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3. High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance

Author

Cortés-López, Mariela, Schulz, Laura, Enculescu, Mihaela, Paret, Claudia, Spiekermann, Bea, Quesnel-Vallières, Mathieu, Torres-Diz, Manuel, Unic, Sebastian, Busch, Anke, Orekhova, Anna, Kuban, Monika, Mesitov, Mikhail, Mulorz, Miriam M., Shraim, Rawan, Kielisch, Fridolin, Faber, Jörg, Barash, Yoseph, Thomas-Tikhonenko, Andrei, Zarnack, Kathi, Legewie, Stefan, and König, Julian

Published
2022
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6. Hereditary Spherocytosis: Can Next-Generation Sequencing of the Five Most Frequently Affected Genes Replace Time-Consuming Functional Investigations?

Author

Häuser, Friederike, Rossmann, Heidi, Adenaeuer, Anke, Shrestha, Annette, Marandiuc, Dana, Paret, Claudia, Faber, Jörg, Lackner, Karl J., Lämmle, Bernhard, and Beck, Olaf

Subjects
NUCLEOTIDE sequencing, GENETIC testing, ERYTHROCYTES, ERYTHROCYTE membranes, GENES, HUMAN abnormalities
Abstract

Congenital defects of the erythrocyte membrane are common in northern Europe and all over the world. The resulting diseases, for example, hereditary spherocytosis (HS), are often underdiagnosed, partly due to their sometimes mild and asymptomatic courses. In addition to a broad clinical spectrum, this is also due to the occasionally complex diagnostics that are not available to every patient. To test whether next-generation sequencing (NGS) could replace time-consuming spherocytosis-specific functional tests, 22 consecutive patients with suspected red cell membranopathy underwent functional blood tests. We were able to identify the causative genetic defect in all patients with suspected HS who underwent genetic testing (n = 17). The sensitivity of the NGS approach, which tests five genes (ANK1 (gene product: ankyrin1), EPB42 (erythrocyte membrane protein band4.2), SLC4A1 (band3), SPTA1 (α-spectrin), and SPTB (β-spectrin)), was 100% (95% confidence interval: 81.5–100.0%). The major advantage of genetic testing in the paediatric setting is the small amount of blood required (<200 µL), and compared to functional assays, sample stability is not an issue. The combination of medical history, basic laboratory parameters, and an NGS panel with five genes is sufficient for diagnosis in most cases. Only in rare cases, a more comprehensive functional screening is required. [ABSTRACT FROM AUTHOR]

Published
2023
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9. Supplementary Tables and Figures S1-S8; Material and Methods from Functional TCR Retrieval from Single Antigen-Specific Human T Cells Reveals Multiple Novel Epitopes

Author

Simon, Petra, primary, Omokoko, Tana A., primary, Breitkreuz, Andrea, primary, Hebich, Lisa, primary, Kreiter, Sebastian, primary, Attig, Sebastian, primary, Konur, Abdo, primary, Britten, Cedrik M., primary, Paret, Claudia, primary, Dhaene, Karl, primary, Türeci, Özlem, primary, and Sahin, Ugur, primary

Published
2023
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10. Supplementary Tables S1-S3 from Colocalization of the Tetraspanins, CO-029 and CD151, with Integrins in Human Pancreatic Adenocarcinoma: Impact on Cell Motility

Author

Gesierich, Sabine, primary, Paret, Claudia, primary, Hildebrand, Dagmar, primary, Weitz, Jürgen, primary, Zgraggen, Kaspar, primary, Schmitz-Winnenthal, Friedrich H., primary, Horejsi, Vaclav, primary, Yoshie, Osamu, primary, Herlyn, Dorothee, primary, Ashman, Leonie K., primary, and Zöller, Margot, primary

Published
2023
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11. Supplementary Tables 1-3 from Colocalization of the Tetraspanins, CO-029 and CD151, with Integrins in Human Pancreatic Adenocarcinoma: Impact on Cell Motility

Author

Gesierich, Sabine, primary, Paret, Claudia, primary, Hildebrand, Dagmar, primary, Weitz, Jürgen, primary, Zgraggen, Kaspar, primary, Schmitz-Winnenthal, Friedrich H., primary, Horejsi, Vaclav, primary, Yoshie, Osamu, primary, Herlyn, Dorothee, primary, Ashman, Leonie K., primary, and Zöller, Margot, primary

Published
2023
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12. Data from Exploiting the Mutanome for Tumor Vaccination

Author

Castle, John C., primary, Kreiter, Sebastian, primary, Diekmann, Jan, primary, Löwer, Martin, primary, van de Roemer, Niels, primary, de Graaf, Jos, primary, Selmi, Abderraouf, primary, Diken, Mustafa, primary, Boegel, Sebastian, primary, Paret, Claudia, primary, Koslowski, Michael, primary, Kuhn, Andreas N., primary, Britten, Cedrik M., primary, Huber, Christoph, primary, Türeci, Özlem, primary, and Sahin, Ugur, primary

