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- Comprehensive Hearing Center, Department of ORL, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, Würzburg, Germany (1)
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Tinnitus is the perception of a phantom sound that affects between 10 and 15% of the general population. Despite this considerable prevalence, treatments for tinnitus are presently lacking. Tinnitus exhibits a diverse array of recognized risk factors and extreme clinical heterogeneity. Furthermore, it can involve an unknown number of auditory and non-auditory networks and molecular pathways. This complex combination has hampered advancements in the field. The identification of specific genetic factors has been at the forefront of several research investigations in the past decade. Nine studies have examined genes in a case-control association approach. Recently, a genome-wide association study has highlighted several potentially significant pathways that are implicated in tinnitus. Two twin studies have calculated a moderate heritability for tinnitus and disclosed a greater concordance rate in monozygotic twins compared to dizygotic twins. Despite the more recent data alluding to genetic factors in tinnitus, a strong association with any specific genetic locus is lacking and a genetic study with sufficient statistical power has yet to be designed. Future research endeavors must overcome the many inherent limitations in previous study designs. This review summarizes the previously embarked upon tinnitus genetic investigations and summarizes the hurdles that have been encountered. The identification of candidate genes responsible for tinnitus may afford gene based diagnostic approaches, effective therapy development, and personalized therapeutic intervention.
Maierhofer, Anna ; Flunkert, Julia ; Dittrich, Marcus ; Müller, Tobias ; Schindler, Detlev ; Nanda, Indrajit ; Haaf, Thomas
Epigenetic alterations may contribute to the generation of cancer cells in a multi-step process of tumorigenesis following irradiation of normal body cells. Primary human fibroblasts with intact cell cycle checkpoints were used as a model to test whether X-ray irradiation with 2 and 4 Gray induces direct epigenetic effects (within the first cell cycle) in the exposed cells. ELISA-based fluorometric assays were consistent with slightly reduced global DNA methylation and hydroxymethylation, however the observed between-group differences were usually not significant. Similarly, bisulfite pyrosequencing of interspersed LINE-1 repeats and centromeric α-satellite DNA did not detect significant methylation differences between irradiated and non-irradiated cultures. Methylation of interspersed ALU repeats appeared to be slightly increased (one percentage point; p = 0.01) at 6 h after irradiation with 4 Gy. Single-cell analysis showed comparable variations in repeat methylation among individual cells in both irradiated and control cultures. Radiation-induced changes in global repeat methylation, if any, were much smaller than methylation variation between different fibroblast strains. Interestingly, α-satellite DNA methylation positively correlated with gestational age. Finally, 450K methylation arrays mainly targeting genes and CpG islands were used for global DNA methylation analysis. There were no detectable methylation differences in genic (promoter, 5' UTR, first exon, gene body, 3' UTR) and intergenic regions between irradiated and control fibroblast cultures. Although we cannot exclude minor effects, i.e. on individual CpG sites, collectively our data suggest that global DNA methylation remains rather stable in irradiated normal body cells in the early phase of DNA damage response.
Haertle, Larissa ; Maierhofer, Anna ; Böck, Julia ; Lehnen, Harald ; Böttcher, Yvonne ; Blüher, Matthias ; Schorsch, Martin ; Potabattula, Ramya ; El Hajj, Nady ; Appenzeller, Silke ; Haaf, Thomas
Imprinted genes show parent-specific activity (functional haploidy), which makes them particularly vulnerable to epigenetic dysregulation. Here we studied the methylation profiles of oppositely imprinted genes at single DNA molecule resolution by two independent parental allele-specific deep bisulfite sequencing (DBS) techniques. Using Roche (GSJunior) next generation sequencing technology, we analyzed the maternally imprinted MEST promoter and the paternally imprinted MEG3 intergenic (IG) differentially methylated region (DMR) in fetal cord blood, adult blood, and visceral adipose tissue. Epimutations were defined as paternal or maternal alleles with >50% aberrantly (de)methylated CpG sites, showing the wrong methylation imprint. The epimutation rates (range 2–66%) of the paternal MEST and the maternal MEG3 IG DMR allele, which should be completely unmethylated, were significantly higher than those (0–15%) of the maternal MEST and paternal MEG3 alleles, which are expected to be fully methylated. This hypermethylation of the non-imprinted allele (HNA) was independent of parental origin. Very low epimutation rates in sperm suggest that HNA occurred after fertilization. DBS with Illumina (MiSeq) technology confirmed HNA for the MEST promoter and the MEG3 IG DMR, and to a lesser extent, for the paternally imprinted secondary MEG3 promoter and the maternally imprinted PEG3 promoter. HNA leads to biallelic methylation of imprinted genes in a considerable proportion of normal body cells (somatic mosaicism) and is highly variable between individuals. We propose that during development and differentiation maintenance of differential methylation at most imprinting control regions may become to some extent redundant. The accumulation of stochastic and environmentally-induced methylation errors on the non-imprinted allele may increase epigenetic diversity between cells and individuals.
