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1. Upfront or delayed surgery in resectable hepatoblastoma: analysis from the childrens hepatic tumors international collaboration database.

Author

Hiyama, Eiso, Hishiki, Tomoro, Yoshimura, Kenichi, Krailo, Mark, Maibach, Rudolf, Haeberle, Beate, Rangaswami, Arun, Lopez-Terrada, Dolores, Malogolowkin, Marcio, Ansari, Marc, Alaggio, Rita, ONeill, Allison, Trobaugh-Lotrario, Angela, Watanabe, Kenichiro, Schmid, Irene, Ranganathan, Sarangarajan, Tanaka, Yukichi, Inoue, Takeshi, Piao, Jin, Lin, Jason, Czauderna, Piotr, Meyers, Rebecka, and Aronson, Daniel

Subjects
Age at diagnosis, Alpha-fetoprotein, Hepatoblastoma, Outcome, Resectable, Up-front surgery
Abstract

BACKGROUND: In the treatment of resectable hepatoblastoma (HB), it has not been established whether upfront surgery (UF) at diagnosis or neoadjuvant chemotherapy and delayed surgery (DL) is preferred. We compared patients with localized HB who underwent either UF, or DL after neoadjuvant chemotherapy in the Childrens Hepatic tumors International Collaboration (CHIC) database of 1605 cases enrolled in eight multicenter hepatoblastoma trials between 1988 and 2010. METHODS: Among the 512 resectable HB patients who had PRETEXT (PRETreament EXTent of disease) I or II unruptured tumors at diagnosis without extrahepatic invasion, distant metastases, or massive vascular invasion, 172 underwent UF and 340 underwent DL. The primary outcomes were event-free and overall survivals after start of treatment in these two groups. Survival analysis was performed using the Kaplan-Maier analysis with long-rank tests and multivariable Cox regression models. FINDINGS: Complete resection rates were comparable (93.6% in UF and 89.7% in DL). The total cycles of chemotherapy of DL (median:6) were significantly more than those of UF (median:4) (P

Published
2024

2. Consensus classification of pediatric hepatocellular tumors: A report from the Children's Hepatic tumors International Collaboration (CHIC)

Author

Cho, Soo‐Jin, Ranganathan, Sarangarajan, Alaggio, Rita, Maibach, Rudolf, Tanaka, Yukichi, Inoue, Takeshi, Leuschner, Ivo, Krijger, Ronald, Vokuhl, Christian, Krailo, Mark, Malogolowkin, Marcio, Meyers, Rebecka, Czauderna, Piotr, Hiyama, Eiso, Ansari, Marc, Morland, Bruce, Trobaugh‐Lotrario, Angela, O'Neill, Allison F, Rangaswami, Arun, Häberle, Beate, and López‐Terrada, Dolores

Subjects
Liver Disease, Pediatric, Digestive Diseases, Rare Diseases, Cancer, hepatoblastoma, international clinical trial, liver tumors, pediatric, Clinical Sciences, Oncology and Carcinogenesis, Paediatrics and Reproductive Medicine, Oncology & Carcinogenesis
Abstract

BackgroundLiver tumors are rare in children with histologic heterogeneity that makes diagnosis challenging. Systematic histopathological review, performed as part of collaborative therapeutic protocols, identified relevant histologic subtypes that are important to distinguish. The Children's Hepatic tumors International Collaboration (CHIC) was established to study pediatric liver tumors on a global scale and led to establishment of a provisional consensus classification for use in international clinical trials. The current study is the validation of this initial classification and first large-scale application by international expert reviewers.ProcedureThe CHIC initiative includes data from 1605 children treated on eight multicenter hepatoblastoma (HB) trials. Review of 605 available tumors was performed by seven expert pathologists from three consortia (US, EU, Japan). Cases with discordant diagnoses were collectively reviewed to reach a final consensus diagnosis.ResultsOf 599 cases with sufficient material for review, 570 (95.2%) were classified as HB by all consortia, and 29 (4.8%) as non-HB, which included "hepatocellular neoplasm, NOS" and malignant rhabdoid tumors. 453 of 570 HBs were classified as epithelial by final consensus. Some patterns (i.e., small cell undifferentiated, macrotrabecular, cholangioblastic) were selectively identified by reviewers from different consortia. All consortia identified a similar number of mixed epithelial-mesenchymal HB.ConclusionsThis study represents the first large-scale application and validation of the pediatric malignant hepatocellular tumors consensus classification. It is a valuable resource to train future generations of investigators on accurate diagnosis of these rare tumors and provides a framework for further international collaborative studies and refinement of the current classification of pediatric liver tumors.

Published
2023

3. Outcomes of Patients Treated for Hepatoblastoma with Low Alpha-Fetoprotein and/or Small Cell Undifferentiated Histology: A Report from the Children's Hepatic Tumors International Collaboration (CHIC).

Author

Trobaugh-Lotrario, Angela D, Maibach, Rudolf, Aronson, Daniel C, Rangaswami, Arun, Häberle, Beate, O'Neill, Allison F, Schmid, Irene, Ansari, Marc, Hishiki, Tomoro, Ranganathan, Sarangarajan, Alaggio, Rita, de Krijger, Ronald R, Tanaka, Yukichi, Cho, Soo-Jin, Vokuhl, Christian, Maxwell, Rebecca, Krailo, Mark, Hiyama, Eiso, Czauderna, Piotr, Finegold, Milton, Feusner, James H, Malogolowkin, Marcio H, Meyers, Rebecka L, and Lopez-Terrada, Dolores

Subjects
AFP, Hepatoblastoma, SCU, SMARCB1, rhabdoid, Cancer, Digestive Diseases, Liver Disease, Oncology and Carcinogenesis
Abstract

