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1. Lack of SMARCB1 expression characterizes a subset of human and murine peripheral T-cell lymphomas

Author

Fischer, Anja, Albert, Thomas K., Moreno, Natalia, Interlandi, Marta, Mormann, Jana, Glaser, Selina, Patil, Paurnima, de Faria, Flavia W., Richter, Mathis, Verma, Archana, Balbach, Sebastian T., Wagener, Rabea, Bens, Susanne, Dahlum, Sonja, Göbel, Carolin, Münter, Daniel, Inserte, Clara, Graf, Monika, Kremer, Eva, Melcher, Viktoria, Di Stefano, Gioia, Santi, Raffaella, Chan, Alexander, Dogan, Ahmet, Bush, Jonathan, Hasselblatt, Martin, Cheng, Sylvia, Spetalen, Signe, Fosså, Alexander, Hartmann, Wolfgang, Herbrüggen, Heidi, Robert, Stella, Oyen, Florian, Dugas, Martin, Walter, Carolin, Sandmann, Sarah, Varghese, Julian, Rossig, Claudia, Schüller, Ulrich, Tzankov, Alexandar, Pedersen, Martin B., d’Amore, Francesco A., Mellgren, Karin, Kontny, Udo, Kancherla, Venkatesh, Veloza, Luis, Missiaglia, Edoardo, Fataccioli, Virginie, Gaulard, Philippe, Burkhardt, Birgit, Soehnlein, Oliver, Klapper, Wolfram, de Leval, Laurence, Siebert, Reiner, and Kerl, Kornelius

Published
2024
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5. Mitochondrial DNA mutations in Medulloblastoma

Author

Funke, Viktoria L. E., Sandmann, Sarah, Melcher, Viktoria, Seggewiss, Jochen, Horvath, Judit, Jäger, Natalie, Kool, Marcel, Jones, David T. W., Pfister, Stefan M., Milde, Till, Rutkowski, Stefan, Mynarek, Martin, Varghese, Julian, Sträter, Ronald, Rust, Stephan, Seelhöfer, Anja, Reunert, Janine, Fiedler, Barbara, Schüller, Ulrich, Marquardt, Thorsten, and Kerl, Kornelius

Published
2023
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11. Early blast clearance during sequential conditioning prior to allogeneic stem cell transplantation in patients with acute myeloid leukaemia

Author

Ronnacker, Julian, primary, Urbahn, Marc‐Andre, additional, Reicherts, Christian, additional, Kolloch, Lina, additional, Berning, Philipp, additional, Sandmann, Sarah, additional, Eßeling, Eva, additional, Call, Simon, additional, Floeth, Matthias, additional, Marx, Julia, additional, Albring, Jörn, additional, Mikesch, Jan‐Henrik, additional, Schliemann, Christoph, additional, Lenz, Georg, additional, and Stelljes, Matthias, additional

Published
2024
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12. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age

Author

Burkhardt, Birgit, Michgehl, Ulf, Rohde, Jonas, Erdmann, Tabea, Berning, Philipp, Reutter, Katrin, Rohde, Marius, Borkhardt, Arndt, Burmeister, Thomas, Dave, Sandeep, Tzankov, Alexandar, Dugas, Martin, Sandmann, Sarah, Fend, Falko, Finger, Jasmin, Mueller, Stephanie, Gökbuget, Nicola, Haferlach, Torsten, Kern, Wolfgang, Hartmann, Wolfgang, Klapper, Wolfram, Oschlies, Ilske, Richter, Julia, Kontny, Udo, Lutz, Mathias, Maecker-Kolhoff, Britta, Ott, German, Rosenwald, Andreas, Siebert, Reiner, von Stackelberg, Arend, Strahm, Brigitte, Woessmann, Wilhelm, Zimmermann, Martin, Zapukhlyak, Myroslav, Grau, Michael, and Lenz, Georg

Published
2022
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17. Research article network analysis of polymicrobial chronic wound infections in Masanga, Sierra Leone

