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1. Predictive potential of dynamic contrast-enhanced MRI and plasma-derived angiogenic factors for response to concurrent chemoradiotherapy in human papillomavirus-negative oropharyngeal cancer

Author

Longo Alja, Hudler Petra, Strojan Primoz, Plavc Gaber, Umek Lan, and Popovic Katarina Surlan

Subjects
dce-mri, angiogenesis, vegf, concurrent chemoradiotherapy, response, head and neck squamous cell carcinoma, Medical physics. Medical radiology. Nuclear medicine, R895-920
Abstract

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) can assess tumour vascularity, which depends on the process of angiogenesis and affects tumour response to treatment. Our study explored the associations between DCE-MRI parameters and the expression of plasma angiogenic factors in human papilloma virus (HPV)-negative oropharyngeal cancer, as well as their predictive value for response to concurrent chemoradiotherapy (cCRT).

Published
2024
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2. Association between polymorphisms in segregation genes BUB1B and TTK and gastric cancer risk

Author

Hudler Petra, Britovsek Nina Kocevar, Grazio Snjezana Frkovic, and Komel Radovan

Subjects
cancer susceptibility, chromosomal instability, chromosome segregation, mitotic checkpoint, serine/threonine kinase, genetic association, Medical physics. Medical radiology. Nuclear medicine, R895-920
Abstract

Malignant transformation of normal gastric cells is a complex and multistep process, resulting in development of heterogeneous tumours. Susceptible genetic background, accumulation of genetic changes, and environmental factors play an important role in gastric carcinogenesis. Single nucleotide polymorphisms (SNPs) in mitotic segregation genes could be responsible for inducing the slow process of accumulation of genetic changes, leading to genome instability.

Published
2016
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3. Exploring US Internal Medicine Resident Career Preferences: A Q-Methodology Study

Author

Roberts, John K., Schub, Micah, Singhal, Surbhi, Norwood, Jamison, Cassini, Thomas, Hudler, Andi, Ramadurai, Deepa, Smith, Christopher C., Desai, Sima S., Weintraub, Jennifer, Hasler, Scott H., Schwiesow, Tyler M., Connors, Geoffrey R., Didwania, Aashish, Hargett, Charles W., and Wolf, Myles

Abstract

Career selection in medicine is a complex and underexplored process. Most medical career studies performed in the U.S. focused on the effect of demographic variables and medical education debt on career choice. Considering ongoing U.S. physician workforce shortages and the trilateral adaptive model of career decision making, a robust assessment of professional attitudes and work-life preferences is necessary. The objective of this study was to explore and define the dominant viewpoints related to career choice selection in a cohort of U.S. IM residents. We administered an electronic Q-sort in which 218 IM residents sorted 50 statements reflecting the spectrum of opinions that influence postgraduate career choice decisions. Participants provided comments that explained the reasoning behind their individual responses. In the final year of residency training, we ascertained participating residents' chosen career. Factor analysis grouped similar sorts and revealed four distinct viewpoints. We characterized the viewpoints as "Fellowship-Bound-Academic," "Altruistic-Longitudinal-Generalist," "Inpatient-Burnout-Aware," and "Lifestyle-Focused-Consultant." There is concordance between residents who loaded significantly onto a viewpoint and their ultimate career choice. Four dominant career choice viewpoints were found among contemporary U.S. IM residents. These viewpoints reflect the intersection of competing priorities, personal interests, professional identity, socio-economic factors, and work/life satisfaction. Better appreciation of determinants of IM residents' career choices may help address workforce shortages and enhance professional satisfaction.

Published
2023
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6. Assessing pathogenicity of MLH1 variants by co-expression of human MLH1 and PMS2 genes in yeast

Author

Hudler Petra, Zupanec Neja, Comino Aleksandra, Vogelsang Matjaz, and Komel Radovan

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Loss of DNA mismatch repair (MMR) in humans, mainly due to mutations in the hMLH1 gene, is linked to hereditary nonpolyposis colorectal cancer (HNPCC). Because not all MLH1 alterations result in loss of MMR function, accurate characterization of variants and their classification in terms of their effect on MMR function is essential for reliable genetic testing and effective treatment. To date, in vivo assays for functional characterization of MLH1 mutations performed in various model systems have used episomal expression of the modified MMR genes. We describe here a novel approach to determine accurately the functional significance of hMLH1 mutations in vivo, based on co-expression of human MLH1 and PMS2 in yeast cells. Methods Yeast MLH1 and PMS1 genes, whose protein products form the MutLα complex, were replaced by human orthologs directly on yeast chromosomes by homologous recombination, and the resulting MMR activity was tested. Results The yeast strain co-expressing hMLH1 and hPMS2 exhibited the same mutation rate as the wild-type. Eight cancer-related MLH1 variants were introduced, using the same approach, into the prepared yeast model, and their effect on MMR function was determined. Five variants (A92P, S93G, I219V, K618R and K618T) were classified as non-pathogenic, whereas variants T117M, Y646C and R659Q were characterized as pathogenic. Conclusion Results of our in vivo yeast-based approach correlate well with clinical data in five out of seven hMLH1 variants and the described model was thus shown to be useful for functional characterization of MLH1 variants in cancer patients found throughout the entire coding region of the gene.

