TY - JOUR A1 - Prelog, Martina A1 - Hilligardt, Deborah A1 - Schmidt, Christian A. A1 - Przybylski, Grzegorz K. A1 - Leierer, Johannes A1 - Almanzar, Giovanni A1 - El Hajj, Nady A1 - Lesch, Klaus-Peter A1 - Arolt, Volker A1 - Zwanzger, Peter A1 - Haaf, Thomas A1 - Domschke, Katharina T1 - Hypermethylation of FOXP3 Promoter and Premature Aging of the Immune System in Female Patients with Panic Disorder? JF - PLoS ONE N2 - Immunological abnormalities associated with pathological conditions, such as higher infection rates, inflammatory diseases, cancer or cardiovascular events are common in patients with panic disorder. In the present study, T cell receptor excision circles (TRECs), Forkhead-Box-Protein P3 gene (FOXP3) methylation of regulatory T cells (Tregs) and relative telomere lengths (RTLs) were investigated in a total and subsamples of 131 patients with panic disorder as compared to 131 age- and sex-matched healthy controls in order to test for a potential dysfunction and premature aging of the immune system in anxiety disorders. Significantly lower TRECs (p = 0.004) as well as significant hypermethylation of the FOXP3 promoter region (p = 0.005) were observed in female (but not in male) patients with panic disorder as compared to healthy controls. No difference in relative telomere length was discerned between patients and controls, but significantly shorter telomeres in females, smokers and older persons within the patient group. The presently observed reduced TRECs in panic disorder patients and FOXP3 hypermethylation in female patients with panic disorder potentially reflect impaired thymus and immunosuppressive Treg function, which might partly account for the known increased morbidity and mortality of anxiety disorders conferred by e.g. cancer and cardiovascular disorders. KW - DNA methylation KW - antidepressants KW - regulatory T cells KW - panic disorder KW - treatment guidelines KW - telomere length KW - inflammatory diseases KW - anxiety disorders Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-179684 VL - 11 IS - 6 ER - TY - JOUR A1 - Bauer, Benedikt A1 - Mally, Angela A1 - Liedtke, Daniel T1 - Zebrafish embryos and larvae as alternative animal models for toxicity testing JF - International Journal of Molecular Sciences N2 - Prerequisite to any biological laboratory assay employing living animals is consideration about its necessity, feasibility, ethics and the potential harm caused during an experiment. The imperative of these thoughts has led to the formulation of the 3R-principle, which today is a pivotal scientific standard of animal experimentation worldwide. The rising amount of laboratory investigations utilizing living animals throughout the last decades, either for regulatory concerns or for basic science, demands the development of alternative methods in accordance with 3R to help reduce experiments in mammals. This demand has resulted in investigation of additional vertebrate species displaying favourable biological properties. One prominent species among these is the zebrafish (Danio rerio), as these small laboratory ray-finned fish are well established in science today and feature outstanding biological characteristics. In this review, we highlight the advantages and general prerequisites of zebrafish embryos and larvae before free-feeding stages for toxicological testing, with a particular focus on cardio-, neuro, hepato- and nephrotoxicity. Furthermore, we discuss toxicokinetics, current advances in utilizing zebrafish for organ toxicity testing and highlight how advanced laboratory methods (such as automation, advanced imaging and genetic techniques) can refine future toxicological studies in this species. KW - danio rerio KW - alternative methods KW - organ toxicity KW - 3R KW - transgenic animals Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-284225 SN - 1422-0067 VL - 22 IS - 24 ER - TY - JOUR A1 - Doll, Julia A1 - Vona, Barbara A1 - Schnapp, Linda A1 - Rüschendorf, Franz A1 - Khan, Imran A1 - Khan, Saadullah A1 - Muhammad, Noor A1 - Alam Khan, Sher A1 - Nawaz, Hamed A1 - Khan, Ajmal A1 - Ahmad, Naseer A1 - Kolb, Susanne M. A1 - Kühlewein, Laura A1 - Labonne, Jonathan D. J. A1 - Layman, Lawrence C. A1 - Hofrichter, Michaela A. H. A1 - Röder, Tabea A1 - Dittrich, Marcus A1 - Müller, Tobias A1 - Graves, Tyler D. A1 - Kong, Il-Keun A1 - Nanda, Indrajit A1 - Kim, Hyung-Goo A1 - Haaf, Thomas T1 - Genetic Spectrum of Syndromic and Non-Syndromic Hearing Loss in Pakistani Families JF - Genes N2 - The current molecular genetic diagnostic rates for hereditary hearing loss (HL) vary considerably according to the population background. Pakistan and other countries with high rates of consanguineous marriages have served as a unique resource for studying rare and novel forms of recessive HL. A combined exome sequencing, bioinformatics analysis, and gene mapping approach for 21 consanguineous Pakistani families revealed 13 pathogenic or likely pathogenic variants in the genes GJB2, MYO7A, FGF3, CDC14A, SLITRK6, CDH23, and MYO15A, with an overall resolve rate of 61.9%. GJB2 and MYO7A were the most frequently involved genes in this cohort. All the identified variants were either homozygous or compound heterozygous, with two of them not previously described in the literature (15.4%). Overall, seven missense variants (53.8%), three nonsense variants (23.1%), two frameshift variants (15.4%), and one splice-site variant (7.7%) were observed. Syndromic HL was identified in five (23.8%) of the 21 families studied. This study reflects the extreme genetic heterogeneity observed in HL and expands the spectrum of variants in deafness-associated genes. KW - genetic diagnosis KW - consanguinity KW - genome-wide linkage analysis KW - hearing loss KW - Pakistan KW - exome sequencing Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-219293 SN - 2073-4425 VL - 11 IS - 11 ER - TY - JOUR A1 - Dumont, Martine A1 - Weber-Lassalle, Nana A1 - Joly-Beauparlant, Charles A1 - Ernst, Corinna A1 - Droit, Arnaud A1 - Feng, Bing-Jian A1 - Dubois, Stéphane A1 - Collin-Deschesnes, Annie-Claude A1 - Soucy, Penny A1 - Vallée, Maxime A1 - Fournier, Frédéric A1 - Lemaçon, Audrey A1 - Adank, Muriel A. A1 - Allen, Jamie A1 - Altmüller, Janine A1 - Arnold, Norbert A1 - Ausems, Margreet G. E. M. A1 - Berutti, Riccardo A1 - Bolla, Manjeet K. A1 - Bull, Shelley A1 - Carvalho, Sara A1 - Cornelissen, Sten A1 - Dufault, Michael R. A1 - Dunning, Alison M. A1 - Engel, Christoph A1 - Gehrig, Andrea A1 - Geurts-Giele, Willemina R. R. A1 - Gieger, Christian A1 - Green, Jessica A1 - Hackmann, Karl A1 - Helmy, Mohamed A1 - Hentschel, Julia A1 - Hogervorst, Frans B. L. A1 - Hollestelle, Antoinette A1 - Hooning, Maartje J. A1 - Horváth, Judit A1 - Ikram, M. Arfan A1 - Kaulfuß, Silke A1 - Keeman, Renske A1 - Kuang, Da A1 - Luccarini, Craig A1 - Maier, Wolfgang A1 - Martens, John W. M. A1 - Niederacher, Dieter A1 - Nürnberg, Peter A1 - Ott, Claus-Eric A1 - Peters, Annette A1 - Pharoah, Paul D. P. A1 - Ramirez, Alfredo A1 - Ramser, Juliane A1 - Riedel-Heller, Steffi A1 - Schmidt, Gunnar A1 - Shah, Mitul A1 - Scherer, Martin A1 - Stäbler, Antje A1 - Strom, Tim M. A1 - Sutter, Christian A1 - Thiele, Holger A1 - van Asperen, Christi J. A1 - van der Kolk, Lizet A1 - van der Luijt, Rob B. A1 - Volk, Alexander E. A1 - Wagner, Michael A1 - Waisfisz, Quinten A1 - Wang, Qin A1 - Wang-Gohrke, Shan A1 - Weber, Bernhard H. F. A1 - Devilee, Peter A1 - Tavtigian, Sean A1 - Bader, Gary D. A1 - Meindl, Alfons A1 - Goldgar, David E. A1 - Andrulis, Irene L. A1 - Schmutzler, Rita K. A1 - Easton, Douglas F. A1 - Schmidt, Marjanka K. A1 - Hahnen, Eric A1 - Simard, Jacques T1 - Uncovering the contribution of moderate-penetrance susceptibility genes to breast cancer by whole-exome sequencing and targeted enrichment sequencing of candidate genes in women of European ancestry JF - Cancers N2 - Rare variants in at least 10 genes, including BRCA1, BRCA2, PALB2, ATM, and CHEK2, are associated with increased risk of breast cancer; however, these variants, in combination with common variants identified through genome-wide association studies, explain only a fraction of the familial aggregation of the disease. To identify further susceptibility genes, we performed a two-stage whole-exome sequencing study. In the discovery stage, samples from 1528 breast cancer cases enriched for breast cancer susceptibility and 3733 geographically matched unaffected controls were sequenced. Using five different filtering and gene prioritization strategies, 198 genes were selected for further validation. These genes, and a panel of 32 known or suspected breast cancer susceptibility genes, were assessed in a validation set of 6211 cases and 6019 controls for their association with risk of breast cancer overall, and by estrogen receptor (ER) disease subtypes, using gene burden tests applied to loss-of-function and rare missense variants. Twenty genes showed nominal evidence of association (p-value < 0.05) with either overall or subtype-specific breast cancer. Our study had the statistical power to detect susceptibility genes with effect sizes similar to ATM, CHEK2, and PALB2, however, it was underpowered to identify genes in which susceptibility variants are rarer or confer smaller effect sizes. Larger sample sizes would be required in order to identify such genes. KW - breast cancer KW - genetic susceptibility KW - whole-exome sequencing KW - moderate-penetrance genes Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-281768 SN - 2072-6694 VL - 14 IS - 14 ER - TY - JOUR A1 - Engel, Christoph A1 - Rhiem, Kerstin A1 - Hahnen, Eric A1 - Loibl, Sibylle A1 - Weber, Karsten E. A1 - Seiler, Sabine A1 - Zachariae, Silke A1 - Hauke, Jan A1 - Wappenschmidt, Barbara A1 - Waha, Anke A1 - Blümcke, Britta A1 - Kiechle, Marion A1 - Meindl, Alfons A1 - Niederacher, Dieter A1 - Bartram, Claus R. A1 - Speiser, Dorothee A1 - Schlegelberger, Brigitte A1 - Arnold, Norbert A1 - Wieacker, Peter A1 - Leinert, Elena A1 - Gehrig, Andrea A1 - Briest, Susanne A1 - Kast, Karin A1 - Riess, Olaf A1 - Emons, Günter A1 - Weber, Bernhard H. F. A1 - Engel, Jutta A1 - Schmutzler, Rita K. T1 - Prevalence of pathogenic BRCA1/2 germline mutations among 802 women with unilateral triple-negative breast cancer without family cancer history JF - BMC Cancer N2 - Background There is no international consensus up to which age women with a diagnosis of triple-negative breast cancer (TNBC) and no family history of breast or ovarian cancer should be offered genetic testing for germline BRCA1 and BRCA2 (gBRCA) mutations. Here, we explored the association of age at TNBC diagnosis with the prevalence of pathogenic gBRCA mutations in this patient group. Methods The study comprised 802 women (median age 40 years, range 19-76) with oestrogen receptor, progesterone receptor, and human epidermal growth factor receptor type 2 negative breast cancers, who had no relatives with breast or ovarian cancer. All women were tested for pathogenic gBRCA mutations. Logistic regression analysis was used to explore the association between age at TNBC diagnosis and the presence of a pathogenic gBRCA mutation. Results A total of 127 women with TNBC(15.8%) were gBRCA mutation carriers (BRCA1: n = 118, 14.7%; BRCA2: n = 9, 1. 