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1. Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4

Author

Grosche, S, Marenholz, I, Esparza-Gordillo, J, Arnau-Soler, A, Pairo-Castineira, E, Rueschendorf, F, Ahluwalia, TS, Almqvist, C, Arnold, A, Baurecht, H, Bisgaard, H, Bonnelykke, K, Brown, SJ, Bustamante, M, Curtin, JA, Custovic, A, Dharmage, SC, Esplugues, A, Falchi, M, Fernandez-Orth, D, Ferreira, MAR, Franke, A, Gerdes, S, Gieger, C, Hakonarson, H, Holt, PG, Homuth, G, Hubner, N, Hysi, PG, Jarvelin, M-R, Karlsson, R, Koppelman, GH, Lau, S, Lutz, M, Magnusson, PKE, Marks, GB, Mueller-Nurasyid, M, Noethen, MM, Paternoster, L, Pennell, CE, Peters, A, Rawlik, K, Robertson, CF, Rodriguez, E, Sebert, S, Simpson, A, Sleiman, PMA, Standl, M, Stoelzl, D, Strauch, K, Szwajda, A, Tenesa, A, Thompson, PJ, Ullemar, V, Visconti, A, Vonk, JM, Wang, CA, Weidinger, S, Wielscher, M, Worth, CL, Xu, C-J, Lee, Y-A, Grosche, S, Marenholz, I, Esparza-Gordillo, J, Arnau-Soler, A, Pairo-Castineira, E, Rueschendorf, F, Ahluwalia, TS, Almqvist, C, Arnold, A, Baurecht, H, Bisgaard, H, Bonnelykke, K, Brown, SJ, Bustamante, M, Curtin, JA, Custovic, A, Dharmage, SC, Esplugues, A, Falchi, M, Fernandez-Orth, D, Ferreira, MAR, Franke, A, Gerdes, S, Gieger, C, Hakonarson, H, Holt, PG, Homuth, G, Hubner, N, Hysi, PG, Jarvelin, M-R, Karlsson, R, Koppelman, GH, Lau, S, Lutz, M, Magnusson, PKE, Marks, GB, Mueller-Nurasyid, M, Noethen, MM, Paternoster, L, Pennell, CE, Peters, A, Rawlik, K, Robertson, CF, Rodriguez, E, Sebert, S, Simpson, A, Sleiman, PMA, Standl, M, Stoelzl, D, Strauch, K, Szwajda, A, Tenesa, A, Thompson, PJ, Ullemar, V, Visconti, A, Vonk, JM, Wang, CA, Weidinger, S, Wielscher, M, Worth, CL, Xu, C-J, and Lee, Y-A

Abstract

Previous genome-wide association studies revealed multiple common variants involved in eczema but the role of rare variants remains to be elucidated. Here, we investigate the role of rare variants in eczema susceptibility. We meta-analyze 21 study populations including 20,016 eczema cases and 380,433 controls. Rare variants are imputed with high accuracy using large population-based reference panels. We identify rare exonic variants in DUSP1, NOTCH4, and SLC9A4 to be associated with eczema. In DUSP1 and NOTCH4 missense variants are predicted to impact conserved functional domains. In addition, five novel common variants at SATB1-AS1/KCNH8, TRIB1/LINC00861, ZBTB1, TBX21/OSBPL7, and CSF2RB are discovered. While genes prioritized based on rare variants are significantly up-regulated in the skin, common variants point to immune cell function. Over 20% of the single nucleotide variant-based heritability is attributable to rare and low-frequency variants. The identified rare/low-frequency variants located in functional protein domains point to promising targets for novel therapeutic approaches to eczema.

Published
2021

2. Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4

Author

Grosche, S. (Sarah), Marenholz, I. (Ingo), Esparza-Gordillo, J. (Jorge), Arnau-Soler, A. (Aleix), Pairo-Castineira, E. (Erola), Rueschendorf, F. (Franz), Ahluwalia, T. S. (Tarunveer S.), Almqvist, C. (Catarina), Arnold, A. (Andreas), Baurecht, H. (Hansjoerg), Bisgaard, H. (Hans), Bonnelykke, K. (Klaus), Brown, S. J. (Sara J.), Bustamante, M. (Mariona), Curtin, J. A. (John A.), Custovic, A. (Adnan), Dharmage, S. C. (Shyamali C.), Esplugues, A. (Ana), Falchi, M. (Mario), Fernandez-Orth, D. (Dietmar), Ferreira, M. A. (Manuel A. R.), Franke, A. (Andre), Gerdes, S. (Sascha), Gieger, C. (Christian), Hakonarson, H. (Hakon), Holt, P. G. (Patrick G.), Homuth, G. (Georg), Hubner, N. (Norbert), Hysi, P. G. (Pirro G.), Järvelin, M.-R. (Marjo-Riitta), Karlsson, R. (Robert), Koppelman, G. H. (Gerard H.), Lau, S. (Susanne), Lutz, M. (Manuel), Magnusson, P. K. (Patrik K. E.), Marks, G. B. (Guy B.), Mueller-Nurasyid, M. (Martina), Noethen, M. M. (Markus M.), Paternoster, L. (Lavinia), Pennell, C. E. (Craig E.), Peters, A. (Annette), Rawlik, K. (Konrad), Robertson, C. F. (Colin F.), Rodriguez, E. (Elke), Sebert, S. (Sylvain), Simpson, A. (Angela), Sleiman, P. M. (Patrick M. A.), Standl, M. (Marie), Stoelzl, D. (Dora), Strauch, K. (Konstantin), Szwajda, A. (Agnieszka), Tenesa, A. (Albert), Thompson, P. J. (Philip J.), Ullemar, V. (Vilhelmina), Visconti, A. (Alessia), Vonk, J. M. (Judith M.), Wang, C. A. (Carol A.), Weidinger, S. (Stephan), Wielscher, M. (Matthias), Worth, C. L. (Catherine L.), Xu, C.-J. (Chen-Jian), Lee, Y.-A. (Young-Ae), Grosche, S. (Sarah), Marenholz, I. (Ingo), Esparza-Gordillo, J. (Jorge), Arnau-Soler, A. (Aleix), Pairo-Castineira, E. (Erola), Rueschendorf, F. (Franz), Ahluwalia, T. S. (Tarunveer S.), Almqvist, C. (Catarina), Arnold, A. (Andreas), Baurecht, H. (Hansjoerg), Bisgaard, H. (Hans), Bonnelykke, K. (Klaus), Brown, S. J. (Sara J.), Bustamante, M. (Mariona), Curtin, J. A. (John A.), Custovic, A. (Adnan), Dharmage, S. C. (Shyamali C.), Esplugues, A. (Ana), Falchi, M. (Mario), Fernandez-Orth, D. (Dietmar), Ferreira, M. A. (Manuel A. R.), Franke, A. (Andre), Gerdes, S. (Sascha), Gieger, C. (Christian), Hakonarson, H. (Hakon), Holt, P. G. (Patrick G.), Homuth, G. (Georg), Hubner, N. (Norbert), Hysi, P. G. (Pirro G.), Järvelin, M.-R. (Marjo-Riitta), Karlsson, R. (Robert), Koppelman, G. H. (Gerard H.), Lau, S. (Susanne), Lutz, M. (Manuel), Magnusson, P. K. (Patrik K. E.), Marks, G. B. (Guy B.), Mueller-Nurasyid, M. (Martina), Noethen, M. M. (Markus M.), Paternoster, L. (Lavinia), Pennell, C. E. (Craig E.), Peters, A. (Annette), Rawlik, K. (Konrad), Robertson, C. F. (Colin F.), Rodriguez, E. (Elke), Sebert, S. (Sylvain), Simpson, A. (Angela), Sleiman, P. M. (Patrick M. A.), Standl, M. (Marie), Stoelzl, D. (Dora), Strauch, K. (Konstantin), Szwajda, A. (Agnieszka), Tenesa, A. (Albert), Thompson, P. J. (Philip J.), Ullemar, V. (Vilhelmina), Visconti, A. (Alessia), Vonk, J. M. (Judith M.), Wang, C. A. (Carol A.), Weidinger, S. (Stephan), Wielscher, M. (Matthias), Worth, C. L. (Catherine L.), Xu, C.-J. (Chen-Jian), and Lee, Y.-A. (Young-Ae)

Abstract

Previous genome-wide association studies revealed multiple common variants involved in eczema but the role of rare variants remains to be elucidated. Here, we investigate the role of rare variants in eczema susceptibility. We meta-analyze 21 study populations including 20,016 eczema cases and 380,433 controls. Rare variants are imputed with high accuracy using large population-based reference panels. We identify rare exonic variants in DUSP1, NOTCH4, and SLC9A4 to be associated with eczema. In DUSP1 and NOTCH4 missense variants are predicted to impact conserved functional domains. In addition, five novel common variants at SATB1-AS1/KCNH8, TRIB1/LINC00861, ZBTB1, TBX21/OSBPL7, and CSF2RB are discovered. While genes prioritized based on rare variants are significantly up-regulated in the skin, common variants point to immune cell function. Over 20% of the single nucleotide variant-based heritability is attributable to rare and low-frequency variants. The identified rare/low-frequency variants located in functional protein domains point to promising targets for novel therapeutic approaches to eczema.