Published
2009
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7. PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease

Author

Adamlje Anton, Leskovar Bostjan, Haarpaintner Guido, Balazic Joze, Zupanic-Pajnic Irena, Jereb Simona, Kenig Anton, Hudler Petra, Bidovec Matjaz, Reiterova Jana, Stekrova Jitka, Strmecki Lana, Vouk Katja, Skoflic Antun, Dovc Reina, Hojs Radovan, and Komel Radovan

Subjects
Internal medicine, RC31-1245, Genetics, QH426-470
Abstract

Abstract Background Autosomal dominant polycystic kidney disease (ADPKD) is a genetically heterogeneous disorder caused by mutations in at least two different loci. Prior to performing mutation screening, if DNA samples of sufficient number of family members are available, it is worthwhile to assign the gene involved in disease progression by the genetic linkage analysis. Methods We collected samples from 36 Slovene ADPKD families and performed linkage analysis in 16 of them. Linkage was assessed by the use of microsatellite polymorphic markers, four in the case of PKD1 (KG8, AC2.5, CW3 and CW2) and five for PKD2 (D4S1534, D4S2929, D4S1542, D4S1563 and D4S423). Partial PKD1 mutation screening was undertaken by analysing exons 23 and 31–46 and PKD2 . Results Lod scores indicated linkage to PKD1 in six families and to PKD2 in two families. One family was linked to none and in seven families linkage to both genes was possible. Partial PKD1 mutation screening was performed in 33 patients (including 20 patients from the families where linkage analysis could not be performed). We analysed PKD2 in 2 patients where lod scores indicated linkage to PKD2 and in 7 families where linkage to both genes was possible. We detected six mutations and eight polymorphisms in PKD1 and one mutation and three polymorphisms in PKD2. Conclusion In our study group of ADPKD patients we detected seven mutations: three frameshift, one missense, two nonsense and one putative splicing mutation. Three have been described previously and 4 are novel. Three newly described framesfift mutations in PKD1 seem to be associated with more severe clinical course of ADPKD. Previously described nonsense mutation in PKD2 seems to be associated with cysts in liver and milder clinical course.

Published
2006
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8. DNA-methylome-assisted classification of patients with poor prognostic subventricular zone associated IDH-wildtype glioblastoma

Author

Adeberg, Sebastian, Knoll, Maximilian, Koelsche, Christian, Bernhardt, Denise, Schrimpf, Daniel, Sahm, Felix, König, Laila, Harrabi, Semi Ben, Hörner-Rieber, Juliane, Verma, Vivek, Bewerunge-Hudler, Melanie, Unterberg, Andreas, Sturm, Dominik, Jungk, Christine, Herold-Mende, Christel, Wick, Wolfgang, von Deimling, Andreas, Debus, Juergen, Rieken, Stefan, and Abdollahi, Amir

Published
2022
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9. Intersectional Sustainability and Student Activism: A Framework for Achieving Social Sustainability on University Campuses

Author

Hudler, Keara, Dennis, Lilly, DiNella, Muriel, Ford, Nataley, Mendez, Joanna, and Long, Joshua

Abstract

In recent decades, universities have made significant progress toward environmental sustainability and have likewise tightened their budgets and restructured economic models in the name of financial sustainability. However, institutions of higher education have failed to address issues of social sustainability and social injustice, many of which are increasing in number and severity on college campuses. This article takes a student activist perspective on these issues, suggesting that a comprehensive and intersectional approach toward university sustainability (with particular re-affirmation of the social sustainability pillar) can empower students and their allies, raise awareness about the causes of these issues, and allow a more constructive environment for collaborative approaches and policy formation on college campuses.

Published
2021
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10. “…the availability of contraceptives is everywhere.”: coordinated and integrated public family planning service delivery in Rwanda

Author

Scanteianu, Adriana, Schwandt, Hilary M., Boulware, Angel, Corey, Julia, Herrera, Ana, Hudler, Ethan, Imbabazi, Claudette, King, Ilia, Linus, Jessica, Manzi, Innocent, Merritt, Madelyn, Mezier, Lyn, Miller, Abigail, Morris, Haley, Musemakweli, Dieudonne, Musekura, Uwase, Mutuyimana, Divine, Ntakarutimana, Chimene, Patel, Nirali, Shemeza, Biganette-Evidente, Sterling-Donaldson, Gi’anna, Umutoni, Chantal, Uwera, Lyse, Zeiler, Madeleine, and Feinberg, Seth

Published
2022
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11. “She is courageous because she does not care what people think about her…”: attitudes toward adolescent contraception use among Rwandan family planning providers and adult female modern contraceptive users