1%). The mutation prevalence was 32.9% in the age group 20-29 years compared to 6.9% in the age group 60-69 years. Logistic regression analysis revealed a significant increase of mutation frequency with decreasing age at diagnosis (odds ratio 1.87 per 10 year decrease, 95% CI 1.50-2.32, p < 0.001). gBRCA mutation risk was predicted to be > 10% for women diagnosed below approximately 50 years. Conclusions Based on the general understanding that a heterozygous mutation probability of 10% or greater justifies gBRCA mutation screening, women with TNBC diagnosed before the age of 50 years and no familial history of breast and ovarian cancer should be tested for gBRCA mutations. In Germany, this would concern approximately 880 women with newly diagnosed TNBC per year, of whom approximately 150 are expected to be identified as carriers of a pathogenic gBRCA mutation. KW - hereditary breast and ovarian cancer KW - BRCA1 KW - BRCA2 KW - triple-negative breast cancer Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-226763 VL - 18 ER - TY - JOUR A1 - Sathyanarayana, Vijaya A1 - Lee, Beth A1 - Wright, Neville B. A1 - Santos, Rui A1 - Bonney, Denise A1 - Wynn, Robert A1 - Patel, Leena A1 - Chandler, Kate A1 - Cheesman, Ed A1 - Schindler, Detlev A1 - Webb, Nicholas J. A. A1 - Meyer, Stefan T1 - Patterns and frequency of renal abnormalities in Fanconi anaemia: implications for long-term management JF - Pediatric Nephrology N2 - Fanconi anaemia (FA) is an inherited disease with bone marrow failure, variable congenital and developmental abnormalities, and cancer predisposition. With improved survival, non-haematological manifestations of FA become increasingly important for long-term management. While renal abnormalities are recognized, detailed data on patterns and frequency and implications for long-term management are sparse. We reviewed clinical course and imaging findings of FA patients with respect to renal complications in our centre over a 25-year period to formulate some practical suggestions for guidelines for management of renal problems associated with FA. Thirty patients including four sibling sets were reviewed. On imaging, 14 had evidence of anatomical abnormalities of the kidneys. Two cases with severe phenotype, including renal abnormalities, had chronic kidney disease (CKD) at diagnosis. Haematopoietic stem cell transplantation was complicated by significant acute kidney injury (AKI) in three cases. In three patients, there was CKD at long-term follow-up. All patients had normal blood pressure. Evaluation of renal anatomy with ultrasound imaging is important at diagnostic workup of FA. While CKD is uncommon at diagnosis, our data suggests that the incidence of CKD increases with age, in particular after haematopoietic stem cell transplantation. Monitoring of renal function is essential for management of FA. Based on these long-term clinical observations, we formulate some practical guidelines for assessment and management of renal abnormalities in FA. KW - Fanconi anaemia KW - Renal abnormalities KW - Long-term follow-up Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-227400 VL - 33 IS - 9 ER - TY - JOUR A1 - Weber-Lassalle, Nana A1 - Hauke, Jan A1 - Ramser, Juliane A1 - Richters, Lisa A1 - Groß, Eva A1 - Blümcke, Britta A1 - Gehrig, Andrea A1 - Kahlert, Anne-Karin A1 - Müller, Clemens R. A1 - Hackmann, Karl A1 - Honisch, Ellen A1 - Weber-Lassalle, Konstantin A1 - Niederacher, Dieter A1 - Borde, Julika A1 - Thiele, Holger A1 - Ernst, Corinna A1 - Altmüller, Janine A1 - Neidhardt, Guido A1 - Nürnberg, Peter A1 - Klaschik, Kristina A1 - Schroeder, Christopher A1 - Platzer, Konrad A1 - Volk, Alexander E. A1 - Wang-Gohrke, Shan A1 - Just, Walter A1 - Auber, Bernd A1 - Kubisch, Christian A1 - Schmidt, Gunnar A1 - Horvath, Judit A1 - Wappenschmidt, Barbara A1 - Engel, Christoph A1 - Arnold, Norbert A1 - Dworniczak, Bernd A1 - Rhiem, Kerstin A1 - Meindl, Alfons A1 - Schmutzler, Rita K. A1 - Hahnen, Eric T1 - BRIP1 loss-of-function mutations confer high risk for familial ovarian cancer, but not familial breast cancer JF - Breast Cancer Research N2 - Background Germline mutations in the BRIP1 gene have been described as conferring a moderate risk for ovarian cancer (OC), while the role of BRIP1 in breast cancer (BC) pathogenesis remains controversial. Methods To assess the role of deleterious BRIP1 germline mutations in BC/OC predisposition, 6341 well-characterized index patients with BC, 706 index patients with OC, and 2189 geographically matched female controls were screened for loss-of-function (LoF) mutations and potentially damaging missense variants. All index patients met the inclusion criteria of the German Consortium for Hereditary Breast and Ovarian Cancer for germline testing and tested negative for pathogenic BRCA1/2 variants. Results BRIP1 LoF mutations confer a high OC risk in familial index patients (odds ratio (OR) = 20.97, 95% confidence interval (CI) = 12.02–36.57, P < 0.0001) and in the subgroup of index patients with late-onset OC (OR = 29.91, 95% CI = 14.99–59.66, P < 0.0001). No significant association of BRIP1 LoF mutations with familial BC was observed (OR = 1.81 95% CI = 1.00–3.30, P = 0.0623). In the subgroup of familial BC index patients without a family history of OC there was also no apparent association (OR = 1.42, 95% CI = 0.70–2.90, P = 0.3030). In 1027 familial BC index patients with a family history of OC, the BRIP1 mutation prevalence was significantly higher than that observed in controls (OR = 3.59, 95% CI = 1.43–9.01; P = 0.0168). Based on the negative association between BRIP1 LoF mutations and familial BC in the absence of an OC family history, we conclude that the elevated mutation prevalence in the latter cohort was driven by the occurrence of OC in these families. Compared with controls, predicted damaging rare missense variants were significantly more prevalent in OC (P = 0.0014) but not in BC (P = 0.0693) patients. Conclusions To avoid ambiguous results, studies aimed at assessing the impact of candidate predisposition gene mutations on BC risk might differentiate between BC index patients with an OC family history and those without. In familial cases, we suggest that BRIP1 is a high-risk gene for late-onset OC but not a BC predisposition gene, though minor effects cannot be excluded. KW - breast cancer KW - ovarian cancer KW - BRIP1 gene KW - germline mutations Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-233433 VL - 20 ER - TY - JOUR A1 - Pluta, Natalie A1 - Hoffjan, Sabine A1 - Zimmer, Frederic A1 - Köhler, Cornelia A1 - Lücke, Thomas A1 - Mohr, Jennifer A1 - Vorgerd, Matthias A1 - Nguyen, Hoa Huu Phuc A1 - Atlan, David A1 - Wolf, Beat A1 - Zaum, Ann-Kathrin A1 - Rost, Simone T1 - Homozygous inversion on chromosome 13 involving SGCG detected by short read whole genome sequencing in a patient suffering from limb-girdle muscular dystrophy JF - Genes N2 - New techniques in molecular genetic diagnostics now allow for accurate diagnosis in a large proportion of patients with muscular diseases. Nevertheless, many patients remain unsolved, although the clinical history and/or the muscle biopsy give a clear indication of the involved genes. In many cases, there is a strong suspicion that the cause must lie in unexplored gene areas, such as deep-intronic or other non-coding regions. In order to find these changes, next-generation sequencing (NGS) methods are constantly evolving, making it possible to sequence entire genomes to reveal these previously uninvestigated regions. Here, we present a young woman who was strongly suspected of having a so far genetically unsolved sarcoglycanopathy based on her clinical history and muscle biopsy. Using short read whole genome sequencing (WGS), a homozygous inversion on chromosome 13 involving SGCG and LINC00621 was detected. The breakpoint in intron 2 of SGCG led to the absence of γ-sarcoglycan, resulting in the manifestation of autosomal recessive limb-girdle muscular dystrophy 5 (LGMDR5) in the young woman. KW - inversion KW - sarcoglycanopathy KW - whole genome sequencing (WGS) KW - next generation sequencing (NGS) KW - LGMDR5 KW - muscle disease KW - genetic diagnostics Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-288122 SN - 2073-4425 VL - 13 IS - 10 ER - TY - JOUR A1 - Nanda, Indrajit A1 - Schröder, Sarah K. A1 - Steinlein, Claus A1 - Haaf, Thomas A1 - Buhl, Eva M. A1 - Grimm, Domink G. A1 - Weiskirchen, Ralf T1 - Rat hepatic stellate cell line CFSC-2G: genetic markers and short tandem repeat profile useful for cell line authentication JF - Cells N2 - Hepatic stellate cells (HSCs) are also known as lipocytes, fat-storing cells, perisinusoidal cells, or Ito cells. These liver-specific mesenchymal cells represent about 5% to 8% of all liver cells, playing a key role in maintaining the microenvironment of the hepatic