Published
2023
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13. Supplementary Table 2 from Exploiting the Mutanome for Tumor Vaccination

Author

Castle, John C., primary, Kreiter, Sebastian, primary, Diekmann, Jan, primary, Löwer, Martin, primary, van de Roemer, Niels, primary, de Graaf, Jos, primary, Selmi, Abderraouf, primary, Diken, Mustafa, primary, Boegel, Sebastian, primary, Paret, Claudia, primary, Koslowski, Michael, primary, Kuhn, Andreas N., primary, Britten, Cedrik M., primary, Huber, Christoph, primary, Türeci, Özlem, primary, and Sahin, Ugur, primary

Published
2023
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14. Supplementary Methods from Exploiting the Mutanome for Tumor Vaccination

Author

Castle, John C., primary, Kreiter, Sebastian, primary, Diekmann, Jan, primary, Löwer, Martin, primary, van de Roemer, Niels, primary, de Graaf, Jos, primary, Selmi, Abderraouf, primary, Diken, Mustafa, primary, Boegel, Sebastian, primary, Paret, Claudia, primary, Koslowski, Michael, primary, Kuhn, Andreas N., primary, Britten, Cedrik M., primary, Huber, Christoph, primary, Türeci, Özlem, primary, and Sahin, Ugur, primary

Published
2023
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15. Supplementary Table 1 from Exploiting the Mutanome for Tumor Vaccination

Author

Castle, John C., primary, Kreiter, Sebastian, primary, Diekmann, Jan, primary, Löwer, Martin, primary, van de Roemer, Niels, primary, de Graaf, Jos, primary, Selmi, Abderraouf, primary, Diken, Mustafa, primary, Boegel, Sebastian, primary, Paret, Claudia, primary, Koslowski, Michael, primary, Kuhn, Andreas N., primary, Britten, Cedrik M., primary, Huber, Christoph, primary, Türeci, Özlem, primary, and Sahin, Ugur, primary

Published
2023
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16. Analysis of RBP expression and binding sites identifies PTBP1 as a regulator of CD19 expression in B-ALL

Author

Ziegler, Nicole, primary, Cortés-López, Mariela, additional, Alt, Francesca, additional, Sprang, Maximilian, additional, Ustjanzew, Arsenij, additional, Lehmann, Nadine, additional, El Malki, Khalifa, additional, Wingerter, Arthur, additional, Russo, Alexandra, additional, Beck, Olaf, additional, Attig, Sebastian, additional, Roth, Lea, additional, König, Julian, additional, Paret, Claudia, additional, and Faber, Jörg, additional

Published
2023
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17. GD2 Expression in Medulloblastoma and Neuroblastoma for Personalized Immunotherapy: A Matter of Subtype

Author

Paret, Claudia, primary, Ustjanzew, Arsenij, additional, Ersali, Sara, additional, Seidmann, Larissa, additional, Jennemann, Richard, additional, Ziegler, Nicole, additional, Malki, Khalifa El, additional, Russo, Alexandra, additional, Wingerter, Arthur, additional, Ortmüller, Franziska, additional, Bornas, Angelina, additional, Wehling, Pia Charlotte, additional, Lepădatu, Adina, additional, Ottenhausen, Malte, additional, Roth, Wilfried, additional, Sommer, Clemens, additional, Fliss, Barbara, additional, Frauenknecht, Katrin B. M., additional, Sandhoff, Roger, additional, and Faber, Jörg, additional

Published
2022
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18. Abstracts of the 52nd Workshop for Pediatric Research: Frankfurt, Germany. 27-28 October 2016