Author

Schwandt, Hilary, Boulware, Angel, Corey, Julia, Herrera, Ana, Hudler, Ethan, Imbabazi, Claudette, King, Ilia, Linus, Jessica, Manzi, Innocent, Merritt, Madelyn, Mezier, Lyn, Miller, Abigail, Morris, Haley, Musemakweli, Dieudonne, Musekura, Uwase, Mutuyimana, Divine, Ntakarutimana, Chimene, Patel, Nirali, Scanteianu, Adriana, Shemeza, Biganette-Evidente, Sterling-Donaldson, Gi’anna, Umutoni, Chantal, Uwera, Lyse, Zeiler, Madeleine, and Feinberg, Seth

Published
2022
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12. DNA methylation-based classification of central nervous system tumours.

Author

Capper, David, Jones, David TW, Sill, Martin, Hovestadt, Volker, Schrimpf, Daniel, Sturm, Dominik, Koelsche, Christian, Sahm, Felix, Chavez, Lukas, Reuss, David E, Kratz, Annekathrin, Wefers, Annika K, Huang, Kristin, Pajtler, Kristian W, Schweizer, Leonille, Stichel, Damian, Olar, Adriana, Engel, Nils W, Lindenberg, Kerstin, Harter, Patrick N, Braczynski, Anne K, Plate, Karl H, Dohmen, Hildegard, Garvalov, Boyan K, Coras, Roland, Hölsken, Annett, Hewer, Ekkehard, Bewerunge-Hudler, Melanie, Schick, Matthias, Fischer, Roger, Beschorner, Rudi, Schittenhelm, Jens, Staszewski, Ori, Wani, Khalida, Varlet, Pascale, Pages, Melanie, Temming, Petra, Lohmann, Dietmar, Selt, Florian, Witt, Hendrik, Milde, Till, Witt, Olaf, Aronica, Eleonora, Giangaspero, Felice, Rushing, Elisabeth, Scheurlen, Wolfram, Geisenberger, Christoph, Rodriguez, Fausto J, Becker, Albert, Preusser, Matthias, Haberler, Christine, Bjerkvig, Rolf, Cryan, Jane, Farrell, Michael, Deckert, Martina, Hench, Jürgen, Frank, Stephan, Serrano, Jonathan, Kannan, Kasthuri, Tsirigos, Aristotelis, Brück, Wolfgang, Hofer, Silvia, Brehmer, Stefanie, Seiz-Rosenhagen, Marcel, Hänggi, Daniel, Hans, Volkmar, Rozsnoki, Stephanie, Hansford, Jordan R, Kohlhof, Patricia, Kristensen, Bjarne W, Lechner, Matt, Lopes, Beatriz, Mawrin, Christian, Ketter, Ralf, Kulozik, Andreas, Khatib, Ziad, Heppner, Frank, Koch, Arend, Jouvet, Anne, Keohane, Catherine, Mühleisen, Helmut, Mueller, Wolf, Pohl, Ute, Prinz, Marco, Benner, Axel, Zapatka, Marc, Gottardo, Nicholas G, Driever, Pablo Hernáiz, Kramm, Christof M, Müller, Hermann L, Rutkowski, Stefan, von Hoff, Katja, Frühwald, Michael C, Gnekow, Astrid, Fleischhack, Gudrun, Tippelt, Stephan, Calaminus, Gabriele, Monoranu, Camelia-Maria, Perry, Arie, and Jones, Chris

Subjects
Humans, Central Nervous System Neoplasms, Cohort Studies, Reproducibility of Results, DNA Methylation, Adolescent, Adult, Aged, Aged, 80 and over, Middle Aged, Child, Child, Preschool, Infant, Female, Male, Young Adult, Unsupervised Machine Learning, and over, Preschool, General Science & Technology
Abstract

Accurate pathological diagnosis is crucial for optimal management of patients with cancer. For the approximately 100 known tumour types of the central nervous system, standardization of the diagnostic process has been shown to be particularly challenging-with substantial inter-observer variability in the histopathological diagnosis of many tumour types. Here we present a comprehensive approach for the DNA methylation-based classification of central nervous system tumours across all entities and age groups, and demonstrate its application in a routine diagnostic setting. We show that the availability of this method may have a substantial impact on diagnostic precision compared to standard methods, resulting in a change of diagnosis in up to 12% of prospective cases. For broader accessibility, we have designed a free online classifier tool, the use of which does not require any additional onsite data processing. Our results provide a blueprint for the generation of machine-learning-based tumour classifiers across other cancer entities, with the potential to fundamentally transform tumour pathology.

Published
2018

13. Family planning demand generation in Rwanda: Government efforts at the national and community level impact interpersonal communication and family norms.

