotype as expected for a recessive condition and the variant was absent in 123,490 subjects from various disease-specific and population genetic studies as well as 150 unrelated individuals and 35 deaf patients of Omani ethnicity. This study, which describes a novel LHFPL5 mutation in a family of Omani origin with hereditary hearing loss, supports previous clinical descriptions of the condition and contributes to the genetic spectrum of mutations in this form of deafness.
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Affiliation(s)
- Ahmed H Al-Amri
- Section of Ophthalmology & Neuroscience, Leeds Institute of Medical Research at St. James's, University of Leeds, United Kingdom; School of Biomedical Sciences, University of Leeds, United Kingdom; National Genetic Centre, Directorate General of Royal Hospital, Ministry of Health, Muscat, Oman
| | - Abeer Al Saegh
- Genetic & Developmental Medicine Clinic, Genetics Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Watfa Al-Mamari
- Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Mohammed E El-Asrag
- Section of Ophthalmology & Neuroscience, Leeds Institute of Medical Research at St. James's, University of Leeds, United Kingdom; Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | | | - Mazin Al Khabouri
- Department of Ear, Nose & Throat, Al Nahdha Hospital, Ministry of Health, Muscat, Oman
| | - Nadia Al Wardy
- Biochemistry Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Khalsa Al Lamki
- Biochemistry Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Ahlam Gabr
- Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Ahmed Idris
- Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Chris F Inglehearn
- Section of Ophthalmology & Neuroscience, Leeds Institute of Medical Research at St. James's, University of Leeds, United Kingdom
| | | | - Manir Ali
- Section of Ophthalmology & Neuroscience, Leeds Institute of Medical Research at St. James's, University of Leeds, United Kingdom.
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20
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Liaqat K, Chiu I, Lee K, Chakchouk I, Andrade-Elizondo PB, Santos-Cortez RLP, Hussain S, Nawaz S, Ansar M, Khan MN, Basit S, Schrauwen I, Ahmad W, Leal SM. Novel missense and 3'-UTR splice site variants in LHFPL5 cause autosomal recessive nonsyndromic hearing impairment. J Hum Genet 2018; 63:1099-1107. [PMID: 30177809 PMCID: PMC6202120 DOI: 10.1038/s10038-018-0502-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 02/07/2023]
Abstract
LHFPL5, the gene for DFNB67, underlies autosomal recessive nonsyndromic hearing impairment. We identified seven Pakistani families that mapped to 6p21.31, which includes the LHFPL5 gene. Sanger sequencing of LHFPL5 using DNA samples from hearing impaired and unaffected members of these seven families identified four variants. Among the identified variants, two were novel: one missense c.452 G > T (p.Gly151Val) and one splice site variant (c.*16 + 1 G > A) were each identified in two families. Two known variants: c.250delC (p.Leu84*) and c.380 A > G (p.Tyr127Cys) were also observed in two families and a single family, respectively. Nucleotides c.452G and c.*16 + 1G and amino-acid residue p.Gly151 are under strong evolutionary conservation. In silico bioinformatics analyses predicted these variants to be damaging. The splice site variant (c.*16 + 1 G > A) is predicted to affect pre-mRNA splicing and a loss of the 5' donor splice site in the 3'-untranslated region (3'-UTR). Further analysis supports the activation of a cryptic splice site approximately 357-bp downstream, leading to an extended 3'-UTR with additional regulatory motifs. In conclusion, we identified two novel variants in LHFPL5, including a unique 3'-UTR splice site variant that is predicted to impact pre-mRNA splicing and regulation through an extended 3'-UTR.
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Affiliation(s)
- Khurram Liaqat
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ilene Chiu
- Bobby R Alford Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Kwanghyuk Lee
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Imen Chakchouk
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Paula B Andrade-Elizondo
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Regie Lyn P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shabir Hussain
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shoaib Nawaz
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Nasim Khan
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunawwarah, Saudi Arabia
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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21
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Lerat J, Bonnet C, Cartault F, Loundon N, Jacquemont ML, Darcel F, Rouillon I, Mezouaghi K, Guichet A, Litzler J, Gesny R, Gherbi S, Aissa IB, Digeon FSJ, Garabedian EN, Bonnefont JP, Genin E, Denoyelle F, Jonard L, Marlin S. High prevalence of congenital deafness on Reunion Island is due to a founder variant of LHFPL5. Clin Genet 2018; 95:177-181. [PMID: 30298622 DOI: 10.1111/cge.13460] [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: 08/30/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 11/28/2022]
Abstract
Reunion Island is a French oversea department in the Indian Ocean with 1.6/1000, an estimated prevalence of deafness that is almost double as compared to the mainland France. Twelve children having isolated bilateral prelingual profound deafness along with motor delay attributed to vestibular areflexia were enrolled. Their mean walking age was 19 months. Electroretinography and temporal bone CT-scans were normal in all cases. A novel homozygous frameshift lipoma HMGIC fusion partner-like 5 (LHFPL5) variant c.185delT p.(Phe62Serfs*23) was identified using whole-exome sequencing. It was found in seven families. Four patients from two different families from both Reunion Island and mainland France, were compound heterozygous: c.185delT p.(Phe62Serfs*23) and c.472C > T p.(Arg158Trp). The phenotype observed in our patients completely mimics the hurry-scurry (hscy) murine Tmhs knock-out model. The recurrent occurrence of same LHFPL5 variant in Reunion Island is attributed to common ancestor couple born in 1693.