sinusoid. Upon chronic liver injury or in primary culture, these cells become activated and transdifferentiate into a contractile phenotype, i.e., the myofibroblast, capable of producing and secreting large quantities of extracellular matrix compounds. Based on their central role in the initiation and progression of chronic liver diseases, cultured HSCs are valuable in vitro tools to study molecular and cellular aspects of liver diseases. However, the isolation of these cells requires special equipment, trained personnel, and in some cases needs approval from respective authorities. To overcome these limitations, several immortalized HSC lines were established. One of these cell lines is CFSC, which was originally established from cirrhotic rat livers induced by carbon tetrachloride. First introduced in 1991, this cell line and derivatives thereof (i.e., CFSC-2G, CFSC-3H, CFSC-5H, and CFSC-8B) are now used in many laboratories as an established in vitro HSC model. We here describe molecular features that are suitable for cell authentication. Importantly, chromosome banding and multicolor spectral karyotyping (SKY) analysis demonstrate that the CFSC-2G genome has accumulated extensive chromosome rearrangements and most chromosomes exist in multiple copies producing a pseudo-triploid karyotype. Furthermore, our study documents a defined short tandem repeat (STR) profile including 31 species-specific markers, and a list of genes expressed in CFSC-2G established by bulk mRNA next-generation sequencing (NGS). KW - liver KW - extracellular matrix KW - hepatic stellate cell KW - myofibroblast KW - fibrosis KW - stress fibers KW - spectral karyotyping KW - rhodamine–phalloidin stain KW - next-generation sequencing KW - STR profile Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-288067 SN - 2073-4409 VL - 11 IS - 18 ER - TY - JOUR A1 - Ferreira, Manuel A. A1 - Gamazon, Eric R. A1 - Al-Ejeh, Fares A1 - Aittomäki, Kristiina A1 - Andrulis, Irene L. A1 - Anton-Culver, Hoda A1 - Arason, Adalgeir A1 - Arndt, Volker A1 - Aronson, Kristan J. A1 - Arun, Banu K. A1 - Asseryanis, Ella A1 - Azzollini, Jacopo A1 - Balmaña, Judith A1 - Barnes, Daniel R. A1 - Barrowdale, Daniel A1 - Beckmann, Matthias W. A1 - Behrens, Sabine A1 - Benitez, Javier A1 - Bermisheva, Marina A1 - Bialkowska, Katarzyna A1 - Blomqvist, Carl A1 - Bogdanova, Natalia V. A1 - Bojesen, Stig E. A1 - Bolla, Manjeet K. A1 - Borg, Ake A1 - Brauch, Hiltrud A1 - Brenner, Hermann A1 - Broeks, Annegien A1 - Burwinkel, Barbara A1 - Caldés, Trinidad A1 - Caligo, Maria A. A1 - Campa, Daniele A1 - Campbell, Ian A1 - Canzian, Federico A1 - Carter, Jonathan A1 - Carter, Brian D. A1 - Castelao, Jose E. A1 - Chang-Claude, Jenny A1 - Chanock, Stephen J. A1 - Christiansen, Hans A1 - Chung, Wendy K. A1 - Claes, Kathleen B. M. A1 - Clarke, Christine L. A1 - Couch, Fergus J. A1 - Cox, Angela A1 - Cross, Simon S. A1 - Czene, Kamila A1 - Daly, Mary B. A1 - de la Hoya, Miguel A1 - Dennis, Joe A1 - Devilee, Peter A1 - Diez, Orland A1 - Dörk, Thilo A1 - Dunning, Alison M. A1 - Dwek, Miriam A1 - Eccles, Diana M. A1 - Ejlertsen, Bent A1 - Ellberg, Carolina A1 - Engel, Christoph A1 - Eriksson, Mikael A1 - Fasching, Peter A. A1 - Fletcher, Olivia A1 - Flyger, Henrik A1 - Friedman, Eitan A1 - Frost, Debra A1 - Gabrielson, Marike A1 - Gago-Dominguez, Manuela A1 - Ganz, Patricia A. A1 - Gapstur, Susan M. A1 - Garber, Judy A1 - García-Closas, Montserrat A1 - García-Sáenz, José A. A1 - Gaudet, Mia M. A1 - Giles, Graham G. A1 - Glendon, Gord A1 - Godwin, Andrew K. A1 - Goldberg, Mark S. A1 - Goldgar, David E. A1 - González-Neira, Anna A1 - Greene, Mark H. A1 - Gronwald, Jacek A1 - Guenél, Pascal A1 - Haimann, Christopher A. A1 - Hall, Per A1 - Hamann, Ute A1 - He, Wei A1 - Heyworth, Jane A1 - Hogervorst, Frans B. L. A1 - Hollestelle, Antoinette A1 - Hoover, Robert N. A1 - Hopper, John L. A1 - Hulick, Peter J. A1 - Humphreys, Keith A1 - Imyanitov, Evgeny N. A1 - Isaacs, Claudine A1 - Jakimovska, Milena A1 - Jakubowska, Anna A1 - James, Paul A. A1 - Janavicius, Ramunas A1 - Jankowitz, Rachel C. A1 - John, Esther M. A1 - Johnson, Nichola A1 - Joseph, Vijai A1 - Karlan, Beth Y. A1 - Khusnutdinova, Elza A1 - Kiiski, Johanna I. A1 - Ko, Yon-Dschun A1 - Jones, Michael E. A1 - Konstantopoulou, Irene A1 - Kristensen, Vessela N. A1 - Laitman, Yael A1 - Lambrechts, Diether A1 - Lazaro, Conxi A1 - Leslie, Goska A1 - Lester, Jenny A1 - Lesueur, Fabienne A1 - Lindström, Sara A1 - Long, Jirong A1 - Loud, Jennifer T. A1 - Lubiński, Jan A1 - Makalic, Enes A1 - Mannermaa, Arto A1 - Manoochehri, Mehdi A1 - Margolin, Sara A1 - Maurer, Tabea A1 - Mavroudis, Dimitrios A1 - McGuffog, Lesley A1 - Meindl, Alfons A1 - Menon, Usha A1 - Michailidou, Kyriaki A1 - Miller, Austin A1 - Montagna, Marco A1 - Moreno, Fernando A1 - Moserle, Lidia A1 - Mulligan, Anna Marie A1 - Nathanson, Katherine L. A1 - Neuhausen, Susan L. A1 - Nevanlinna, Heli A1 - Nevelsteen, Ines A1 - Nielsen, Finn C. A1 - Nikitina-Zake, Liene A1 - Nussbaum, Robert L. A1 - Offit, Kenneth A1 - Olah, Edith A1 - Olopade, Olufunmilayo I. A1 - Olsson, Håkan A1 - Osorio, Ana A1 - Papp, Janos A1 - Park-Simon, Tjoung-Won A1 - Parsons, Michael T. A1 - Pedersen, Inge Sokilde A1 - Peixoto, Ana A1 - Peterlongo, Paolo A1 - Pharaoh, Paul D. P. A1 - Plaseska-Karanfilska, Dijana A1 - Poppe, Bruce A1 - Presneau, Nadege A1 - Radice, Paolo A1 - Rantala, Johanna A1 - Rennert, Gad A1 - Risch, Harvey A. A1 - Saloustros, Emmanouil A1 - Sanden, Kristin A1 - Sawyer, Elinor J. A1 - Schmidt, Marjanka K. A1 - Schmutzler, Rita K. A1 - Sharma, Priyanka A1 - Shu, Xiao-Ou A1 - Simard, Jaques A1 - Singer, Christian F. A1 - Soucy, Penny A1 - Southey, Melissa C. A1 - Spinelli, John J. A1 - Spurdle, Amanda B. A1 - Stone, Jennifer A1 - Swerdlow, Anthony J. A1 - Tapper, William J. A1 - Taylor, Jack A. A1 - Teixeira, Manuel R. A1 - Terry, Mary Beth A1 - Teulé, Alex A1 - Thomassen, Mads A1 - Thöne, Kathrin A1 - Thull, Darcy L. A1 - Tischkowitz, Marc A1 - Toland, Amanda E. A1 - Torres, Diana A1 - Truong, Thérèse A1 - Tung, Nadine A1 - Vachon, Celine M. A1 - van Asperen, Christi J. A1 - van den Ouweland, Ans M. W. A1 - van Rensburg, Elizabeth J. A1 - Vega, Ana A1 - Viel, Alexandra A1 - Wang, Qin A1 - Wappenschmidt, Barbara A1 - Weitzel, Jeffrey N. A1 - Wendt, Camilla A1 - Winqvist, Robert A1 - Yang, Xiaohong R. A1 - Yannoukakos, Drakoulis A1 - Ziogas, Argyrios A1 - Kraft, Peter A1 - Antoniou, Antonis C. A1 - Zheng, Wei A1 - Easton, Douglas F. A1 - Milne, Roger L. A1 - Beesley, Jonathan A1 - Chenevix-Trench, Georgia T1 - Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer JF - Nature Communications N2 - Genome-wide association studies (GWAS) have identified more than 170 breast cancer susceptibility loci. Here we hypothesize that some risk-associated variants might act in non-breast tissues, specifically adipose tissue and immune cells from blood and spleen. Using expression quantitative trait loci (eQTL) reported in these tissues, we identify 26 previously unreported, likely target genes of overall breast cancer risk variants, and 17 for estrogen receptor (ER)-negative breast cancer, several with a known immune function. We determine the directional effect of gene expression on disease risk measured based on single and multiple eQTL. In addition, using a gene-based test of association that considers eQTL from multiple tissues, we identify seven (and four) regions with variants associated with overall (and ER-negative) breast cancer risk, which were not reported in previous GWAS. Further investigation of the function of the implicated genes in breast and immune cells may provide insights into the etiology of breast cancer. KW - cancer KW - genetics Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-228024 VL - 10 ER - TY - JOUR A1 - Dubail, Johanne A1 - Huber, Céline A1 - Chantepie, Sandrine A1 - Sonntag, Stephan A1 - Tüysüz, Beyhan A1 - Mihci, Ercan A1 - Gordon, Christopher T. A1 - Steichen-Gersdorf, Elisabeth A1 - Amiel, Jeanne A1 - Nur, Banu A1 - Stolte-Dijkstra, Irene A1 - van Eerde, Albertien M. A1 - van Gassen, Koen L. A1 - Breugem, Corstiaan C. A1 - Stegmann, Alexander A1 - Lekszas, Caroline A1 - Maroofian, Reza A1 - Karimiani, Ehsan Ghayoor A1 - Bruneel, Arnaud A1 - Seta, Nathalie A1 - Munnich, Arnold A1 - Papy-Garcia, Dulce A1 - De La Dure-Molla, Muriel A1 - Cormier-Daire, Valérie T1 - SLC10A7 mutations cause a skeletal dysplasia with amelogenesis imperfecta mediated by GAG biosynthesis defects JF - Nature Communications N2 - Skeletal dysplasia with multiple dislocations are severe disorders characterized by dislocations of large joints and short stature. The majority of them have been linked to pathogenic variants in genes encoding glycosyltransferases, sulfotransferases or epimerases required for glycosaminoglycan synthesis. Using exome sequencing, we identify homozygous mutations in SLC10A7 in six individuals with skeletal dysplasia with multiple dislocations and amelogenesis imperfecta. SLC10A7 encodes a 10-transmembrane-domain transporter located at the plasma membrane. Functional studies in vitro demonstrate that SLC10A7 mutations reduce SLC10A7 protein expression. We generate a Slc10a7−/− mouse model, which displays shortened long bones, growth plate disorganization and tooth enamel anomalies, recapitulating the human phenotype. Furthermore, we identify decreased heparan sulfate levels in Slc10a7−/− mouse cartilage and patient fibroblasts. Finally, we find an abnormal N-glycoprotein electrophoretic profile in patient blood samples. Together, our findings support the involvement of SLC10A7 in glycosaminoglycan synthesis and specifically in skeletal development. KW - bone development KW - disease genetics KW - medical genetics Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-226377 VL - 9 ER - TY - JOUR A1 - Haertle, Larissa A1 - Maierhofer, Anna A1 - Böck, Julia A1 - Lehnen, Harald A1 - Böttcher, Yvonne A1 - Blüher, Matthias A1 - Schorsch, Martin A1 - Potabattula, Ramya A1 - El Hajj, Nady A1 - Appenzeller, Silke A1 - Haaf, Thomas T1 - Hypermethylation of the