Author

Julia Corey, Hilary Schwandt, Angel Boulware, Ana Herrera, Ethan Hudler, Claudette Imbabazi, Ilia King, Jessica Linus, Innocent Manzi, Madelyn Merrit, Lyn Mezier, Abigail Miller, Haley Morris, Dieudonne Musemakweli, Uwase Musekura, Divine Mutuyimana, Chimene Ntakarutimana, Nirali Patel, Adriana Scanteianu, Biganette-Evidente Shemeza, Gi'anna Sterling-Donaldson, Chantal Umutoni, Lyse Uwera, Madeleine Zeiler, and Seth Feinberg

Subjects
Medicine, Science
Abstract

Between 2005 and 2020, total contraceptive use among married women in Rwanda increased from 17% to 64%. The aim of this study is to better understand how the Rwandan government's mobilization and demand generation efforts have impacted community norms and interpersonal discourse surrounding family planning. Eight focus group discussions with family planning providers and 32 in-depth interviews with experienced modern contraceptive users were conducted in 2018 in the two Rwandan districts with the highest and the lowest contraceptive prevalence rates. Results suggest that outspoken government support, mass media, and community meetings were valuable sources of information about family planning. Information received through these channels generated interpersonal dialogue about contraceptives through both conversation and observation; however, rumors and misinformation remained a significant barrier to use. A once taboo subject is now normative among married couples. Continuing to address common fears and misinformation through communication channels such as mass media and community meetings may help to further increase contraceptive uptake in Rwanda.

Published
2022
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14. “… the way we welcome them is how we will lead them to love family planning.”: family planning providers in Rwanda foster compassionate relationships with clients despite workplace challenges

Author

Schwandt, Hilary M., Boulware, Angel, Corey, Julia, Herrera, Ana, Hudler, Ethan, Imbabazi, Claudette, King, Ilia, Linus, Jessica, Manzi, Innocent, Merritt, Madelyn, Mezier, Lyn, Miller, Abigail, Morris, Haley, Musemakweli, Dieudonne, Musekura, Uwase, Mutuyimana, Divine, Ntakarutimana, Chimene, Patel, Nirali, Scanteianu, Adriana, Shemeza, Biganette-Evidente, Sterling-Donaldson, Giànna, Umutoni, Chantal, Uwera, Lyse, Zeiler, Madeleine, and Feinberg, Seth

Published
2021
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15. Sarcoma classification by DNA methylation profiling

Author

Koelsche, Christian, Schrimpf, Daniel, Stichel, Damian, Sill, Martin, Sahm, Felix, Reuss, David E., Blattner, Mirjam, Worst, Barbara, Heilig, Christoph E., Beck, Katja, Horak, Peter, Kreutzfeldt, Simon, Paff, Elke, Stark, Sebastian, Johann, Pascal, Selt, Florian, Ecker, Jonas, Sturm, Dominik, Pajtler, Kristian W., Reinhardt, Annekathrin, Wefers, Annika K., Sievers, Philipp, Ebrahimi, Azadeh, Suwala, Abigail, Fernández-Klett, Francisco, Casalini, Belén, Korshunov, Andrey, Hovestadt, Volker, Kommoss, Felix K. F., Kriegsmann, Mark, Schick, Matthias, Bewerunge-Hudler, Melanie, Milde, Till, Witt, Olaf, Kulozik, Andreas E., Kool, Marcel, Romero-Pérez, Laura, Grünewald, Thomas G. P., Kirchner, Thomas, Wick, Wolfgang, Platten, Michael, Unterberg, Andreas, Uhl, Matthias, Abdollahi, Amir, Debus, Jürgen, Lehner, Burkhard, Thomas, Christian, Hasselblatt, Martin, Paulus, Werner, Hartmann, Christian, Staszewski, Ori, Prinz, Marco, Hench, Jürgen, Frank, Stephan, Versleijen-Jonkers, Yvonne M. H., Weidema, Marije E., Mentzel, Thomas, Griewank, Klaus, de Álava, Enrique, Martín, Juan Díaz, Gastearena, Miguel A. Idoate, Chang, Kenneth Tou-En, Low, Sharon Yin Yee, Cuevas-Bourdier, Adrian, Mittelbronn, Michel, Mynarek, Martin, Rutkowski, Stefan, Schüller, Ulrich, Mautner, Viktor F., Schittenhelm, Jens, Serrano, Jonathan, Snuderl, Matija, Büttner, Reinhard, Klingebiel, Thomas, Buslei, Rolf, Gessler, Manfred, Wesseling, Pieter, Dinjens, Winand N. M., Brandner, Sebastian, Jaunmuktane, Zane, Lyskjær, Iben, Schirmacher, Peter, Stenzinger, Albrecht, Brors, Benedikt, Glimm, Hanno, Heining, Christoph, Tirado, Oscar M., Sáinz-Jaspeado, Miguel, Mora, Jaume, Alonso, Javier, del Muro, Xavier Garcia, Moran, Sebastian, Esteller, Manel, Benhamida, Jamal K., Ladanyi, Marc, Wardelmann, Eva, Antonescu, Cristina, Flanagan, Adrienne, Dirksen, Uta, Hohenberger, Peter, Baumhoer, Daniel, Hartmann, Wolfgang, Vokuhl, Christian, Flucke, Uta, Petersen, Iver, Mechtersheimer, Gunhild, Capper, David, Jones, David T. W., Fröhling, Stefan, Pfister, Stefan M., and von Deimling, Andreas