Small cell undifferentiated (SCU) histology and alpha-fetoprotein (AFP) levels below 100 ng/mL have been reported as poor prognostic factors in hepatoblastoma (HB); subsequent studies reported SMARCB1 mutations in some SCU HBs confirming the diagnosis of rhabdoid tumor. The Children's Hepatic tumors International Collaboration (CHIC) database was queried for patients with HB who had AFP levels less than 100 ng/mL at diagnosis or were historically diagnosed as SCU HBs. Seventy-three of 1605 patients in the CHIC database were originally identified as SCU HB, HB with SCU component, or HB with low AFP levels. Upon retrospective review, they were re-classified as rhabdoid tumors (n = 11), HB with SCU component (n = 41), and HB with low AFP (n = 14). Seven were excluded for erroneously low AFP levels. Overall survival was 0% for patients with rhabdoid tumors, 76% for patients with HB with SCU component, and 64% for patients with HB with AFP less than 100 ng/mL. Patients with HB with SCU component or low AFP should be assessed for SMARCB1 mutations and, if confirmed, treated as rhabdoid tumors. When rhabdoid tumors are excluded, the presence of SCU component and low AFP at diagnosis were not associated with poor prognosis in patients diagnosed with HB.

Published
2023

4. Remote Collaboration in Higher Game Development Education. Online Practices and Learning Processes of Students between Professional Routines and Psychosocial Challenges

Author

Czauderna, André and Guardiola, Emmanuel

Abstract

The development of digital games over physical distance is a common practice in the gaming industry, yet widely neglected in the curricula of digital game development programs at university level. The coronavirus pandemic, however, pushed project-oriented game programs all over the world towards an implementation of ad hoc approaches to remote development in their project-based courses. The present article demonstrates practice-based research examining such a course and its 30 third-year undergraduate students of game arts, game design, and game programming, who remotely collaborated in interdisciplinary groups of two to five persons over the course of half a semester during Germany's logdown in spring 2020. Applying a mixed-method approach including quantitative and qualitative analyses of survey data (n=22) and qualitative content analyses of students' postmortem documentations (n=30), this exploratory study reconstructed the online practices, experiences, and learning processes of these students between their professional routines and psychosocial challenges. The results of this study can be used in curriculum development to inform the advancement of courses focused on the development of prototypes over physical distance, which may not only be relevant for the field of games education, but also for related creative and project-oriented fields of higher education, such as design, digital media, and software engineering.

Published
2021

5. How Digital Strategy and Management Games Can Facilitate the Practice of Dynamic Decision-Making

Author

Czauderna, André and Budke, Alexandra

Abstract

This paper examines how digital strategy and management games that have been initially designed for entertainment can facilitate the practice of dynamic decision-making. Based on a comparative qualitative analysis of 17 games--organized into categories derived from a conceptual model of decision-making design--this article illustrates two ways in which these games may be useful in supporting the learning of dynamic decision-making in educational practice: (1) Players must take over the role of a decider and solve situations in which players must pursue different conflicting goals by making a continuous series of decisions on a variety of actions and measures; (2) three of the features of the games are considered to structure players' practice of decision-making and foster processes of learning through the curation of possible decisions, the offering of lucid feedback and the modification of time. This article also highlights the games' shortcomings, from an educational perspective, as players' decisions are restricted by the numbers of choices they can make within the game, and certain choices are rewarded more than others. An educational application of the games must, therefore, entail a critical reflection of players' limited choices inside a necessarily biased system.

Published
2020

9. The Gameplay Loop Methodology as a Tool for Educational Game Design

Author

Czauderna, André and Guardiola, Emmanuel

Abstract

The field of game design for educational content lacks a focus on methodologies that merge gameplay and learning. Existing methodologies typically fall short in three ways: they neglect the unfolding of gameplay through players' actions over a short period of time as a significant unit of analysis; they lack a common consideration of game and learning mechanics; and they falsely separate the acts of playing and learning. This paper recommends the gameplay loop methodology as a valuable tool for educational game design, as it addresses these major shortcomings. Furthermore, this paper outlines how this methodology can be supported by knowledge from subject-specific didactics--considering both the curriculum and its mediation (contributed by experts from educational practice) as well as methods of player-centered design--in order to ensure the appropriateness of learning objectives and techniques of mediation in the context of a particular field of knowledge, the game's appeal to its target group, and the effectiveness of the learning mechanics. A case study of the design and production phases of Antura and the Letters, a literacy game for Arabic refugee children, illustrates the uses of the gameplay loop methodology situated in the described broader approach to educational game design. Finally, this paper explains the results of an impact study revealing that the approach indeed provides the opportunity to merge playing and learning.

Published
2019

10. OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies

Author

Yang, Ying, Wybrow, Michael, Li, Yuan-Fang, Czauderna, Tobias, and He, Yongqun

Subjects
Computer Science - Human-Computer Interaction, Computer Science - Artificial Intelligence
Abstract

Ontologies are formal representations of concepts and complex relationships among them. They have been widely used to capture comprehensive domain knowledge in areas such as biology and medicine, where large and complex ontologies can contain hundreds of thousands of concepts. Especially due to the large size of ontologies, visualisation is useful for authoring, exploring and understanding their underlying data. Existing ontology visualisation tools generally focus on the hierarchical structure, giving much less emphasis to non-hierarchical associations. In this paper we present OntoPlot, a novel visualisation specifically designed to facilitate the exploration of all concept associations whilst still showing an ontology's large hierarchical structure. This hybrid visualisation combines icicle plots, visual compression techniques and interactivity, improving space-efficiency and reducing visual structural complexity. We conducted a user study with domain experts to evaluate the usability of OntoPlot, comparing it with the de facto ontology editor Prot{\'e}g{\'e}. The results confirm that OntoPlot attains our design goals for association-related tasks and is strongly favoured by domain experts., Comment: Accepted at IEEE InfoVis 2019