non-imprinted maternal MEG3 and paternal MEST alleles is highly variable among normal individuals JF - PLoS ONE N2 - 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. KW - DNA methylation KW - genomic imprinting KW - polymerase chain reaction KW - blood KW - epigenetics KW - sequence alignment KW - sperm Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-170433 VL - 12 IS - 8 ER - TY - JOUR A1 - Klughammer, Johanna A1 - Dittrich, Marcus A1 - Blom, Jochen A1 - Mitesser, Vera A1 - Vogel, Ulrich A1 - Frosch, Matthias A1 - Goesmann, Alexander A1 - Müller, Tobias A1 - Schoen, Christoph T1 - Comparative genome sequencing reveals within-host genetic changes in Neisseria meningitidis during invasive disease JF - PLoS ONE N2 - Some members of the physiological human microbiome occasionally cause life-threatening disease even in immunocompetent individuals. A prime example of such a commensal pathogen is Neisseria meningitidis, which normally resides in the human nasopharynx but is also a leading cause of sepsis and epidemic meningitis. Using N. meningitidis as model organism, we tested the hypothesis that virulence of commensal pathogens is a consequence of within host evolution and selection of invasive variants due to mutations at contingency genes, a mechanism called phase variation. In line with the hypothesis that phase variation evolved as an adaptation to colonize diverse hosts, computational comparisons of all 27 to date completely sequenced and annotated meningococcal genomes retrieved from public databases showed that contingency genes are indeed enriched for genes involved in host interactions. To assess within-host genetic changes in meningococci, we further used ultra-deep whole-genome sequencing of throat-blood strain pairs isolated from four patients suffering from invasive meningococcal disease. We detected up to three mutations per strain pair, affecting predominantly contingency genes involved in type IV pilus biogenesis. However, there was not a single (set) of mutation(s) that could invariably be found in all four pairs of strains. Phenotypic assays further showed that these genetic changes were generally not associated with increased serum resistance, higher fitness in human blood ex vivo or differences in the interaction with human epithelial and endothelial cells in vitro. In conclusion, we hypothesize that virulence of meningococci results from accidental emergence of invasive variants during carriage and without within host evolution of invasive phenotypes during disease progression in vivo. KW - blood KW - comparative genomics KW - throat KW - genetic loci KW - Neisseria meningitidis KW - genomic libraries KW - genome sequencing KW - sequence assembly tools Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-159547 VL - 12 IS - 1 ER - TY - JOUR A1 - Nanda, Indrajit A1 - Schories, Susanne A1 - Simeonov, Ivan A1 - Adolfi, Mateus Contar A1 - Du, Kang A1 - Steinlein, Claus A1 - Alsheimer, Manfred A1 - Haaf, Thomas A1 - Schartl, Manfred T1 - Evolution of the degenerated Y-chromosome of the swamp guppy, Micropoecilia picta JF - Cells N2 - The conspicuous colour sexual dimorphism of guppies has made them paradigmatic study objects for sex-linked traits and sex chromosome evolution. Both the X- and Y-chromosomes of the common guppy (Poecilia reticulata) are genetically active and homomorphic, with a large homologous part and a small sex specific region. This feature is considered to emulate the initial stage of sex chromosome evolution. A similar situation has been documented in the related Endler’s and Oropuche guppies (P. wingei, P. obscura) indicating a common origin of the Y in this group. A recent molecular study in the swamp guppy (Micropoecilia. picta) reported a low SNP density on the Y, indicating Y-chromosome deterioration. We performed a series of cytological studies on M. picta to show that the Y-chromosome is quite small compared to the X and has accumulated a high content of heterochromatin. Furthermore, the Y-chromosome stands out in displaying CpG clusters around the centromeric region. These cytological findings evidently illustrate that the Y-chromosome in M. picta is indeed highly degenerated. Immunostaining for SYCP3 and MLH1 in pachytene meiocytes revealed that a substantial part of the Y remains associated with the X. A specific MLH1 hotspot site was persistently marked at the distal end of the associated XY structure. These results unveil a landmark of a recombining pseudoautosomal region on the otherwise strongly degenerated Y chromosome of M. picta. Hormone treatments of females revealed that, unexpectedly, no sexually antagonistic color gene is Y-linked in M. picta. All these differences to the Poecilia group of guppies indicate that the trajectories associated with the evolution of sex chromosomes are not in parallel. KW - sex chromosomes KW - heterochromatin KW - Y chromosome degeneration KW - meiosis KW - synaptonemal complex KW - recombination KW - 5-methylcytosine KW - testosterone KW - sexual antagonistic genes KW - sex linked pigmentation pattern Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-267242 SN - 2073-4409 VL - 11 IS - 7 ER - TY - JOUR A1 - Prell, Andreas A1 - Sen, Mustafa Orkun A1 - Potabattula, Ramya A1 - Bernhardt, Laura A1 - Dittrich, Marcus A1 - Hahn, Thomas A1 - Schorsch, Martin A1 - Zacchini, Federica A1 - Ptak, Grazyna Ewa A1 - Niemann, Heiner A1 - Haaf, Thomas T1 - Species-specific paternal age effects and sperm methylation levels of developmentally important genes JF - Cells N2 - A growing number of sperm methylome analyses have identified genomic loci that are susceptible to paternal age effects in a variety of mammalian species, including human, bovine, and mouse. However, there is little overlap between different data sets. Here, we studied whether or not paternal age effects on the sperm epigenome have been conserved in mammalian evolution and compared methylation patterns of orthologous regulatory regions (mainly gene promoters) containing both conserved and non-conserved CpG sites in 94 human, 36 bovine, and 94 mouse sperm samples, using bisulfite pyrosequencing. We discovered three (NFKB2, RASGEF1C, and RPL6) age-related differentially methylated regions (ageDMRs) in humans, four (CHD7, HDAC11, PAK1, and PTK2B) in bovines, and three (Def6, Nrxn2, and Tbx19) in mice. Remarkably, the identified sperm ageDMRs were all species-specific. Most ageDMRs were in genomic regions with medium methylation levels and large methylation variation. Orthologous regions in species not showing this age effect were either hypermethylated (>80%) or hypomethylated (<20%). In humans and mice, ageDMRs lost methylation, whereas bovine ageDMRs gained methylation with age. Our results are in line with the hypothesis that sperm ageDMRs are in regions under epigenomic evolution and may be part of an epigenetic mechanism(s) for lineage-specific environmental adaptations and provide a solid basis for studies on downstream effects in the genes analyzed here. KW - age-related differentially methylated regions (ageDMRs) KW - bisulfite pyrosequencing KW - mammalian male germline KW - paternal age effect KW - species-specific epigenetic marks KW - sperm DNA methylation Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-262301 SN - 2073-4409 VL - 11 IS - 4 ER - TY - THES A1 - Zaum, Ann-Kathrin T1 - Erweiterte Diagnostik bei neuromuskulären Erkrankungen: vom Genpanel zum Whole Genome Sequencing T1 - Extended diagnostics in neuromuscular disease: from gene panel to whole genome sequencing N2 - Muskeln und Nerven bilden eine essentielle funktionelle Einheit für den Bewegungsapparat. Neuromuskuläre Erkrankungen lassen sich unterteilen in Krankheiten, denen ein muskuläres Problem zu Grunde liegt, wie zum Beispiel Muskeldystrophien (Muskeldystrophie Duchenne, DMD) und Myopathien (Myofibrilläre Myopathie, MFM), und in Erkrankungen aufgrund von Nervenschädigungen, wie zum Beispiel Neuropathien und spastische Paraplegien (SPG). In den vier Teilen der vorliegenden Arbeit konnte sowohl das genetische wie auch das phänotypische Spektrum von neuromuskulären Krankheiten erweitert werden. Die dafür verwendeten Methoden reichen von der Sanger-Sequenzierung einzelner Gene über Next-Generation Sequencing (NGS)-Panel-Diagnostik, zu Whole Exome Sequencing (WES) und schließlich zu Whole Genome Sequencing (WGS). Zusätzlich wurde cDNA zur Detektion von Veränderungen im Transkriptom sequenziert. Im ersten Teil wurde der klinische Phänotyp der Seipinopathien erweitert, der jetzt auch amyotrophe Lateralsklerose (ALS) und multifokale motorische Neuropathie (MMN) beinhaltet. Dafür wurde eine Panel-Analyse durchgeführt, die eine bekannte Mutation in BSCL2 aufdeckte. Aufgrund des hiermit erweiterten Phänotyps der Seipinopathien sollten Mutationen in BSCL2 auch bei anderen Verdachtsdiagnosen, wie ALS oder MMN, berücksichtigt werden. Außerdem wurde gezeigt, dass in der Diagnostik SPGs und Charcot-Marie-Tooth Erkrankungen (CMTs) eine Überlappung zeigen und bei der Diagnose von Verdachtsfällen Gene aus beiden Krankheitsbereichen berücksichtigt werden sollten. Die Suche mit Hilfe eines Phänotyp-Filters hat sich dabei als erfolgreich erwiesen. Ungelöste Fälle sollten aber in regelmäßigen Abständen neu analysiert werden, da immer neue Gene mit den Phänotypen assoziiert werden. Der zweite Teil befasst sich mit der Untersuchung von DMD-Patienten mit bisher ungeklärtem Genotyp. Durch eine RNA-Analyse des gesamten DMD-Transkripts wurden tief-intronische Mutationen aufgedeckt, die Einfluss auf das Spleißen haben. Durch diese Mutationen wurden intronische Sequenzen als Pseudoexons in die mRNA eingefügt. Diese Mutationsart scheint häufig unter ungeklärten DMD-Fällen zu sein, in unserer Kohorte von 5 DMD-Patienten wurden in zwei Fällen Pseudoexons entdeckt. Eine Besonderheit besteht darin, dass in der RNA-Analyse immer noch ein Rest Wildtyp-Transkript vorhanden war, wodurch die Patienten vermutlich einen milderen Becker-Phänotyp aufweisen. Ein weiterer ungeklärter DMD-Fall konnte durch die Sequenzierung