Published
2021

3. Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4

Author

Grosche, S. (Sarah), Marenholz, I. (Ingo), Esparza-Gordillo, J. (Jorge), Arnau-Soler, A. (Aleix), Pairo-Castineira, E. (Erola), Rueschendorf, F. (Franz), Ahluwalia, T. S. (Tarunveer S.), Almqvist, C. (Catarina), Arnold, A. (Andreas), Baurecht, H. (Hansjoerg), Bisgaard, H. (Hans), Bonnelykke, K. (Klaus), Brown, S. J. (Sara J.), Bustamante, M. (Mariona), Curtin, J. A. (John A.), Custovic, A. (Adnan), Dharmage, S. C. (Shyamali C.), Esplugues, A. (Ana), Falchi, M. (Mario), Fernandez-Orth, D. (Dietmar), Ferreira, M. A. (Manuel A. R.), Franke, A. (Andre), Gerdes, S. (Sascha), Gieger, C. (Christian), Hakonarson, H. (Hakon), Holt, P. G. (Patrick G.), Homuth, G. (Georg), Hubner, N. (Norbert), Hysi, P. G. (Pirro G.), Järvelin, M.-R. (Marjo-Riitta), Karlsson, R. (Robert), Koppelman, G. H. (Gerard H.), Lau, S. (Susanne), Lutz, M. (Manuel), Magnusson, P. K. (Patrik K. E.), Marks, G. B. (Guy B.), Mueller-Nurasyid, M. (Martina), Noethen, M. M. (Markus M.), Paternoster, L. (Lavinia), Pennell, C. E. (Craig E.), Peters, A. (Annette), Rawlik, K. (Konrad), Robertson, C. F. (Colin F.), Rodriguez, E. (Elke), Sebert, S. (Sylvain), Simpson, A. (Angela), Sleiman, P. M. (Patrick M. A.), Standl, M. (Marie), Stoelzl, D. (Dora), Strauch, K. (Konstantin), Szwajda, A. (Agnieszka), Tenesa, A. (Albert), Thompson, P. J. (Philip J.), Ullemar, V. (Vilhelmina), Visconti, A. (Alessia), Vonk, J. M. (Judith M.), Wang, C. A. (Carol A.), Weidinger, S. (Stephan), Wielscher, M. (Matthias), Worth, C. L. (Catherine L.), Xu, C.-J. (Chen-Jian), Lee, Y.-A. (Young-Ae), and Groningen Research Institute for Asthma and COPD (GRIAC)

Subjects
Sodium-Hydrogen Exchangers, Genotype, Eczema, Gene Expression, Genetic predisposition to disease, Dual Specificity Phosphatase 1, Rare variants, Matrix Attachment Region Binding Proteins, Polymorphism, Single Nucleotide, Genome-wide association studies, Article, Cytokine Receptor Common beta Subunit, Skin diseases, Rare Diseases, Cardiovascular and Metabolic Diseases, Humans, Receptor, Notch4, Genome-Wide Association Study, Atopic dermatitis
Abstract

Previous genome-wide association studies revealed multiple common variants involved in eczema but the role of rare variants remains to be elucidated. Here, we investigate the role of rare variants in eczema susceptibility. We meta-analyze 21 study populations including 20,016 eczema cases and 380,433 controls. Rare variants are imputed with high accuracy using large population-based reference panels. We identify rare exonic variants in DUSP1, NOTCH4, and SLC9A4 to be associated with eczema. In DUSP1 and NOTCH4 missense variants are predicted to impact conserved functional domains. In addition, five novel common variants at SATB1-AS1/KCNH8, TRIB1/LINC00861, ZBTB1, TBX21/OSBPL7, and CSF2RB are discovered. While genes prioritized based on rare variants are significantly up-regulated in the skin, common variants point to immune cell function. Over 20% of the single nucleotide variant-based heritability is attributable to rare and low-frequency variants. The identified rare/low-frequency variants located in functional protein domains point to promising targets for novel therapeutic approaches to eczema., Genetic studies of eczema to date have mostly explored common genetic variation. Here, the authors perform a large meta-analysis for common and rare variants and discover 8 loci associated with eczema. Over 20% of the heritability of the condition is attributable to rare variants.

Published
2020

4. International interdependence between cash crop and staple food futures price indices: A wavelet-BEKK-GARCH assessment

Author

Heckelei, T., Amrouk, E.M., and Grosche, S.

Subjects
Demand and Price Analysis
Abstract

This study examines the price level and volatility interaction between international staple food and cash crop futures price indices. Understanding the relationship between these commodities bears significant implication for net food importing developing countries that depend on cash crop to finance food import bills. We use a wavelet analysis to decompose and denoise the price indices and then apply a BEKK-MGARCH approach to analyze the relationship across time-frequency domains. Results indicate the level of correlation and volatility linkages are strongest at lower frequencies (i.e. longer run), with markets adjusting quickly to volatility shocks after a high initial impact. Acknowledgement

Published
2018
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5. Financial and Commodity-specific expectations in soybean futures markets

Author

Cao, A.N.Q. and Grosche, S.-C.

Subjects
Marketing, FOS: Economics and business
Abstract

We conceptualize the futures price of an agricultural commodity as an aggregate expectation for the spot price of a commodity. The market agents have divergent opinions about the price development and the price drivers, which initiates trading. In informationally efficient markets, the price will thus reflect expectations about its influencing variables. Using historical decompositions from an SVARX model, we analyze the contribution of financial and commodity- specific expectation shocks to changes in a trading-volume weighted price index for corn and soybean futures on the Chicago Board of Trade (CBOT) over the time period 2005- 2016. Financial expectations are instrumented with the DJ REIT Index, commodity demand expectations with the CNY/USD exchange rate and supply expectations with changes in the vapor pressure deficit. Results show that the price index was affected by cumulative shocks in the REIT index during the time of the food price crisis, but these shocks are only of small magnitude. Weather fluctuations have a minimal impact on the week-to-week fluctuation of the commodity price index. Acknowledgement

Published
2018
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6. Genome-wide association study identifies the SERPINB gene cluster as a susceptibility locus for food allergy

Author

Marenholz, I., Grosche, S., Kalb, B., Rüschendorf, F., Blümchen, K., Schlags, R., Harandi, N., Price, M., Hansen, G., Seidenberg, J., Röblitz, H., Yürek, S., Tschirner, S., Hong, X., Wang, X., Homuth, G., Schmidt, C.O., Nöthen, M.M., Hübner, N., Niggemann, B., Beyer, K., and Lee, Y.A.

Subjects
Cardiovascular and Metabolic Diseases
Abstract

Genetic factors and mechanisms underlying food allergy are largely unknown. Due to heterogeneity of symptoms a reliable diagnosis is often difficult to make. Here, we report a genome-wide association study on food allergy diagnosed by oral food challenge in 497 cases and 2387 controls. We identify five loci at genome-wide significance, the clade B serpin (SERPINB) gene cluster at 18q21.3, the cytokine gene cluster at 5q31.1, the filaggrin gene, the C11orf30/LRRC32 locus, and the human leukocyte antigen (HLA) region. Stratifying the results for the causative food demonstrates that association of the HLA locus is peanut allergy-specific whereas the other four loci increase the risk for any food allergy. Variants in the SERPINB gene cluster are associated with SERPINB10 expression in leukocytes. Moreover, SERPINB genes are highly expressed in the esophagus. All identified loci are involved in immunological regulation or epithelial barrier function, emphasizing the role of both mechanisms in food allergy.