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Affiliation(s)
- Justine Lerat
- INSERM UMR_S1163 IHU Imagine - Institut des Maladies Génétiques - Université Paris Descartes, Paris, France.,Génétique Moléculaire, Necker, AP-HP, Paris, France.,Otorhinolaryngologie, CHU, Limoges, France
| | - Crystel Bonnet
- Institut de la Vision, UMRS 1120 INSERM/UPMC, Paris, France
| | - François Cartault
- Génétique Moléculaire, CHU La Réunion site Felix Guyon, Paris, France
| | - Natalie Loundon
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | | | | | - Isabelle Rouillon
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | - Kheira Mezouaghi
- Centre Régional de Compétences en Surdité Infantile, Sainte-Clothilde, France
| | | | | | | | - Souad Gherbi
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
| | - Ines Ben Aissa
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
| | | | - Eréa-Nöel Garabedian
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | | | - Emmanuelle Genin
- UMR1078 Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, CHU Brest, France
| | - Françoise Denoyelle
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | - Laurence Jonard
- Génétique Moléculaire, Necker, AP-HP, Paris, France.,Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
| | - Sandrine Marlin
- INSERM UMR_S1163 IHU Imagine - Institut des Maladies Génétiques - Université Paris Descartes, Paris, France.,Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
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22
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Wang L, Kempton JB, Brigande JV. Gene Therapy in Mouse Models of Deafness and Balance Dysfunction. Front Mol Neurosci 2018; 11:300. [PMID: 30210291 PMCID: PMC6123355 DOI: 10.3389/fnmol.2018.00300] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/06/2018] [Indexed: 12/16/2022] Open
Abstract
Therapeutic strategies to restore hearing and balance in mouse models of inner ear disease aim to rescue sensory function by gene replacement, augmentation, knock down or knock out. Modalities to achieve therapeutic effects have utilized virus-mediated transfer of wild type genes and small interfering ribonucleic acids; systemic and focal administration of antisense oligonucleotides (ASO) and designer small molecules; and lipid-mediated transfer of Cas 9 ribonucleoprotein (RNP) complexes. This work has established that gene or drug administration to the structurally and functionally immature, early neonatal mouse inner ear prior to hearing onset is a prerequisite for the most robust therapeutic responses. These observations may have significant implications for translating mouse inner ear gene therapies to patients. The human fetus hears by gestational week 19, suggesting that a corollary window of therapeutic efficacy closes early in the second trimester of pregnancy. We hypothesize that fetal therapeutics deployed prior to hearing onset may be the most effective approach to preemptively manage genetic mutations that cause deafness and vestibular dysfunction. We assert that gene therapy studies in higher vertebrate model systems with fetal hearing onset and a comparable acoustic range and sensitivity to that of humans are an essential step to safely and effectively translate murine gene therapies to the clinic.
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Affiliation(s)
- Lingyan Wang
- Oregon Hearing Research Center, Department of Otolaryngology, Oregon Health & Science University, Portland, OR, United States
| | - J Beth Kempton
- Oregon Hearing Research Center, Department of Otolaryngology, Oregon Health & Science University, Portland, OR, United States
| | - John V Brigande
- Oregon Hearing Research Center, Department of Otolaryngology, Oregon Health & Science University, Portland, OR, United States
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23
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Oxidative stress-induced chromosome breaks within the ABL gene: a model for chromosome rearrangement in nasopharyngeal carcinoma. Hum Genomics 2018; 12:29. [PMID: 29914565 PMCID: PMC6006577 DOI: 10.1186/s40246-018-0160-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/28/2018] [Indexed: 12/15/2022] Open
Abstract
Background The mechanism underlying chromosome rearrangement in nasopharyngeal carcinoma (NPC) remains elusive. It is known that most of the aetiological factors of NPC trigger oxidative stress. Oxidative stress is a potent apoptotic inducer. During apoptosis, chromatin cleavage and DNA fragmentation occur. However, cells may undergo DNA repair and survive apoptosis. Non-homologous end joining (NHEJ) pathway has been known as the primary DNA repair system in human cells. The NHEJ process may repair DNA ends without any homology, although region of microhomology (a few nucleotides) is usually utilised by this DNA repair system. Cells that evade apoptosis via erroneous DNA repair may carry chromosomal aberration. Apoptotic nuclease was found to be associated with nuclear matrix during apoptosis. Matrix association region/scaffold attachment region (MAR/SAR) is the binding site of the chromosomal DNA loop structure to the nuclear matrix. When apoptotic nuclease is associated with nuclear matrix during apoptosis, it potentially cleaves at MAR/SAR. Cells that survive apoptosis via compromised DNA repair may carry chromosome rearrangement contributing to NPC tumourigenesis. The Abelson murine leukaemia (ABL) gene at 9q34 was targeted in this study as 9q34 is a common region of loss in NPC. This study aimed to identify the chromosome breakages and/or rearrangements in the ABL gene in cells undergoing oxidative stress-induced apoptosis. Results In the present study, in silico prediction of MAR/SAR was performed in the ABL gene. More than 80% of the predicted MAR/SAR sites are closely associated with previously reported patient breakpoint cluster regions (BCR). By using inverse polymerase chain reaction (IPCR), we demonstrated that hydrogen peroxide (H2O2)-induced apoptosis in normal nasopharyngeal epithelial and NPC cells led to chromosomal breakages within the ABL BCR that contains a MAR/SAR. Intriguingly, we detected two translocations in H2O2-treated cells. Region of microhomology was found at the translocation junctions. This observation is consistent with the operation of microhomology-mediated NHEJ. Conclusions Our findings suggested that oxidative stress-induced apoptosis may participate in chromosome rearrangements of NPC. A revised model for oxidative stress-induced apoptosis mediating chromosome rearrangement in NPC is proposed. Electronic supplementary material The online version of this article (10.1186/s40246-018-0160-8) contains supplementary material, which is available to authorized users.