der gesamten genomischen Sequenz aufgeklärt werden. Es wurde eine perizentrische Inversion entdeckt (46,Y,inv(X)(p21.1q13.3). Dies zeigt, dass WGS auch zur Detektion von großen Strukturvariationen geeignet ist. Im dritten Teil wurden Spleißmutationen untersucht. Spleißmutationen wurden bisher nicht in TMEM5-assoziierter alpha-Dystroglykanopathie beschrieben und somit als neue Mutationsart für diese Erkrankung nachgewiesen. Dabei wurde auch die funktionelle Exostosin-Domäne in TMEM5 bestätigt. Eine RNA-Untersuchung verschiedener Spleißmutationen zeigte, dass Spleißmutationen häufig zu einem veränderten Transkript führen, auch wenn diese Mutationen weiter von der Konsensussequenz entfernt sind. Spleißmutation sollten daher häufiger in der Diagnostik berücksichtig und überprüft werden. Im letzten Teil wurde eine strukturierte Diagnostik von MFM-Patienten beschrieben und neue Kandidaten-Gene für MFM vorgestellt. Es ist zu vermuten, dass auch Mutationen in Genen, die bisher für Kardiomyopathien, Kollagen Typ VI-Myopathien und Neuropathien beschrieben sind, einen MFM-Phänotyp verursachen können. Diese Ergebnisse erweitern das genetische Spektrum der MFM, was sich auf die Diagnostik dieser Erkrankungen auswirken sollte. Im Laufe dieser Arbeit konnten damit die neuromuskulären Erkrankungen vieler Patienten genetisch geklärt werden. Neue Phänotypen und genetische Ursachen wurden beschrieben und es wurde gezeigt, dass sich WGS technisch für die Diagnostik, auch zur Detektion von großen Strukturvarianten, eignet. N2 - Muscles and nerves form an essential functional unit for the locomotor system. Neuromuscular disorders are divided in diseases that have a muscular origin, such as muscular dystrophies (Duchenne muscular dystrophy, DMD) and myopathies (myofibrillar myopathies, MFM) and diseases based on neuron denervation, for instance neuropathies and spastic paraplegias (SPG). The four parts of the present work expand the genetic and phenotypic spectrum of neuromuscular disorders. The used methods range from Sanger sequencing of single genes to panel next-generation sequencing (NGS) diagnostics, whole exome sequencing (WES) and finally to whole genome sequencing (WGS). Additionally, cDNA was sequenced to detect transcriptome changes. In the first part, the clinical phenotype of seipinopathies has been expanded to include amyotrophic lateral sclerosis (ALS) and multifocal motor neuropathy (MMN). An NGS panel was sequenced in three patients suffering from ALS, MMN and neuropathy. A known mutation in BSCL2 was detected which expands the phenotype of seipinopathies. Therefore, mutations in BSCL2 should be considered in patients with diagnosis such as ALS and MMN. Moreover, it was demonstrated that SPGs and Charcot-Marie-Tooth disease (CMT) show a genetic overlap and genes of both diseases should be considered in genetic analysis. The use of a phenotype filter for variant analysis was successful. However, unsolved cases should be re-analysed in intervals, as new genes are frequently connected to phenotypes. The second part concerns DMD patients with unresolved genotype. RNA-analysis of the whole DMD transcripts revealed deep-intronic variants that influence splicing and insert intronic sequences as pseudoexons in the mRNA. This kind of mutation appears to be common, as two of our five analysed patients had pseudoexons. What is particular about these cases is the fact that a rest of wild type DMD transcript remained, which possibly contributes to a milder Becker phenotype in the patients. In another unsolved DMD case WGS was performed and a pericentric inversion including DMD was discovered (46,Y,inv(X)(p21.1q13.3), which demonstrates that WGS is capable of detecting large structural anomalies. In the third part splice mutations were analysed. Splice mutations were unknown for TMEM5-related alpha-dystroglycanopathy and are now a new kind of mutation in this disease. At the same time the functional exostosin domain in TMEM5 was confirmed. RNA analysis of further splice mutations showed a frequent influence on splicing even if the mutation was far from the canonical splice site. Therefore, splice mutations should be verified and considered in diagnostics more often. The last part describes a structured approach when diagnosing MFM patients and introduces new candidate genes for MFM. It appears that mutations in genes formerly associated with cardiomyopathies, collagen type VI-related myopathies and neuropathies can cause an MFM phenotype. These results expand the genetic spectrum of MFM which should be considered in diagnostics. In the course of this dissertation the neuromuscular diseases of many patients could be solved genetically. New phenotypes and genotypes were described and it was proven that WGS is technically suitable for genetic diagnostic, even for the detection of large structural variants. KW - Neuromuskuläre Krankheit KW - Mensch KW - Next-Generation Sequencing KW - Neuromuskuläre Erkrankungen KW - Molekulargenetik KW - Humangenetik KW - Human genetics Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-176314 ER - TY - JOUR A1 - Liedtke, Daniel A1 - Hofmann, Christine A1 - Jakob, Franz A1 - Klopocki, Eva A1 - Graser, Stephanie T1 - Tissue-Nonspecific Alkaline Phosphatase—A Gatekeeper of Physiological Conditions in Health and a Modulator of Biological Environments in Disease JF - Biomolecules N2 - Tissue-nonspecific alkaline phosphatase (TNAP) is a ubiquitously expressed enzyme that is best known for its role during mineralization processes in bones and skeleton. The enzyme metabolizes phosphate compounds like inorganic pyrophosphate and pyridoxal-5′-phosphate to provide, among others, inorganic phosphate for the mineralization and transportable vitamin B6 molecules. Patients with inherited loss of function mutations in the ALPL gene and consequently altered TNAP activity are suffering from the rare metabolic disease hypophosphatasia (HPP). This systemic disease is mainly characterized by impaired bone and dental mineralization but may also be accompanied by neurological symptoms, like anxiety disorders, seizures, and depression. HPP characteristically affects all ages and shows a wide range of clinical symptoms and disease severity, which results in the classification into different clinical subtypes. This review describes the molecular function of TNAP during the mineralization of bones and teeth, further discusses the current knowledge on the enzyme’s role in the nervous system and in sensory perception. An additional focus is set on the molecular role of TNAP in health and on functional observations reported in common laboratory vertebrate disease models, like rodents and zebrafish. KW - TNAP KW - hypophosphatasia KW - HPP KW - zebrafish KW - mineralization KW - ALPL KW - craniosynostosis KW - teeth KW - nervous system Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-220096 SN - 2218-273X VL - 10 IS - 12 PB - MDPI ER - TY - JOUR A1 - Hofrichter, Michaela A. H. A1 - Mojarad, Majid A1 - Doll, Julia A1 - Grimm, Clemens A1 - Eslahi, Atiye A1 - Hosseini, Neda Sadat A1 - Rajati, Mohsen A1 - Müller, Tobias A1 - Dittrich, Marcus A1 - Maroofian, Reza A1 - Haaf, Thomas A1 - Vona, Barbara T1 - The conserved p.Arg108 residue in S1PR2 (DFNB68) is fundamental for proper hearing: evidence from a consanguineous Iranian family JF - BMC Medical Genetics N2 - Background: Genetic heterogeneity and consanguineous marriages make recessive inherited hearing loss in Iran the second most common genetic disorder. Only two reported pathogenic variants (c.323G>C, p.Arg108Pro and c.419A>G, p.Tyr140Cys) in the S1PR2 gene have previously been linked to autosomal recessive hearing loss (DFNB68) in two Pakistani families. We describe a segregating novel homozygous c.323G>A, p.Arg108Gln pathogenic variant in S1PR2 that was identified in four affected individuals from a consanguineous five generation Iranian family. Methods: Whole exome sequencing and bioinformatics analysis of 116 hearing loss-associated genes was performed in an affected individual from a five generation Iranian family. Segregation analysis and 3D protein modeling of the p.Arg108 exchange was performed. Results: The two Pakistani families previously identified with S1PR2 pathogenic variants presented profound hearing loss that is also observed in the affected Iranian individuals described in the current study. Interestingly, we confirmed mixed hearing loss in one affected individual. 3D protein modeling suggests that the p.Arg108 position plays a key role in ligand receptor interaction, which is disturbed by the p.Arg108Gln change. Conclusion: In summary, we report the third overall mutation in S1PR2 and the first report outside the Pakistani population. Furthermore, we describe a novel variant that causes an amino acid exchange (p.Arg108Gln) in the same amino acid residue as one of the previously reported Pakistani families (p.Arg108Pro). This finding emphasizes the importance of the p.Arg108 amino acid in normal hearing and confirms and consolidates the role of S1PR2 in autosomal recessive hearing loss. KW - 3D modeling KW - autosomal recessive non-synstromic hearing loss KW - DFNB68 KW - mixed hearing loss KW - whole exome sequencing KW - S1PR2 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-175755 VL - 19 IS - 81 ER - TY - JOUR A1 - Fiedler, David A1 - Hirsch, Daniela A1 - El Hajj, Nady A1 - Yang, Howard H. A1 - Hu, Yue A1 - Sticht, Carsten A1 - Nanda, Indrajit A1 - Belle, Sebastian A1 - Rueschoff, Josef A1 - Lee, Maxwell P. A1 - Ried, Thomas A1 - Haaf, Thomas A1 - Gaiser, Timo T1 - Genome‐wide DNA methylation analysis of colorectal adenomas with and without recurrence reveals an association between cytosine‐phosphate‐guanine methylation and histological subtypes JF - Genes, Chromosomes and Cancer N2 - Aberrant methylation of DNA is supposed to be a major and early driver of colonic adenoma development, which may result in colorectal cancer (CRC). Although gene methylation assays are used already for CRC screening, differential epigenetic alterations of