Published
2021
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16. An examination of the barriers to and benefits from collaborative couple contraceptive use in Rwanda

Author

Schwandt, Hilary, Boulware, Angel, Corey, Julia, Herrera, Ana, Hudler, Ethan, Imbabazi, Claudette, King, Ilia, Linus, Jessica, Manzi, Innocent, Merritt, Madelyn, Mezier, Lyn, Miller, Abigail, Morris, Haley, Musemakweli, Dieudonne, Musekura, Uwase, Mutuyimana, Divine, Ntakarutimana, Chimene, Patel, Nirali, Scanteianu, Adriana, Shemeza, Biganette-Evidente, Stapleton, Madi, Sterling-Donaldson, Gi’anna, Umutoni, Chantal, Uwera, Lyse, Zeiler, Madeleine, and Feinberg, Seth

Published
2021
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18. Mutational patterns and regulatory networks in epigenetic subgroups of meningioma

Author

Paramasivam, Nagarajan, Hübschmann, Daniel, Toprak, Umut H, Ishaque, Naveed, Neidert, Marian, Schrimpf, Daniel, Stichel, Damian, Reuss, David, Sievers, Philipp, Reinhardt, Annekathrin, Wefers, Annika K., Jones, David T. W., Gu, Zuguang, Werner, Johannes, Uhrig, Sebastian, Wirsching, Hans-Georg, Schick, Matthias, Bewerunge-Hudler, Melanie, Beck, Katja, Brehmer, Stephanie, Urbschat, Steffi, Seiz-Rosenhagen, Marcel, Hänggi, Daniel, Herold-Mende, Christel, Ketter, Ralf, Eils, Roland, Ram, Zvi, Pfister, Stefan M., Wick, Wolfgang, Weller, Michael, Grossmann, Rachel, von Deimling, Andreas, Schlesner, Matthias, and Sahm, Felix

Published
2019
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19. Chordoid meningiomas can be sub-stratified into prognostically distinct DNA methylation classes and are enriched for heterozygous deletions of chromosomal arm 2p

Author

Sievers, Philipp, Stichel, Damian, Hielscher, Thomas, Schrimpf, Daniel, Reinhardt, Annekathrin, Wefers, Annika K., Reuss, David, Jones, David T. W., Bewerunge-Hudler, Melanie, Hartmann, Christian, Baumgarten, Peter, Wirsching, Hans-Georg, Winther-Kristensen, Bjarne, Brokinkel, Benjamin, Ketter, Ralf, Idoate Gastearena, Miguel Angel, Lamszus, Katrin, Seiz-Rosenhagen, Marcel, Mawrin, Christian, Harter, Patrick N., Felsberg, Jörg, Hänggi, Daniel, Herold-Mende, Christel, Berghoff, Anna Sophie, Weller, Michael, Pfister, Stefan M., Wick, Wolfgang, Reifenberger, Guido, Preusser, Matthias, von Deimling, Andreas, and Sahm, Felix

Published
2018
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21. Array-based DNA-methylation profiling in sarcomas with small blue round cell histology provides valuable diagnostic information

Author

Koelsche, Christian, Hartmann, Wolfgang, Schrimpf, Daniel, Stichel, Damian, Jabar, Susanne, Ranft, Andreas, Reuss, David E., Sahm, Felix, Jones, David T. W., Bewerunge-Hudler, Melanie, Trautmann, Marcel, Klingebiel, Thomas, Vokuhl, Christian, Gessler, Manfred, Wardelmann, Eva, Petersen, Iver, Baumhoer, Daniel, Flucke, Uta, Antonescu, Cristina, Esteller, Manel, Fröhling, Stefan, Kool, Marcel, Pfister, Stefan M., Mechtersheimer, Gunhild, Dirksen, Uta, and von Deimling, Andreas

Published
2018
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24. Profiling of gallbladder carcinoma reveals distinct miRNA profiles and activation of STAT1 by the tumor suppressive miRNA-145-5p

Author

Goeppert, Benjamin, Truckenmueller, Felicia, Ori, Alessandro, Fritz, Valerie, Albrecht, Thomas, Fraas, Angelika, Scherer, Dominique, Silos, Rosa González, Sticht, Carsten, Gretz, Norbert, Mehrabi, Arianeb, Bewerunge-Hudler, Melanie, Pusch, Stefan, Bermejo, Justo Lorenzo, Dietrich, Peter, Schirmacher, Peter, Renner, Marcus, and Roessler, Stephanie