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24
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An Essential Role for the Tetraspanin LHFPL4 in the Cell-Type-Specific Targeting and Clustering of Synaptic GABA A Receptors. Cell Rep 2018; 21:70-83. [PMID: 28978485 PMCID: PMC5640807 DOI: 10.1016/j.celrep.2017.09.025] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/17/2017] [Accepted: 09/06/2017] [Indexed: 02/04/2023] Open
Abstract
Inhibitory synaptic transmission requires the targeting and stabilization of GABAA receptors (GABAARs) at synapses. The mechanisms responsible remain poorly understood, and roles for transmembrane accessory proteins have not been established. Using molecular, imaging, and electrophysiological approaches, we identify the tetraspanin LHFPL4 as a critical regulator of postsynaptic GABAAR clustering in hippocampal pyramidal neurons. LHFPL4 interacts tightly with GABAAR subunits and is selectively enriched at inhibitory synapses. In LHFPL4 knockout mice, there is a dramatic cell-type-specific reduction in GABAAR and gephyrin clusters and an accumulation of large intracellular gephyrin aggregates in vivo. While GABAARs are still trafficked to the neuronal surface in pyramidal neurons, they are no longer localized at synapses, resulting in a profound loss of fast inhibitory postsynaptic currents. Hippocampal interneuron currents remain unaffected. Our results establish LHFPL4 as a synapse-specific tetraspanin essential for inhibitory synapse function and provide fresh insights into the molecular make-up of inhibitory synapses. LHFPL4 is a tetraspanin enriched at inhibitory synapses that complexes with GABAARs LHFPL4 is important for GABAAR clustering both in vitro and in vivo LHFPL4 is required for the surface clustering but not the trafficking of GABAARs GABAergic synaptic inputs on CA1 pyramidal neurons, but not interneurons, require LHFPL4
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Qiu X, Müller U. Mechanically Gated Ion Channels in Mammalian Hair Cells. Front Cell Neurosci 2018; 12:100. [PMID: 29755320 PMCID: PMC5932396 DOI: 10.3389/fncel.2018.00100] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/26/2018] [Indexed: 01/05/2023] Open
Abstract
Hair cells in the inner ear convert mechanical stimuli provided by sound waves and head movements into electrical signal. Several mechanically evoked ionic currents with different properties have been recorded in hair cells. The search for the proteins that form the underlying ion channels is still in progress. The mechanoelectrical transduction (MET) channel near the tips of stereociliary in hair cells, which is responsible for sensory transduction, has been studied most extensively. Several components of the sensory mechanotransduction machinery in stereocilia have been identified, including the multi-transmembrane proteins tetraspan membrane protein in hair cell stereocilia (TMHS)/LHFPL5, transmembrane inner ear (TMIE) and transmembrane channel-like proteins 1 and 2 (TMC1/2). However, there remains considerable uncertainty regarding the molecules that form the channel pore. In addition to the sensory MET channel, hair cells express the mechanically gated ion channel PIEZO2, which is localized near the base of stereocilia and not essential for sensory transduction. The function of PIEZO2 in hair cells is not entirely clear but it might have a role in damage sensing and repair processes. Additional stretch-activated channels of unknown molecular identity and function have been found to localize at the basolateral membrane of hair cells. Here, we review current knowledge regarding the different mechanically gated ion channels in hair cells and discuss open questions concerning their molecular composition and function.
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Affiliation(s)
- Xufeng Qiu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ulrich Müller
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Targeted Next-Generation Sequencing of a Deafness Gene Panel (MiamiOtoGenes) Analysis in Families Unsuitable for Linkage Analysis. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3103986. [PMID: 29568747 PMCID: PMC5820677 DOI: 10.1155/2018/3103986] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/28/2017] [Accepted: 11/01/2017] [Indexed: 11/18/2022]
Abstract
Hearing loss (HL) is a common sensory disorder in humans with high genetic heterogeneity. To date, over 145 loci have been identified to cause nonsyndromic deafness. Furthermore, there are countless families unsuitable for the conventional linkage analysis. In the present study, we used a custom capture panel (MiamiOtoGenes) to target sequence 180 deafness-associated genes in 5 GJB2 negative deaf probands with autosomal recessive nonsyndromic HL from Iran. In these 5 families, we detected one reported and six novel mutations in 5 different deafness autosomal recessive (DFNB) genes (TRIOBP, LHFPL5, CDH23, PCDH15, and MYO7A). The custom capture panel in our study provided an efficient and comprehensive diagnosis for known deafness genes in small families.
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Mutations in eight small DFNB genes are not a frequent cause of non-syndromic hereditary hearing loss in Czech patients. Int J Pediatr Otorhinolaryngol 2016; 86:27-33. [PMID: 27260575 DOI: 10.1016/j.ijporl.2016.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/03/2016] [Accepted: 04/04/2016] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To evaluate the contribution of eight small NSHL-AR (non-syndromic deafness, autosomal recessive) genes to hereditary hearing loss in Czech patients. PATIENTS AND METHODS Unrelated Czech patients, adults and children, diagnosed with pre-lingual hereditary hearing loss with at least one similarly affected deaf sibling and with previously excluded mutations in the GJB2 gene were investigated by Sanger sequencing of the selected eight small NSHL-AR associated genes (CABP2 - 51 patients, CIB2 - 45 patients, PJVK/DFNB59 - 53 patients, GJB3 - 46 patients, ILDR1 - 48 patients, LHFPL5 - 66 patients, LRTOMT - 60 patients, TMIE - 64 patients). RESULTS Mutations were detected in the LHFPL5 (DFNB67) gene. The patient is heterozygote for two already described pathogenic variants (p.Tyr127Cys, p.Thr165Met). In five samples, five rare heterozygous variants (two novel) predicted as pathogenic were detected in genes CABP2, ILDR1, LHFPL5 and LRTOMT. CONCLUSION Mutations in eight small NSHL-AR genes are not a frequent cause of hereditary hearing loss in the Czech Republic. This diagnostic approach permitted the clarification of HL in only one patient - two heterozygous mutations were detected in LHFPL5 gene for the first time in Central Europe. As the use of panel base MPS certainly improves the diagnostic yield, future studies should rather profit from that diagnostic strategy.