Published
2017

7. Abstracts from the Food Allergy and Anaphylaxis Meeting 2016

Author

Pouessel, G, Claverie, C, Labreuche, J, Renaudin, J-M, Dorkenoo, A, Eb, M, Moneret-Vautrin, A, Deschildre, A, Leteurtre, S, Grabenhenrich, L, Worm, M, Dölle, S, Scherer, K, Hutteger, I, Christensen, M, Bindslev-Jensen, C, Mortz, C, Eller, E, Kjaer, HF, Carneiro-Leão, L, Badas, J, Coimbra, A, Levy, DP, Ben-Shoshan, M, Rimon, A, Benor, S, Arends, NJT, Edelbroek, N, de Groot, H, Emons, JAM, Brand, HKA, Verhoeven, D, van Veen, LN, de Jong, NW, Noh, G, Jang, EH, Pascal, M, Dominguez, O, Piquer, M, Alvaro, M, Jimenez-Feijoo, R, Lozano, J, Machinena, A, del Mar Folqué, M, Giner, MT, Plaza, AM, Turner, P, Patel, N, Vazquez-Ortiz, M, Lindsley, S, Walker, L, Rosenberg, S, Mari, A, Alessandri, C, Giangrieco, I, Tuppo, L, Rafaiani, C, Mitterer, G, Ciancamerla, M, Ferrara, R, Bernardi, ML, Zennaro, D, Tamburrini, M, Ciardiello, MA, Harwanegg, C, Fernandez, A, Selb, R, Egenmann, P, Epstein, M, Hoffmann-Sommergruber, K, Koning, F, Lovik, M, Clare Mills, EN, Moreno, J, van Loveren, H, Wal, J-M, Diesner, S, Bergmayr, C, Pfitzner, B, Assmann, VE, Starkl, P, Endesfelder, D, Eiwegger, T, Szepfalusi, Z, Fehrenbach, H, Jensen-Jarolim, E, Hartmann, A, Pali-Schöll, I, Untersmayr, E, Wille, S, Meyer, P, Klingebiel, C, Lidholm, J, Ehrenberg, A, Östling, J, Cleach, I, Mège, J-L, Vitte, J, Aina, R, Dubiela, P, Pfeifer, S, Bublin, M, Radauer, C, Humeniuk, P, Kabasser, S, Asero, R, Bogas, G, Gomez, F, Campo, P, Salas, M, Doña, I, Barrionuevo, E, Guerrero, MA, Mayorga, C, Prieto, A, Barber, D, Torres, MJ, Jamin, A, Wangorsch, A, Ballmer, B, Vieths, S, Scheurer, S, Apostolovic, D, Mihailovic, J, Krstic, M, Starkhammar, M, Velickovic, TC, Hamsten, C, van Hage, M, van Erp, FC, Knol, EF, Kansen, HM, Pontoppidan, B, Meijer, Y, van der Ent, CK, Knulst, AC, Sayers, R, Brown, H, Custovic, A, Simpson, A, Mills, C, Schulz, J, Akkerdaas, J, Totis, M, Capt, A, Herouet-Guicheney, C, van Ree, R, Banerjee, T, Banerjee, A, Claude, M, Bouchaud, G, Lupi, R, Castan, L, Tranquet, O, Denery-Papini, S, Bodinier, M, Brossard, C, De Poi, R, Gritti, E, De Dominicis, E, Popping, B, de Laureto, PP, Palosuo, K, Kukkonen, AK, Pelkonen, A, Mäkelä, M, Lee, NA, Rost, J, Muralidharan, S, Campbell, D, Mehr, S, Nock, C, Baumert, J, Taylor, S, Mastrorilli, C, Tripodi, S, Caffarelli, C, Perna, S, Di Rienzo Businco, A, Sfika, I, Dondi, A, Bianchi, A, Dascola, CP, Ricci, G, Cipriani, F, Maiello, N, del Giudice, MM, Frediani, T, Frediani, S, Macrì, F, Pistoletti, C, Iacono, ID, Patria, MF, Varin, E, Peroni, D, Comberiati, P, Chini, L, Moschese, V, Lucarelli, S, Bernardini, R, Pingitore, G, Pelosi, U, Olcese, R, Moretti, M, Cirisano, A, Faggian, D, Travaglini, A, Plebani, M, Verga, MC, Calvani, M, Giordani, P, Matricardi, PM, Ontiveros, N, Cabrera-Chavez, F, Galand, J, Beaudouin, E, Pineau, F, Sakai, S, Matsunaga, K, Teshima, R, Larré, C, Denery, S, Tschirner, S, Trendelenburg, V, Schulz, G, Niggemann, B, Beyer, K, Bouferkas, Y, Belabbas, Y, Saidi, D, Kheroua, O, Mecherfi, KEE, Guendouz, M, Haddi, A, Kaddouri, H, Amaral, L, Pereira, A, Rodrigues, S, Datema, M, Jongejan, L, Clausen, M, Knulst, A, Papadopoulos, N, Kowalski, M, de Blay, F, Zwinderman, A, Hoffman-Sommergruber, K, Ballmer-Weber, B, Fernandez-Rivas, M, Deng, S, Yin, J, Eisenmann, C, Nassiri, M, Reinert, R, van der Valk, JPM, van Wijk, RG, Vergouwe, Y, Steyerberg, EW, Reitsma, M, Wichers, HJ, Savelkoul, HFJ, Vlieg-Boerstra, B, Dubois, AEJ, Carolino, F, Rodolfo, A, Cernadas, J, Roa-Medellín, D, Rodriguez-Fernandez, A, Navarro, J, Albendiz, V, Baeza, ML, Intente-Herrero, S, Mikkelsen, A, Mehlig, K, Lissner, L, Verrill, L, Luccioli, S, van Bilsen, J, Kuper, F, Wolterbeek, A, Rankouhi, TR, Verschuren, L, Cnossen, H, Jeurink, P, Garssen, J, Knippels, L, Garthoff, J, Houben, G, Leeman, W, Eleonore Pettersson, M, Schins, AMM, Koppelman, GH, Kollen, BJ, Zubchenko, S, Kuntz, S, Mérida, P, Álvaro, M, Riggioni, C, Castellanos, JH, Jimenez, R, Cap, M, Drumez, E, Lejeune, S, Thumerelle, C, Mordacq, C, Nève, V, Ricò, S, Varini, M, Nocerino, R, Cosenza, L, Amoroso, A, Di Costanzo, M, Di Scala, C, Bedogni, G, Canani, RB, Turner, PJ, Poza-Guedes, P, González-Pérez, R, Sánchez-Machín, I, Matheu-Delgado, V, Wambre, E, Ballegaard, A-S, Madsen, C, Gregersen, J, Bøgh, KL, Aubert, P, Neunlist, M, Magnan, A, Lozano-Ojalvo, D, Pablos-Tanarro, A, Pérez-Rodríguez, L, Molina, E, López-Fandiño, R, Rekima, A, Macchiaverni, P, Turfkruyer, M, Holvoet, S, Dupuis, L, Baiz, N, Annesi-Maesano, I, Mercenier, A, Nutten, S, Verhasselt, V, Mrakovcic-Sutic, I, Banac, S, Sutic, I, Baricev-Novakovic, Z, Pavisic, V, Muñoz-Cano, R, Jiménez-Rodríguez, T, Corbacho, D, Roca-Ferrer, J, Bartra, J, Bulog, A, Micovic, V, Markiewicz, L, Szymkiewicz, A, Szyc, A, Wróblewska, B, Harvey, BM, Harthoorn, LF, Wesley Burks, A, Rentzos, G, Björk, A-LB, Bengtsson, U, Barber, C, Kalicinsky, C, Breynaert, C, Coorevits, L, Jansen, C, Van Hoeyveld, E, Verbeke, K, Kochuyt, A-M, Schrijvers, R, Deleanu, D, Muntean, A, Konstantakopoulou, M, Pasioti, M, Papadopoulou, A, Iliopoulou, A, Mikos, N, Kompoti, E, de Castro, ED, Bartalomé, B, Ue, KL, Griffiths, E, Till, S, Grimshaw, K, Roberts, G, Selby, A, Butiene, I, Larco, JI, Dubakiene, R, Fiandor, A, Fiocchi, A, Sigurdardottir, S, Sprikkelman, A, Schoemaker, A-F, Xepapadaki, P, Keil, T, Cojocariu, Z, Barbado, BS, Iancu, V, Arroabarren, E, Esarte, MG, Arteaga, M, Andrade, MC, Borges, D, Kalil, J, Bianchi, PG, Agondi, RC, Gupta, RK, Sharma, A, Gupta, K, Das, M, Dwivedi, P, Karseladze, R, Jorjoliani, L, Saginadze, L, Tskhakaia, M, Basello, K, Piuri, G, Speciani, AF, Speciani, MC, Camerotto, C, Zinno, F, Pakholchuk, O, Nedelska, S, Pattini, S, Costantino, MT, Peveri, S, Villalta, D, Savi, E, Costanzi, A, Revyakina, VA, Kiseleva, MA, Kuvshinova, ED, Larkova, IA, Shekhetov, AA, Silva, D, Moreira, A, Plácido, J, van