Author

van den Bruck, Rhea, Weil, Patrick P., Ziegenhals, Thomas, Schreiner, Philipp, Juranek, Stefan, Gödde, Daniel, Vogel, Silvia, Schuster, Frauke, Orth, Valerie, Dörner, Johannes, Pembaur, Daniel, Röper, Meike, Störkel, Stefan, Zirngibl, Hubert, Wirth, Stefan, Jenke, Andreas C. W., Postberg, Jan, Boy, Nikolas, Heringer, Jana, Haege, Gisela, Glahn, Esther M., Hoffmann, Georg F., Garbade, Sven F., Burgard, Peter, Kölker, Stefan, Chao, Cho-Ming, Yahya, Faady, Moiseenko, Alena, Shrestha, Amit, Ahmadvand, Negah, Quantius, Jennifer, Wilhelm, Jochen, El-Agha, Elie, Zimmer, Klaus-Peter, Bellusci, Saverio, Staufner, Christian, Kölker, Stefan, Prokisch, Holger, Hoffmann, Georg F., Seeliger, Stephan, Müller, Matthias, Hippe, Andreas, Steinkraus, Henrik, Wauer, Roland, Lachmann, Burkhard, Hofmann, Sigrun R., Hedrich, Christian M., Zierk, Jakob, Arzideh, Farhad, Haeckel, Rainer, Rascher, Wolfgang, Rauh, Manfred, Metzler, Markus, Thieme, Sebastian, Bandoła, Joanna, Richter, Cornelia, Ryser, Martin, Jamal, Arshad, Ashton, Michelle P., von Bonin, Malte, Kuhn, Matthias, Hedrich, Christian M., Bonifacio, Ezio, Berner, Reinhard, Brenner, Sebastian, Hammersen, Johanna, Has, Cristina, Naumann-Bartsch, Nora, Stachel, Daniel, Kiritsi, Dimitra, Söder, Stephan, Tardieu, Mathilde, Metzler, Markus, Bruckner-Tuderman, Leena, Schneider, Holm, Bohne, F., Langer, D., Cencic, R., Eggermann, T., Zechner, U., Pelletier, J., Zepp, F., Enklaar, T., Prawitt, D., Pech, Martin, Weckmann, Markus, Heinsen, Femke-Anouska, Franke, Andre, Happle, Christine, Dittrich, Anna-Maria, Hansen, Gesine, Fuchs, Oliver, von Mutius, Erika, Oliver, Brian G., Kopp, Matthias V., Paret, Claudia, Russo, Alexandra, Theruvath, Johanna, Keller, Bettina, El Malki, Khalifa, Lehmann, Nadine, Wingerter, Arthur, Neu, Marie A., Aslihan, Gerhold-Ay, Wagner, Wolfgang, Sommer, Clemens, Pietsch, Torsten, Seidmann, Larissa, Faber, Jörg, Schreiner, Felix, Ackermann, Merle, Michalik, Michael, Rother, Eva, Bilkei-Gorzo, Andras, Racz, Ildiko, Bindila, Laura, Lutz, Beat, Dötsch, Jörg, Zimmer, Andreas, Woelfle, Joachim, Fischer, Hendrik S., Ullrich, Tim L., Bührer, Christoph, Czernik, Christoph, Schmalisch, Gerd, Stein, Robert, Hofmann, Sigrun R., Hagenbuchner, Judith, Kiechl-Kohlendorfer, Ursula, Obexer, Petra, Ausserlechner, Michael J., Loges, Niki T., Frommer, Adrien Tobias, Wallmeier, Julia, Omran, Heymut, Öner-Sieben, Soner, Gimpfl, Martina, Rozman, Jan, Irmler, Martin, Beckers, Johannes, De Angelis, Martin Hrabe, Roscher, Adelbert, Wolf, Eckhard, Ensenauer, Regina, Nemes, Karolina, Frühwald, Michael, Hasselblatt, Martin, Siebert, Reiner, Kordes, Uwe, Kool, Marcel, Wang, Haicui, Hardy, Holly, Refai, Osama, Barwick, Katy E. S., Zimmerman, Holly H., Weis, Joachim, Baple, Emma L., Crosby, Andrew H., Cirak, Sebahattin, Hellmuth, C., Uhl, O., Standl, M., Heinrich, J., Thiering, E., Koletzko, B., Blümel, Lena, Kerl, Kornelius, Picard, Daniel, Frühwald, Michael C., Liebau, Max C., Reifenberger, Guido, Borkhardt, Arndt, Hasselblatt, Martin, Remke, Marc, Tews, D., Wabitsch, M., Fischer-Posovszky, P., Westhoff, Mike-Andrew, Nonnenmacher, Lisa, Langhans, Julia, Schneele, Lukas, Trenkler, Nancy, and Debatin, Klaus-Michael

Published
2017
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19. Glucosylceramide Synthase Inhibitors Induce Ceramide Accumulation and Sensitize H3K27 Mutant Diffuse Midline Glioma to Irradiation.