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Novel function of LHFPL2 in female and male distal reproductive tract development. Sci Rep 2016; 6:23037. [PMID: 26964900 PMCID: PMC4786858 DOI: 10.1038/srep23037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/29/2016] [Indexed: 01/04/2023] Open
Abstract
Congenital reproductive tract anomalies could impair fertility. Female and male reproductive tracts are developed from Müllerian ducts and Wolffian ducts, respectively, involving initiation, elongation and differentiation. Genetic basis solely for distal reproductive tract development is largely unknown. Lhfpl2 (lipoma HMGIC fusion partner-like 2) encodes a tetra-transmembrane protein with unknown functions. It is expressed in follicle cells of ovary and epithelial cells of reproductive tracts. A spontaneous point mutation of Lhfpl2 (LHFPL2G102E) leads to infertility in 100% female mice, which have normal ovarian development, ovulation, uterine development, and uterine response to exogenous estrogen stimulation, but abnormal upper longitudinal vaginal septum and lower vaginal agenesis. Infertility is also observed in ~70% mutant males, which have normal mating behavior and sperm counts, but abnormal distal vas deferens convolution resulting in complete and incomplete blockage of reproductive tract in infertile and fertile males, respectively. On embryonic day 15.5, mutant Müllerian ducts and Wolffian ducts have elongated but their duct tips are enlarged and fail to merge with the urogenital sinus. These findings provide a novel function of LHFPL2 and a novel genetic basis for distal reproductive tract development; they also emphasize the importance of an additional merging phase for proper reproductive tract development.
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Bianchi M, Dahlgren S, Massey J, Dietschi E, Kierczak M, Lund-Ziener M, Sundberg K, Thoresen SI, Kämpe O, Andersson G, Ollier WER, Hedhammar Å, Leeb T, Lindblad-Toh K, Kennedy LJ, Lingaas F, Rosengren Pielberg G. A Multi-Breed Genome-Wide Association Analysis for Canine Hypothyroidism Identifies a Shared Major Risk Locus on CFA12. PLoS One 2015; 10:e0134720. [PMID: 26261983 PMCID: PMC4532498 DOI: 10.1371/journal.pone.0134720] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/13/2015] [Indexed: 01/12/2023] Open
Abstract
Hypothyroidism is a complex clinical condition found in both humans and dogs, thought to be caused by a combination of genetic and environmental factors. In this study we present a multi-breed analysis of predisposing genetic risk factors for hypothyroidism in dogs using three high-risk breeds—the Gordon Setter, Hovawart and the Rhodesian Ridgeback. Using a genome-wide association approach and meta-analysis, we identified a major hypothyroidism risk locus shared by these breeds on chromosome 12 (p = 2.1x10-11). Further characterisation of the candidate region revealed a shared ~167 kb risk haplotype (4,915,018–5,081,823 bp), tagged by two SNPs in almost complete linkage disequilibrium. This breed-shared risk haplotype includes three genes (LHFPL5, SRPK1 and SLC26A8) and does not extend to the dog leukocyte antigen (DLA) class II gene cluster located in the vicinity. These three genes have not been identified as candidate genes for hypothyroid disease previously, but have functions that could potentially contribute to the development of the disease. Our results implicate the potential involvement of novel genes and pathways for the development of canine hypothyroidism, raising new possibilities for screening, breeding programmes and treatments in dogs. This study may also contribute to our understanding of the genetic etiology of human hypothyroid disease, which is one of the most common endocrine disorders in humans.
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Affiliation(s)
- Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Stina Dahlgren
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Jonathan Massey
- Centre for Integrated Genomic Medical Research, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Elisabeth Dietschi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Marcin Kierczak
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Martine Lund-Ziener
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Katarina Sundberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Stein Istre Thoresen
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Olle Kämpe
- Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - William E. R. Ollier
- Centre for Integrated Genomic Medical Research, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Lorna J. Kennedy
- Centre for Integrated Genomic Medical Research, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Frode Lingaas
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Gerli Rosengren Pielberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail:
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Pan B, Holt JR. The molecules that mediate sensory transduction in the mammalian inner ear. Curr Opin Neurobiol 2015. [PMID: 26218316 DOI: 10.1016/j.conb.2015.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Years of searching and researching have finally yielded a few leads in the quest to identify molecules required for mechanosensory transduction in the mammalian inner ear. Studies of human and mouse genetics have raised the profile of several molecules that are crucial for the function sensory hair cells. Follow up studies have begun to define the molecular function and biochemical interactions of several key proteins. These studies have exposed a sensory transduction apparatus that is more complex than originally envisioned and have reinvigorated the search for additional molecular components required for normal inner ear function.
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Affiliation(s)
- Bifeng Pan
- Department of Otolaryngology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Jeffrey R Holt
- Department of Otolaryngology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States.
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Characterization of the transcriptome of nascent hair cells and identification of direct targets of the Atoh1 transcription factor. J Neurosci 2015; 35:5870-83. [PMID: 25855195 DOI: 10.1523/jneurosci.5083-14.2015] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hair cells are sensory receptors for the auditory and vestibular system in vertebrates. The transcription factor Atoh1 is both necessary and sufficient for the differentiation of hair cells, and is strongly upregulated during hair-cell regeneration in nonmammalian vertebrates. To identify genes involved in hair cell development and function, we performed RNA-seq profiling of purified Atoh1-expressing hair cells from the neonatal mouse cochlea. We identified >600 enriched transcripts in cochlear hair cells, of which 90% have not been previously shown to be expressed in hair cells. We identified 233 of these hair cell genes as candidates to be directly regulated by Atoh1 based on the presence of Atoh1 binding sites in their regulatory regions and by analyzing Atoh1 ChIP-seq datasets from the cerebellum and small intestine. We confirmed 10 of these genes as being direct Atoh1 targets in the cochlea by ChIP-PCR. The identification of candidate Atoh1 target genes is a first step in identifying gene regulatory networks for hair-cell development and may inform future studies on the potential role of Atoh1 in mammalian hair cell regeneration.
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Abstract
Hearing loss is the most common form of sensory impairment in humans and affects more than 40 million people in the United States alone. No drug-based therapy has been approved by the Food and Drug Administration, and treatment mostly relies on devices such as hearing aids and cochlear implants. Over recent years, more than 100 genetic loci have been linked to hearing loss and many of the affected genes have been identified. This understanding of the genetic pathways that regulate auditory function has revealed new targets for pharmacological treatment of the disease. Moreover, approaches that are based on stem cells and gene therapy, which may have the potential to restore or maintain auditory function, are beginning to emerge.