Published
2019
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11. Risk-stratified staging in paediatric hepatoblastoma: a unified analysis from the Children's Hepatic tumors International Collaboration

Author

Meyers, Rebecka L, Maibach, Rudolf, Hiyama, Eiso, Häberle, Beate, Krailo, Mark, Rangaswami, Arun, Aronson, Daniel C, Malogolowkin, Marcio H, Perilongo, Giorgio, von Schweinitz, Dietrich, Ansari, Marc, Lopez-Terrada, Dolores, Tanaka, Yukichi, Alaggio, Rita, Leuschner, Ivo, Hishiki, Tomoro, Schmid, Irene, Watanabe, Kenichiro, Yoshimura, Kenichi, Feng, Yurong, Rinaldi, Eugenia, Saraceno, Davide, Derosa, Marisa, and Czauderna, Piotr

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Liver Disease, Pediatric, Digestive Diseases, Cancer, Adolescent, Child, Child, Preschool, Combined Modality Therapy, Cooperative Behavior, Databases, Factual, Female, Follow-Up Studies, Hepatoblastoma, Humans, Infant, Infant, Newborn, International Agencies, Japan, Liver Neoplasms, Lymphatic Metastasis, Male, Neoplasm Staging, Prognosis, Prospective Studies, Risk Factors, Survival Rate, alpha-Fetoproteins, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

BackgroundComparative assessment of treatment results in paediatric hepatoblastoma trials has been hampered by small patient numbers and the use of multiple disparate staging systems by the four major trial groups. To address this challenge, we formed a global coalition, the Children's Hepatic tumors International Collaboration (CHIC), with the aim of creating a common approach to staging and risk stratification in this rare cancer.MethodsThe CHIC steering committee-consisting of leadership from the four major cooperative trial groups (the International Childhood Liver Tumours Strategy Group, Children's Oncology Group, the German Society for Paediatric Oncology and Haematology, and the Japanese Study Group for Paediatric Liver Tumours)-created a shared international database that includes comprehensive data from 1605 children treated in eight multicentre hepatoblastoma trials over 25 years. Diagnostic factors found to be most prognostic on initial analysis were PRETreatment EXTent of disease (PRETEXT) group; age younger than 3 years, 3-7 years, and 8 years or older; α fetoprotein (AFP) concentration of 100 ng/mL or lower and 101-1000 ng/mL; and the PRETEXT annotation factors metastatic disease (M), macrovascular involvement of all hepatic veins (V) or portal bifurcation (P), contiguous extrahepatic tumour (E), multifocal tumour (F), and spontaneous rupture (R). We defined five clinically relevant backbone groups on the basis of established prognostic factors: PRETEXT I/II, PRETEXT III, PRETEXT IV, metastatic disease, and AFP concentration of 100 ng/mL or lower at diagnosis. We then carried the additional factors into a hierarchical backwards elimination multivariable analysis and used the results to create a new international staging system.ResultsWithin each backbone group, we identified constellations of factors that were most predictive of outcome in that group. The robustness of candidate models was then interrogated using the bootstrapping procedure. Using the clinically established PRETEXT groups I, II, III, and IV as our stems, we created risk stratification trees based on 5 year event-free survival and clinical applicability. We defined and adopted four risk groups: very low, low, intermediate, and high.InterpretationWe have created a unified global approach to risk stratification in children with hepatoblastoma on the basis of rigorous statistical interrogation of what is, to the best of our knowledge, the largest dataset ever assembled for this rare paediatric tumour. This achievement provides the structural framework for further collaboration and prospective international cooperative study, such as the Paediatric Hepatic International Tumour Trial (PHITT).FundingEuropean Network for Cancer Research in Children and Adolescents, funded through the Framework Program 7 of the European Commission (grant number 261474); Children's Oncology Group CureSearch grant contributed by the Hepatoblastoma Foundation; Practical Research for Innovative Cancer Control and Project Promoting Clinical Trials for Development of New Drugs and Medical Devices, Japan Agency for Medical Research; and Swiss Cancer Research grant.

Published
2017

12. Large-scale generation of computational models from biochemical pathway maps

Author

Büchel, Finja, Rodriguez, Nicolas, Swainston, Neil, Wrzodek, Clemens, Czauderna, Tobias, Keller, Roland, Mittag, Florian, Schubert, Michael, Glont, Mihai, Golebiewski, Martin, van Iersel, Martijn, Keating, Sarah, Rall, Matthias, Wybrow, Michael, Hermjakob, Henning, Hucka, Michael, Kell, Douglas B., Müller, Wolfgang, Mendes, Pedro, Zell, Andreas, Chaouiya, Claudine, Saez-Rodriguez, Julio, Schreiber, Falk, Laibe, Camille, Dräger, Andreas, and Novère, Nicolas Le

Subjects
Quantitative Biology - Molecular Networks
Abstract

Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway reconstructions. However, mathematical models are still most often created de novo, based on reading the literature and processing pathway data manually. Results: To increase the efficiency with which such models can be created, we automatically generated mathematical models from pathway representations using a suite of freely available software. We produced models that combine data from KEGG PATHWAY, BioCarta, MetaCyc and SABIO-RK; According to the source data, three types of models are provided: kinetic, logical and constraint-based. All models are encoded using SBML Core and Qual packages, and available through BioModels Database. Each model contains the list of participants, the interactions, and the relevant mathematical constructs, but, in most cases, no meaningful parameter values. Most models are also available as easy to understand graphical SBGN maps. Conclusions: to date, the project has resulted in more than 140000 models freely available. We believe this resource can tremendously accelerate the development of mathematical models by providing initial starting points ready for parametrization., Comment: 29 pages, 8 figures

Published
2013
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13. Erratum To: COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms

Author

Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, D A B, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff‐Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2021
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14. Association of Lesion Location and Functional Parameters with Vision-Related Quality of Life in Geographic Atrophy Secondary to Age-related Macular Degeneration

Author

Künzel, Sandrine H., Broadbent, Eliza, Möller, Philipp T., Lindner, Moritz, Goerdt, Lukas, Czauderna, Joanna, Schmitz-Valckenberg, Steffen, Holz, Frank G., Pfau, Maximilian, and Fleckenstein, Monika

Abstract

The primary goal of this study was to determine how structural and functional parameters influence the vision-related quality of life (VRQoL) in patients suffering from geographic atrophy (GA) secondary to age-related macular degeneration.