Author

El Malki, Khalifa, Wehling, Pia, Alt, Francesca, Sandhoff, Roger, Zahnreich, Sebastian, Ustjanzew, Arsenij, Wilzius, Carolin, Brockmann, Marc A., Wingerter, Arthur, Russo, Alexandra, Beck, Olaf, Sommer, Clemens, Ottenhausen, Malte, Frauenknecht, Katrin B. M., Paret, Claudia, and Faber, Jörg

Subjects
CERAMIDES, GLIOMAS, CHILD patients, NIEMANN-Pick diseases, IONIZING radiation
Abstract

H3K27M mutant (mut) diffuse midline glioma (DMG) is a lethal cancer with no effective cure. The glycosphingolipids (GSL) metabolism is altered in these tumors and could be exploited to develop new therapies. We tested the effect of the glucosylceramide synthase inhibitors (GSI) miglustat and eliglustat on cell proliferation, alone or in combination with temozolomide or ionizing radiation. Miglustat was included in the therapy protocol of two pediatric patients. The effect of H3.3K27 trimethylation on GSL composition was analyzed in ependymoma. GSI reduced the expression of the ganglioside GD2 in a concentration and time-dependent manner and increased the expression of ceramide, ceramide 1-phosphate, sphingosine, and sphingomyelin but not of sphingosine 1-phosphate. Miglustat significantly increased the efficacy of irradiation. Treatment with miglustat according to dose recommendations for patients with Niemann–Pick disease was well tolerated with manageable toxicities. One patient showed a mixed response. In ependymoma, a high concentration of GD2 was found only in the presence of the loss of H3.3K27 trimethylation. In conclusion, treatment with miglustat and, in general, targeting GSL metabolism may offer a new therapeutic opportunity and can be administered in close proximity to radiation therapy. Alterations in H3K27 could be useful to identify patients with a deregulated GSL metabolism. [ABSTRACT FROM AUTHOR]

Published
2023
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22. Deregulation in binding and expression of RNA binding proteins as a mechanism of CD19-negative B-ALL

Author

Ziegler, Nicole, primary, Cortés-López, Mariela, additional, Alt, Francesca, additional, Sprang, Maximilian, additional, Lehmann, Nadine, additional, Malki, Khalifa El, additional, Wingerter, Arthur, additional, Russo, Alexandra, additional, Beck, Olaf, additional, Attig, Sebastian, additional, Roth, Lea, additional, König, Julian, additional, Paret, Claudia, additional, and Faber, Jörg, additional

Published
2022
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24. Identification of an Immunogenic Medulloblastoma-Specific Fusion Involving EPC2 and GULP1

Author

Paret, Claudia, primary, Lehmann, Nadine, additional, Bender, Hannah, additional, Sprang, Maximilian, additional, Sommer, Clemens J., additional, Cana, Denis, additional, Seidmann, Larissa, additional, Wingerter, Arthur, additional, Neu, Marie A., additional, El Malki, Khalifa, additional, Alt, Francesca, additional, Roth, Lea, additional, Marini, Federico, additional, Ottenhausen, Malte, additional, Glaser, Martin, additional, Knuf, Markus, additional, Russo, Alexandra, additional, and Faber, Joerg, additional

Published
2021
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25. High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance

Author

Cortés-López, Mariela, primary, Schulz, Laura, additional, Enculescu, Mihaela, additional, Paret, Claudia, additional, Spiekermann, Bea, additional, Busch, Anke, additional, Orekhova, Anna, additional, Kielisch, Fridolin, additional, Quesnel-Vallières, Mathieu, additional, Torres-Diz, Manuel, additional, Faber, Jörg, additional, Barash, Yoseph, additional, Thomas-Tikhonenko, Andrei, additional, Zarnack, Kathi, additional, Legewie, Stefan, additional, and König, Julian, additional

Published
2021
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27. CpG-Islands as Markers for Liquid Biopsies of Cancer Patients

Author

Sprang, Maximilian, Paret, Claudia, and Faber, Joerg

Subjects
Carcinoma, Hepatocellular, liquid biopsy, Liver Neoplasms, 610 Medizin, Article, 570 Life sciences, CpG islands, lcsh:Biology (General), 610 Medical sciences, Biomarkers, Tumor, 500 Natural sciences and mathematics, Humans, 500 Naturwissenschaften, HCC, lcsh:QH301-705.5, 570 Biowissenschaften
Abstract

The analysis of tumours using biomarkers in blood is transforming cancer diagnosis and therapy. Cancers are characterised by evolving genetic alterations, making it difficult to develop reliable and broadly applicable DNA-based biomarkers for liquid biopsy. In contrast to the variability in gene mutations, the methylation pattern remains generally constant during carcinogenesis. Thus, methylation more than mutation analysis may be exploited to recognise tumour features in the blood of patients. In this work, we investigated the possibility of using global CpG (CpG means a CG motif in the context of methylation. The p represents the phosphate. This is used to distinguish CG sites meant for methylation from other CG motifs or from mentions of CG content) island methylation profiles as a basis for the prediction of cancer state of patients utilising liquid biopsy samples. We retrieved existing GEO methylation datasets on hepatocellular carcinoma (HCC) and cell-free DNA (cfDNA) from HCC patients and healthy donors, as well as healthy whole blood and purified peripheral blood mononuclear cell (PBMC) samples, and used a random forest classifier as a predictor. Additionally, we tested three different feature selection techniques in combination. When using cfDNA samples together with solid tumour samples and healthy blood samples of different origin, we could achieve an average accuracy of 0.98 in a 10-fold cross-validation. In this setting, all the feature selection methods we tested in this work showed promising results. We could also show that it is possible to use solid tumour samples and purified PBMCs as a training set and correctly predict a cfDNA sample as cancerous or healthy. In contrast to the complete set of samples, the feature selections led to varying results of the respective random forests. ANOVA feature selection worked well with this training set, and the selected features allowed the random forest to predict all cfDNA samples correctly. Feature selection based on mutual information could also lead to better than random results, but LASSO feature selection would not lead to a confident prediction. Our results show the relevance of CpG islands as tumour markers in blood.