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Affiliation(s)
- Ulrich Müller
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, San Diego, California 92037, USA
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center, Vollum Institute, Oregon Health &Science University, 3181 South West Sam Jackson Park Road, Portland, Oregon 97239, USA
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Ammar-Khodja F, Bonnet C, Dahmani M, Ouhab S, Lefèvre GM, Ibrahim H, Hardelin JP, Weil D, Louha M, Petit C. Diversity of the causal genes in hearing impaired Algerian individuals identified by whole exome sequencing. Mol Genet Genomic Med 2015; 3:189-96. [PMID: 26029705 PMCID: PMC4444160 DOI: 10.1002/mgg3.131] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 12/05/2014] [Accepted: 12/06/2014] [Indexed: 11/15/2022] Open
Abstract
The genetic heterogeneity of congenital hearing disorders makes molecular diagnosis expensive and time-consuming using conventional techniques such as Sanger sequencing of DNA. In order to design an appropriate strategy of molecular diagnosis in the Algerian population, we explored the diversity of the involved mutations by studying 65 families affected by autosomal recessive forms of nonsyndromic hearing impairment (DFNB forms), which are the most prevalent early onset forms. We first carried out a systematic screening for mutations in GJB2 and the recurrent p.(Arg34*) mutation in TMC1, which were found in 31 (47.7%) families and 1 (1.5%) family, respectively. We then performed whole exome sequencing in nine of the remaining families, and identified the causative mutations in all the patients analyzed, either in the homozygous state (eight families) or in the compound heterozygous state (one family): (c.709C>T: p.(Arg237*)) and (c.2122C>T: p.(Arg708*)) in OTOF, (c.1334T>G: p.(Leu445Trp)) in SLC26A4, (c.764T>A: p.(Met255Lys)) in GIPC3, (c.518T>A: p.(Cys173Ser)) in LHFPL5, (c.5336T>C: p.(Leu1779Pro)) in MYO15A, (c.1807G>T: p.(Val603Phe)) in OTOA, (c.6080dup: p.(Asn2027Lys*9)) in PTPRQ, and (c.6017del: p.(Gly2006Alafs*13); c.7188_7189ins14: p.(Val2397Leufs*2)) in GPR98. Notably, 7 of these 10 mutations affecting 8 different genes had not been reported previously. These results highlight for the first time the genetic heterogeneity of the early onset forms of nonsyndromic deafness in Algerian families.
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Affiliation(s)
- Fatima Ammar-Khodja
- Equipe de Génétique, Laboratoire de Biologie Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène (USTHB) Alger, Algeria
| | - Crystel Bonnet
- Institut de la Vision, UMRS 1120 INSERM/UPMC/Institut Pasteur Paris, France
| | - Malika Dahmani
- Equipe de Génétique, Laboratoire de Biologie Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène (USTHB) Alger, Algeria
| | - Sofiane Ouhab
- Service d'Otorhinolaryngologie (ORL), Hôpital de Kouba-Bachir Mentouri Alger, Algeria
| | - Gaelle M Lefèvre
- Institut de la Vision, UMRS 1120 INSERM/UPMC/Institut Pasteur Paris, France
| | - Hassina Ibrahim
- Service d'Otorhinolaryngologie (ORL), Hôpital Mustapha Pacha Alger, Algeria
| | - Jean-Pierre Hardelin
- Institut Pasteur, Unité de Génétique et Physiologie de l'Audition UMRS 1120 INSERM/UPMC Paris 6, Paris, France
| | - Dominique Weil
- Institut Pasteur, Unité de Génétique et Physiologie de l'Audition UMRS 1120 INSERM/UPMC Paris 6, Paris, France
| | - Malek Louha
- Service de Biochimie, Hôpital Armand Trousseau UMRS 1120 INSERM, Paris, France
| | - Christine Petit
- Institut de la Vision, UMRS 1120 INSERM/UPMC/Institut Pasteur Paris, France ; Institut Pasteur, Unité de Génétique et Physiologie de l'Audition UMRS 1120 INSERM/UPMC Paris 6, Paris, France ; Collège de France Paris, France
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Subunit determination of the conductance of hair-cell mechanotransducer channels. Proc Natl Acad Sci U S A 2014; 112:1589-94. [PMID: 25550511 DOI: 10.1073/pnas.1420906112] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Cochlear hair cells convert sound stimuli into electrical signals by gating of mechanically sensitive ion channels in their stereociliary (hair) bundle. The molecular identity of this ion channel is still unclear, but its properties are modulated by accessory proteins. Two such proteins are transmembrane channel-like protein isoform 1 (TMC1) and tetraspan membrane protein of hair cell stereocilia (TMHS, also known as lipoma HMGIC fusion partner-like 5, LHFPL5), both thought to be integral components of the mechanotransduction machinery. Here we show that, in mice harboring an Lhfpl5 null mutation, the unitary conductance of outer hair cell mechanotransducer (MT) channels was reduced relative to wild type, and the tonotopic gradient in conductance, where channels from the cochlear base are nearly twice as conducting as those at the apex, was almost absent. The macroscopic MT current in these mutants was attenuated and the tonotopic gradient in amplitude was also lost, although the current was not completely extinguished. The consequences of Lhfpl5 mutation mirror those due to Tmc1 mutation, suggesting a part of the MT-channel conferring a large and tonotopically variable conductance is similarly disrupted in the absence of Lhfpl5 or Tmc1. Immunolabelling demonstrated TMC1 throughout the stereociliary bundles in wild type but not in Lhfpl5 mutants, implying the channel effect of Lhfpl5 mutations stems from down-regulation of TMC1. Both LHFPL5 and TMC1 were shown to interact with protocadherin-15, a component of the tip link, which applies force to the MT channel. We propose that titration of the TMC1 content of the MT channel sets the gradient in unitary conductance along the cochlea.