der Kleij, H, van Twuijver, E, Sutorius, R, de Kam, P-J, van Odijk, J, Lindqvist, H, Lustig, E, Jácome, AAA, Aguilar, KLB, Domínguez, MG, Hernández, DAM, Caruso, C, Casale, C, Rapaccini, GL, Romano, A, De Vitis, I, Cocco, RR, Aranda, C, Mallozi, MC, Motta, JF, Moraes, L, Pastorino, A, Rosario, N, Goudouris, E, Porto, A, Wandalsen, NF, Sarinho, E, Sano, F, Solé, D, Pitsios, C, Petrodimopoulou, M, Papadopoulou, E, Passioti, M, Kontogianni, M, Adamia, N, Khaleva, E, del Prado, AP, Du Toit, G, Krzych, E, Samolinska-Zawisza, U, Furmanczyk, K, Tomaszewska, A, Raciborski, F, Lipiec, A, Samel-Kowalik, P, Walkiewicz, A, Borowicz, J, Samolinski, B, Nano, AL, Recto, M, Somoza, ML, López, NB, Alzate, DP, Ruano, FJ, Garcimartín, MI, Haroun, E, de la Torre, MV, Rojas, A, Onieva, ML, Canto, G, Rodrigues, A, Forno, A, Cabral, AJ, Gonçalves, R, Vorozhko, I, Sentsova, T, Chernyak, O, Denisova, S, Ilènko, L, Muhortnich, V, Zimmermann, C, Rohrbach, A, Bakhsh, FR, Boudewijn, K, Oomkes-Pilon, A-M, Van Ginkle, D, Šilar, M, Jeverica, A, Vesel, T, Avčin, T, Korošec, P, van der Valk, J, Berends, I, Arends, N, van Maaren, M, Wichers, H, Emons, J, Dubois, A, de Jong, N, Matsyura, O, Besh, L, Huang, C-H, Jan, T-R, 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Cooke, R, Yrjänä, J, Hanni, A-M, Vähäsarja, P, Mustonen, O, Dunder, T, Kulmala, P, Lasa, E, D’Amelio, C, Martínez, S, Joral, A, Gastaminza, G, Goikoetxea, MJ, Candy, DCA, Van Ampting, MTJ, Oude Nijhuis, MM, Butt, AM, Peroni, DG, Fox, AT, Knol, J, Michaelis, LJ, Padua, I, Padrao, P, Moreira, P, Barros, R, Sharif, H, Ahmed, M, Gomaa, N, Mens, J, Smit, K, Timmermans, F, Poredoš, T, Jeverica, AK, Sedmak, M, Benedik, E, Accetto, M, Zupančič, M, Yonamine, G, Soldateli, G, Aquilante, B, Pastorino, AC, de Moraes Beck, CL, Gushken, AK, de Barros Dorna, M, dos Santos, CN, Castro, APM, Al-Qahtani, A, Arnaout, R, Khaliq, AR, Amin, R, Sheikh, F, Alvarez, J, Anda, M, Palacios, M, De Prada, M, Ponce, C, Balbino, B, Sibilano, R, Marichal, T, Gaudenzio, N, Karasuyama, H, Bruhns, P, Tsai, M, Reber, LL, Galli, SJ, Ferreira, AR, Cernadas, JR, del Campo García, A, Fernández, SP, Carrera, NS, Sánchez-Cruz, FB, Lorenzo, JRF, Claus, S, Pföhler, C, Ruëff, F, Treudler, R, Jaume, ME, Madroñero, A, Perez, MTG, Julia, JC, Plovdiv, CH, Gethings, L, Langridge, J, Adel-Patient, K, Bernard, H, Barcievic-Jones, I, Sokolova, R, Yankova, R, Ivanovska, M, Murdjeva, M, Popova, T, Dermendzhiev, S, Karjalainen, M, Lehnigk, U, Brown, D, Locklear, JC, Locklear, J, Maris, I, Hourihane, J, Ornelas, C, Caiado, J, Ferreira, MB, Pereira-Barbosa, M, Puente, Y, Daza, JC, Monteseirin, FJ, Ukleja-Sokolowska, N, Gawronska-Ukleja, E, Zbikowska-Gotz, M, Bartuzi, Z, Sokolowski, L, Adams, A, Mahon, B, English, K, Gourdon-Dubois, N, Sellam, L, Pereira, B, Michaud, E, Messaoudi, K, Evrard, B, Fauquert, J-L, Palomares, F, Gomez, G, Rodriguez, MJ, Galindo, L, Molina, A, Paparo, L, Mennini, M, Aitoro, R, Wawrzeńczyk, A, Przybyszewski, M, Sarıcoban, HE, Ugras, M, Yalvac, Z, Flokstra-de Blok, BMJ, van der Velde, JL, Vereda, A, Ippolito, C, Traversa, A, Adriano, D, Bianchi, DM, Gallina, S, Decastelli, L, Makatsori, M, Miles, A, Devetak, SP, Devetak, I, Tabet, SA, Trandbohus, JF, Winther, P, Malling, H-J, Hansen, KS, Garvey, LH, Wang, C-C, Cheng, Y-H, Tung, C-W, Dietrich, M, Marenholz, I, Kalb, B, Grosche, S, Blümchen, K, Schlags, R, Price, M, Rietz, S, Esparza-Gordillo, J, Lau, S, Lee, Y-A, Almontasheri, A, Bahkali, MA, Elshorbagi, S, Alfhaid, A, Altamimi, M, Madbouly, E, Al-Dhekri, H, Arnaout, RK, Basagaña, M, Miquel, S, Bartolomé, B, Brix, B, Rohwer, S, Brandhoff, S, Berger, A, Suer, W, Weimann, A, Bueno, C, Martín-Pedraza, L, Abián, S, Segundo-Acosta, PS, López-Rodríguez, JC, Barderas, R, Batanero, E, Cuesta-Herranz, J, Villalba, MT, Correia, M, Benito-Garcia, F, Arêde, C, Piedade, S, Morais-Almeida, M, Hindley, J, Yarham, R, Kuklinska-Pijanka, A, Gillick, D, Patient, K, Chapman, MD, Miranda, A, Matos, E, Sokolova, A, Rao, H, Baricevic-Jones, I, Smith, F, Xue, W, Magnusdottir, H, Vidarsdottir, AG, Lund, S, Jensen, AB, Ludviksson, BR, Simon, R, Elfont, R, Bennett, S, Voyksner, R, de Lurdes Torre, M, Yürek, S, Faber, MA, Bastiaensen, A, Mangodt, E, van Gasse, A, Decuyper, I, Sabato, V, Hagendorens, MM, Bridts, CH, De Clerck, LS, Ebo, D, Schwarz, S, Ziegert, M, Albroscheit, S, Schwager, C, Kull, S, Behrends, J, Röckendorf, N, Schocker, F, Frey, A, Homann, A, Becker, W-M, Jappe, U, Zaabat, N, Osscini, S, Agabriel, C, Sterling, B, Carsin, A, Liabeuf, V, Maćków, M, Zbróg, A, Bronkowska, M, Courtois, J, Gadisseur, R, Bertholet, C, Lukas, P, Cavalier, E, Delahaut, P, Quinting, B, Gertmo, MB, Hasseus, ET, Barzylovych, V, Oliveira, J, Ensina, LF, Aranda, CS, Dopazo, L, Lopez, R, Perez, R, Santos-Diez, L, Bilbao, A, Garcia, JM, Núñez, IG, Mármol, MÁA, Villarejo, MJB, Martos, JAB, Vergara, MS, García, JMI, Michalska, A, Sergiejko, G, Zacniewski, R, Ghiordanescu, I-M, Deaconu, C, Popescu, M, Bumbacea, RS, Ibranji, A, Nikolla, E, Loloci, G, Juel-Berg, N, Larsen, LF, Poulsen, LK, Marcelino, J, Prata, R, Costa, AC, Duarte, F, Neto, M, Santos, J, Pestana, LC, Sampaio, D, Minale, P, Dignetti, P, Bignardi, D, Nedelea, I, Popescu, F-D, Vieru, M, Secureanu, F-A, Ganea, CS, Vieira, M, Silva, JPM, Watts, T, Watts, S, Lomikovska, M, Peredelskaya, M, Nenasheva, N, Filipovic, I, Zivkovic, Z, Filipovic, D, Higgs, J, Warner, A, and Jones, C