Published
2019
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25. Genome-wide methylation profiling and copy number analysis in atypical fibroxanthomas and pleomorphic dermal sarcomas indicate a similar molecular phenotype

Author

Koelsche, Christian, Stichel, Damian, Griewank, Klaus G., Schrimpf, Daniel, Reuss, David E., Bewerunge-Hudler, Melanie, Vokuhl, Christian, Dinjens, Winand N. M., Petersen, Iver, Mittelbronn, Michel, Cuevas-Bourdier, Adrian, Buslei, Rolf, Pfister, Stefan M., Flucke, Uta, Mechtersheimer, Gunhild, Mentzel, Thomas, and von Deimling, Andreas

Published
2019
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26. Meningiomas induced by low-dose radiation carry structural variants of NF2 and a distinct mutational signature

Author

Sahm, Felix, Toprak, Umut H., Hübschmann, Daniel, Kleinheinz, Kortine, Buchhalter, Ivo, Sill, Martin, Stichel, Damian, Schick, Matthias, Bewerunge-Hudler, Melanie, Schrimpf, Daniel, Zadeh, Gelareh, Aldape, Ken, Herold-Mende, Christel, Beck, Katja, Staszewski, Ori, Prinz, Marco, Harosh, Carmit Ben, Eils, Roland, Sturm, Dominik, Jones, David T. W., Pfister, Stefan M., Paulus, Werner, Ram, Zvi, Schlesner, Matthias, Grossman, Rachel, and von Deimling, Andreas

Published
2017
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27. MEST mediates the impact of prenatal bisphenol A exposure on long-term body weight development

Author

Junge, Kristin M., Leppert, Beate, Jahreis, Susanne, Wissenbach, Dirk K., Feltens, Ralph, Grützmann, Konrad, Thürmann, Loreen, Bauer, Tobias, Ishaque, Naveed, Schick, Matthias, Bewerunge-Hudler, Melanie, Röder, Stefan, Bauer, Mario, Schulz, Angela, Borte, Michael, Landgraf, Kathrin, Körner, Antje, Kiess, Wieland, von Bergen, Martin, Stangl, Gabriele I., Trump, Saskia, Eils, Roland, Polte, Tobias, and Lehmann, Irina

Published
2018
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28. Gain of 12p encompassing CCND2 is associated with gemistocytic histology in IDH mutant astrocytomas

Author

Sahm, Felix, Korshunov, Andrey, Schrimpf, Daniel, Stichel, Damian, Jones, David T. W., Capper, David, Koelsche, Christian, Reuss, David, Kratz, Annekathrin, Huang, Kristin, Wefers, Annika K., Schick, Matthias, Bewerunge-Hudler, Melanie, Mittelbronn, Michel, Platten, Michael, Hänggi, Daniel, Jeibmann, Astrid, Unterberg, Andreas, Herold-Mende, Christel, Pfister, Stefan M., Brandner, Sebastian, Wick, Wolfgang, and von Deimling, Andreas

Published
2017
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29. Next-generation sequencing in routine brain tumor diagnostics enables an integrated diagnosis and identifies actionable targets

Author

Sahm, Felix, Schrimpf, Daniel, Jones, David T. W., Meyer, Jochen, Kratz, Annekathrin, Reuss, David, Capper, David, Koelsche, Christian, Korshunov, Andrey, Wiestler, Benedikt, Buchhalter, Ivo, Milde, Till, Selt, Florian, Sturm, Dominik, Kool, Marcel, Hummel, Manuela, Bewerunge-Hudler, Melanie, Mawrin, Christian, Schüller, Ulrich, Jungk, Christine, Wick, Antje, Witt, Olaf, Platten, Michael, Herold-Mende, Christel, Unterberg, Andreas, Pfister, Stefan M., Wick, Wolfgang, and von Deimling, Andreas

Published
2016
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30. Methylation-based classification of benign and malignant peripheral nerve sheath tumors

Author

Röhrich, Manuel, Koelsche, Christian, Schrimpf, Daniel, Capper, David, Sahm, Felix, Kratz, Annekathrin, Reuss, Jana, Hovestadt, Volker, Jones, David T. W., Bewerunge-Hudler, Melanie, Becker, Albert, Weis, Joachim, Mawrin, Christian, Mittelbronn, Michel, Perry, Arie, Mautner, Victor-Felix, Mechtersheimer, Gunhild, Hartmann, Christian, Okuducu, Ali Fuat, Arp, Mirko, Seiz-Rosenhagen, Marcel, Hänggi, Daniel, Heim, Stefanie, Paulus, Werner, Schittenhelm, Jens, Ahmadi, Rezvan, Herold-Mende, Christel, Unterberg, Andreas, Pfister, Stefan M., von Deimling, Andreas, and Reuss, David E.