Published
2020

28. Benefits from Exercise Training in Pediatric Oncology: Results from the Randomized Controlled Mucki-Trial

Author

Stoessel, Sandra, Neu, Marie Astrid, Wingerter, Arthur, Bloch, Wilhelm, Zimmer, Philipp, Paret, Claudia, El Malki, Khalifa, Baumann, Freerk T., Henninger, Nicole, Russo, Alexandra, Lehmann, Nadine, Otto, Henrike, Faber, Joerg, Stoessel, Sandra, Neu, Marie Astrid, Wingerter, Arthur, Bloch, Wilhelm, Zimmer, Philipp, Paret, Claudia, El Malki, Khalifa, Baumann, Freerk T., Henninger, Nicole, Russo, Alexandra, Lehmann, Nadine, Otto, Henrike, and Faber, Joerg

Published
2020

29. Benefits of Exercise Training for Children and Adolescents Undergoing Cancer Treatment: Results From the Randomized Controlled MUCKI Trial

Author

Stoessel, Sandra, Neu, Marie A., Wingerter, Arthur, Bloch, Wilhelm, Zimmer, Philipp, Paret, Claudia, El Malki, Khalifa, Baumann, Freerk T., Russo, Alexandra, Henninger, Nicole, Lehmann, Nadine, Otto, Henrike, Faber, Joerg, Stoessel, Sandra, Neu, Marie A., Wingerter, Arthur, Bloch, Wilhelm, Zimmer, Philipp, Paret, Claudia, El Malki, Khalifa, Baumann, Freerk T., Russo, Alexandra, Henninger, Nicole, Lehmann, Nadine, Otto, Henrike, and Faber, Joerg

Abstract

Objective:In cancer patients, the impairment in muscle function is a frequently observed phenomenon. However, comprehensive evaluation of the effect of exercise training on muscle function in childhood cancer patients (CCPs) is sparse and therefore investigated in the MUCKI trial. Study Design:In the randomized controlled MUCKI trial, CCPs during intensive cancer treatment and aged 4-18 years were recruited. Eligible patients were enrolled soon after diagnosis as long as they were physically and mentally able to participate in exercise testing and training. Patients of the exercise group (n= 16) participated in average 2.7 +/- 1.2 times per week in a combined resistance and endurance training with moderate exercise intensity, for a time period of 8.0 +/- 2.1 weeks, while patients of the control group (n= 17) received usual care. Leg strength was evaluated as the primary endpoint. Secondary endpoints were 6-min walk performance, arm strength, body composition, fatigue, and health-related quality of life. Results:Comparisons of pre- and post-intervention results were evaluated by baseline and stratification criteria adjusted analysis and showed positive effects for the exercise group regarding leg strength [F-(1,F- 20)= 5.733;p= 0.027*;eta p2= 0.223], walking performance [F-(1,F- 25)= 4.270;p= 0.049*;eta p2= 0.146], fatigue [F-(1,F- 13)= 8.353;p= 0.013*;eta p2= 0.391], self-esteem [F-(1,F- 6)= 6.823;p= 0.040*;eta p2= 0.532], and self-reported strength and endurance capacity [F-(1,F- 6)= 6.273;p= 0.046*;eta p2= 0.511]. No significant differences were found for the other parameters. Conclusion:Within one of the first randomized controlled trials, the present study provides evidence for a positive effect of combined training in CCPs during intensive cancer treatment. Further research is needed to confirm these results and to evaluate their clinical impact.