Author

Sandmann, Sarah, Nunes, Jonathan Vas, Grobusch, Martin P., Sesay, Maxwell, Kriegel, Martin A., Varghese, Julian, Schaumburg, Frieder, Infectious diseases, AII - Infectious diseases, and APH - Global Health

Subjects
Wound infection, Africa, Staphylococcus aureus, Pseudomonas aeruginosa, Microbiome, Community networks, Panton-Valentine leukocidin
Abstract

Background: Chronic wounds are frequently colonized or infected with multiple bacterial or fungal species, which can both promote or inhibit each other. Network analyses are helpful to understand the interplay of these species in polymicrobial infections. Our aim was to analyse the network of bacterial and fungal species in chronic wounds. Methods: Swabs (n = 163) from chronic wound infections (Masanga, Sierra Leone, 2019–2020) were screened for bacterial and fungal species using non-selective agars. Some of these wounds were suspected but not confirmed Buruli ulcer. Species identification was done with MALDI-TOF mass spectrometry. Network analysis was performed to investigate co-occurrence of different species within one patient. All species with n ≥ 10 isolates were taken into account. Results: Of the 163 patients, 156 had a positive wound culture (median of three different species per patient; range 1–7). Pseudomonas aeruginosa (n = 75) was the dominating species with frequent co-detections of Klebsiella pneumoniae (21 cases; OR = 1.36, 95%CI: 0.63–2.96, p = 0.47), Staphylococcus aureus (14 cases; OR = 1.06, 95%CI: 0.44–2.55, p = 1) and Proteus mirabilis (13 cases; OR = 0.84, 95%CI: 0.35–1.99, p = 0.69). Conclusion: The culturome of chronic wounds in Sierra Leonean patients is highly diverse and characterized by the co-occurrence of P. aeruginosa, K. pneumoniae and S. aureus.

Published
2023

18. Genome-wide DNA methylation changes in human spermatogenesis

Author

Siebert-Kuss, Lara M, primary, Dietrich, Verena, additional, Di Persio, Sara, additional, Bhaskaran, Jahnavi, additional, Stehling, Martin, additional, Cremers, Jann-Frederik, additional, Sandmann, Sarah, additional, Varghese, Julian, additional, Kliesch, Sabine, additional, Schlatt, Stefan, additional, Vaquerizas, Juan Manuel, additional, Neuhaus, Nina, additional, and Laurentino, Sandra, additional

Published
2023
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20. Knockout of the Cardiac Transcription Factor NKX2-5 Results in Stem Cell-Derived Cardiac Cells with Typical Purkinje Cell-like Signal Transduction and Extracellular Matrix Formation

Author

Disse, Paul, primary, Aymanns, Isabel, additional, Mücher, Lena, additional, Sandmann, Sarah, additional, Varghese, Julian, additional, Ritter, Nadine, additional, Strutz-Seebohm, Nathalie, additional, Seebohm, Guiscard, additional, and Peischard, Stefan, additional

Published
2023
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21. Pharyngeal Communities and Antimicrobial Resistance in Pangolins in Gabon

Author

Wiethoff, Johanna P., primary, Sandmann, Sarah, additional, Theiler, Tom, additional, Nze Nkogue, Chimene, additional, Akomo-Okoue, Etienne-François, additional, Varghese, Julian, additional, Kreidenweiss, Andrea, additional, Mellmann, Alexander, additional, Lell, Bertrand, additional, Adegnika, Ayôla A., additional, Held, Jana, additional, and Schaumburg, Frieder, additional

Published
2023
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23. Genetische und diagnostische Charakterisierung einer großen israelischen PCD-Kohorte – Notwendigkeit der geografischen Anpassungen der aktuellen diagnostischen Leitlinien?