Published
2017

8. Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology

Author

Ferreira, MA, Vonk, JM, Baurecht, H, Marenholz, I, Tian, C, Hoffman, JD, Helmer, Q, Tillander, A, Ullemar, V, van Dongen, J, Lu, Y, Rueschendorf, F, Esparza-Gordillo, J, Medway, CW, Mountjoy, E, Burrows, K, Hummel, O, Grosche, S, Brumpton, BM, Witte, JS, Hottenga, J-J, Willemsen, G, Zheng, J, Rodriguez, E, Hotze, M, Franke, A, Revez, JA, Beesley, J, Matheson, MC, Dharmage, SC, Bain, LM, Fritsche, LG, Gabrielsen, ME, Balliu, B, Nielsen, JB, Zhou, W, Hveem, K, Langhammer, A, Holmen, OL, Loset, M, Abecasis, GR, Willer, CJ, Arnold, A, Homuth, G, Schmidt, CO, Thompson, PJ, Martin, NG, Duffy, DL, Novak, N, Schulz, H, Karrasch, S, Gieger, C, Strauch, K, Melles, RB, Hinds, DA, Huebner, N, Weidinger, S, Magnusson, PKE, Jansen, R, Jorgenson, E, Lee, Y-A, Boomsma, DI, Almqvist, C, Karlsson, R, Koppelman, GH, Paternoster, L, Ferreira, MA, Vonk, JM, Baurecht, H, Marenholz, I, Tian, C, Hoffman, JD, Helmer, Q, Tillander, A, Ullemar, V, van Dongen, J, Lu, Y, Rueschendorf, F, Esparza-Gordillo, J, Medway, CW, Mountjoy, E, Burrows, K, Hummel, O, Grosche, S, Brumpton, BM, Witte, JS, Hottenga, J-J, Willemsen, G, Zheng, J, Rodriguez, E, Hotze, M, Franke, A, Revez, JA, Beesley, J, Matheson, MC, Dharmage, SC, Bain, LM, Fritsche, LG, Gabrielsen, ME, Balliu, B, Nielsen, JB, Zhou, W, Hveem, K, Langhammer, A, Holmen, OL, Loset, M, Abecasis, GR, Willer, CJ, Arnold, A, Homuth, G, Schmidt, CO, Thompson, PJ, Martin, NG, Duffy, DL, Novak, N, Schulz, H, Karrasch, S, Gieger, C, Strauch, K, Melles, RB, Hinds, DA, Huebner, N, Weidinger, S, Magnusson, PKE, Jansen, R, Jorgenson, E, Lee, Y-A, Boomsma, DI, Almqvist, C, Karlsson, R, Koppelman, GH, and Paternoster, L

Abstract

Asthma, hay fever (or allergic rhinitis) and eczema (or atopic dermatitis) often coexist in the same individuals, partly because of a shared genetic origin. To identify shared risk variants, we performed a genome-wide association study (GWAS; n = 360,838) of a broad allergic disease phenotype that considers the presence of any one of these three diseases. We identified 136 independent risk variants (P < 3 × 10-8), including 73 not previously reported, which implicate 132 nearby genes in allergic disease pathophysiology. Disease-specific effects were detected for only six variants, confirming that most represent shared risk factors. Tissue-specific heritability and biological process enrichment analyses suggest that shared risk variants influence lymphocyte-mediated immunity. Six target genes provide an opportunity for drug repositioning, while for 36 genes CpG methylation was found to influence transcription independently of genetic effects. Asthma, hay fever and eczema partly coexist because they share many genetic risk variants that dysregulate the expression of immune-related genes.

Published
2017

9. EU-Wide (Regional and Farm Level) Effects of Premium Decoupling and Harmonisation Following the Health Check Reform

Author

Wolfgang Britz, Gocht, A., Domínguez, I. P., Jansson, T., Grosche, S. -C, and Zhao, N.

Subjects
decoupling, direct payments, Common Agricultural Policy, Health Check reform, land rents, income distribution, Entkopplung, Direktzahlungen, Gemeinsame Agrarpolitik, Health-Check-Reform, Landrenten, Einkommensverteilung, Agricultural and Food Policy, Land Economics/Use
Abstract

This article investigates the income effects of decoupled payments distributed at the farm-type or uniformly at the regional level within the European Union. The analysis was conducted using detailed information on the implementation of the Health Check policy package for agricultural activities in each of the 27 member states, which is included in the Common Agricultural Policy Regionalised Impact (CAPRI) model. In the simulation experiments, the transition from individual to uniform per-hectare rates at the country level was explicitly modelled. The results show significant income shifts only for single products, such as durum wheat. Moreover, income was redistributed away from traditional “Grandes Cultures†crop production to fodder production, an effect primarily caused by the capitalisation of decoupled premiums on previously unsubsidised land. Cattle, sheep and goat production was primarily affected in the animal sector. Land values are expected to increase considerably, especially those of grasslands. Der Artikel untersucht die Einkommenswirkungen von entkoppelten Zahlungen, die nach Betriebstypen oder einheitlich auf regionaler Ebene der Europäischen Union verteilt werden. Die Analyse wird durchgeführt basierend auf detaillierten Informationen über die Implementierung des Health-Check-Reform-Paketes pro landwirtschaftlicher Aktivität in jeder der 27 Mitgliedstaaten, die dann im CAPRI (Common Agricultural Policy Regionalized Impact)-Modell einfließen. In den Szenarien wird der Übergang von individuellen zu einheitlichen Hektarprämien auf der Ebene der Mitgliedsländer explizit modelliert. Ergebnisse zeigen signifikante Einkommensänderungen nur für einzelne Produkte wie Hartweizen. Außerdem wird Einkommen von den traditionellen Grandes Cultures zum Futterbau umverteilt, ein Effekt, der hauptsächlich durch die Kapitalisierung der entkoppelten Zahlungen von Land, welches vorher nicht subventioniert war, zustande kommt. Im tierischen Sektor sind besonders Rindfleisch, Schafe und Ziegenproduktion betroffen. Es wird erwartet, dass Landrenten deutlich steigen, insbesondere für Grünland.

Published
2012

25. Genetic dependencies associated with transcription factor activities in human cancer cell lines.

Author

Thatikonda V, Supper V, Wachter J, Kaya O, Kombara A, Bilgilier C, Ravichandran MC, Lipp JJ, Sharma R, Badertscher L, Boghossian AS, Rees MG, Ronan MM, Roth JA, Grosche S, Neumüller RA, Mair B, Mauri F, and Popa A

Subjects
Humans, Cell Line, Tumor, TEA Domain Transcription Factors metabolism, Gene Expression Regulation, Neoplastic, DNA-Binding Proteins metabolism, DNA-Binding Proteins genetics, Biomarkers, Tumor metabolism, Biomarkers, Tumor genetics, Cell Proliferation, Transcription Factors metabolism, Transcription Factors genetics, Neoplasms genetics, Neoplasms metabolism, Neoplasms pathology
Abstract

Transcription factors (TFs) are important mediators of aberrant transcriptional programs in cancer cells. In this study, we focus on TF activity (TFa) as a biomarker for cell-line-selective anti-proliferative effects, in that high TFa predicts sensitivity to loss of function of a given gene (i.e., genetic dependencies [GDs]). Our linear-regression-based framework identifies 3,047 pan-cancer and 3,952 cancer-type-specific candidate TFa-GD associations from cell line data, which are then cross-examined for impact on survival in patient cohorts. One of the most prominent biomarkers is TEAD1 activity, whose associations with its predicted GDs are validated through experimental evidence as proof of concept. Overall, these TFa-GD associations represent an attractive resource for identifying innovative, biomarker-driven hypotheses for drug discovery programs in oncology., Competing Interests: Declaration of interests All authors, except A.S.B., M.G.R., M.M.R., J.A.R., R.S., and L.B. are full-time employees of Boehringer Ingelheim RCV. V.T. is now a full-time employee of Exscientia GmbH., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Published
2024
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26. Efficiency of moderately hypofractionated radiotherapy in NSCLC cell model.

Author

Lüdeking M, Stemwedel K, Ramachandran D, Grosche S, Christiansen H, Merten R, Henkenberens C, and Bogdanova NV

Abstract

Background: The current standard of radiotherapy for inoperable locally advanced NSCLCs with single fraction doses of 2.0 Gy, results in poor outcomes. Several fractionation schedules have been explored that developed over the past decades to increasingly more hypofractionated treatments. Moderate hypofractionated radiotherapy, as an alternative treatment, has gained clinical importance due to shorter duration and higher patient convenience. However, clinical trials show controversial results, adding to the need for pre-clinical radiobiological studies of this schedule., Methods: We examined in comparative analysis the efficiency of moderate hypofractionation and normofractionation in four different NSCLC cell lines and fibroblasts using several molecular-biological approaches. Cells were daily irradiated with 24x2.75 Gy (moderate hypofractionation) or with 30x2 Gy (normofractionation), imitating the clinical situation. Proliferation and growth rate via direct counting of cell numbers, MTT assay and measurements of DNA-synthesizing cells (EdU assay), DNA repair efficiency via immunocytochemical staining of residual γH2AX/53BP1 foci and cell surviving via clonogenic assay (CSA) were experimentally evaluated., Results: Overall, the four tumor cell lines and fibroblasts showed different sensitivity to both radiation regimes, indicating cell specificity of the effect. The absolute cell numbers and the CSA revealed significant differences between schedules (P < 0.0001 for all employed cell lines and both assays) with a stronger effect of moderate hypofractionation., Conclusion: Our results provide evidence for the similar effectiveness and toxicity of both regimes, with some favorable evidence towards a moderate hypofractionation. This indicates that increasing the dose per fraction may improve patient survival and therapy outcomes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Lüdeking, Stemwedel, Ramachandran, Grosche, Christiansen, Merten, Henkenberens and Bogdanova.)