Published
2016
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32. Adult IDH wild type astrocytomas biologically and clinically resolve into other tumor entities

Author

Reuss, David E., Kratz, Annekathrin, Sahm, Felix, Capper, David, Schrimpf, Daniel, Koelsche, Christian, Hovestadt, Volker, Bewerunge-Hudler, Melanie, Jones, David T. W., Schittenhelm, Jens, Mittelbronn, Michel, Rushing, Elisabeth, Simon, Matthias, Westphal, Manfred, Unterberg, Andreas, Platten, Michael, Paulus, Werner, Reifenberger, Guido, Tonn, Joerg-Christian, Aldape, Kenneth, Pfister, Stefan M., Korshunov, Andrey, Weller, Michael, Herold-Mende, Christel, Wick, Wolfgang, Brandner, Sebastian, and von Deimling, Andreas

Published
2015
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35. Proteomic Approaches in Biomarker Discovery: New Perspectives in Cancer Diagnostics

Author

Petra Hudler, Nina Kocevar, and Radovan Komel

Subjects
Technology, Medicine, Science
Abstract

Despite remarkable progress in proteomic methods, including improved detection limits and sensitivity, these methods have not yet been established in routine clinical practice. The main limitations, which prevent their integration into clinics, are high cost of equipment, the need for highly trained personnel, and last, but not least, the establishment of reliable and accurate protein biomarkers or panels of protein biomarkers for detection of neoplasms. Furthermore, the complexity and heterogeneity of most solid tumours present obstacles in the discovery of specific protein signatures, which could be used for early detection of cancers, for prediction of disease outcome, and for determining the response to specific therapies. However, cancer proteome, as the end-point of pathological processes that underlie cancer development and progression, could represent an important source for the discovery of new biomarkers and molecular targets for tailored therapies.

Published
2014
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36. Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumour material using high-density DNA methylation arrays

Author

Hovestadt, Volker, Remke, Marc, Kool, Marcel, Pietsch, Torsten, Northcott, Paul A., Fischer, Roger, Cavalli, Florence M. G., Ramaswamy, Vijay, Zapatka, Marc, Reifenberger, Guido, Rutkowski, Stefan, Schick, Matthias, Bewerunge-Hudler, Melanie, Korshunov, Andrey, Lichter, Peter, Taylor, Michael D., Pfister, Stefan M., and Jones, David T. W.

Published
2013
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39. Pathophysiology of Asthma-Chronic Obstructive Pulmonary Disease Overlap

Author

Hudler, Andi, Holguin, Fernando, and Sharma, Sunita

Abstract

Asthma-chronic obstructive pulmonary disease (COPD) overlap (ACO) is a condition in which a person has clinical and biological features of both asthma and COPD. The pathophysiology behind the development of ACO is complex, with various inflammatory cells, cytokines, environmental factors, and architectural changes within the airways, all affecting a patient’s clinical manifestation. A better understanding of the pathophysiologic mechanisms resulting in the development of ACO will help us to better identify potential drug targets and improve symptom burden and overall quality of life for patients living with ACO.

Published
2022
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45. Blood‐derived DNA methylation predictors of mortality discriminate tumor and healthy tissue in multiple organs.

Author

Zhang, Yan, Bewerunge‐Hudler, Melanie, Schick, Matthias, Burwinkel, Barbara, Herpel, Esther, Hoffmeister, Michael, and Brenner, Hermann

Abstract

Evidence has shown that certain methylation markers derived from blood can mirror corresponding methylation signatures in internal tissues. In the current study, we aimed to investigate two strong epigenetic predictors for life span, derived from blood DNA methylation data, in tissue samples of solid cancer patients. Using data from the Cancer Genome Atlas (TCGA) and the German DACHS study, we compared a mortality risk score (MRscore) and DNAmPhenoAge in paired tumor and adjacent normal tissue samples of patients with lung (N = 69), colorectal (n = 299), breast (n = 90), head/neck (n = 50), prostate (n = 50), and liver (n = 50) cancer. To explore the concordance across tissue and blood, we additionally assessed the two markers in blood samples of colorectal cancer (CRC) cases and matched controls (n = 93) in the DACHS+ study. The MRscore was significantly elevated in tumor tissues compared to normal tissues of all cancers except prostate cancer, for which an opposite pattern was observed. DNAmPhenoAge was consistently higher in all tumor tissues. The MRscore discriminated lung, colorectal, and prostate tumor tissues from normal tissues with very high accuracy [AUCs of 0.87, 0.99 (TCGA) /0.94 (DACHS), and 0.92, respectively]. DNAmPhenoAge accurately discriminated five types of tumor tissues from normal tissues (except prostate cancer), with AUCs of 0.82–0.93. The MRscore was also significantly higher in blood samples of CRC cases than in controls, with areas under the curve (AUC) of 0.74, whereas DNAmPhenoAge did not distinguish cases from controls, with AUC of 0.54. This study provides compelling evidence that blood‐derived DNAm markers could reflect methylation changes in less accessible tissues. Further research should explore the potential use of these findings for cancer diagnosis and early detection. [ABSTRACT FROM AUTHOR]