recurring and nonrecurring colorectal adenomas have yet not been systematically investigated. Here, we collected a sample set of formalin‐fixed paraffin‐embedded colorectal low‐grade adenomas (n = 72) consisting of primary adenomas without and with recurrence (n = 59), recurrent adenomas (n = 10), and normal mucosa specimens (n = 3). We aimed to unveil differentially methylated CpG positions (DMPs) across the methylome comparing not only primary adenomas without recurrence vs primary adenomas with recurrence but also primary adenomas vs recurrent adenomas using the Illumina Human Methylation 450K BeadChip array. Unsupervised hierarchical clustering exhibited a significant association of methylation patterns with histological adenoma subtypes. No significant DMPs were identified comparing primary adenomas with and without recurrence. Despite that, a total of 5094 DMPs (false discovery rate <0.05; fold change >10%) were identified in the comparisons of recurrent adenomas vs primary adenomas with recurrence (674; 98% hypermethylated), recurrent adenomas vs primary adenomas with and without recurrence (241; 99% hypermethylated) and colorectal adenomas vs normal mucosa (4179; 46% hypermethylated). DMPs in cytosine‐phosphate‐guanine (CpG) islands were frequently hypermethylated, whereas open sea‐ and shelf‐regions exhibited hypomethylation. Gene ontology analysis revealed enrichment of genes associated with the immune system, inflammatory processes, and cancer pathways. In conclusion, our methylation data could assist in establishing a more robust and reproducible histological adenoma classification, which is a prerequisite for improving surveillance guidelines. KW - adenoma KW - DNA methylation KW - epigenetics KW - histological subtype KW - recurrence Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-212676 VL - 58 IS - 11 SP - 783 EP - 797 ER - TY - JOUR A1 - Kolokotronis, Konstantinos A1 - Pluta, Natalie A1 - Klopocki, Eva A1 - Kunstmann, Erdmute A1 - Messroghli, Daniel A1 - Maack, Christoph A1 - Tejman-Yarden, Shai A1 - Arad, Michael A1 - Rost, Simone A1 - Gerull, Brenda T1 - New Insights on Genetic Diagnostics in Cardiomyopathy and Arrhythmia Patients Gained by Stepwise Exome Data Analysis JF - Journal of Clinical Medicine N2 - Inherited cardiomyopathies are characterized by clinical and genetic heterogeneity that challenge genetic diagnostics. In this study, we examined the diagnostic benefit of exome data compared to targeted gene panel analyses, and we propose new candidate genes. We performed exome sequencing in a cohort of 61 consecutive patients with a diagnosis of cardiomyopathy or primary arrhythmia, and we analyzed the data following a stepwise approach. Overall, in 64% of patients, a variant of interest (VOI) was detected. The detection rate in the main sub-cohort consisting of patients with dilated cardiomyopathy (DCM) was much higher than previously reported (25/36; 69%). The majority of VOIs were found in disease-specific panels, while a further analysis of an extended panel and exome data led to an additional diagnostic yield of 13% and 5%, respectively. Exome data analysis also detected variants in candidate genes whose functional profile suggested a probable pathogenetic role, the strongest candidate being a truncating variant in STK38. In conclusion, although the diagnostic yield of gene panels is acceptable for routine diagnostics, the genetic heterogeneity of cardiomyopathies and the presence of still-unknown causes favor exome sequencing, which enables the detection of interesting phenotype–genotype correlations, as well as the identification of novel candidate genes. KW - cardiomyopathy KW - cardiogenetics KW - whole exome sequencing KW - targeted gene panel KW - candidate genes Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-236094 VL - 9 IS - 7 ER - TY - JOUR A1 - Wagenhäuser, Laura A1 - Rickert, Vanessa A1 - Sommer, Claudia A1 - Wanner, Christoph A1 - Nordbeck, Peter A1 - Rost, Simone A1 - Üçeyler, Nurcan T1 - X-chromosomal inactivation patterns in women with Fabry disease JF - Molecular Genetics & Genomic Medicine N2 - Background Although Fabry disease (FD) is an X-linked lysosomal storage disorder caused by mutations in the α-galactosidase A gene (GLA), women may develop severe symptoms. We investigated X-chromosomal inactivation patterns (XCI) as a potential determinant of symptom severity in FD women. Patients and Methods We included 95 women with mutations in GLA (n = 18 with variants of unknown pathogenicity) and 50 related men, and collected mouth epithelial cells, venous blood, and skin fibroblasts for XCI analysis using the methylation status of the androgen receptor gene. The mutated X-chromosome was identified by comparison of samples from relatives. Patients underwent genotype categorization and deep clinical phenotyping of symptom severity. Results 43/95 (45%) women carried mutations categorized as classic. The XCI pattern was skewed (i.e., ≥75:25% distribution) in 6/87 (7%) mouth epithelial cell samples, 31/88 (35%) blood samples, and 9/27 (33%) skin fibroblast samples. Clinical phenotype, α-galactosidase A (GAL) activity, and lyso-Gb3 levels did not show intergroup differences when stratified for X-chromosomal skewing and activity status of the mutated X-chromosome. Conclusions X-inactivation patterns alone do not reliably reflect the clinical phenotype of women with FD when investigated in biomaterial not directly affected by FD. However, while XCI patterns may vary between tissues, blood frequently shows skewing of XCI patterns. KW - Fabry disease KW - Fabry genotype KW - Fabry phenotype KW - female Fabry patients KW - X-chromosomal inactivation Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-312795 VL - 10 IS - 9 ER - TY - JOUR A1 - Lekszas, Caroline A1 - Nanda, Indrajit A1 - Vona, Barbara A1 - Böck, Julia A1 - Ashrafzadeh, Farah A1 - Donyadideh, Nahid A1 - Ebrahimzadeh, Farnoosh A1 - Ahangari, Najmeh A1 - Maroofian, Reza A1 - Karimiani, Ehsan Ghayoor A1 - Haaf, Thomas T1 - Unbalanced segregation of a paternal t(9;11)(p24.3;p15.4) translocation causing familial Beckwith-Wiedemann syndrome: a case report JF - BMC Medical Genomics N2 - Background The vast majority of cases with Beckwith-Wiedemann syndrome (BWS) are caused by a molecular defect in the imprinted chromosome region 11p15.5. The underlying mechanisms include epimutations, uniparental disomy, copy number variations, and structural rearrangements. In addition, maternal loss-of-function mutations in CDKN1C are found. Despite growing knowledge on BWS pathogenesis, up to 20% of patients with BWS phenotype remain without molecular diagnosis. Case presentation Herein, we report an Iranian family with two females affected with BWS in different generations. Bisulfite pyrosequencing revealed hypermethylation of the H19/IGF2: intergenic differentially methylated region (IG DMR), also known as imprinting center 1 (IC1) and hypomethylation of the KCNQ1OT1: transcriptional start site (TSS) DMR (IC2). Array CGH demonstrated an 8 Mb duplication on chromosome 11p15.5p15.4 (205,827-8,150,933) and a 1 Mb deletion on chromosome 9p24.3 (209,020-1,288,114). Chromosome painting revealed that this duplication-deficiency in both patients is due to unbalanced segregation of a paternal reciprocal t(9;11)(p24.3;p15.4) translocation. Conclusions This is the first report of a paternally inherited unbalanced translocation between the chromosome 9 and 11 short arms underlying familial BWS. Copy number variations involving the 11p15.5 region are detected by the consensus diagnostic algorithm. However, in complex cases which do not only affect the BWS region itself, characterization of submicroscopic chromosome rearrangements can assist to estimate the recurrence risk and possible phenotypic outcomes. KW - Familial Beckwith-Wiedemann syndrome KW - copy number variation KW - duplication-deficiency KW - genomic imprinting KW - submicroscopic chromosome rearrangement KW - reciprocal translocation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-200422 VL - 12 ER - TY - JOUR A1 - Appel, Mirjam A1 - Scholz, Claus-Jürgen A1 - Müller, Tobias A1 - Dittrich, Marcus A1 - König, Christian A1 - Bockstaller, Marie A1 - Oguz, Tuba A1 - Khalili, Afshin A1 - Antwi-Adjei, Emmanuel A1 - Schauer, Tamas A1 - Margulies, Carla A1 - Tanimoto, Hiromu A1 - Yarali, Ayse T1 - Genome-Wide Association Analyses Point to Candidate Genes for Electric Shock Avoidance in Drosophila melanogaster JF - PLoS ONE N2 - Electric shock is a common stimulus for nociception-research and the most widely used reinforcement in aversive associative learning experiments. Yet, nothing is known about the mechanisms it recruits at the periphery. To help fill this gap, we undertook a genome-wide association analysis using 38 inbred Drosophila melanogaster strains, which avoided shock to varying extents. We identified 514 genes whose expression levels and/or sequences covaried with shock avoidance scores. We independently scrutinized 14 of these genes using mutants, validating the effect of 7 of them on shock avoidance. This emphasizes the value of our candidate gene list as a guide for follow-up research. In addition, by integrating our association results with external protein-protein interaction data we obtained a shock avoidance- associated network of 38 genes. Both this network and the original candidate list contained a substantial number of genes that affect mechanosensory bristles, which are hairlike organs distributed across the fly's body. These results may point to a potential role for mechanosensory bristles in shock sensation. Thus, we not only provide a first list of candidate genes for shock avoidance, but also point to an interesting new hypothesis on nociceptive mechanisms. KW - functional analysis KW - disruption project KW - natural variation KW - complex traits KW - networks KW - behavior KW - flies KW - temperature KW - genetics KW - painful Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-152006 VL - 10 IS - 5 ER - TY - JOUR A1 - Vona, Barbara A1 - Mazaheri, Neda A1 - Lin, Sheng-Jia A1 - Dunbar, Lucy A. A1 - Maroofian, Reza A1 - Azaiez, Hela A1 - Booth, Kevin T. A1 - Vitry, Sandrine A1 - Rad, Aboulfazl A1 - Rüschendorf, Franz A1 - Varshney, Pratishtha A1 - Fowler, Ben A1 - Beetz, Christian A1 - Alagramam, Kumar N. A1 - Murphy, David A1 - Shariati, Gholamreza A1 - Sedaghat, Alireza A1 - Houlden, Henry A1 - Petree, Cassidy A1 - VijayKumar, Shruthi A1 - Smith, Richard J. H. A1 - Haaf, Thomas A1 - El-Amraoui, Aziz A1 - Bowl, Michael R. A1 - Varshney, Gaurav K. A1 - Galehdari, Hamid T1 - A biallelic variant in CLRN2 causes non-syndromic hearing loss in humans JF - Human Genetics N2 - Deafness, the most frequent sensory deficit in humans, is extremely heterogeneous with hundreds of genes involved. Clinical and genetic analyses of an extended consanguineous family with pre-lingual, moderate-to-profound autosomal recessive sensorineural hearing loss, allowed us to identify CLRN2, encoding a tetraspan protein, as a new deafness gene. Homozygosity mapping followed by exome sequencing identified a 14.96 Mb locus on chromosome 4p15.32p15.1 containing a likely pathogenic missense variant in CLRN2 (c.494C > A, NM_001079827.2) segregating with the disease. Using in vitro RNA splicing analysis, we show that the CLRN2 c.494C > A variant leads to two events: (1) the substitution of a highly conserved threonine (uncharged amino acid) to lysine (charged amino acid) at position 165, p.