Published
2020

30. Benefits On Cancer-related Fatigue In Children After Exercise Training: Results From The Randomized, Controlled Mucki-trial

Author

Stoessel, Sandra, Neu, Marie A., Wingerter, Arthur, Bloch, Wilhelm, Zimmer, Philipp, Paret, Claudia, Baumann, Freerk T., Henninger, Nicole, Russo, Alexandra, Lehmann, Nadine, Otto, Henrike, Faber, Joerg, Stoessel, Sandra, Neu, Marie A., Wingerter, Arthur, Bloch, Wilhelm, Zimmer, Philipp, Paret, Claudia, Baumann, Freerk T., Henninger, Nicole, Russo, Alexandra, Lehmann, Nadine, Otto, Henrike, and Faber, Joerg

Published
2020

31. Requirements analysis and specification for a molecular tumor board platform based on cBioPortal

Author

Buechner, Philipp, Hinderer, Marc, Unberath, Philipp, Metzger, Patrick, Boeker, Martin, Acker, Till, Haller, Florian, Mack, Elisabeth, Nowak, Daniel, Paret, Claudia, Schanze, Denny, Bubnoff, Nikolas von, Wagner, Sebastian Alexander, Busch, Hauke, Börries, Melanie, Christoph, Jan, Buechner, Philipp, Hinderer, Marc, Unberath, Philipp, Metzger, Patrick, Boeker, Martin, Acker, Till, Haller, Florian, Mack, Elisabeth, Nowak, Daniel, Paret, Claudia, Schanze, Denny, Bubnoff, Nikolas von, Wagner, Sebastian Alexander, Busch, Hauke, Börries, Melanie, and Christoph, Jan

Abstract

Clinicians in molecular tumor boards (MTB) are confronted with a growing amount of genetic high-throughput sequencing data. Today, at German university hospitals, these data are usually handled in complex spreadsheets from which clinicians have to obtain the necessary information. The aim of this work was to gather a comprehensive list of requirements to be met by cBioPortal to support processes in MTBs according to clinical needs. Therefore, oncology experts at nine German university hospitals were surveyed in two rounds of interviews. To generate an interview guideline a scoping review was conducted. For visual support in the second round, screenshot mockups illustrating the requirements from the first round were created. Requirements that cBioPortal already meets were skipped during the second round. In the end, 24 requirements with sometimes several conceivable options were identified and 54 screenshot mockups were created. Some of the identified requirements have already been suggested to the community by other users or are currently being implemented in cBioPortal. This shows, that the results are in line with the needs expressed by various disciplines. According to our findings, cBioPortal has the potential to significantly improve the processes and analyses of an MTB after the implementation of the identified requirements.

Published
2020

32. Exploiting Gangliosides for the Therapy of Ewing’s Sarcoma and H3K27M-Mutant Diffuse Midline Glioma

Author

Wingerter, Arthur, primary, El Malki, Khalifa, additional, Sandhoff, Roger, additional, Seidmann, Larissa, additional, Wagner, Daniel-Christoph, additional, Lehmann, Nadine, additional, Vewinger, Nadine, additional, Frauenknecht, Katrin B. M., additional, Sommer, Clemens J., additional, Traub, Frank, additional, Kindler, Thomas, additional, Russo, Alexandra, additional, Otto, Henrike, additional, Lollert, André, additional, Staatz, Gundula, additional, Roth, Lea, additional, Paret, Claudia, additional, and Faber, Jörg, additional

Published
2021
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33. Tumor Lipids of Pediatric Papillary Renal Cell Carcinoma Stimulate Unconventional T Cells

Author

Lehmann, Nadine, primary, Paret, Claudia, additional, El Malki, Khalifa, additional, Russo, Alexandra, additional, Neu, Marie Astrid, additional, Wingerter, Arthur, additional, Seidmann, Larissa, additional, Foersch, Sebastian, additional, Ziegler, Nicole, additional, Roth, Lea, additional, Backes, Nora, additional, Sandhoff, Roger, additional, and Faber, Joerg, additional

Published
2020
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34. Benefits of Exercise Training for Children and Adolescents Undergoing Cancer Treatment: Results From the Randomized Controlled MUCKI Trial

Author

Stössel, Sandra, primary, Neu, Marie A., additional, Wingerter, Arthur, additional, Bloch, Wilhelm, additional, Zimmer, Philipp, additional, Paret, Claudia, additional, Malki, Khalifa El, additional, Baumann, Freerk T., additional, Russo, Alexandra, additional, Henninger, Nicole, additional, Lehmann, Nadine, additional, Otto, Henrike, additional, and Faber, Jörg, additional

Published
2020
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36. Safety and Activity of the Combination of Ceritinib and Dasatinib in Osteosarcoma

Author

Beck, Olaf, primary, Paret, Claudia, additional, Russo, Alexandra, additional, Burhenne, Jürgen, additional, Fresnais, Margaux, additional, Steimel, Kevin, additional, Seidmann, Larissa, additional, Wagner, Daniel-Christoph, additional, Vewinger, Nadine, additional, Lehmann, Nadine, additional, Sprang, Maximilian, additional, Backes, Nora, additional, Roth, Lea, additional, Neu, Marie Astrid, additional, Wingerter, Arthur, additional, Henninger, Nicole, additional, El Malki, Khalifa, additional, Otto, Henrike, additional, Alt, Francesca, additional, Desuki, Alexander, additional, Kindler, Thomas, additional, and Faber, Joerg, additional