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Challenges and solutions for gene identification in the presence of familial locus heterogeneity. Eur J Hum Genet 2014; 23:1207-15. [PMID: 25491636 PMCID: PMC4538203 DOI: 10.1038/ejhg.2014.266] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/25/2014] [Accepted: 10/31/2014] [Indexed: 11/08/2022] Open
Abstract
Next-generation sequencing (NGS) of exomes and genomes has accelerated the identification of genes involved in Mendelian phenotypes. However, many NGS studies fall short of identifying causal variants, with estimates for success rates as low as 25% for uncovering the pathological variant underlying disease etiology. An important reason for such failures is familial locus heterogeneity, where within a single pedigree causal variants in two or more genes underlie Mendelian trait etiology. As examples of intra- and inter-sibship familial locus heterogeneity, we present 10 consanguineous Pakistani families segregating hearing impairment due to homozygous variants in two different hearing impairment genes and a European-American pedigree in which hearing impairment is caused by four variants in three different genes. We have identified 41 additional pedigrees with syndromic and nonsyndromic hearing impairment for which a single previously reported hearing impairment gene has been identified but only segregates with the phenotype in a subset of affected pedigree members. We estimate that locus heterogeneity occurs in 15.3% (95% confidence interval: 11.9%, 19.9%) of the families in our collection. We demonstrate novel approaches to apply linkage analysis and homozygosity mapping (for autosomal recessive consanguineous pedigrees), which can be used to detect locus heterogeneity using either NGS or SNP array data. Results from linkage analysis and homozygosity mapping can also be used to group sibships or individuals most likely to be segregating the same causal variants and thereby increase the success rate of gene identification.
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Najmabadi H, Kahrizi K. Genetics of non-syndromic hearing loss in the Middle East. Int J Pediatr Otorhinolaryngol 2014; 78:2026-36. [PMID: 25281338 DOI: 10.1016/j.ijporl.2014.08.036] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/24/2014] [Accepted: 08/25/2014] [Indexed: 12/23/2022]
Abstract
Hearing impairment is the most common sensory disorder, present 1 in every 500 newborns. About 80% of genetic HL is classified as non-syndromic deafness. To date, over 115 non-syndromic loci have been identified of which fifty associated with autosomal recessive non-syndromic hearing loss (ARNSHL). In this review article, we represent the 40 genes function and contribution to genetic deafness in different Middle Eastern populations as well as gene frequencies and mutation spectrum. The wide variety of mutations have so far detected in 19 countries reflects the heterogeneity of the genes involved in HL in this region. The deafness genes can cause dysfunction of cochlear homeostasis, cellular organization, neuronal transmission, cell growth, differentiation, and survival, some coding for tectorial membrane-associated proteins, and the remaining with unknown functions. Non-syndromic deafness is highly heterogeneous and mutations in the GJB2 are responsible for almost 30-50% in northwest to as low as 0-5% in south and southeast of the Middle East, it remain as major gene in ARNSHL in Middle East. The other genes contributing to AR/ADNSHL in some countries have been determined while for many other countries in the Middle East have not been studied or little study has been done. With the advancement of next generation sequencing one could expect in next coming year many of the remaining genes to be determine and to understand their function in the inner ear.
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Affiliation(s)
- Hossein Najmabadi
- Genetics Research Centre (GRC), University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| | - Kimia Kahrizi
- Genetics Research Centre (GRC), University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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von Ameln S, Wang G, Boulouiz R, Rutherford M, Smith G, Li Y, Pogoda HM, Nürnberg G, Stiller B, Volk A, Borck G, Hong J, Goodyear R, Abidi O, Nürnberg P, Hofmann K, Richardson G, Hammerschmidt M, Moser T, Wollnik B, Koehler C, Teitell M, Barakat A, Kubisch C. A mutation in PNPT1, encoding mitochondrial-RNA-import protein PNPase, causes hereditary hearing loss. Am J Hum Genet 2012; 91:919-27. [PMID: 23084290 PMCID: PMC3487123 DOI: 10.1016/j.ajhg.2012.09.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 08/22/2012] [Accepted: 09/04/2012] [Indexed: 11/24/2022] Open
Abstract
A subset of nuclear-encoded RNAs has to be imported into mitochondria for the proper replication and transcription of the mitochondrial genome and, hence, for proper mitochondrial function. Polynucleotide phosphorylase (PNPase or PNPT1) is one of the very few components known to be involved in this poorly characterized process in mammals. At the organismal level, however, the effect of PNPase dysfunction and impaired mitochondrial RNA import are unknown. By positional cloning, we identified a homozygous PNPT1 missense mutation (c.1424A>G predicting the protein substitution p.Glu475Gly) of a highly conserved PNPase residue within the second RNase-PH domain in a family affected by autosomal-recessive nonsyndromic hearing impairment. In vitro analyses in bacteria, yeast, and mammalian cells showed that the identified mutation results in a hypofunctional protein leading to disturbed PNPase trimerization and impaired mitochondrial RNA import. Immunohistochemistry revealed strong PNPase staining in the murine cochlea, including the sensory hair cells and the auditory ganglion neurons. In summary, we show that a component of the mitochondrial RNA-import machinery is specifically required for auditory function.