(Thr165Lys), and (2) aberrant splicing, with the retention of intron 2 resulting in a stop codon after 26 additional amino acids, p.(Gly146Lysfs*26). Expression studies and phenotyping of newly produced zebrafish and mouse models deficient for clarin 2 further confirm that clarin 2, expressed in the inner ear hair cells, is essential for normal organization and maintenance of the auditory hair bundles, and for hearing function. Together, our findings identify CLRN2 as a new deafness gene, which will impact future diagnosis and treatment for deaf patients. KW - deafness KW - CLRN2 KW - gene Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-267740 SN - 1432-1203 VL - 140 IS - 6 ER - TY - JOUR A1 - Jansch, Charline A1 - Günther, Katharina A1 - Waider, Jonas A1 - Ziegler, Georg C. A1 - Forero, Andrea A1 - Kollert, Sina A1 - Svirin, Evgeniy A1 - Pühringer, Dirk A1 - Kwok, Chee Keong A1 - Ullmann, Reinhard A1 - Maierhofer, Anna A1 - Flunkert, Julia A1 - Haaf, Thomas A1 - Edenhofer, Frank A1 - Lesch, Klaus-Peter T1 - Generation of a human induced pluripotent stem cell (iPSC) line from a 51-year-old female with attention-deficit/hyperactivity disorder (ADHD) carrying a duplication of SLC2A3 JF - Stem Cell Research N2 - 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. KW - ADHD KW - SLC2A3 KW - induced pluripotent stem cells Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-176654 VL - 28 ER - TY - JOUR A1 - Mahyera, Alexis S. A1 - Schneider, Tamara A1 - Halliger-Keller, Birgit A1 - Schrooten, Katja A1 - Hörner, Eva-Maria A1 - Rost, Simone A1 - Kress, Wolfram T1 - Distribution and Structure of DM2 Repeat Tract Alleles in the German Population JF - Frontiers in Neurology N2 - Autosomal dominant inherited Myotonic dystrophy type 1 and 2 (DM1 and DM2) are the most frequent muscle dystrophies in the European population and are caused by repeat expansion mutations. For Germany cumulative empiric evidence suggests an estimated prevalence of DM2 of roughly 9 in 100,000, therefore being as prevalent as DM1. In DM2, a (CCTG)n repeat tract located in the first intron of the CNBP gene is expanded. The CCTG repeat tract is part of a complex repeat structure comprising not only CCTG tetraplets but also repeated TG dinucleotides and TCTG tetraplet elements as well as NCTG interruptions. Here, we provide the distribution of normal sized alleles in the German population, which was found to be highly similar to the Slovak population. Sequencing of 34 unexpanded healthy range alleles in DM2 positive patients (heterozygous for a full expansion) revealed that the CCTG repeat tract is usually interrupted by at least three tetraplets which according to current opinion is supposed to render it stable against expansion. Interestingly, only the largest analyzed normal allele had 23 uninterrupted CCTGs and consequently could represent an instable early premutation allele. In our diagnostic history of DM2 cases, a total of 18 premutations were detected in 16 independent cases. Here, we describe two premutation families, one with an expansion from a premutation allele and the other with a contraction of a full expansion down to a premutation allele. Our diagnostic results support the general assumption that the premutation range of unstable CCTG stretches lies obviously between 25 and 75 CCTGs. However, the clinical significance of premutation alleles is still unclear. In the light of the two described families we suggest incomplete penetrance. Thus, as it was proposed for other repeat expansion diseases (e.g., Huntington's disease), a fluid transition of penetrance is more likely rather than a clear cut CCTG number threshold. KW - DM2 KW - intergenerational contraction KW - expansion KW - premutation KW - penetrance KW - prevalence Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-196252 SN - 1664-2295 VL - 9 IS - 463 ER - TY - JOUR A1 - Haertle, Larissa A1 - El Hajj, Nady A1 - Dittrich, Marcus A1 - Müller, Tobias A1 - Nanda, Indrajit A1 - Lehnen, Harald A1 - Haaf, Thomas T1 - Epigenetic signatures of gestational diabetes mellitus on cord blood methylation JF - Clinical Epigenetics N2 - Background: Intrauterine exposure to gestational diabetes mellitus (GDM) confers a lifelong increased risk for metabolic and other complex disorders to the offspring. GDM-induced epigenetic modifications modulating gene regulation and persisting into later life are generally assumed to mediate these elevated disease susceptibilities. To identify candidate genes for fetal programming, we compared genome-wide methylation patterns of fetal cord bloods (FCBs) from GDM and control pregnancies. Methods and results: Using Illumina’s 450K methylation arrays and following correction for multiple testing, 65 CpG sites (52 associated with genes) displayed significant methylation differences between GDM and control samples. Four candidate genes, ATP5A1, MFAP4, PRKCH, and SLC17A4, from our methylation screen and one, HIF3A, from the literature were validated by bisulfite pyrosequencing. The effects remained significant after adjustment for the confounding factors maternal BMI, gestational week, and fetal sex in a multivariate regression model. In general, GDM effects on FCB methylation were more pronounced in women with insulin-dependent GDM who had a more severe metabolic phenotype than women with dietetically treated GDM. Conclusions: Our study supports an association between maternal GDM and the epigenetic status of the exposed offspring. Consistent with a multifactorial disease model, the observed FCB methylation changes are of small effect size but affect multiple genes/loci. The identified genes are primary candidates for transmitting GDM effects to the next generation. They also may provide useful biomarkers for the diagnosis, prognosis, and treatment of adverse prenatal exposures. KW - fetal programming KW - insulin treatment KW - DNA methylation KW - fetal cord blood KW - gestational diabetes mellitus Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-159459 VL - 9 IS - 28 ER - TY - JOUR A1 - Blümel, Rabea A1 - Zink, Miriam A1 - Klopocki, Eva A1 - Liedtke, Daniel T1 - On the traces of tcf12: Investigation of the gene expression pattern during development and cranial suture patterning in zebrafish (Danio rerio) JF - PLoS ONE N2 - The transcription factor 12 (tcf12) is a basic Helix-Loop-Helix protein (bHLH) of the E-protein family, proven to play an important role in developmental processes like neurogenesis, mesoderm formation, and cranial vault development. In humans, mutations in TCF12 lead to craniosynostosis, a congenital birth disorder characterized by the premature fusion of one or several of the cranial sutures. Current research has been primarily focused on functional studies of TCF12, hence the cellular expression profile of this gene during embryonic development and early stages of ossification remains poorly understood. Here we present the establishment and detailed analysis of two transgenic tcf12:EGFP fluorescent zebrafish (Danio rerio) reporter lines. Using these transgenic lines, we analyzed the general spatiotemporal expression pattern of tcf12 during different developmental stages and put emphasis on skeletal development and cranial suture patterning. We identified robust tcf12 promoter-driven EGFP expression in the central nervous system (CNS), the heart, the pronephros, and the somites of zebrafish embryos. Additionally, expression was observed inside the muscles and bones of the viscerocranium in juvenile and adult fish. During cranial vault development, the transgenic fish show a high amount of tcf12 expressing cells at the growth fronts of the ossifying frontal and parietal bones and inside the emerging cranial sutures. Subsequently, we tested the transcriptional activity of three evolutionary conserved non-coding elements (CNEs) located in the tcf12 locus by transient transgenic assays and compared their in vivo activity to the expression pattern determined in the transgenic tcf12:EGFP lines. We could validate two of them as tcf12 enhancer elements driving specific gene expression in the CNS during embryogenesis. Our newly established transgenic lines enhance the understanding of tcf12 gene regulation and open up the possibilities for further functional investigation of these novel tcf12 enhancer elements in zebrafish. KW - Zebrafish KW - Neurons KW - Skull KW - Enhancer elements KW - Hindbrain KW - Cranial sutures KW - Embryos KW - Somites Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-201428 VL - 14 IS - 6 ER - TY - JOUR A1 - Liedtke, Daniel A1 - Orth, Melanie A1 - Meissler, Michelle