Die Pierre-Robin-Sequenz ist eine angeborene kraniofaziale Fehlbildung, bei der häufig eine Triade von Symptomen, bestehend aus mandibulärer Mikrognathie/Retrognathie, Glossoptose und einer Gaumenspalte, beobachtet werden kann. Aufgrund der Heterogenität der PRS und der häufigen Vergesellschaftung mit Syndromen, konnten Ätiologie und Pathogenese der PRS bisher nur unzureichend geklärt werden. Für einen Teil der Patienten mit isolierter PRS konnte eine familiäre Häufung von PRS-Fällen nachgewiesen werden, was auf eine erbliche Komponente als krankheitsauslösenden Faktor hinweist. In diesem Zusammenhang konnten bei Patienten mit isolierter PRS gehäuft genetische Veränderungen mit einer Entfernung von über 1Mb zentromerisch (5´) von SOX9 auf dem Chromosom 17 detektiert werden. Es wird vermutet, dass diese genetischen Aberrationen am SOX9 Lokus eine gewebsspezifische Fehlregulation von SOX9 während der Embryonalentwicklung auslösen und somit ursächlich für die Entstehung von PRS sein können.
Das Ziel dieser Arbeit war es, eine Würzburger Patientenkohorte mit isolierter PRS zu gewinnen und Informationen über die phänotypischen Merkmale der Studienteilnehmer auszuwerten. Im Anschluss sollte die Patienten-DNS mittels molekulargenetischen Analysemethoden auf potenziell krankheitsauslösende genetische Aberrationen am SOX9 Lokus untersucht werden.
Zunächst konnte eine Kohorte mit sieben PRS-Patienten erstellt und Informationen über die phänotypischen Krankheitsmerkmale erfasst und ausgewertet werden. Anschließend wurden bei den Studienteilnehmern eine Array-CGH, eine quantitative Echtzeit-Polymerase-Kettenreaktion und im Bereich von drei konservierten, potenziell regulatorischen Elementen des SOX9 Lokus eine Sanger Sequenzierung durchgeführt. Die Array-CGH ergab zunächst bei einem Patienten zwei große Deletionen im regulativen Umfeld des SOX9 Lokus, welche im Weiteren nicht durch qPCR bestätigt werden konnten. Letztendlich konnten durch die Sanger Sequenzierung 22 Varianten detektiert werden, wovon für drei Einzelnukleotid-Polymorphismen eine prädisponierende Wirkung diskutierbar und für zwei Einzelnukleotid-Varianten eine ursächlich pathogene Wirkung nicht auszuschließen ist.
Die Arbeit zeigt, dass die Symptome der HPP sehr variabel und unterschiedlich stark auftreten können. Dies erschwert die klinische Diagnosestellung der Erkrankung. Nahezu alle Patienten berichteten von starken Knochen-, Gelenk,- und Muskelschmerzen, von Karies und Parodontose sowie von vermehrten Frakturen, die zum Teil weitere chronische Schmerzen und Wiederholungsfrakturen erzeugen. Eine deutlich verminderte Leistungsfähigkeit im Vergleich zu Gleichaltrigen wurde ebenso häufig angegeben. Es konnte keine eindeutige Phänotyp - Genotyp Korrelation gefunden werden, allerdings geben die Daten einen deutlichen Hinweis, dass Patienten mit zwei Mutationen am stärksten symptomatisch betroffen sind.
Ebenfalls konnten keine Unterschiede zwischen dominant negativen Mutationen und nicht dominant negativen Mutationen gefunden werden.
Rodríguez-Mari, Adriana ; Wilson, Catherine ; Titus, Tom A. ; Canestro, Cristian ; BreMiller, Ruth A. ; Yan, Yi-Lin ; Nanda, Indrajit ; Johnston, Adam ; Kanki, John P. ; Gray, Erin M. ; He, Xinjun ; Spitsbergen, Jan ; Schindler, Detlev ; Postlethwait, John H.