Published
2024
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27. Effectiveness of hypofractionated and normofractionated radiotherapy in a triple-negative breast cancer model.

Author

Grosche S, Bogdanova NV, Ramachandran D, Lüdeking M, Stemwedel K, Christiansen H, Henkenberens C, and Merten R

Abstract

Breast cancer (BC) is one of the most diagnosed malignant carcinomas in women with a triple-negative breast cancer (TNBC) phenotype being correlated with poorer prognosis. Fractionated radiotherapy (RT) is a central component of breast cancer management, especially after breast conserving surgery and is increasingly important for TNBC subtype prognosis. In recent years, moderately hypofractionated radiation schedules are established as a standard of care, but many professionals remain skeptical and are concerned about their efficiency and side effects. In the present study, two different triple-negative breast cancer cell lines, a non-malignant breast epithelial cell line and fibroblasts, were irradiated daily under normofractionated and hypofractionated schedules to evaluate the impact of different irradiation regimens on radiation-induced cell-biological effects. During the series of radiotherapy, proliferation, growth rate, double-strand DNA break-repair (DDR), cellular senescence, and cell survival were measured. Investigated normal and cancer cells differed in their responses and receptivity to different irradiation regimens, indicating cell line/cell type specificity of the effect. At the end of both therapy concepts, normal and malignant cells reach almost the same endpoint of cell count and proliferation inhibition, confirming the clinical observations in the follow-up at the cellular level. These result in cell lines closely replicating the irradiation schedules in clinical practice and, to some extent, contributing to the understanding of growth rate or remission of tumors and the development of fibrosis., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Grosche, Bogdanova, Ramachandran, Lüdeking, Stemwedel, Christiansen, Henkenberens and Merten.)

Published
2022
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28. Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.

Author

Grosche S, Marenholz I, Esparza-Gordillo J, Arnau-Soler A, Pairo-Castineira E, Rüschendorf F, Ahluwalia TS, Almqvist C, Arnold A, Baurecht H, Bisgaard H, Bønnelykke K, Brown SJ, Bustamante M, Curtin JA, Custovic A, Dharmage SC, Esplugues A, Falchi M, Fernandez-Orth D, Ferreira MAR, Franke A, Gerdes S, Gieger C, Hakonarson H, Holt PG, Homuth G, Hubner N, Hysi PG, Jarvelin MR, Karlsson R, Koppelman GH, Lau S, Lutz M, Magnusson PKE, Marks GB, Müller-Nurasyid M, Nöthen MM, Paternoster L, Pennell CE, Peters A, Rawlik K, Robertson CF, Rodriguez E, Sebert S, Simpson A, Sleiman PMA, Standl M, Stölzl D, Strauch K, Szwajda A, Tenesa A, Thompson PJ, Ullemar V, Visconti A, Vonk JM, Wang CA, Weidinger S, Wielscher M, Worth CL, Xu CJ, and Lee YA

Subjects
Cytokine Receptor Common beta Subunit, Dual Specificity Phosphatase 1 chemistry, Dual Specificity Phosphatase 1 metabolism, Gene Expression, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Matrix Attachment Region Binding Proteins, Polymorphism, Single Nucleotide, Rare Diseases genetics, Receptor, Notch4 chemistry, Receptor, Notch4 metabolism, Sodium-Hydrogen Exchangers chemistry, Sodium-Hydrogen Exchangers metabolism, Dual Specificity Phosphatase 1 genetics, Eczema diagnosis, Eczema genetics, Receptor, Notch4 genetics, Sodium-Hydrogen Exchangers genetics
Abstract

Previous genome-wide association studies revealed multiple common variants involved in eczema but the role of rare variants remains to be elucidated. Here, we investigate the role of rare variants in eczema susceptibility. We meta-analyze 21 study populations including 20,016 eczema cases and 380,433 controls. Rare variants are imputed with high accuracy using large population-based reference panels. We identify rare exonic variants in DUSP1, NOTCH4, and SLC9A4 to be associated with eczema. In DUSP1 and NOTCH4 missense variants are predicted to impact conserved functional domains. In addition, five novel common variants at SATB1-AS1/KCNH8, TRIB1/LINC00861, ZBTB1, TBX21/OSBPL7, and CSF2RB are discovered. While genes prioritized based on rare variants are significantly up-regulated in the skin, common variants point to immune cell function. Over 20% of the single nucleotide variant-based heritability is attributable to rare and low-frequency variants. The identified rare/low-frequency variants located in functional protein domains point to promising targets for novel therapeutic approaches to eczema., (© 2021. The Author(s).)

Published
2021
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29. Cell-surface SLC nucleoside transporters and purine levels modulate BRD4-dependent chromatin states.

Author

Li KC, Girardi E, Kartnig F, Grosche S, Pemovska T, Bigenzahn JW, Goldmann U, Sedlyarov V, Bensimon A, Schick S, Lin JG, Gürtl B, Reil D, Klavins K, Kubicek S, Sdelci S, and Superti-Furga G

Subjects
Adenine metabolism, Biosynthetic Pathways, Cell Cycle Proteins antagonists & inhibitors, Cell Line, Chromatin genetics, DNA-Binding Proteins metabolism, Gene Expression Regulation, Gene Knockdown Techniques, Humans, Membrane Transport Proteins, Models, Biological, Solute Carrier Proteins genetics, Transcription Factors antagonists & inhibitors, Transcription, Genetic, Cell Cycle Proteins metabolism, Chromatin metabolism, Nucleoside Transport Proteins metabolism, Purines metabolism, Solute Carrier Proteins metabolism, Transcription Factors metabolism
Abstract

Metabolism negotiates cell-endogenous requirements of energy, nutrients and building blocks with the immediate environment to enable various processes, including growth and differentiation. While there is an increasing number of examples of crosstalk between metabolism and chromatin, few involve uptake of exogenous metabolites. Solute carriers (SLCs) represent the largest group of transporters in the human genome and are responsible for the transport of a wide variety of substrates, including nutrients and metabolites. We aimed to investigate the possible involvement of SLC-mediated solutes uptake and cellular metabolism in regulating cellular epigenetic states. Here, we perform a CRISPR-Cas9 transporter-focused genetic screen and a metabolic compound library screen for the regulation of BRD4-dependent chromatin states in human myeloid leukaemia cells. Intersection of the two orthogonal approaches reveal that loss of transporters involved with purine transport or inhibition of de novo purine synthesis lead to dysfunction of BRD4-dependent transcriptional regulation. Through mechanistic characterization of the metabolic circuitry, we elucidate the convergence of SLC-mediated purine uptake and de novo purine synthesis on BRD4-chromatin occupancy. Moreover, adenine-related metabolite supplementation effectively restores BRD4 functionality on purine impairment. Our study highlights the specific role of purine/adenine metabolism in modulating BRD4-dependent epigenetic states.

Published
2021
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30. Acute BAF perturbation causes immediate changes in chromatin accessibility.

Author

Schick S, Grosche S, Kohl KE, Drpic D, Jaeger MG, Marella NC, Imrichova H, Lin JG, Hofstätter G, Schuster M, Rendeiro AF, Koren A, Petronczki M, Bock C, Müller AC, Winter GE, and Kubicek S

Subjects
Acetylation, Animals, Cell Line, Chromatin metabolism, DNA Helicases genetics, DNA-Binding Proteins genetics, DNA-Binding Proteins metabolism, Drosophila cytology, Enhancer Elements, Genetic, Gene Knockout Techniques, Histones genetics, Histones metabolism, Humans, Multiprotein Complexes metabolism, Nuclear Proteins genetics, Transcription Factors genetics, Chromatin genetics, DNA Helicases metabolism, Multiprotein Complexes genetics, Nuclear Proteins metabolism, Transcription Factors metabolism
Abstract

Cancer-associated, loss-of-function mutations in genes encoding subunits of the BRG1/BRM-associated factor (BAF) chromatin-remodeling complexes 1-8 often cause drastic chromatin accessibility changes, especially in important regulatory regions 9-19 . However, it remains unknown how these changes are established over time (for example, immediate consequences or long-term adaptations), and whether they are causative for intracomplex synthetic lethalities, abrogating the formation or activity of BAF complexes 9,20-24 . In the present study, we use the dTAG system to induce acute degradation of BAF subunits and show that chromatin alterations are established faster than the duration of one cell cycle. Using a pharmacological inhibitor and a chemical degrader of the BAF complex ATPase subunits 25,26 , we show that maintaining genome accessibility requires constant ATP-dependent remodeling. Completely abolishing BAF complex function by acute degradation of a synthetic lethal subunit in a paralog-deficient background results in an almost complete loss of chromatin accessibility at BAF-controlled sites, especially also at superenhancers, providing a mechanism for intracomplex synthetic lethalities.

Published
2021
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31. Age-of-onset information helps identify 76 genetic variants associated with allergic disease.