Author

Raidt, Johanna, additional, Loges, Niki T., additional, Amirav, Israel, additional, Sandmann, Sarah, additional, Krenz, Henrike, additional, Abitbul, Revital, additional, Lavie, Moran, additional, Mussafi, Huda, additional, Mandelberg, Avigdor, additional, Wolter, Alexander, additional, Dougherty, Gerard W., additional, Nöthe-Menchen, Tabea, additional, Wallmeier, Julia, additional, Cindric, Sandra, additional, Werner, Claudius, additional, Pennekamp, Petra, additional, Dworniczak, Bernd, additional, Schmidts, Miriam, additional, Olbrich, Heike, additional, Dugas, Martin, additional, and Omran, Heymut, additional

Published
2023
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26. Additional file 1 of Group-specific cellular metabolism in Medulloblastoma

Author

Funke, Viktoria L. E., Walter, Carolin, Melcher, Viktoria, Wei, Lanying, Sandmann, Sarah, Hotfilder, Marc, Varghese, Julian, Jäger, Natalie, Kool, Marcel, Jones, David T. W., Pfister, Stefan M., Milde, Till, Mynarek, Martin, Rutkowski, Stefan, Seggewiss, Jochen, Jeising, Daniela, de Faria, Flavia W., Marquardt, Thorsten, Albert, Thomas K., Schüller, Ulrich, and Kerl, Kornelius

Abstract

Additional file 1: Supplementary materials. Supplementary materials include supplementary methods, references and the Supplementary Figures S1–S15.

Published
2023
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29. Group-specific cellular metabolism in Medulloblastoma.

Author

Funke, Viktoria L. E., Walter, Carolin, Melcher, Viktoria, Wei, Lanying, Sandmann, Sarah, Hotfilder, Marc, Varghese, Julian, Jäger, Natalie, Kool, Marcel, Jones, David T. W., Pfister, Stefan M., Milde, Till, Mynarek, Martin, Rutkowski, Stefan, Seggewiss, Jochen, Jeising, Daniela, de Faria, Flavia W., Marquardt, Thorsten, Albert, Thomas K., and Schüller, Ulrich

Subjects
MEDULLOBLASTOMA, GENE expression, INOSITOL phosphates, PHOSPHATE metabolism, REGULATOR genes
Abstract

Background: Cancer metabolism influences multiple aspects of tumorigenesis and causes diversity across malignancies. Although comprehensive research has extended our knowledge of molecular subgroups in medulloblastoma (MB), discrete analysis of metabolic heterogeneity is currently lacking. This study seeks to improve our understanding of metabolic phenotypes in MB and their impact on patients' outcomes. Methods: Data from four independent MB cohorts encompassing 1,288 patients were analysed. We explored metabolic characteristics of 902 patients (ICGC and MAGIC cohorts) on bulk RNA level. Moreover, data from 491 patients (ICGC cohort) were searched for DNA alterations in genes regulating cell metabolism. To determine the role of intratumoral metabolic differences, we examined single-cell RNA-sequencing (scRNA-seq) data from 34 additional patients. Findings on metabolic heterogeneity were correlated to clinical data. Results: Established MB groups exhibit substantial differences in metabolic gene expression. By employing unsupervised analyses, we identified three clusters of group 3 and 4 samples with distinct metabolic features in ICGC and MAGIC cohorts. Analysis of scRNA-seq data confirmed our results of intertumoral heterogeneity underlying the according differences in metabolic gene expression. On DNA level, we discovered clear associations between altered regulatory genes involved in MB development and lipid metabolism. Additionally, we determined the prognostic value of metabolic gene expression in MB and showed that expression of genes involved in metabolism of inositol phosphates and nucleotides correlates with patient survival. Conclusion: Our research underlines the biological and clinical relevance of metabolic alterations in MB. Thus, distinct metabolic signatures presented here might be the first step towards future metabolism-targeted therapeutic options. [ABSTRACT FROM AUTHOR]

Published
2023
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31. Clonal Evolution at First Sight: A Combined Visualization of Diverse Diagnostic Methods Improves Understanding of Leukemic Progression