Functional near-infrared spectroscopy (fNIRS) is an established optical neuroimaging method for measuring functional hemodynamic responses to infer neural activation. However, the impact of individual anatomy on the sensitivity of fNIRS measuring hemodynamics within cortical gray matter is still unknown. By means of Monte Carlo simulations and structural MRI of 23 healthy subjects (mean age: (25.0 +/- 2.8) years), we characterized the individual distribution of tissue-specific NIR-light absorption underneath 24 prefrontal fNIRS channels. We, thereby, investigated the impact of scalp-cortex distance (SCD), frontal sinus volume as well as sulcal morphology on gray matter volumes (V(gray)) traversed by NIR-light, i.e. anatomy-dependent fNIRS sensitivity. The NIR-light absorption between optodes was distributed describing a rotational ellipsoid with a mean penetration depth of (23.6 +/- 0.7) mm considering the deepest 5% of light. Of the detected photon packages scalp and bone absorbed (96.4 +/- 9: 7)% and V(gray) absorbed (3.1 +/- 1.8)% of the energy. The mean V(gray) volume (1.1 +/- 0.4)cm(3) was negatively correlated (r = - .76) with the SCD and frontal sinus volume (r = - .57) and was reduced by 41.5% in subjects with relatively large compared to small frontal sinus. Head circumference was significantly positively correlated with the mean SCD (r = .46) and the traversed frontal sinus volume (r = .43). Sulcal morphology had no significant impact on V(gray). Our findings suggest to consider individual SCD and frontal sinus volume as anatomical factors impacting fNIRS sensitivity. Head circumference may represent a practical measure to partly control for these sources of error variance.
Vigorito, Elena ; Kuchenbaecker, Karoline B. ; Beesley, Jonathan ; Adlard, Julian ; Agnarsson, Bjarni A. ; Andrulis, Irene L. ; Arun, Banu K. ; Barjhoux, Laure ; Belotti, Muriel ; Benitez, Javier ; Berger, Andreas ; Bojesen, Anders ; Bonanni, Bernardo ; Brewer, Carole ; Caldes, Trinidad ; Caligo, Maria A. ; Campbell, Ian ; Chan, Salina B. ; Claes, Kathleen B. M. ; Cohn, David E. ; Cook, Jackie ; Daly, Mary B. ; Damiola, Francesca ; Davidson, Rosemarie ; de Pauw, Antoine ; Delnatte, Capucine ; Diez, Orland ; Domchek, Susan M. ; Dumont, Martine ; Durda, Katarzyna ; Dworniczak, Bernd ; Easton, Douglas F. ; Eccles, Diana ; Ardnor, Christina Edwinsdotter ; Eeles, Ros ; Ejlertsen, Bent ; Ellis, Steve ; Evans, D. Gareth ; Feliubadalo, Lidia ; Fostira, Florentia ; Foulkes, William D. ; Friedman, Eitan ; Frost, Debra ; Gaddam, Pragna ; Ganz, Patricia A. ; Garber, Judy ; Garcia-Barberan, Vanesa ; Gauthier-Villars, Marion ; Gehrig, Andrea ; Gerdes, Anne-Marie ; Giraud, Sophie ; Godwin, Andrew K. ; Goldgar, David E. ; Hake, Christopher R. ; Hansen, Thomas V. O. ; Healey, Sue ; Hodgson, Shirley ; Hogervorst, Frans B. L. ; Houdayer, Claude ; Hulick, Peter J. ; Imyanitov, Evgeny N. ; Isaacs, Claudine ; Izatt, Louise ; Izquierdo, Angel ; Jacobs, Lauren ; Jakubowska, Anna ; Janavicius, Ramunas ; Jaworska-Bieniek, Katarzyna ; Jensen, Uffe Birk ; John, Esther M. ; Vijai, Joseph ; Karlan, Beth Y. ; Kast, Karin ; Khan, Sofia ; Kwong, Ava ; Laitman, Yael ; Lester, Jenny ; Lesueur, Fabienne ; Liljegren, Annelie ; Lubinski, Jan ; Mai, Phuong L. ; Manoukian, Siranoush ; Mazoyer, Sylvie ; Meindl, Alfons ; Mensenkamp, Arjen R. ; Montagna, Marco ; Nathanson, Katherine L. ; Neuhausen, Susan L. ; Nevanlinna, Heli ; Niederacher, Dieter ; Olah, Edith ; Olopade, Olufunmilayo I. ; Ong, Kai-ren ; Osorio, Ana ; Park, Sue Kyung ; Paulsson-Karlsson, Ylva ; Pedersen, Inge Sokilde ; Peissel, Bernard ; Peterlongo, Paolo ; Pfeiler, Georg ; Phelan, Catherine M. ; Piedmonte, Marion ; Poppe, Bruce ; Pujana, Miquel Angel ; Radice, Paolo ; Rennert, Gad ; Rodriguez, Gustavo C. ; Rookus, Matti A. ; Ross, Eric A. ; Schmutzler, Rita Katharina ; Simard, Jacques ; Singer, Christian F. ; Slavin, Thomas P. ; Soucy, Penny ; Southey, Melissa ; Steinemann, Doris ; Stoppa-Lyonnet, Dominique ; Sukiennicki, Grzegorz ; Sutter, Christian ; Szabo, Csilla I. ; Tea, Muy-Kheng ; Teixeira, Manuel R. ; Teo, Soo-Hwang ; Terry, Mary Beth ; Thomassen, Mads ; Tibiletti, Maria Grazia ; Tihomirova, Laima ; Tognazzo, Silvia ; van Rensburg, Elizabeth J. ; Varesco, Liliana ; Varon-Mateeva, Raymonda ; Vratimos, Athanassios ; Weitzel, Jeffrey N. ; McGuffog, Lesley ; Kirk, Judy ; Toland, Amanda Ewart ; Hamann, Ute ; Lindor, Noralane ; Ramus, Susan J. ; Greene, Mark H. ; Couch, Fergus J. ; Offit, Kenneth ; Pharoah, Paul D. P. ; Chenevix-Trench, Georgia ; Antoniou, Antonis C.
Population-based genome wide association studies have identified a locus at 9p22.2 associated with ovarian cancer risk, which also modifies ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. We conducted fine-scale mapping at 9p22.2 to identify potential causal variants in BRCA1 and BRCA2 mutation carriers. Genotype data were available for 15,252 (2,462 ovarian cancer cases) BRCA1 and 8,211 (631 ovarian cancer cases) BRCA2 mutation carriers. Following genotype imputation, ovarian cancer associations were assessed for 4,873 and 5,020 SNPs in BRCA1 and BRCA 2 mutation carriers respectively, within a retrospective cohort analytical framework. In BRCA1 mutation carriers one set of eight correlated candidate causal variants for ovarian cancer risk modification was identified (top SNP rs10124837, HR: 0.73, 95%CI: 0.68 to 0.79, p-value 2× 10−16). These variants were located up to 20 kb upstream of BNC2. In BRCA2 mutation carriers one region, up to 45 kb upstream of BNC2, and containing 100 correlated SNPs was identified as candidate causal (top SNP rs62543585, HR: 0.69, 95%CI: 0.59 to 0.80, p-value 1.0 × 10−6). The candidate causal in BRCA1 mutation carriers did not include the strongest associated variant at this locus in the general population. In sum, we identified a set of candidate causal variants in a region that encompasses the BNC2 transcription start site. The ovarian cancer association at 9p22.2 may be mediated by different variants in BRCA1 mutation carriers and in the general population. Thus, potentially different mechanisms may underlie ovarian cancer risk for mutation carriers and the general population.
Jansch, Charline ; Günther, Katharina ; Waider, Jonas ; Ziegler, Georg C. ; Forero, Andrea ; Kollert, Sina ; Svirin, Evgeniy ; Pühringer, Dirk ; Kwok, Chee Keong ; Ullmann, Reinhard ; Maierhofer, Anna ; Flunkert, Julia ; Haaf, Thomas ; Edenhofer, Frank ; Lesch, Klaus-Peter
Fibroblasts were isolated from a skin biopsy of a clinically diagnosed 51-year-old female attention-deficit/hyperactivity disorder (ADHD) patient carrying a duplication of SLC2A3, a gene encoding neuronal glucose transporter-3 (GLUT3). Patient fibroblasts were infected with Sendai virus, a single-stranded RNA virus, to generate transgene-free human induced pluripotent stem cells (iPSCs). SLC2A3-D2-iPSCs showed expression of pluripotency-associated markers, were able to differentiate into cells of the three germ layers in vitro and had a normal female karyotype. This in vitro cellular model can be used to study the role of risk genes in the pathogenesis of ADHD, in a patient-specific manner.