Published
2024
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15. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Author

Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff-Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2021
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16. Path2Models: large-scale generation of computational models from biochemical pathway maps

Author

Büchel, Finja, Rodriguez, Nicolas, Swainston, Neil, Wrzodek, Clemens, Czauderna, Tobias, Keller, Roland, Mittag, Florian, Schubert, Michael, Glont, Mihai, Golebiewski, Martin, van Iersel, Martijn, Keating, Sarah, Rall, Matthias, Wybrow, Michael, Hermjakob, Henning, Hucka, Michael, Kell, Douglas B, Müller, Wolfgang, Mendes, Pedro, Zell, Andreas, Chaouiya, Claudine, Saez-Rodriguez, Julio, Schreiber, Falk, Laibe, Camille, Dräger, Andreas, and Le Novère, Nicolas

Abstract

Abstract Background Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data. Results To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2 600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at http://www.ebi.ac.uk/biomodels-main/path2models. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understand graphical SBGN maps. Conclusions To date, the project has resulted in more than 140 000 freely available models. Such a resource can tremendously accelerate the development of mathematical models by providing initial starting models for simulation and analysis, which can be subsequently curated and further parameterized.

Published
2013

20. Heme oxygenase‐1 deficiency triggers exhaustion of hematopoietic stem cells

Author

Szade, Krzysztof, Zukowska, Monika, Szade, Agata, Nowak, Witold, Skulimowska, Izabella, Ciesla, Maciej, Bukowska‐Strakova, Karolina, Gulati, Gunsagar Singh, Kachamakova‐Trojanowska, Neli, Kusienicka, Anna, Einwallner, Elisa, Kijowski, Jacek, Czauderna, Szymon, Esterbauer, Harald, Benes, Vladimir, L Weissman, Irving, Dulak, Jozef, and Jozkowicz, Alicja

Published
2020
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24. Global effort to evacuate Ukrainian children with cancer and blood disorders who have been affected by war