A1 - Geuer, Sinje A1 - Knaup, Sabine A1 - Köblitz, Isabell A1 - Klopocki, Eva T1 - ECM alterations in fndc3a (fibronectin domain containing protein 3A) deficient zebrafish cause temporal fin development and regeneration defects JF - Scientific Reports N2 - Fin development and regeneration are complex biological processes that are highly relevant in teleost fish. They share genetic factors, signaling pathways and cellular properties to coordinate formation of regularly shaped extremities. Especially correct tissue structure defined by extracellular matrix (ECM) formation is essential. Gene expression and protein localization studies demonstrated expression of fndc3a (fibronectin domain containing protein 3a) in both developing and regenerating caudal fins of zebrafish (Danio rerio). We established a hypomorphic fndc3a mutant line (fndc3a\(^{wue1/wue1}\)) via CRISPR/Cas9, exhibiting phenotypic malformations and changed gene expression patterns during early stages of median fin fold development. These developmental effects are mostly temporary, but result in a fraction of adults with permanent tail fin deformations. In addition, caudal fin regeneration in adult fndc3a\(^{wue1/wue1}\) mutants is hampered by interference with actinotrichia formation and epidermal cell organization. Investigation of the ECM implies that loss of epidermal tissue structure is a common cause for both of the observed defects. Our results thereby provide a molecular link between these developmental processes and foreshadow Fndc3a as a novel temporal regulator of epidermal cell properties during extremity development and regeneration in zebrafish. KW - Extracellular matrix KW - Limb development KW - Self-renewal Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-202141 VL - 9 ER - TY - JOUR A1 - Manukjan, Georgi A1 - Wiegering, Verena A1 - Reindl, Tobias A1 - Strauß, Gabriele A1 - Klopocki, Eva A1 - Schulze, Harald A1 - Andres, Oliver T1 - Novel variants in FERMT3 and RASGRP2 - Genetic linkage in Glanzmann-like bleeding disorders JF - Pediatric Blood & Cancer N2 - Defects of platelet intracellular signaling can result in severe platelet dysfunction. Several mutations in each of the linked genes FERMT3 and RASGRP2 on chromosome 11 causing a Glanzmann‐like bleeding phenotype have been identified so far. We report on novel variants in two unrelated pediatric patients with severe bleeding diathesis—one with leukocyte adhesion deficiency type III due to a homozygous frameshift in FERMT3 and the other with homozygous variants in both, FERMT3 and RASGRP2 . We focus on the challenging genetic and functional variant assessment and aim to accentuate the risk of obtaining misleading results due to the phenomenon of genetic linkage. KW - bleding disorders other than hemophilia KW - hematology KW - hemostasis and thrombosis KW - platelet disorders Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-208129 VL - 67 IS - 2 ER - TY - JOUR A1 - Hauer, Nadine N. A1 - Popp, Bernt A1 - Taher, Leila A1 - Vogl, Carina A1 - Dhandapany, Perundurai S. A1 - Büttner, Christian A1 - Uebe, Steffen A1 - Sticht, Heinrich A1 - Ferrazzi, Fulvia A1 - Ekici, Arif B. A1 - De Luca, Alessandro A1 - Klinger, Patrizia A1 - Kraus, Cornelia A1 - Zweier, Christiane A1 - Wiesener, Antje A1 - Abou Jamra, Rami A1 - Kunstmann, Erdmute A1 - Rauch, Anita A1 - Wieczorek, Dagmar A1 - Jung, Anna-Marie A1 - Rohrer, Tilman R. A1 - Zenker, Martin A1 - Doerr, Helmuth-Guenther A1 - Reis, André A1 - Thiel, Christian T. T1 - Evolutionary conserved networks of human height identify multiple Mendelian causes of short stature JF - European Journal of Human Genetics N2 - Height is a heritable and highly heterogeneous trait. Short stature affects 3% of the population and in most cases is genetic in origin. After excluding known causes, 67% of affected individuals remain without diagnosis. To identify novel candidate genes for short stature, we performed exome sequencing in 254 unrelated families with short stature of unknown cause and identified variants in 63 candidate genes in 92 (36%) independent families. Based on systematic characterization of variants and functional analysis including expression in chondrocytes, we classified 13 genes as strong candidates. Whereas variants in at least two families were detected for all 13 candidates, two genes had variants in 6 (UBR4) and 8 (LAMA5) families, respectively. To facilitate their characterization, we established a clustered network of 1025 known growth and short stature genes, which yielded 29 significantly enriched clusters, including skeletal system development, appendage development, metabolic processes, and ciliopathy. Eleven of the candidate genes mapped to 21 of these clusters, including CPZ, EDEM3, FBRS, IFT81, KCND1, PLXNA3, RASA3, SLC7A8, UBR4, USP45, and ZFHX3. Fifty additional growth-related candidates we identified await confirmation in other affected families. Our study identifies Mendelian forms of growth retardation as an important component of idiopathic short stature. KW - disease genetics KW - DNA sequencing KW - genetic counselling Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-227899 VL - 27 ER - TY - JOUR A1 - Ghosh, Sujal A1 - Hönscheid, Andrea A1 - Dückers, Gregor A1 - Ginzel, Sebastian A1 - Gohlke, Holger A1 - Gombert, Michael A1 - Kempkes, Bettina A1 - Klapper, Wolfram A1 - Kuhlen, Michaela A1 - Laws, Hans-Jürgen A1 - Linka, René Martin A1 - Meisel, Roland A1 - Mielke, Christian A1 - Niehues, Tim A1 - Schindler, Detlev A1 - Schneider, Dominik A1 - Schuster, Friedhelm R. A1 - Speckmann, Carsten A1 - Borkhardt, Arndt T1 - Human RAD52 - a novel player in DNA repair in cancer and immunodeficiency JF - Haematologica N2 - No abstract available. KW - human medicine KW - DNA-Repair KW - cancer KW - immunodeficiency KW - RAD52 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-180862 VL - 102 IS - 2 ER - TY - JOUR A1 - Hernández, Gonzalo A1 - José Ramírez, María A1 - Minguillón, Jordi A1 - Quiles, Paco A1 - Ruiz de Garibay, Gorka A1 - Aza-Carmona, Miriam A1 - Bogliolo, Massimo A1 - Pujol, Roser A1 - Prados-Carvajal, Rosario A1 - Fernández, Juana A1 - García, Nadia A1 - López, Adrià A1 - Gutiérrez-Enríquez, Sara A1 - Diez, Orland A1 - Benítez, Javier A1 - Salinas, Mónica A1 - Teulé, Alex A1 - Brunet, Joan A1 - Radice, Paolo A1 - Peterlongo, Paolo A1 - Schindler, Detlev A1 - Huertas, Pablo A1 - Puente, Xose S. A1 - Lázaro, Conxi A1 - Àngel Pujana, Miquel A1 - Surrallés, Jordi T1 - Decapping protein EDC4 regulates DNA repair and phenocopies BRCA1 JF - Nature Communications N2 - BRCA1 is a tumor suppressor that regulates DNA repair by homologous recombination. Germline mutations in BRCA1 are associated with increased risk of breast and ovarian cancer and BRCA1 deficient tumors are exquisitely sensitive to poly (ADP-ribose) polymerase (PARP) inhibitors. Therefore, uncovering additional components of this DNA repair pathway is of extreme importance for further understanding cancer development and therapeutic vulnerabilities. Here, we identify EDC4, a known component of processing-bodies and regulator of mRNA decapping, as a member of the BRCA1-BRIP1-TOPBP1 complex. EDC4 plays a key role in homologous recombination by stimulating end resection at double-strand breaks. EDC4 deficiency leads to genome instability and hypersensitivity to DNA interstrand cross-linking drugs and PARP inhibitors. Lack-of-function mutations in EDC4 were detected in BRCA1/2-mutation-negative breast cancer cases, suggesting a role in breast cancer susceptibility. Collectively, this study recognizes EDC4 with a dual role in decapping and DNA repair whose inactivation phenocopies BRCA1 deficiency. KW - cancer KW - double-strand DNA breaks KW - genomic instability KW - RNA metabolism Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-319929 VL - 9 ER - TY - JOUR A1 - Hauer, Nadine N. A1 - Popp, Bernt A1 - Schoeller, Eva A1 - Schuhmann, Sarah A1 - Heath, Karen E. A1 - Hisado-Oliva, Alfonso A1 - Klinger, Patricia A1 - Kraus, Cornelia A1 - Trautmann, Udo A1 - Zenker, Martin A1 - Zweier, Christiane A1 - Wiesener, Antje A1 - Jamra, Rami Abou A1 - Kunstmann, Erdmute A1 - Wieczorek, Dagmar A1 - Uebe, Steffen A1 - Ferrazzi, Fulvia A1 - Büttner, Christian A1 - Ekici, Arif B. A1 - Rauch, Anita A1 - Sticht, Heinrich A1 - Dörr, Helmuth-Günther A1 - Reis, André A1 - Thiel, Christian T. T1 - Clinical relevance of systematic phenotyping and exome sequencing in patients with short stature JF - Genetics in Medicine N2 - Purpose Short stature is a common condition of great concern to patients and their families. Mostly genetic in origin, the underlying cause often remains elusive due to clinical and genetic heterogeneity. Methods We systematically phenotyped 565 patients where common nongenetic causes of short stature were excluded, selected 200 representative patients for whole-exome sequencing, and analyzed the identified variants for pathogenicity and the affected genes regarding their functional relevance for growth. Results By standard targeted diagnostic and phenotype assessment, we identified a known disease cause in only 13.6% of the 565 patients. Whole-exome sequencing in 200 patients identified additional mutations in known short-stature genes in 16.5% of these patients who manifested only part of the symptomatology. In 15.5% of the 200 patients our findings were of significant clinical relevance. Heterozygous carriers of recessive skeletal dysplasia alleles represented 3.5% of the cases. Conclusion A combined approach of systematic phenotyping, targeted genetic testing, and whole-exome sequencing allows the identification of the underlying cause of short stature in at least 33% of cases, enabling physicians to improve diagnosis, treatment, and genetic counseling. Exome sequencing significantly increases the diagnostic yield and consequently care in patients with short stature. KW - growth KW - phenotypic spectrum KW - short stature KW - skeletal dysplasia KW - whole-exome sequencing Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-227888 VL - 20 ER -