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Affiliation(s)
- Simon von Ameln
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
| | - Geng Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Redouane Boulouiz
- Department of Genetics, Institut Pasteur du Maroc, 20100 Casablanca, Morocco
| | - Mark A. Rutherford
- InnerEarLab, Department of Otolaryngology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Geoffrey M. Smith
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yun Li
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50674 Cologne, Germany
| | - Hans-Martin Pogoda
- Institute for Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | - Gudrun Nürnberg
- Cologne Center for Genomics, University of Cologne, 50674 Cologne, Germany
| | - Barbara Stiller
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
| | - Alexander E. Volk
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
| | - Guntram Borck
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
| | - Jason S. Hong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Omar Abidi
- Department of Genetics, Institut Pasteur du Maroc, 20100 Casablanca, Morocco
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne, University of Cologne, 50674 Cologne, Germany
- Cologne Center for Genomics, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50674 Cologne, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Guy P. Richardson
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Matthias Hammerschmidt
- Center for Molecular Medicine Cologne, University of Cologne, 50674 Cologne, Germany
- Institute for Developmental Biology, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50674 Cologne, Germany
| | - Tobias Moser
- InnerEarLab, Department of Otolaryngology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Center for Molecular Physiology of the Brain, University of Göttingen, 37073 Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50674 Cologne, Germany
| | - Carla M. Koehler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael A. Teitell
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, Broad Stem Cell Research Center, California NanoSystems Institute and Center for Cell Control, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Abdelhamid Barakat
- Department of Genetics, Institut Pasteur du Maroc, 20100 Casablanca, Morocco
| | - Christian Kubisch
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
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Obholzer N, Swinburne IA, Schwab E, Nechiporuk AV, Nicolson T, Megason SG. Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing. Development 2012; 139:4280-90. [PMID: 23052906 DOI: 10.1242/dev.083931] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Forward genetic screens in zebrafish have identified >9000 mutants, many of which are potential disease models. Most mutants remain molecularly uncharacterized because of the high cost, time and labor investment required for positional cloning. These costs limit the benefit of previous genetic screens and discourage future screens. Drastic improvements in DNA sequencing technology could dramatically improve the efficiency of positional cloning in zebrafish and other model organisms, but the best strategy for cloning by sequencing has yet to be established. Using four zebrafish inner ear mutants, we developed and compared two approaches for 'cloning by sequencing': one based on bulk segregant linkage (BSFseq) and one based on homozygosity mapping (HMFseq). Using BSFseq we discovered that mutations in lmx1b and jagged1b cause abnormal ear morphogenesis. With HMFseq we validated that the disruption of cdh23 abolishes the ear's sensory functions and identified a candidate lesion in lhfpl5a predicted to cause nonsyndromic deafness. The success of HMFseq shows that the high intrastrain polymorphism rate in zebrafish eliminates the need for time-consuming map crosses. Additionally, we analyzed diversity in zebrafish laboratory strains to find areas of elevated diversity and areas of fixed homozygosity, reinforcing recent findings that genome diversity is clustered. We present a database of >15 million sequence variants that provides much of this approach's power. In our four test cases, only a single candidate single nucleotide polymorphism (SNP) remained after subtracting all database SNPs from a mutant's critical region. The saturation of the common SNP database and our open source analysis pipeline MegaMapper will improve the pace at which the zebrafish community makes unique discoveries relevant to human health.
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Affiliation(s)
- Nikolaus Obholzer
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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Bensaïd M, Hmani-Aifa M, Hammami B, Tlili A, Hakim B, Charfeddine I, Ayadi H, Ghorbel A, Castillo ID, Masmoudi S. DFNB66 and DFNB67 loci are non allelic and rarely contribute to autosomal recessive nonsyndromic hearing loss. Eur J Med Genet 2011; 54:e565-9. [PMID: 21816241 DOI: 10.1016/j.ejmg.2011.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 07/08/2011] [Indexed: 11/17/2022]
Abstract
We previously mapped the DFNB66 locus to an interval overlapping the DFNB67 region. Mutations in the LHFPL5 gene were identified as a cause of DFNB67 hearing loss (HL). However, screening of the coding exons of LHFPL5 did not reveal any mutation in the DFNB66 family. The objective of this study was to check whether DFNB66 and DFNB67 are distinctive loci and determining their contribution to HL. In the DFNB66 family, sequencing showed absence of mutations in the untranslated regions and the predicted promoter sequence of LHFPL5. Analysis of five microsatellites in the 6p21.31-22.3 region and screening of the LHFPL5 gene by DNA heteroduplex analysis in DHPLC revealed a novel mutation (c.89dup) in one out of 129 unrelated Tunisian families with autosomal recessive nonsyndromic (ARNS) HL. Our findings suggest that two distinct genes are responsible for DFNB66 and DFNB67 HL. These loci are likely to be a rare cause of ARNSHL.
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Affiliation(s)
- Mariem Bensaïd
- Equipe Procédés de Criblages Moléculaires et Cellulaires, Laboratoire de Microorganismes et de Biomolécules, Centre de Biotechnologie de Sfax, Université de Sfax, Tunisia
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Finding new genes for non-syndromic hearing loss through an in silico prioritization study. PLoS One 2010; 5. [PMID: 20927407 PMCID: PMC2946934 DOI: 10.1371/journal.pone.0012742] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 08/17/2010] [Indexed: 11/19/2022] Open
Abstract
At present, 51 genes are already known to be responsible for Non-Syndromic hereditary Hearing Loss (NSHL), but the knowledge of 121 NSHL-linked chromosomal regions brings to the hypothesis that a number of disease genes have still to be uncovered. To help scientists to find new NSHL genes, we built a gene-scoring system, integrating Gene Ontology, NCBI Gene and Map Viewer databases, which prioritizes the candidate genes according to their probability to cause NSHL. We defined a set of candidates and measured their functional similarity with respect to the disease gene set, computing a score () that relies on the assumption that functionally related genes might contribute to the same (disease) phenotype. A Kolmogorov-Smirnov test, comparing the pair-wise distribution on the disease gene set with the distribution on the remaining human genes, provided a statistical assessment of this assumption. We found at a p-value that the former pair-wise is greater than the latter, justifying a prioritization strategy based on the functional similarity of candidate genes respect to the disease gene set. A cross-validation test measured to what extent the ranking for NSHL is different from a random ordering: adding 15% of the disease genes to the candidate gene set, the ranking of the disease genes in the first eight positions resulted statistically different from a hypergeometric distribution with a p-value and a power. The twenty top-scored genes were finally examined to evaluate their possible involvement in NSHL. We found that half of them are known to be expressed in human inner ear or cochlea and are mainly involved in remodeling and organization of actin formation and maintenance of the cilia and the endocochlear potential. These findings strongly indicate that our metric was able to suggest excellent NSHL candidates to be screened in patients and controls for causative mutations.
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Abstract
Hearing loss (HL), or deafness in its most severe form, affects an estimated 28 and 22.5 million Americans and Europeans, respectively. The numbers are higher in regions such as India and the Middle East, where consanguinity contributes to larger numbers of recessively inherited hearing impairment (HI). As a result of work-related difficulties, educational and developmental delays, and social stigmas and exclusion, the economic impact of HL is very high. At the other end of the spectrum, a rich deaf culture, particularly for individuals whose parents and even grandparents were deaf, is a social movement that believes that deafness is a difference in human experience rather than a disability. This review attempts to cover the remarkable progress made in the field of the genetics of HL over the past 20 years. Mutations in a significant number of genes have been discovered over the years that contribute to clinically heterogeneous forms of HL, enabling genetic counseling and prediction of progression of HL. Cell biological assays, protein localization in the inner ear, and detailed analysis of spontaneous and transgenic mouse models have provided an incredibly rich resource for elucidating mechanisms of hereditary hearing loss (HHL). This knowledge is providing answers for the families with HL, who contribute a great deal to the research being performed worldwide.