Published
2020
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47. Outlook on Epigenetic Therapeutic Approaches for Treatment of Gastric Cancer

Author

Hudler, Petra

Abstract

The incidence of gastric cancer has been declining globally in the last decades. Despite the improvements in the diagnostic procedures, most cases are still detected at advanced stages due to lack of specific symptoms associated with early phases of tumour development. Consequently, gastric cancer poses a major health burden worldwide due to high mortality rates. Continuing advances in high-throughput technologies are revealing an intricate network of genetic and epigenetic changes associated with carcinogenesis. In addition, several risk factors, both environmental and genetic, have been recognized, which promote accumulation of diverse alterations affecting the expression of oncogenes, tumour suppressor genes, DNA repair genes, and other genes, implicated in normal gastric cell functions. A plethora of aberrant molecular events found in patients with this disease and intragenic heterogeneity of tumours from individuals are delaying the development of targeted biological therapies. Frequent occurrence of characteristic CpG island methylator phenotypes (CIMP phenotypes) in gastric cancers, particularly in association with Helicobacter pylori or EBV infection, could lead to introduction of epigenetic modulators into standard treatment regimens used against early and advanced forms of adenocarcinomas. This review highlights aberrant DNA methylation events in the development of gastric tumours and addresses the different aspects associated with the application of therapeutic epigenetic modulation in the management of the disease.

Published
2018
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48. Are there geographical differences in the frequency of SYT-SSX1 and SYT-SSX2 chimeric transcripts in synovial sarcoma?

Author

Kokovic, I., Bracko, M., Golouh, R., Ligtenberg, M.J.L., Krieken, J.H.J.M. van, Hudler, P., Komel, R., Kokovic, I., Bracko, M., Golouh, R., Ligtenberg, M.J.L., Krieken, J.H.J.M. van, Hudler, P., and Komel, R.

Abstract

Contains fulltext : 58287.pdf (publisher's version ) (Closed access), Synovial sarcoma (SS) is characterized by the t(X;18)(p11.2;q11.2) chromosomal translocation, which results in generating either SYT-SSX1, SYT-SSX2 or, infrequently, SYT-SSX4 fusion gene. The ratio of SYT-SSX1:SYT-SSX2 fusions is close to 2:1 in the majority of studies, and SYT-SSX2 fusion has been only rarely observed in biphasic SS. In the present study, we compared two series of patients with SS, Slovenian (37 cases) and Dutch (14 cases), with respect to clinical, pathological and molecular findings. The two groups did not differ with regard to clinicopathological features. Whereas the frequency of different SYT-SSX fusions in the Dutch group was similar to that reported in the literature, we found an unexpectedly high number of tumors with SYT-SSX2 fusion in the Slovenian group. The ratio of SYT-SSX1:SYT-SSX2 fusion was 7:18 for monophasic and 2:7 for biphasic tumors in the Slovenian group. This distribution differs significantly from that observed in the Dutch group in the present study (P = 0.041) as well as from data reported in the recent large multi-institutional study on 243 patients (P = 0.0001). Our findings indicate possible geographical differences in the frequency of two SYT-SSX fusion transcripts in patients with synovial sarcoma.

Published
2004

50. Pythium soft rot of ginger: Detection and identification of the causal pathogens, and their control.

Author

Le, Duy Phu, Smith, Mike, Hudler, George William, and Aitken, Elizabeth

Subjects
BIOLOGICAL control of pythium diseases, GINGER, CONTROL of phytopathogenic microorganisms, CHINESE medicine, ANTI-inflammatory agents, ANTIBACTERIAL agents, COOKING
Abstract

Ginger is considered by many people to be the outstanding member among 1400 other species in the family Zingiberaceae. Not only it is a valuable spice used by cooks throughout the world to impart unique flavour to their dishes but it also has a long track record in some Chinese and Indian cultures for treating common human ailments such as colds and headaches. Ginger has recently attracted considerable attention for its anti-inflammatory, antibacterial and antifungal properties. However, ginger as a crop is also susceptible to at least 24 different plant pathogens, including viruses, bacteria, fungi and nematodes. Of these, Pythium spp. (within the kingdom Stramenopila, phyllum Oomycota) are of most concern because various species can cause rotting and yield loss on ginger at any of the growth stages including during postharvest storage. Pythium gracile was the first species in the genus to be reported as a ginger pathogen, causing Pythium soft rot disease in India in 1907. Thereafter, numerous other Pythium spp. have been recorded from ginger growing regions throughout the world. Today, 15 Pythium species have been implicated as pathogens of the soft rot disease. Because accurate identification of a pathogen is the cornerstone of effective disease management programs, this review will focus on how to detect, identify and control Pythium spp. in general, with special emphasis on Pythium spp. associated with soft rot on ginger. [ABSTRACT FROM AUTHOR]

Published
2014
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