Author

Agulnik, A, Kizyma, R, Salek, M, Wlodarski, M, Pogorelyy, M, Oszer, A, Yakimkova, T, Nogovitsyna, Y, Dutkiewicz, M, Dalle, J, Dirksen, U, Eggert, A, Fernandez-Teijeiro, A, Greiner, J, Kraal, K, Mueller, A, Sramkova, L, Zecca, M, Wise, P, Mlynarski, W, Avula, M, Adyrov, M, Berlanga, P, Blackwood, C, Bouffet, E, Czauderna, P, de Koning, L, dos Reis Farinha, N, Foster, W, Graetz, D, Gupta, S, Holter, W, Hough, R, Kliuchkivska, K, Kolenova, A, Kolodrubiec, J, Moreira, D, Mukkada, S, Mykychak, I, Raciborska, A, Salman, Z, Sopilnyak, A, Tyupa, S, Vinitsky, A, Wobst, N, Miller, B, Rasul, S, Rodriguez-Galindo, C, Alanbousi, I, Alexander, S, Apel, A, Bal, W, Balwierz, W, Basset-Salom, L, Bastardo Blanco, D, Bauer, K, Bayazitov, I, Bhakta, N, Bien, E, Bieniek, K, Blair, S, Bodak, K, Bordeianu, I, Braganca, J, Bucurenci, M, Budny, E, Budzyn, A, Bumgardner, C, Burditt, R, Burnside Clapp, V, Bykov, V, Canete, A, Carnelli, M, Cela, E, Cepowska, Z, Chaber, R, Cherner-Drieux, A, Chubata, M, Clough, H, Czernicka - Siwecka, J, Czyzewski, K, Dashchakovska, O, Dembowska-Baginska, B, Derwich, K, Dommett, R, Dorosh, O, Drabko, K, Dragomir, M, Dworzak, M, Dyma, S, Earl, J, English, M, Evseev, D, Farren, B, Fedyk, N, Ferneza, S, Fox Irwin, L, Galazkowski, R, Ganieva, G, Garanzha, V, Gelman, M, Godzinski, J, Goeres, A, Golban, R, Griksaitis, M, Hampel, M, Hastings, S, Heenen, D, Hill, M, Holiuk, I, Hutnik, L, Irga-Jaworska, N, Istomin, O, Janczar, S, Kacharian, A, Kalwak, K, Karolczyk, G, Karpenko, N, Katsubo, H, Kaznowska, B, Kentsis, A, Ketteler, P, Kienesberger, A, Kiselev, R, Kizyma, Z, Klymniuk, H, Kostiuk, Y, Kowalik, T, Kozlova, O, Kozubenko, V, Kramar, T, Krawczuk-Rybak, M, Kulemzina, I, Kurkowska, P, Kuzyk, A, Ladenstein, R, Laguna, P, Lassaletta, A, Lehmberg, K, Leontieva, O, Liashenko, S, Loizou, L, Lucchetta, S, Lupo, M, Lysytsia, L, Lysytsia, O, Machnik, K, Mainland, J, Matczak, K, Matysiak, M, Mayeur, P, Minervina, A, Mishkova, V, Mizia-Malarz, A, Morales La Madrid, A, Moreno, L, Moskvin, V, Muszynska-Roslan, K, Nelson, A, Ociepa, T, Oltolini, S, Onipko, N, Pappas, A, Patel, A, Patrahau, A, Pauley, J, Pavlenko, Y, Pavlovych, A, Peregud-Pogorzelski, J, Perek-Polnik, M, Perez, V, Perez-Martinez, A, Pikman, Y, Pitozzi, G, Portugal, R, Posternak, V, Prete, A, Pritchard-Jones, K, Radaelli, A, Reeves, T, Reinhardt, D, Reshetnyak, A, Rider, A, Rizzari, C, Rizzi, D, Rodriguez Hermosillo, K, Ronenko, O, Rostowska, A, Rudko, L, Sakaan, F, Sakhar, N, Savva, N, Scaccaglia, D, Schaeffer, E, Schneider, C, Scobie, N, Semeniuk, O, Shevchyk, R, Shuler, A, Shvets, S, Skoczen, S, Smeal, W, Sokolowski, I, Sonkin, A, Stepanjuk, A, Spota, A, Sterba, J, Styczynski, J, Svintsova, O, Synyuta, A, Szczepanski, T, Szczucinski, P, Szmyd, B, Tasso Cereceda, M, Teliuk, A, Tomanek, I, Topping, P, Torrent, M, Trelinska, J, Troyanovska, O, Trubnikova, E, Tsurkan, L, Tsymbalyuk-Voloshyn, I, Urasinski, T, Urbanek-Dadela, A, Vasilieva, N, Vasilyeva, A, Verdu-Amoros, J, Vilcu-Bajurean, N, Vinitsky, L, Volpe, G, Vorobel, O, Wachowiak, J, Wasiak, M, Wiedower, L, Wuenschel, L, Wysocki, M, Yurieva, M, Zagurska, A, Zakharenko, S, Zakharenko, A, Zapotochna, K, Zawitkowska, J, Agulnik A., Kizyma R., Salek M., Wlodarski M. W., Pogorelyy M., Oszer A., Yakimkova T., Nogovitsyna Y., Dutkiewicz M., Dalle J. -H., Dirksen U., Eggert A., Fernandez-Teijeiro A., Greiner J., Kraal K., Mueller A., Sramkova L., Zecca M., Wise P. H., Mlynarski W., Avula M., Adyrov M. V., Berlanga P., Blackwood C. A., Bouffet E., Czauderna P. S., de Koning L. A., dos Reis Farinha N. J., Foster W. B., Graetz D. E., Gupta S., Holter W., Hough R. E., Kliuchkivska K., Kolenova A., Kolodrubiec J., Moreira D. C., Mukkada S. T., Mykychak I., Raciborska A., Salman Z. S., Sopilnyak A., Tyupa S., Vinitsky A., Wobst N. M., Miller B. A., Rasul S. S., Rodriguez-Galindo C., Alanbousi I., Alexander S. W., Apel A., Bal W. A., Balwierz W. A., Basset-Salom L., Bastardo Blanco D., Bauer K. J., Bayazitov I. T., Bhakta N. H., Bien E. I., Bieniek K. A., Blair S. J., Bodak K. I., Bordeianu I. M., Braganca J. M., Bucurenci M. S., Budny E. B., Budzyn A., Bumgardner C. C., Burditt R. N., Burnside Clapp V. G., Bykov V., Canete A., Carnelli M., Cela E., Cepowska Z. P., Chaber R., Cherner-Drieux A., Chubata M., Clough H. M., Czernicka - Siwecka J., Czyzewski K., Dashchakovska O., Dembowska-Baginska B. M., Derwich K., Dommett R., Dorosh O., Drabko K. A., Dragomir M. D., Dworzak