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Affiliation(s)
- Amiel A Dror
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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Ahmed ZM, Riazuddin S, Khan SN, Friedman PL, Riazuddin S, Friedman TB. USH1H, a novel locus for type I Usher syndrome, maps to chromosome 15q22-23. Clin Genet 2008; 75:86-91. [PMID: 18505454 DOI: 10.1111/j.1399-0004.2008.01038.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Usher syndrome (USH) is a hereditary disorder associated with sensorineural hearing impairment, progressive loss of vision attributable to retinitis pigmentosa (RP) and variable vestibular function. Three clinical types have been described with type I (USH1) being the most severe. To date, six USH1 loci have been reported. We ascertained two large Pakistani consanguineous families segregating profound hearing loss, vestibular dysfunction, and RP, the defining features of USH1. In these families, we excluded linkage of USH to the 11 known USH loci and subsequently performed a genome-wide linkage screen. We found a novel USH1 locus designated USH1H that mapped to chromosome 15q22-23 in a 4.92-cM interval. This locus overlaps the non-syndromic deafness locus DFNB48 raising the possibility that the two disorders may be caused by allelic mutations.
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Affiliation(s)
- Z M Ahmed
- Section on Human Genetics, Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, MD 20850, USA
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Abstract
Mechanical stimuli generated by head movements and changes in sound pressure are detected by hair cells with amazing speed and sensitivity. The mechanosensitive organelle, the hair bundle, is a highly elaborated structure of actin-based stereocilia arranged in precise rows of increasing height. Extracellular linkages contribute to its cohesion and convey forces to mechanically gated channels. Channel opening is nearly instantaneous and is followed by a process of sensory adaptation that keeps the channels poised in their most sensitive range. This process is served by motors, scaffolds, and homeostatic mechanisms. The molecular constituents of this process are rapidly being elucidated, especially by the discovery of deafness genes and antibody targets.
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Affiliation(s)
- Melissa A Vollrath
- Howard Hughes Medical Institute and Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA.
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Longo-Guess CM, Gagnon LH, Fritzsch B, Johnson KR. Targeted knockout and lacZ reporter expression of the mouse Tmhs deafness gene and characterization of the hscy-2J mutation. Mamm Genome 2007; 18:646-56. [PMID: 17876667 PMCID: PMC2613174 DOI: 10.1007/s00335-007-9049-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Accepted: 06/14/2007] [Indexed: 01/03/2023]
Abstract
The Tmhs gene codes for a tetraspan transmembrane protein that is expressed in hair cell stereocilia. We previously showed that a spontaneous missense mutation of Tmhs underlies deafness and vestibular dysfunction in the hurry-scurry (hscy) mouse. Subsequently, mutations in the human TMHS gene were shown to be responsible for DFNB67, an autosomal recessive nonsyndromic deafness locus. Here we describe a genetically engineered null mutation of the mouse Tmhs gene (Tmhs ( tm1Kjn )) and show that its phenotype is identical to that of the hscy missense mutation, confirming the deleterious nature of the hscy cysteine-to-phenylalanine substitution. In the targeted null allele, the Tmhs promoter drives expression of a lacZ reporter gene. Visualization of beta-galactosidase activity in Tmhs ( tm1Kjn ) heterozygous mice indicates that Tmhs is highly expressed in the cochlear and vestibular hair cells of the inner ear. Expression is first detectable at E15.5, peaks around P0, decreases slightly at P6, and is absent by P15, a duration that supports the involvement of Tmhs in stereocilia development. Tmhs reporter gene expression also was detected in several cranial and cervical sensory ganglia, but not in the vestibular or spiral ganglia. We also describe a new nontargeted mutation of the Tmhs gene, hscy-2J, that causes abnormal splicing from a cryptic splice site within exon 2 and is predicted to produce a functionally null protein lacking 51 amino acids of the wild-type sequence.
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Tekin M, Arici ZS. Genetic epidemiological studies of congenital/prelingual deafness in Turkey: Population structure and mating type are major determinants of mutation identification. Am J Med Genet A 2007; 143A:1583-91. [PMID: 17444514 DOI: 10.1002/ajmg.a.31702] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In order to evaluate the genetic epidemiology of deafness in Turkey, we first analyzed the pedigree data obtained from 2,169 families whose children were students of the schools for hearing loss/deafness in 31 cities of Turkey. Single major locus segregation analysis was performed after families were grouped according to hearing status of the parents. The results showed that sporadic phenocopies, autosomal dominant, and autosomal recessive transmission account for 18.2%, 4.9%, and 76.9% of the cases respectively, after exclusion of probands with unequivocal evidence for environmental etiologies. The high frequency of autosomal recessive transmission of this study differs from those of previous ones in Western populations. We subsequently analyzed the data from a subset of 574 unrelated families that were evaluated clinically, including mutation analysis of the GJB2 gene in 406 probands. Biallelic mutations were detected in 22.4% of all probands. They were present in 68.8% of probands whose parents were both deaf, yet in only 9.3% when both parents were hearing and consanguineous without a family history of deafness. Our study shows that GJB2 is the major gene for deafness in Turkey and was amplified in deaf by deaf matings, since assortative mating preferentially affects common genes. Deafness in the remaining families appears to result from mutations at many loci that are less frequent causes of deafness, because consanguinity has a proportionally greater effect on rare genes. Conclusions of this study may be relevant to other populations where consanguineous or assortative mating is present with various frequencies.
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Affiliation(s)
- Mustafa Tekin
- Division of Clinical Molecular Pathology and Genetics, Department of Pediatrics, Ankara University School of Medicine, Ankara, Turkey.
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