Author

Ferreira MAR, Vonk JM, Baurecht H, Marenholz I, Tian C, Hoffman JD, Helmer Q, Tillander A, Ullemar V, Lu Y, Grosche S, Rüschendorf F, Granell R, Brumpton BM, Fritsche LG, Bhatta L, Gabrielsen ME, Nielsen JB, Zhou W, Hveem K, Langhammer A, Holmen OL, Løset M, Abecasis GR, Willer CJ, Emami NC, Cavazos TB, Witte JS, Szwajda A, Hinds DA, Hübner N, Weidinger S, Magnusson PK, Jorgenson E, Karlsson R, Paternoster L, Boomsma DI, Almqvist C, Lee YA, and Koppelman GH

Subjects
Adolescent, Adult, Age of Onset, Aged, Asthma pathology, Child, Eczema pathology, Female, Genetic Loci, Genome-Wide Association Study methods, Humans, Male, Middle Aged, Rhinitis, Allergic, Seasonal pathology, Asthma genetics, Eczema genetics, Polymorphism, Single Nucleotide, Rhinitis, Allergic, Seasonal genetics
Abstract

Risk factors that contribute to inter-individual differences in the age-of-onset of allergic diseases are poorly understood. The aim of this study was to identify genetic risk variants associated with the age at which symptoms of allergic disease first develop, considering information from asthma, hay fever and eczema. Self-reported age-of-onset information was available for 117,130 genotyped individuals of European ancestry from the UK Biobank study. For each individual, we identified the earliest age at which asthma, hay fever and/or eczema was first diagnosed and performed a genome-wide association study (GWAS) of this combined age-of-onset phenotype. We identified 50 variants with a significant independent association (P<3x10-8) with age-of-onset. Forty-five variants had comparable effects on the onset of the three individual diseases and 38 were also associated with allergic disease case-control status in an independent study (n = 222,484). We observed a strong negative genetic correlation between age-of-onset and case-control status of allergic disease (rg = -0.63, P = 4.5x10-61), indicating that cases with early disease onset have a greater burden of allergy risk alleles than those with late disease onset. Subsequently, a multivariate GWAS of age-of-onset and case-control status identified a further 26 associations that were missed by the univariate analyses of age-of-onset or case-control status only. Collectively, of the 76 variants identified, 18 represent novel associations for allergic disease. We identified 81 likely target genes of the 76 associated variants based on information from expression quantitative trait loci (eQTL) and non-synonymous variants, of which we highlight ADAM15, FOSL2, TRIM8, BMPR2, CD200R1, PRKCQ, NOD2, SMAD4, ABCA7 and UBE2L3. Our results support the notion that early and late onset allergic disease have partly distinct genetic architectures, potentially explaining known differences in pathophysiology between individuals., Competing Interests: C. Tian and D. A. Hinds both report support from 23andMe during the conduct of the study. C. Almqvist received grant 2017-00641 from Swedish Research Council and Swedish Initiative for Research on Microdata in the Social And Medical Sciences (SIMSAM) framework grant (340-2013-5867) for this work. G. H. Koppelman's institution received grants from the Lung Foundation of The Netherlands, the Ubbo Emmius Foundation, TEVA (The Netherlands), GlaxoSmithKline, Vertex, and the Tetri Foundation for other works. L. Paternoster received grant MR/J012165/1 from the UK Medical Research Council for this work and personal fees from Merck. The rest of the authors declare that they have no relevant conflicts of interest.

Published
2020
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32. Protein-coding variants contribute to the risk of atopic dermatitis and skin-specific gene expression.

Author

Mucha S, Baurecht H, Novak N, Rodríguez E, Bej S, Mayr G, Emmert H, Stölzl D, Gerdes S, Jung ES, Degenhardt F, Hübenthal M, Ellinghaus E, Kässens JC, Wienbrandt L, Lieb W, Müller-Nurasyid M, Hotze M, Dand N, Grosche S, Marenholz I, Arnold A, Homuth G, Schmidt CO, Wehkamp U, Nöthen MM, Hoffmann P, Paternoster L, Standl M, Bønnelykke K, Ahluwalia TS, Bisgaard H, Peters A, Gieger C, Waldenberger M, Schulz H, Strauch K, Werfel T, Lee YA, Wolfien M, Rosenstiel P, Wolkenhauer O, Schreiber S, Franke A, Weidinger S, and Ellinghaus D

Subjects
Adult, Cohort Studies, Filaggrin Proteins, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Organ Specificity, Polymorphism, Genetic, Risk, Transcriptome, Adaptor Proteins, Signal Transducing genetics, Dermatitis, Atopic genetics, Genotype, Orexin Receptors genetics, Phosphoproteins genetics, Skin metabolism
Abstract

Background: Fifteen percent of atopic dermatitis (AD) liability-scale heritability could be attributed to 31 susceptibility loci identified by using genome-wide association studies, with only 3 of them (IL13, IL-6 receptor [IL6R], and filaggrin [FLG]) resolved to protein-coding variants., Objective: We examined whether a significant portion of unexplained AD heritability is further explained by low-frequency and rare variants in the gene-coding sequence., Methods: We evaluated common, low-frequency, and rare protein-coding variants using exome chip and replication genotype data of 15,574 patients and 377,839 control subjects combined with whole-transcriptome data on lesional, nonlesional, and healthy skin samples of 27 patients and 38 control subjects., Results: An additional 12.56% (SE, 0.74%) of AD heritability is explained by rare protein-coding variation. We identified docking protein 2 (DOK2) and CD200 receptor 1 (CD200R1) as novel genome-wide significant susceptibility genes. Rare coding variants associated with AD are further enriched in 5 genes (IL-4 receptor [IL4R], IL13, Janus kinase 1 [JAK1], JAK2, and tyrosine kinase 2 [TYK2]) of the IL13 pathway, all of which are targets for novel systemic AD therapeutics. Multiomics-based network and RNA sequencing analysis revealed DOK2 as a central hub interacting with, among others, CD200R1, IL6R, and signal transducer and activator of transcription 3 (STAT3). Multitissue gene expression profile analysis for 53 tissue types from the Genotype-Tissue Expression project showed that disease-associated protein-coding variants exert their greatest effect in skin tissues., Conclusion: Our discoveries highlight a major role of rare coding variants in AD acting independently of common variants. Further extensive functional studies are required to detect all potential causal variants and to specify the contribution of the novel susceptibility genes DOK2 and CD200R1 to overall disease susceptibility., (Copyright © 2019. Published by Elsevier Inc.)

Published
2020
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33. Towards polarization-based excitation tailoring for extended Raman spectroscopy.

Author

Grosche S, Hünermann R, Sarau G, Christiansen S, Boyd RW, Leuchs G, and Banzer P

Abstract

Undoubtedly, Raman spectroscopy is one of the most elaborate spectroscopy tools in materials science, chemistry, medicine and optics. However, when it comes to the analysis of nanostructured specimens or individual sub-wavelength-sized systems, the access to Raman spectra resulting from different excitation schemes is usually very limited. For instance, the excitation with an electric field component oriented perpendicularly to the substrate plane is a difficult task. Conventionally, this can only be achieved by mechanically tilting the sample or by sophisticated sample preparation. Here, we propose a novel experimental method based on the utilization of polarization tailored light for Raman spectroscopy of individual nanostructures. As a proof of principle, we create three-dimensional electromagnetic field distributions at the nanoscale using tightly focused cylindrical vector beams impinging normally onto the specimen, hence keeping the traditional beam-path of commercial Raman systems. In order to demonstrate the convenience of this excitation scheme, we use a sub-wavelength diameter gallium-nitride nanostructure as a test platform and show experimentally that its Raman spectra depend sensitively on its location relative to the focal vector field. The observed Raman spectra can be attributed to the interaction with transverse and pure longitudinal electric field components. This novel technique may pave the way towards a characterization of Raman active nanosystems, granting direct access to growth-related parameters such as strain or defects in the material by using the full information of all Raman modes.

Published
2020
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34. The Enigmatic Canal-Associated Neurons Regulate Caenorhabditis elegans Larval Development Through a cAMP Signaling Pathway.

