SFB 1243 Publications
The SFB 1243 ended in March 2021, and this site is no longer updated.
2021
Landspersky T, Saçma M, Rivière J, Hecker JS, Hettler F, Hameister E, Brandstetter K, Istvanffy R, Romero Marquez S, Ludwig R, Götz M, Buck MC, Wolf M, Schiemann M, Ruland J, Strunk D, Shimamura A, Myers KC, Yamaguchi TP, Kieslinger M, Leonhardt H, Bassermann F, Götze KS, Geiger H, Schreck C, Oostendorp RAJ. Autophagy In Mesenchymal Progenitors Protects Mice Against Bone Marrow Failure After Severe Intermittent Stress. Blood. 2021 Oct 17:blood.2021011775. doi: 10.1182/blood.2021011775. PMID: 34657154.
Kempf JM, Weser S, Bartoschek MD, Metzeler KH, Vick B, Herold T, Völse K, Mattes R, Scholz M, Wange LE, Festini M, Ugur E, Roas M, Weigert O, Bultmann S, Leonhardt H, Schotta G, Hiddemann W, Jeremias I and Spiekermann K (2021). Loss-of-function mutations in the histone methyltransferase EZH2 promote chemotherapy resistance in AML. Sci Rep., 11, 5838. https://doi.org/10.1038/s41598-021-84708-6
2020
Mulholland CB, Nishiyama A, Ryan J, Nakamura R, Yiğit M, Glück IM, Trummer C, Qin W, Bartoschek MD, Traube FR, Parsa E, Ugur E, Modic M, Acharya A, Stolz P, Ziegenhain C, Wierer M, Enard W, Carell T, Lamb DC, Takeda H, Nakanashi M, Bultmann S and Leonhardt H (2020). Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. Nat Commun., 11, 5972. https://doi.org/10.1038/s41467-020-19603-1
Schmitt S, Tahk S, Lohner A, Hänel G, Maiser A, Hauke M, Patel L, Rothe M, Josenhans C, Leonhardt H, Griffioen M, Deiser K, Fenn NC, Hopfner KP* and Subklewe M* (2020 Nov 12) Fusion of Bacterial Flagellin to a Dendritic Cell-Targeting aCD40 Antibody Construct Coupled With Viral or Leukemia-Specific Antigens Enhances Dendritic Cell Maturation and Activates Peptide-Responsive T Cells. Front. Immunol. 11:602802. doi: 10.3389/fimmu.2020.602802
Romero Marquez S, Hettler F, Hausinger R, Schreck C, Landspersky T, Henkel L, Angerpointner C, Demir IE, Schiemann M, Bassermann F, Götze KS, Istvánffy R, Oostendorp RAJ. Secreted factors from Mouse embryonic fibroblasts maintain repopulating function of single cultures hematopoietic stem cells. Haematologica. Accepted for Publication, Nov. 10th, 2020
Brauchle B, Goldstein RL, Karbowski CM , Henn A, Li C-M, Bücklein VL, Krupka C, Boyle MC, Koppikar P, Haubner S, Wahl J, Dahlhoff C, Raum T, Rardin MJ, Sastri C, Rock DA, von Bergwelt-Baildon M, Frank B, Metzeler KH, Case R, Friedrich M, Balazs M, Spiekermann K, Coxon A, Subklewe M, Arvedson T (2020) Characterization of a Novel FLT3 BiTE Antibody Construct for the Treatment of Acute Myeloid Leukemia. Mol Cancer Ther. (June 9, 2020, online ahead of print) DOI: 10.1158/1535-7163.MCT-19-1093
Müller-Thomas C, Heider M, Piontek G, Schlensog M, Bassermann F, Kirchner T, Germing U, Götze KS, Rudelieus M (2020) Prognostic value of indoleamine 2,3 dioxygenase in patients with higher-risk myelodysplastic syndromes treated with azacytidine [published online ahead of print, 2020 Apr 29]. Br J Haematol. doi:10.1111/bjh.16652
Kober-Hasslacher M, Oh-Strauß H, Kumar D, Soberon V, Diehl C, Lech M, Engleitner T, Katab E, Fernández-Sáiz V, Piontek G, Li H, Menze B, Ziegenhain C, Enard W, Rad R, Rudelius M, Schmidt-Supprian M (2020) c-Rel gain in B cells drives germinal center reactions and autoantibody production. J Clin Invest 120, 2991. doi: 10.1172/JCI124382