Author

Sandmann, Sarah, primary, Behrens, Yvonne Lisa, additional, Davenport, Claudia, additional, Thol, Felicitas, additional, Heuser, Michael, additional, Dörfel, Daniela, additional, Löhr, Friederike, additional, Castrup, Agnes, additional, Steinemann, Doris, additional, Varghese, Julian, additional, Schlegelberger, Brigitte, additional, Dugas, Martin, additional, and Göhring, Gudrun, additional

Published
2022
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33. ETMR-05. Single-cell transcriptomics of ETMR reveals developmental cellular programs and tumor-pericyte communications in the microenvironment

Author

de Faria, Flavia W, primary, Walter, Carolin, additional, Interlandi, Marta, additional, Melcher, Viktoria, additional, Riedel, Nicole, additional, Graf, Monika, additional, Moreno, Natalia, additional, Schoof, Melanie, additional, Holdhof, Dörthe, additional, Thomas, Christian, additional, Frühwald, Michael C, additional, Maerkl, Bruno, additional, Ho, Ben, additional, Sandmann, Sarah, additional, Varghese, Julian, additional, Ebinger, Martin, additional, Schuhmann, Martin, additional, Canak, Aysegül, additional, Huang, Annie, additional, Schüller, Ulrich, additional, Albert, Thomas K, additional, and Kerl, Kornelius, additional

Published
2022
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34. Design of a targeted next‐generation DNA sequencing panel for pediatric T‐cell lymphoblastic lymphoma to unravel biology and optimize treatment

Author

Ruether, Charlotte, primary, Wuensch, Christian, additional, Randau, Gerrit, additional, Michgehl, Ulf, additional, Trautmann, Marcel, additional, Hartmann, Wolfgang, additional, Sandmann, Sarah, additional, Dugas, Martin, additional, Khanam, Tasneem, additional, and Burkhardt, Birgit, additional

Published
2022
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36. Divergent Effects of EZH1 and EZH2 Protein Expression on the Prognosis of Patients with T-Cell Lymphomas

Author

Schümann, Franziska Lea, primary, Groß, Elisabeth, additional, Bauer, Marcus, additional, Rohde, Christian, additional, Sandmann, Sarah, additional, Terziev, Denis, additional, Müller, Lutz P., additional, Posern, Guido, additional, Wienke, Andreas, additional, Fend, Falko, additional, Hansmann, Martin-Leo, additional, Klapper, Wolfram, additional, Rosenwald, Andreas, additional, Stein, Harald, additional, Dugas, Martin, additional, Müller-Tidow, Carsten, additional, Wickenhauser, Claudia, additional, Binder, Mascha, additional, and Weber, Thomas, additional

Published
2021
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37. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age

Author

Burkhardt, Birgit, Michgehl, Ulf, Tzankov, Alexandar, Dugas, Martin, Sandmann, Sarah, Fend, Falko, Finger, Jasmin, Mueller, Stephanie, Gökbuget, Nicola, Haferlach, Torsten, Kern, Wolfgang, Hartmann, Wolfgang, Rohde, Jonas, Klapper, Wolfram, Oschlies, Ilske, Richter, Julia, Kontny, Udo, Lutz, Mathias, Maecker-Kolhoff, Britta, Ott, German, Rosenwald, Andreas, Siebert, Reiner, von Stackelberg, Arend, Erdmann, Tabea, Strahm, Brigitte, Woessmann, Wilhelm, Zimmermann, Martin, Zapukhlyak, Myroslav, Grau, Michael, Lenz, Georg, Berning, Philipp, Reutter, Katrin, Rohde, Marius, Borkhardt, Arndt, Burmeister, Thomas, and Dave, Sandeep

Subjects
Adult, Genes, cdc, Mutation Rate, Mutation, DNA Helicases, Humans, Nuclear Proteins, Cell Cycle Proteins, ddc:610, Neoplasm Recurrence, Local, Child, Burkitt Lymphoma, Transcription Factors
Abstract

Nature Communications 13(1), 3881 (2022). doi:10.1038/s41467-022-31355-8, Published by Nature Publishing Group UK, [London]

Published
2021

38. clevRvis: visualization techniques for clonal evolution.