Author

Chien J, Wolf FW, Grosche S, Yosef N, Garriga G, and Mörck C

Subjects
Adenylyl Cyclases metabolism, Animals, Caenorhabditis elegans genetics, Caenorhabditis elegans Proteins chemistry, Caenorhabditis elegans Proteins genetics, Caenorhabditis elegans Proteins metabolism, Cyclic AMP-Dependent Protein Kinases metabolism, Larva growth & development, Models, Biological, Mutation genetics, Phenotype, Protein Domains, Subcutaneous Tissue, Up-Regulation, Caenorhabditis elegans growth & development, Caenorhabditis elegans metabolism, Cyclic AMP metabolism, Neurons metabolism, Signal Transduction
Abstract

Caenorhabditis elegans larval development requires the function of the two Canal-Associated Neurons (CANs): killing the CANs by laser microsurgery or disrupting their development by mutating the gene ceh-10 results in early larval arrest. How these cells promote larval development, however, remains a mystery. In screens for mutations that bypass CAN function, we identified the gene kin-29 , which encodes a member of the Salt-Inducible Kinase (SIK) family and a component of a conserved pathway that regulates various C. elegans phenotypes. Like kin-29 loss, gain-of-function mutations in genes that may act upstream of kin-29 or growth in cyclic-AMP analogs bypassed ceh-10 larval arrest, suggesting that a conserved adenylyl cyclase/PKA pathway inhibits KIN-29 to promote larval development, and that loss of CAN function results in dysregulation of KIN-29 and larval arrest. The adenylyl cyclase ACY-2 mediates CAN-dependent larval development: acy-2 mutant larvae arrested development with a similar phenotype to ceh-10 mutants, and the arrest phenotype was suppressed by mutations in kin-29 ACY-2 is expressed predominantly in the CANs, and we provide evidence that the acy-2 functions in the CANs to promote larval development. By contrast, cell-specific expression experiments suggest that kin-29 acts in both the hypodermis and neurons, but not in the CANs. Based on our findings, we propose two models for how ACY-2 activity in the CANs regulates KIN-29 in target cells., (Copyright © 2019 by the Genetics Society of America.)

Published
2019
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35. Evaluation of food allergy candidate loci in the Genetics of Food Allergy study.

Author

Marenholz I, Grosche S, Rüschendorf F, Kalb B, Blumchen K, Schlags R, Harandi N, Price M, Hansen G, Seidenberg J, Yürek S, Homuth G, Schmidt CO, Nöthen MM, Hubner N, Niggemann B, Beyer K, and Lee YA

Subjects
Child, Preschool, Female, Genotype, Humans, Infant, Male, Polymorphism, Single Nucleotide, Chromosomes, Human, Pair 11, Food Hypersensitivity genetics
Published
2018
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36. A Canadian genome-wide association study and meta-analysis confirm HLA as a risk factor for peanut allergy independent of asthma.

Author

Asai Y, Eslami A, van Ginkel CD, Akhabir L, Wan M, Yin D, Ellis G, Ben-Shoshan M, Marenholz I, Martino D, Ferreira MA, Allen K, Mazer B, de Groot H, de Jong NW, Gerth van Wijk R, Dubois AEJ, Grosche S, Ashley S, Rüschendorf F, Kalb B, Beyer K, Nöthen MM, Lee YA, Chin R, Cheuk S, Hoffman J, Jorgensen E, Witte JS, Melles RB, Hong X, Wang X, Hui J, Musk AWB, Hunter M, James AL, Koppelman GH, Sandford AJ, Clarke AE, and Daley D

Subjects
Adolescent, Adult, Aged, Aged, 80 and over, Canada, Child, Child, Preschool, Female, Genetic Predisposition to Disease genetics, Genome-Wide Association Study methods, Humans, Infant, Male, Middle Aged, Polymorphism, Single Nucleotide genetics, Risk Factors, Young Adult, Arachis immunology, Asthma genetics, Asthma immunology, HLA Antigens genetics, Peanut Hypersensitivity genetics, Peanut Hypersensitivity immunology
Published
2018
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37. Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology.

Author

Ferreira MA, Vonk JM, Baurecht H, Marenholz I, Tian C, Hoffman JD, Helmer Q, Tillander A, Ullemar V, van Dongen J, Lu Y, Rüschendorf F, Esparza-Gordillo J, Medway CW, Mountjoy E, Burrows K, Hummel O, Grosche S, Brumpton BM, Witte JS, Hottenga JJ, Willemsen G, Zheng J, Rodríguez E, Hotze M, Franke A, Revez JA, Beesley J, Matheson MC, Dharmage SC, Bain LM, Fritsche LG, Gabrielsen ME, Balliu B, Nielsen JB, Zhou W, Hveem K, Langhammer A, Holmen OL, Løset M, Abecasis GR, Willer CJ, Arnold A, Homuth G, Schmidt CO, Thompson PJ, Martin NG, Duffy DL, Novak N, Schulz H, Karrasch S, Gieger C, Strauch K, Melles RB, Hinds DA, Hübner N, Weidinger S, Magnusson PKE, Jansen R, Jorgenson E, Lee YA, Boomsma DI, Almqvist C, Karlsson R, Koppelman GH, and Paternoster L

Subjects
Genome-Wide Association Study methods, Humans, Phenotype, Polymorphism, Single Nucleotide, Risk Factors, Asthma genetics, Eczema genetics, Genetic Predisposition to Disease genetics, Hypersensitivity genetics, Rhinitis, Allergic, Seasonal genetics
Abstract

Asthma, hay fever (or allergic rhinitis) and eczema (or atopic dermatitis) often coexist in the same individuals, partly because of a shared genetic origin. To identify shared risk variants, we performed a genome-wide association study (GWAS; n = 360,838) of a broad allergic disease phenotype that considers the presence of any one of these three diseases. We identified 136 independent risk variants (P < 3 × 10 -8 ), including 73 not previously reported, which implicate 132 nearby genes in allergic disease pathophysiology. Disease-specific effects were detected for only six variants, confirming that most represent shared risk factors. Tissue-specific heritability and biological process enrichment analyses suggest that shared risk variants influence lymphocyte-mediated immunity. Six target genes provide an opportunity for drug repositioning, while for 36 genes CpG methylation was found to influence transcription independently of genetic effects. Asthma, hay fever and eczema partly coexist because they share many genetic risk variants that dysregulate the expression of immune-related genes.

Published
2017
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38. Genome-wide association study identifies the SERPINB gene cluster as a susceptibility locus for food allergy.

Author

Marenholz I, Grosche S, Kalb B, Rüschendorf F, Blümchen K, Schlags R, Harandi N, Price M, Hansen G, Seidenberg J, Röblitz H, Yürek S, Tschirner S, Hong X, Wang X, Homuth G, Schmidt CO, Nöthen MM, Hübner N, Niggemann B, Beyer K, and Lee YA

Subjects
Case-Control Studies, Child, Preschool, Female, Filaggrin Proteins, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Multigene Family, Food Hypersensitivity genetics, Serpins genetics
Abstract

Genetic factors and mechanisms underlying food allergy are largely unknown. Due to heterogeneity of symptoms a reliable diagnosis is often difficult to make. Here, we report a genome-wide association study on food allergy diagnosed by oral food challenge in 497 cases and 2387 controls. We identify five loci at genome-wide significance, the clade B serpin (SERPINB) gene cluster at 18q21.3, the cytokine gene cluster at 5q31.1, the filaggrin gene, the C11orf30/LRRC32 locus, and the human leukocyte antigen (HLA) region. Stratifying the results for the causative food demonstrates that association of the HLA locus is peanut allergy-specific whereas the other four loci increase the risk for any food allergy. Variants in the SERPINB gene cluster are associated with SERPINB10 expression in leukocytes. Moreover, SERPINB genes are highly expressed in the esophagus. All identified loci are involved in immunological regulation or epithelial barrier function, emphasizing the role of both mechanisms in food allergy.

Published
2017
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39. Lateral spin transport in paraxial beams of light.

Author

Neugebauer M, Grosche S, Rothau S, Leuchs G, and Banzer P

Abstract

We investigate the lateral transport of (longitudinal) spin angular momentum in a special polarization tailored light beam composed of a superposition of a y-polarized zero-order and an x-polarized first-order Hermite-Gaussian mode. This phenomenon is linked to the relative Gouy phase shift between the individual modes upon propagation, but can also be interpreted as a geometric phase effect. Experimentally, we demonstrate the implementation of such a mode and measure the spin density upon propagation.

Published
2016
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40. Goos-Hänchen and Imbert-Fedorov shifts for Gaussian beams impinging on graphene-coated surfaces.

Author

Grosche S, Ornigotti M, and Szameit A

Abstract

We present a theoretical study of the Goos-Hänchen and Imbert-Fedorov shifts for a fundamental Gaussian beam impinging on a surface coated with a single layer of graphene. We show that the graphene surface conductivity σ(ω) is responsible for the appearance of a giant and negative spatial Goos-Hänchen shift.

Published
2015
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41. [Left-sided thoracic pain in a 56-year old man followed by double vision and paresthesias of the left hand].

Author

Grosche S, Schöne W, Borgmann H, Hempel K, Schubert C, and Wihsgott C

Subjects
Brain Stem Infarctions complications, Brain Stem Infarctions pathology, Brain Stem Infarctions therapy, Functional Laterality, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Risk Factors, Ataxia etiology, Brain Stem Infarctions diagnosis, Chest Pain etiology, Diplopia etiology, Hand physiopathology, Paresthesia etiology
Published
2000
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