M., Dyma S., Earl J. D., English M. W., Evseev D. A., Farren B. S., Fedyk N., Ferneza S., Fox Irwin L. E., Galazkowski R. M., Ganieva G., Garanzha V., Gelman M. S., Godzinski J. K., Goeres A. F., Golban R., Griksaitis M. J., Hampel M. A., Hastings S. G., Heenen D. L., Hill M. C., Holiuk I., Hutnik L. M., Irga-Jaworska N., Istomin O., Janczar S. L., Kacharian A., Kalwak K., Karolczyk G. M., Karpenko N. M., Katsubo H., Kaznowska B. J., Kentsis A., Ketteler P., Kienesberger A., Kiselev R., Kizyma Z., Klymniuk H., Kostiuk Y., Kowalik T., Kozlova O., Kozubenko V., Kramar T., Krawczuk-Rybak M., Kulemzina I., Kurkowska P., Kuzyk A. S., Ladenstein R. L., Laguna P. J., Lassaletta A., Lehmberg K., Leontieva O., Liashenko S., Loizou L. G., Lucchetta S. A., Lupo M. W., Lysytsia L., Lysytsia O., Machnik K. A., Mainland J. A., Matczak K. E., Matysiak M. J., Mayeur P., Minervina A. A., Mishkova V., Mizia-Malarz A. J., Morales La Madrid A., Moreno L., Moskvin V. P., Muszynska-Roslan K. M., Nelson A. J., Ociepa T., Oltolini S., Onipko N., Pappas A., Patel A. B., Patrahau A., Pauley J. L., Pavlenko Y., Pavlovych A., Peregud-Pogorzelski J., Perek-Polnik M., Perez V., Perez-Martinez A., Pikman Y., Pitozzi G., Portugal R. G., Posternak V. V., Prete A., Pritchard-Jones K., Radaelli A., Reeves T., Reinhardt D., Reshetnyak A. V., Rider A. J., Rizzari C., Rizzi D., Rodriguez Hermosillo K. G., Ronenko O., Rostowska A. O., Rudko L., Sakaan F. M., Sakhar N., Savva N. N., Scaccaglia D., Schaeffer E. H., Schneider C. U., Scobie N., Semeniuk O., Shevchyk R., Shuler A. I., Shvets S., Skoczen S. P., Smeal W. J., Sokolowski I., Sonkin A. A., Stepanjuk A. I., Spota A., Sterba J., Styczynski J., Svintsova O., Synyuta A. V., Szczepanski T., Szczucinski P. K., Szmyd B. M., Tasso Cereceda M., Teliuk A., Tomanek I., Topping P., Torrent M., Trelinska J., Troyanovska O., Trubnikova E., Tsurkan L. G., Tsymbalyuk-Voloshyn I., Urasinski T. F., Urbanek-Dadela A., Vasilieva N., Vasilyeva A., Verdu-Amoros J., Vilcu-Bajurean N., Vinitsky L., Volpe G., Vorobel O., Wachowiak J. T., Wasiak M. S., Wiedower L. A., Wuenschel L. I., Wysocki M. S., Yurieva M., Zagurska A., Zakharenko S. S., Zakharenko A. V., Zapotochna K., Zawitkowska J. E., Agulnik, A, Kizyma, R, Salek, M, Wlodarski, M, Pogorelyy, M, Oszer, A, Yakimkova, T, Nogovitsyna, Y, Dutkiewicz, M, Dalle, J, Dirksen, U, Eggert, A, Fernandez-Teijeiro, A, Greiner, J, Kraal, K, Mueller, A, Sramkova, L, Zecca, M, Wise, P, Mlynarski, W, Avula, M, Adyrov, M, Berlanga, P, Blackwood, C, Bouffet, E, Czauderna, P, de Koning, L, dos Reis Farinha, N, Foster, W, Graetz, D, Gupta, S, Holter, W, Hough, R, Kliuchkivska, K, Kolenova, A, Kolodrubiec, J, Moreira, D, Mukkada, S, Mykychak, I, Raciborska, A, Salman, Z, Sopilnyak, A, Tyupa, S, Vinitsky, A, Wobst, N, Miller, B, Rasul, S, Rodriguez-Galindo, C, Alanbousi, I, Alexander, S, Apel, A, Bal, W, Balwierz, W, Basset-Salom, L, Bastardo Blanco, D, Bauer, K, Bayazitov, I, Bhakta, N, Bien, E, Bieniek, K, Blair, S, Bodak, K, Bordeianu, I, Braganca, J, Bucurenci, M, Budny, E, Budzyn, A, Bumgardner, C, Burditt, R, Burnside Clapp, V, Bykov, V, Canete, A, Carnelli, M, Cela, E, Cepowska, Z, Chaber, R, Cherner-Drieux, A, Chubata, M, Clough, H, Czernicka - Siwecka, J, Czyzewski, K, Dashchakovska, O, Dembowska-Baginska, B, Derwich, K, Dommett, R, Dorosh, O, Drabko, K, Dragomir, M, Dworzak, M, Dyma, S, Earl, J, English, M, Evseev, D, Farren, B, Fedyk, N, Ferneza, S, Fox Irwin, L, Galazkowski, R, Ganieva, G, Garanzha, V, Gelman, M, Godzinski, J, Goeres, A, Golban, R, Griksaitis, M, Hampel, M, Hastings, S, Heenen, D, Hill, M, Holiuk, I, Hutnik, L, Irga-Jaworska, N, Istomin, O, Janczar, S, Kacharian, A, Kalwak, K, Karolczyk, G, Karpenko, N, Katsubo, H, Kaznowska, B, Kentsis, A, Ketteler, P, Kienesberger, A, Kiselev, R, Kizyma, Z, Klymniuk, H, Kostiuk, Y, Kowalik, T, Kozlova, O, Kozubenko, V, Kramar, T, Krawczuk-Rybak, M, Kulemzina, I, Kurkowska, P, Kuzyk, A, Ladenstein, R, Laguna, P, Lassaletta, A, Lehmberg, K, Leontieva, O, Liashenko, S, Loizou, L, Lucchetta, S, Lupo, M, Lysytsia, L, Lysytsia, O, Machnik, K, Mainland, J, Matczak, K, Matysiak, M, Mayeur, P, Minervina, A, Mishkova, V, Mizia-Malarz, A, Morales La Madrid, A, Moreno, L, Moskvin, V, Muszynska-Roslan, K, Nelson, A, Ociepa, T, Oltolini, S, Onipko, N, Pappas, A, Patel, A, Patrahau, A, Pauley, J, Pavlenko, Y, Pavlovych, A, Peregud-Pogorzelski, J, Perek-Polnik, M, Perez, V, Perez-Martinez, A, Pikman, Y, Pitozzi, G, Portugal, R, Posternak, V, Prete, A, Pritchard-Jones, K, Radaelli, A, Reeves, T, Reinhardt, D, Reshetnyak, A, Rider, A, Rizzari, C, Rizzi, D, Rodriguez