Author

Sandmann, Sarah, Inserte, Clara, and Varghese, Julian

Subjects
*GRAPHICAL user interfaces, *COLOR codes, *NUCLEOTIDE sequencing, *PLAICE
Abstract

Background A thorough analysis of clonal evolution commonly requires integration of diverse sources of data (e.g. karyotyping, next-generation sequencing, and clinical information). Subsequent to actual reconstruction of clonal evolution, detailed analysis and interpretation of the results are essential. Often, however, only few tumor samples per patient are available. Thus, information on clonal development and therapy effect may be incomplete. Furthermore, analysis of biallelic events—considered of high relevance with respect to disease course—can commonly only be realized by time-consuming analysis of the raw results and even raw sequencing data. Results We developed clevRvis, an R/Bioconductor package providing an extensive set of visualization techniques for clonal evolution. In addition to common approaches for visualization, clevRvis offers a unique option for allele-aware representation: plaice plots. Biallelic events may be visualized and inspected at a glance. Analyzing 4 public datasets, we show that plaice plots help to gain new insights into tumor development and investigate hypotheses on disease progression and therapy resistance. In addition to a graphical user interface, automatic phylogeny-aware color coding of the plots, and an approach to explore alternative trees, clevRvis provides 2 algorithms for fully automatic time point interpolation and therapy effect estimation. Analyzing 2 public datasets, we show that both approaches allow for valid approximation of a tumor's development in between measured time points. Conclusions clevRvis represents a novel option for user-friendly analysis of clonal evolution, contributing to gaining new insights into tumor development. [ABSTRACT FROM AUTHOR]

Published
2023
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42. Integrative genomic analysis of pediatric T-cell lymphoblastic lymphoma reveals candidates of clinical significance

Author

Khanam, Tasneem, Sandmann, Sarah, Seggewiss, Jochen, Ruether, Charlotte, Zimmermann, Martin, Norvil, Allison B., Bartenhagen, Christoph, Randau, Gerrit, Mueller, Stephanie, Herbrueggen, Heidi, Hoffmann, Per, Herms, Stefan, Wei, Lanying, Woeste, Marius, Wuensch, Christian, Gowher, Humaira, Oschlies, Ilske, Klapper, Wolfram, Woessmann, Wilhelm, Dugas, Martin, Burkhardt, Birgit, Khanam, Tasneem, Sandmann, Sarah, Seggewiss, Jochen, Ruether, Charlotte, Zimmermann, Martin, Norvil, Allison B., Bartenhagen, Christoph, Randau, Gerrit, Mueller, Stephanie, Herbrueggen, Heidi, Hoffmann, Per, Herms, Stefan, Wei, Lanying, Woeste, Marius, Wuensch, Christian, Gowher, Humaira, Oschlies, Ilske, Klapper, Wolfram, Woessmann, Wilhelm, Dugas, Martin, and Burkhardt, Birgit

Abstract

T-cell lymphoblastic lymphoma (T-LBL) is a heterogeneous malignancy of lymphoblasts committed to T-cell lineage. The dismal outcomes (15%-30%) after T-LBL relapse warrant establishing risk-based treatment. To our knowledge, this study presents the first comprehensive, systematic, integrated, genome-wide analysis including relapsed cases that identifies molecular markers of prognostic relevance for T-LBL. NOTCH1 was identified as the putative driver for T-LBL. An activated NOTCH/PI3K-AKT signaling axis and alterations in cell cycle regulators constitute the core oncogenic program for T-LBL. Mutated KMT2D was identified as a prognostic marker. The cumulative incidence of relapse was 47% +/- 17% in patients with KMT2D mutations, compared with 14% +/- 3% in wild-type KMT2D. Structural analysis of the mutated domains of KMT2D revealed a plausible impact on structure and functional consequences. These findings provide new insights into the pathogenesis of T-LBL, including high translational potential. The ongoing LBL 2018 trial (www.clinicaltrials.gov #NCT04043494) allows for prospective validation and subsequent fine tuning of the stratification criteria for T-LBL risk groups to improve survival of pediatric patients.