Published
2020
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37. Requirements Analysis and Specification for a Molecular Tumor Board Platform Based on cBioPortal

Author

Buechner, Philipp, primary, Hinderer, Marc, additional, Unberath, Philipp, additional, Metzger, Patrick, additional, Boeker, Martin, additional, Acker, Till, additional, Haller, Florian, additional, Mack, Elisabeth, additional, Nowak, Daniel, additional, Paret, Claudia, additional, Schanze, Denny, additional, von Bubnoff, Nikolas, additional, Wagner, Sebastian, additional, Busch, Hauke, additional, Boerries, Melanie, additional, and Christoph, Jan, additional

Published
2020
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38. Definition of an annotation pipeline for a molecular tumor board focused on the processing of the result and oncological drugs in terms of usability and approval status

Author

Walther, Désirée, Paret, Claudia, Ritzel, Christoph, Büchner, Philipp, Unberath, Philipp, Maier, Wolfgang, Metzger, Patrick, Christoph, Jan, Storf, Holger, Börries, Melanie, and Wagner, Sebastian

Subjects
Molecular Tumor Board, ddc: 610, cancer, next-generation sequencing, 610 Medical sciences, Medicine
Abstract

Introduction: The annotation of genetic variants is an important step in high-throughput sequencing data analysis pipelines. In the context of cancer sequencing, the annotation of somatic variants plays an essential role for clinical interpretation. As part of the BMBF-funded project MIRACUM, an annotation[for full text, please go to the a.m. URL], 64. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS)

Published
2019

39. IGF1R is a potential new therapeutic target for HGNET-BCOR brain tumor patients

Author

Vewinger, Nadine, Huprich, Sabrina, Seidmann, Larissa, Russo, Alexandra, Alt, Francesca, Bender, Hannah, Sommer, Clemens, Samuel, David, Lehmann, Nadine, Backes, Nora, Roth, Lea, Harter, Patrick N., Filipski, Katharina, Faber, Jörg, and Paret, Claudia

Subjects
Male, HGNET-BCOR, Medizin, 610 Medizin, Antineoplastic Agents, Article, Receptor, IGF Type 1, lcsh:Chemistry, Insulin-Like Growth Factor II, IGF1R, Proto-Oncogene Proteins, 610 Medical sciences, vinblastine, Tumor Cells, Cultured, Humans, ceritinib, Molecular Targeted Therapy, Sulfones, lcsh:QH301-705.5, Brain Neoplasms, IGF2, Receptors, Somatomedin, DNA Methylation, Neoplasms, Neuroepithelial, body regions, Gene Expression Regulation, Neoplastic, Repressor Proteins, Pyrimidines, lcsh:Biology (General), lcsh:QD1-999, Female
Abstract

(1) Background: The high-grade neuroepithelial tumor of the central nervous system with BCOR alteration (HGNET-BCOR) is a highly malignant tumor. Preclinical models and molecular targets are urgently required for this cancer. Previous data suggest a potential role of insulin-like growth factor (IGF) signaling in HGNET-BCOR. (2) Methods: The primary HGNET-BCOR cells PhKh1 were characterized by western blot, copy number variation, and methylation analysis and by electron microscopy. The expression of IGF2 and IGF1R was assessed by qRT-PCR. The effect of chemotherapeutics and IGF1R inhibitors on PhKh1 proliferation was tested. The phosphorylation of IGF1R and downstream molecules was assessed by western blot. (3) Results: Phkh1 cells showed a DNA methylation profile compatible with the DNA methylation class &ldquo, HGNET-BCOR&rdquo, and morphologic features of cellular cannibalism. IGF2 and IGF1R were highly expressed by three HGNET-BCOR tumor samples and PhKh1 cells. PhKh1 cells were particularly sensitive to vincristine, vinblastine, actinomycin D (IC50 &lt, 10 nM for all drugs), and ceritinib (IC50 = 310 nM). Ceritinib was able to abrogate the proliferation of PhKh1 cells and blocked the phosphorylation of IGF1R and AKT. (4) Conclusion: IGF1R is as an attractive target for the development of new therapy protocols for HGNET-BCOR patients, which may include ceritinib and vinblastine.