Hermosillo, K, Ronenko, O, Rostowska, A, Rudko, L, Sakaan, F, Sakhar, N, Savva, N, Scaccaglia, D, Schaeffer, E, Schneider, C, Scobie, N, Semeniuk, O, Shevchyk, R, Shuler, A, Shvets, S, Skoczen, S, Smeal, W, Sokolowski, I, Sonkin, A, Stepanjuk, A, Spota, A, Sterba, J, Styczynski, J, Svintsova, O, Synyuta, A, Szczepanski, T, Szczucinski, P, Szmyd, B, Tasso Cereceda, M, Teliuk, A, Tomanek, I, Topping, P, Torrent, M, Trelinska, J, Troyanovska, O, Trubnikova, E, Tsurkan, L, Tsymbalyuk-Voloshyn, I, Urasinski, T, Urbanek-Dadela, A, Vasilieva, N, Vasilyeva, A, Verdu-Amoros, J, Vilcu-Bajurean, N, Vinitsky, L, Volpe, G, Vorobel, O, Wachowiak, J, Wasiak, M, Wiedower, L, Wuenschel, L, Wysocki, M, Yurieva, M, Zagurska, A, Zakharenko, S, Zakharenko, A, Zapotochna, K, Zawitkowska, J, Agulnik A., Kizyma R., Salek M., Wlodarski M. W., Pogorelyy M., Oszer A., Yakimkova T., Nogovitsyna Y., Dutkiewicz M., Dalle J. -H., Dirksen U., Eggert A., Fernandez-Teijeiro A., Greiner J., Kraal K., Mueller A., Sramkova L., Zecca M., Wise P. H., Mlynarski W., Avula M., Adyrov M. V., Berlanga P., Blackwood C. A., Bouffet E., Czauderna P. S., de Koning L. A., dos Reis Farinha N. J., Foster W. B., Graetz D. E., Gupta S., Holter W., Hough R. E., Kliuchkivska K., Kolenova A., Kolodrubiec J., Moreira D. C., Mukkada S. T., Mykychak I., Raciborska A., Salman Z. S., Sopilnyak A., Tyupa S., Vinitsky A., Wobst N. M., Miller B. A., Rasul S. S., Rodriguez-Galindo C., Alanbousi I., Alexander S. W., Apel A., Bal W. A., Balwierz W. A., Basset-Salom L., Bastardo Blanco D., Bauer K. J., Bayazitov I. T., Bhakta N. H., Bien E. I., Bieniek K. A., Blair S. J., Bodak K. I., Bordeianu I. M., Braganca J. M., Bucurenci M. S., Budny E. B., Budzyn A., Bumgardner C. C., Burditt R. N., Burnside Clapp V. G., Bykov V., Canete A., Carnelli M., Cela E., Cepowska Z. P., Chaber R., Cherner-Drieux A., Chubata M., Clough H. M., Czernicka - Siwecka J., Czyzewski K., Dashchakovska O., Dembowska-Baginska B. M., Derwich K., Dommett R., Dorosh O., Drabko K. A., Dragomir M. D., Dworzak M., Dyma S., Earl J. D., English M. W., Evseev D. A., Farren B. S., Fedyk N., Ferneza S., Fox Irwin L. E., Galazkowski R. M., Ganieva G., Garanzha V., Gelman M. S., Godzinski J. K., Goeres A. F., Golban R., Griksaitis M. J., Hampel M. A., Hastings S. G., Heenen D. L., Hill M. C., Holiuk I., Hutnik L. M., Irga-Jaworska N., Istomin O., Janczar S. L., Kacharian A., Kalwak K., Karolczyk G. M., Karpenko N. M., Katsubo H., Kaznowska B. J., Kentsis A., Ketteler P., Kienesberger A., Kiselev R., Kizyma Z., Klymniuk H., Kostiuk Y., Kowalik T., Kozlova O., Kozubenko V., Kramar T., Krawczuk-Rybak M., Kulemzina I., Kurkowska P., Kuzyk A. S., Ladenstein R. L., Laguna P. J., Lassaletta A., Lehmberg K., Leontieva O., Liashenko S., Loizou L. G., Lucchetta S. A., Lupo M. W., Lysytsia L., Lysytsia O., Machnik K. A., Mainland J. A., Matczak K. E., Matysiak M. J., Mayeur P., Minervina A. A., Mishkova V., Mizia-Malarz A. J., Morales La Madrid A., Moreno L., Moskvin V. P., Muszynska-Roslan K. M., Nelson A. J., Ociepa T., Oltolini S., Onipko N., Pappas A., Patel A. B., Patrahau A., Pauley J. L., Pavlenko Y., Pavlovych A., Peregud-Pogorzelski J., Perek-Polnik M., Perez V., Perez-Martinez A., Pikman Y., Pitozzi G., Portugal R. G., Posternak V. V., Prete A., Pritchard-Jones K., Radaelli A., Reeves T., Reinhardt D., Reshetnyak A. V., Rider A. J., Rizzari C., Rizzi D., Rodriguez Hermosillo K. G., Ronenko O., Rostowska A. O., Rudko L., Sakaan F. M., Sakhar N., Savva N. N., Scaccaglia D., Schaeffer E. H., Schneider C. U., Scobie N., Semeniuk O., Shevchyk R., Shuler A. I., Shvets S., Skoczen S. P., Smeal W. J., Sokolowski I., Sonkin A. A., Stepanjuk A. I., Spota A., Sterba J., Styczynski J., Svintsova O., Synyuta A. V., Szczepanski T., Szczucinski P. K., Szmyd B. M., Tasso Cereceda M., Teliuk A., Tomanek I., Topping P., Torrent M., Trelinska J., Troyanovska O., Trubnikova E., Tsurkan L. G., Tsymbalyuk-Voloshyn I., Urasinski T. F., Urbanek-Dadela A., Vasilieva N., Vasilyeva A., Verdu-Amoros J., Vilcu-Bajurean N., Vinitsky L., Volpe G., Vorobel O., Wachowiak J. T., Wasiak M. S., Wiedower L. A., Wuenschel L. I., Wysocki M. S., Yurieva M., Zagurska A., Zakharenko S. S., Zakharenko A. V., Zapotochna K., and Zawitkowska J. E.