Vona, Barbara ; Maroofian, Reza ; Bellacchio, Emanuele ; Najafi, Maryam ; Thompson, Kyle ; Alahmad, Ahmad ; He, Langping ; Ahangari, Najmeh ; Rad, Abolfazl ; Shahrokhzadeh, Sima ; Bahena, Paulina ; Mittag, Falk ; Traub, Frank ; Movaffagh, Jebrail ; Amiri, Nafise ; Doosti, Mohammad ; Boostani, Reza ; Shirzadeh, Ebrahim ; Haaf, Thomas ; Diodato, Daria ; Schmidts, Miriam ; Taylor, Robert W. ; Karimiani, Ehsan Ghayoor
Background:
IARS2 encodes a mitochondrial isoleucyl-tRNA synthetase, a highly conserved nuclear-encoded enzyme required for the charging of tRNAs with their cognate amino acid for translation. Recently, pathogenic IARS2 variants have been identified in a number of patients presenting broad clinical phenotypes with autosomal recessive inheritance. These phenotypes range from Leigh and West syndrome to a new syndrome abbreviated CAGSSS that is characterised by cataracts, growth hormone deficiency, sensory neuropathy, sensorineural hearing loss, and skeletal dysplasia, as well as cataract with no additional anomalies.
Methods:
Genomic DNA from Iranian probands from two families with consanguineous parental background and overlapping CAGSSS features were subjected to exome sequencing and bioinformatics analysis.
Results:
Exome sequencing and data analysis revealed a novel homozygous missense variant (c.2625C > T, p.Pro909Ser, NM_018060.3) within a 14.3 Mb run of homozygosity in proband 1 and a novel homozygous missense variant (c.2282A > G, p.His761Arg) residing in an ~ 8 Mb region of homozygosity in a proband of the second family. Patient-derived fibroblasts from proband 1 showed normal respiratory chain enzyme activity, as well as unchanged oxidative phosphorylation protein subunits and IARS2 levels. Homology modelling of the known and novel amino acid residue substitutions in IARS2 provided insight into the possible consequence of these variants on function and structure of the protein.
Conclusions:
This study further expands the phenotypic spectrum of IARS2 pathogenic variants to include two patients (patients 2 and 3) with cataract and skeletal dysplasia and no other features of CAGSSS to the possible presentation of the defects in IARS2. Additionally, this study suggests that adult patients with CAGSSS may manifest central adrenal insufficiency and type II esophageal achalasia and proposes that a variable sensorineural hearing loss onset, proportionate short stature, polyneuropathy, and mild dysmorphic features are possible, as seen in patient 1. Our findings support that even though biallelic IARS2 pathogenic variants can result in a distinctive, clinically recognisable phenotype in humans, it can also show a wide range of clinical presentation from severe pediatric neurological disorders of Leigh and West syndrome to both non-syndromic cataract and cataract accompanied by skeletal dysplasia.
Vona, Barbara ; Hofrichter, Michaela A. H. ; Schröder, Jörg ; Shehata-Dieler, Wafaa ; Nanda, Indrajit ; Haaf, Thomas
Objectives:
Despite recent advancements in diagnostic tools, the genomic landscape of hereditary hearing loss remains largely uncharacterized. One strategy to understand genome-wide aberrations includes the analysis of copy number variation that can be mapped using SNP-microarray technology. A growing collection of literature has begun to uncover the importance of copy number variation in hereditary hearing loss. This pilot study underpins a larger effort that involves the stage-wise analysis of hearing loss patients, many of whom have advanced to high-throughput sequencing analysis.
Data description:
Our data originate from the Infinium HumanOmni1-Quad v1.0 SNP-microarrays (Illumina) that provide useful markers for genome-wide association studies and copy number variation analysis. This dataset comprises a cohort of 108 individuals (99 with hearing loss, 9 normal hearing family members) for the purpose of understanding the genetic contribution of copy number variations to hereditary hearing loss. These anonymized SNP-microarray data have been uploaded to the NCBI Gene Expression Omnibus and are intended to benefit other investigators interested in aggregating platform-matched array patient datasets or as part of a supporting reference tool for other laboratories to better understand recurring copy number variations in other genetic disorders.