Published
2019
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41. Ceritinib-induced regression of an insulin-like growth factor-driven neuroepithelial brain tumor

Author

Russo, Alexandra, Paret, Claudia, Alt, Francesca, Burhenne, Jürgen, Fresnais, Margaux, Wagner, Wolfgang, Glaser, Martin, Bender, Hannah, Huprich, Sabrina, Harter, Patrick Nikolaus, Filipski, Katharina Johanna, Lehmann, Nadine, Backes, Nora, Roth, Lea, Seidmann, Larissa, Sommer, Clemens, Brockmann, Marc Alexander, Pietsch, Torsten, Neu, Marie Astrid, Wingerter, Arthur, Faber, Jörg, Russo, Alexandra, Paret, Claudia, Alt, Francesca, Burhenne, Jürgen, Fresnais, Margaux, Wagner, Wolfgang, Glaser, Martin, Bender, Hannah, Huprich, Sabrina, Harter, Patrick Nikolaus, Filipski, Katharina Johanna, Lehmann, Nadine, Backes, Nora, Roth, Lea, Seidmann, Larissa, Sommer, Clemens, Brockmann, Marc Alexander, Pietsch, Torsten, Neu, Marie Astrid, Wingerter, Arthur, and Faber, Jörg

Abstract

The insulin-like growth factor (IGF) pathway plays an important role in several brain tumor entities. However, the lack of inhibitors crossing the blood–brain barrier remains a significant obstacle for clinical translation. Here, we targeted the IGF pathway using ceritinib, an off-target inhibitor of the IGF1 receptor (IGF1R) and insulin receptor (INSR), in a pediatric patient with an unclassified brain tumor and a notch receptor 1 (NOTCH1) germline mutation. Pathway analysis of the tumor revealed activation of the sonic hedgehog (SHH), the wingless and integrated-1 (WNT), the IGF, and the Notch pathway. The proliferation of the patient tumor cells (225ZL) was inhibited by arsenic trioxide (ATO), which is an inhibitor of the SHH pathway, by linsitinib, which is an inhibitor of IGF1R and INSR, and by ceritinib. 225ZL expressed INSR but not IGF1R at the protein level, and ceritinib blocked the phosphorylation of INSR. Our first personalized treatment included ATO, but because of side effects, we switched to ceritinib. After 46 days, we achieved a concentration of 1.70 µM of ceritinib in the plasma, and after 58 days, MRI confirmed that there was a response to the treatment. Ceritinib accumulated in the tumor at a concentration of 2.72 µM. Our data suggest ceritinib as a promising drug for the treatment of IGF-driven brain tumors.

Published
2019

43. Ceritinib-Induced Regression of an Insulin-Like Growth Factor-Driven Neuroepithelial Brain Tumor

Author

Russo, Alexandra, primary, Paret, Claudia, additional, Alt, Francesca, additional, Burhenne, Jürgen, additional, Fresnais, Margaux, additional, Wagner, Wolfgang, additional, Glaser, Martin, additional, Bender, Hannah, additional, Huprich, Sabrina, additional, Harter, Patrick N., additional, Filipski, Katharina, additional, Lehmann, Nadine, additional, Backes, Nora, additional, Roth, Lea, additional, Seidmann, Larissa, additional, Sommer, Clemens, additional, Brockmann, Marc A., additional, Pietsch, Torsten, additional, Neu, Marie A., additional, Wingerter, Arthur, additional, and Faber, Jörg, additional

Published
2019
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44. IGF1R Is a Potential New Therapeutic Target for HGNET-BCOR Brain Tumor Patients

Author

Vewinger, Nadine, primary, Huprich, Sabrina, additional, Seidmann, Larissa, additional, Russo, Alexandra, additional, Alt, Francesca, additional, Bender, Hannah, additional, Sommer, Clemens, additional, Samuel, David, additional, Lehmann, Nadine, additional, Backes, Nora, additional, Roth, Lea, additional, Harter, Patrick N., additional, Filipski, Katharina, additional, Faber, Jörg, additional, and Paret, Claudia, additional

Published
2019
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49. Personalized therapy: CNS HGNET-BCOR responsiveness to arsenic trioxide combined with radiotherapy

Author

Paret, Claudia, primary, Russo, Alexandra, additional, Otto, Henrike, additional, Mayer, Arnulf, additional, Zahnreich, Sebastian, additional, Wagner, Wolfgang, additional, Samuel, David, additional, Scharnhorst, David, additional, Solomon, David A., additional, Dhall, Girish, additional, Wong, Kenneth, additional, Bender, Hannah, additional, Alt, Francesca, additional, Wingerter, Arthur, additional, Neu, Marie A., additional, Beck, Olaf, additional, Prawitt, Dirk, additional, Eder, Stefan, additional, Henninger, Nicole, additional, El Malki, Khalifa, additional, Lehmann, Nadine, additional, Backes, Nora, additional, Roth, Lea, additional, Seidmann, Larissa, additional, Sommer, Clemens, additional, Brockmann, Marc A., additional, Staatz, Gundula, additional, Schmidberger, Heinz, additional, and Faber, Jörg, additional

Published
2017
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