Published
2022

25. Second Malignant Neoplasms Following Treatment for Hepatoblastoma: An International Report and Review of the Literature

Author

Trobaugh-Lotrario, Angela, Watanabe, Kenichiro, O’Neill, Allison F., Dembowska-Bagińska, Bozenna, Häberle, Beate, Murphy, Andrew, Hiyama, Eiso, Czauderna, Piotr, Meyers, Rebecka L., Langham, Max, and Feusner, James

Abstract

Treatment intensification has improved survival in patients with hepatoblastoma (HB); however, these treatments are associated with an increased risk of late effects, including second malignant neoplasms (SMNs). Data is limited regarding SMNs following HB treatment. Cases of SMNs following treatment for HB reported in the literature and from personal communication were analyzed to further assess this late effect. Thirty-eight patients were identified. The median age at diagnosis of HB was 16 months (range: 3 to 168 mo). All patients had received a platinum agent, and almost all had anthracycline exposure. The SMNs reported were hematopoietic malignancies (n=19), solid tumors (n=12), and post-transplant lymphoproliferative disorder (n=7). Of the 36 patients with outcome data, 19 survived. SMNs following HB treatment were primarily seen in patients with chemotherapy exposure, a history of liver transplantation, hereditary tumor predisposition syndromes, and/or a history of radiation treatment. Hematopoietic malignancies were the most common SMN reported in this cohort and were diagnosed earlier than other SMNs. Prospective collection of data through a companion late effects study or international registry could be used to further evaluate the rates and risks of SMNs as well as tumor predisposition syndromes in patients treated for HB.

Published
2024
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29. Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Author

Waltemath, Dagmar, Bergmann, Frank T., Chaouiya, Claudine, Czauderna, Tobias, Gleeson, Padraig, Goble, Carole, Golebiewski, Martin, Hucka, Michael, Juty, Nick, Krebs, Olga, Le Novère, Nicolas, Mi, Huaiyu, Moraru, Ion I., Myers, Chris J., Nickerson, David, Olivier, Brett G., Rodriguez, Nicolas, Schreiber, Falk, Smith, Lucian, Zhang, Fengkai, and Bonnet, Eric

Published
2018
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30. Fibrolamellar variant of hepatocellular carcinoma does not have a better survival than conventional hepatocellular carcinoma – Results and treatment recommendations from the Childhood Liver Tumour Strategy Group (SIOPEL) experience

Author

Weeda, V.B., Murawski, M., McCabe, A.J., Maibach, R., Brugières, L., Roebuck, D., Fabre, M., Zimmermann, A., Otte, J.B., Sullivan, M., Perilongo, G., Childs, M., Brock, P., Zsíros, J., Plaschkes, J., Czauderna, P., and Aronson, D.C.

Published
2013
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32. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Author

Waltemath, Dagmar, Bergmann, Frank T., Chaouiya, Claudine, Czauderna, Tobias, Gleeson, Padraig, Goble, Carole, Golebiewski, Martin, Hucka, Michael, Juty, Nick, Krebs, Olga, Le Novère, Nicolas, Mi, Huaiyu, Moraru, Ion I., Myers, Chris J., Nickerson, David, Olivier, Brett G., Rodriguez, Nicolas, Schreiber, Falk, Smith, Lucian, Zhang, Fengkai, and Bonnet, Eric

Published
2014
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38. A 3-proteomic score to improve the clinical management of childhood liver cancer

Author

Carrillo, J, Simon-Coma, M, Azkargorta, M, Royo, L, Guerra, L, Alvaro, D, Failli, M, Hernansaiz, R, Kimura, H, Garrido, M, Oliveros, FH, Porta-Pardo, E, Ng, IOL, Domingo-Sabat, M, Lopez-Santamaria, M, Morland, B, Czauderna, P, Childs, M, Maibach, R, Valencia, A, Elortza, F, Sala, M, Buendia, MA, Akuchi, A, Saez-Rodriguez, J, Di Bernardo, D, Sarrias, MR, and Armengol, C

Published
2021

39. Intestinal carbapenem-resistant Klebsiella pneumoniaeundergoes complex transcriptional reprogramming following immune activation

Author

David, Clement, Czauderna, Aleksander, Cheng, Liqing, Lagune, Marion, Jung, Hea-Jin, Kim, Sohn G., Pamer, Eric G., Prados, Julien, Chen, Liang, and Becattini, Simone

Abstract

ABSTRACTCarbapenem-resistant Klebsiella pneumoniae(CR-Kp) is a significant threat to public health worldwide. The primary reservoir for CR-Kp is the intestinal tract. There, the bacterium is usually present at low density but can bloom following antibiotic treatment, mostly in hospital settings. The impact of disturbances in the intestinal environment on the fitness, survival, expansion, and drug susceptibility of this pathogen is not well-understood, yet it may be relevant to devise strategies to tackle CR-Kp colonization and infection. Here, we adopted an in vivomodel to examine the transcriptional adaptation of a CR-Kp clinical isolate to immune activation in the intestine. We report that as early as 6 hours following host treatment with anti-CD3 antibody, CR-Kp underwent rapid transcriptional changes including downregulation of genes involved in sugar utilization and amino acid biosynthesis and upregulation of genes involved in amino acid uptake and catabolism, antibiotic resistance, and stress response. In agreement with these findings, treatment increased the concentration of oxidative species and amino acids in the mouse intestine. Genes encoding for proteins containing the domain of unknown function (DUF) 1471 were strongly upregulated, however their deletion did not impair CR-Kp fitness in vivoupon immune activation. Transcription factor enrichment analysis identified the global regulator cAMP-Receptor Protein, CRP, as a potential orchestrator of the observed transcriptional signature. In keeping with the recognized role of CRP in regulating utilization of alternative carbon sources, crpdeletion in CR-Kp resulted in strongly impaired gut colonization, although this effect was not amplified by immune activation. Thus, following intestinal colonization, which occurs in a CRP-dependent manner, CR-Kp can rapidly respond to immune cues by implementing a well-defined and complex transcriptional program whose direct relevance toward bacterial fitness warrants further investigation. Additional analyses utilizing this model may identify key factors to tackle CR-Kp colonization of the intestine.

Published
2024
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