Published
2021

43. Somatic Mutations and DNA Hypermethylation at Enhancers and Promoters Identify Distinct Subtypes within Lower-Risk Myelodysplastic Syndromes

Author

Rombaut, David, Tekath, Tobias, Sandmann, Sarah, Crouch, Simon, de Graaf, Aniek O., Kosmider, Olivier, Tobiasson, Magnus, Lennartsson, Andreas, Van der Reijden, Bert A., Park, Sophie, D'Aveni, Maud, Slama, Bohrane, Clappier, Emmanuelle, Fenaux, Pierre, Ades, Lionel, van de Loosdrecht, Arjan A., Langemeijer, Saskia MC, Symeonidis, Argiris S., Čermák, Jaroslav, Preudhomme, Claude, Savic, Aleksandar, Germing, Ulrich, Stauder, Reinhard, Bowen, David T., Van Marrewijk, Corine J., Bernard, Elsa, Smith, Alexandra, Painter, Daniel, de Witte, Theo J.M., Hellstrom Lindberg, Eva, Varghese, Julian, Dugas, Martin, Martens, Joost H.A., Malcovati, Luca, Jansen, Joop H., and Fontenay, Michaela

Published
2023
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44. Integrative genomic analysis of pediatric T-cell lymphoblastic lymphoma reveals candidates of clinical significance

Author

Khanam, Tasneem, primary, Sandmann, Sarah, additional, Seggewiss, Jochen, additional, Ruether, Charlotte, additional, Zimmermann, Martin, additional, Norvil, Allison B., additional, Bartenhagen, Christoph, additional, Randau, Gerrit, additional, Mueller, Stephanie, additional, Herbrueggen, Heidi, additional, Hoffmann, Per, additional, Herms, Stefan, additional, Wei, Lanying, additional, Woeste, Marius, additional, Wuensch, Christian, additional, Gowher, Humaira, additional, Oschlies, Ilske, additional, Klapper, Wolfram, additional, Woessmann, Wilhelm, additional, Dugas, Martin, additional, and Burkhardt, Birgit, additional

Published
2021
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45. Multicenter Next-Generation Sequencing Studies between Theory and Practice

Author

Sandmann, Sarah, primary, de Graaf, Aniek O., additional, Tobiasson, Magnus, additional, Kosmider, Olivier, additional, Abáigar, María, additional, Clappier, Emmanuelle, additional, Gallì, Anna, additional, van der Reijden, Bert A., additional, Malcovati, Luca, additional, Fenaux, Pierre, additional, Díez-Campelo, María, additional, Fontenay, Michaela, additional, Hellström-Lindberg, Eva, additional, Jansen, Joop H., additional, and Dugas, Martin, additional

Published
2021
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49. Mutation Profiles Identify Distinct Clusters of Lower Risk Myelodysplastic Syndromes with Unique Clinical and Biological Features and Clinical Endpoints

Author

Malcovati, Luca, primary, Crouch, Simon, additional, De Graaf, Aniek O., additional, Sandmann, Sarah, additional, Tobiasson, Magnus, additional, Kosmider, Olivier, additional, van der Reijden, Bert A., additional, Painter, Daniel, additional, Van de Loosdrecht, Arjan A., additional, Symeonidis, Argiris, additional, Cermak, Jaroslav, additional, Clappier, Emmanuelle, additional, Preudhomme, Claude, additional, Stauder, Reinhard, additional, Mittelman, Moshe, additional, Germing, Ulrich, additional, Bowen, David, additional, Fenaux, Pierre, additional, Van Marrewijk, Corine, additional, Smith, Alexandra, additional, Dugas, Martin, additional, Hellstrom Lindberg, Eva, additional, de Witte, Theo M, additional, Fontenay, Michaela, additional, and Jansen, Joop, additional

Published
2020
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