Bararia D, Hildebrand JA, Stolz S, Haebe S, Alig S, Trevisani CP, Osorio-Barrios F, Bartoschek MD, Mentz M, Pastore A, Gaitzsch E, Heide M, Jurinovic V, Rautter K, Gunawardana J, Sabdia M, Szczepanowski M, Richter J, Klapper W, Louissaint A Jr, Ludwig C, Bultmann S, Leonhardt H, Eustermann S, Hopfner KP, Hiddemann W, von Bergwelt-Baildon M, Steid C, Kridel R, Tobin JWD, Gandhi MK, Weinstock DM, Schmidt-Supprian M, Sárosi MB, Rudelius M, Passerini V, Mautner J and Weigert O (2020) Cathepsin S Alterations Induce a Tumor-Promoting Immune Microenvironment in Follicular Lymphoma. Cell Reports https://doi.org/10.1016/j.celrep.2020.107522
Kober-Hasslacher M, Oh-Strauß H, Kumar D, Soberon V, Diehl C, Lech M, Engleitner T, Katab E, Fernández-Sáiz V, Piontek G, Li H, Menze B, Ziegenhain C, Enard W, Rad R, Böttcher JP, Anders HJ, Rudelius M, Schmidt-Supprian M (2020). c-Rel gain in B cells drives germinal center reactions and autoantibody production. J Clin Invest 120, 2991. doi: 10.1172/JCI124382
Grosser K, Metzler D (2020) Modeling methylation dynamics with simultaneous changes in CpG islands. BMC Bioinformatics 21, 115. https://doi.org/10.1186/s12859-020-3438-5
Redondo Monte E, Wilding A, Leubolt G, Kerbs P, Bagnoli JW, Hartmann L, Hiddemann W, Chen-Wichmann L, Krebs S, Blum H, Cusan M, Vick B, Jeremias I, Enard W, Theurich S, Wichmann C, Greif PA (2020 Mar 2) ZBTB7A prevents RUNX1-RUNX1T1-dependent clonal expansion of human hematopoietic stem and progenitor cells. Oncogene. doi: 10.1038/s41388-020-1209-4, PubMed PMID:32115572.
Nishiyama A, Mulholland CB, Bultmann S, Kori S, Endo A, Saeki Y, Qin W, Trummer C, Chiba Y, Yokoyama H, Kumamoto S, Kawakami T, Hojo H, Nagae G, Aburatani H, Tanaka K, Arita K, Leonhardt H and Nakanishi M (2020). Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation. Nature Communications 11: 1222. https://doi.org/10.1038/s41467-020-15006-4
Schneider M, Trummer C, Stengl A, Zhang P, Szwagierczak A, Cardoso MC, Leonhardt H, Bauer C and Antes I (2020 Feb 21). Systematic analysis of the binding behaviour of UHRF1 towards different methyl- and carboxylcytosine modification patterns at CpG dyads. PLoS One, 15, e0229144. https://doi.org/10.1371/journal.pone.0229144
Deng W, Bates JA, Wei H, Bartoschek MD, Conradt B and Leonhardt H (2020 Jan 16) Tunable light and drug induced depletion of target proteins. Nature Communications 11:304. https://doi.org/10.1038/s41467-019-14160-8
Park E, Chen J, Moore A, Mangolini M, Santoro A, Boyd JR, Schjerven H, Ecker V, Buchner M, Williamson JC, Lehner PJ, Gasparoli L, Williams O, Bloehdorn J, Stilgenbauer S, Leitges M, Egle A, Schmidt-Supprian M, Frietze S, Ringshausen I (2020 Jan 15) Stromal cell protein kinase C-β inhibition enhances chemosensitivity in B cell malignancies and overcomes drug resistance. Science Translational Medicine 12, eaax9340. doi:10.1126/scitranslmed.aax9340
Opatz S, Bamopoulos S, Metzeler K, Herold T, Ksienzyk B, Braeundl, K Tschuri S, Vosberg S, Konstandin N, Wang C, Hartmann L, Graf A, Krebs S, Blum H, Schneider S, Thiede C, Middeke JM, Stölzel F, Roellig C, Schetelig J, Ehninger G, Krämer A, Braess J, Görlich D, Sauerland C, Berdel W, Wörmann B, Hiddemann W, Spiekermann K, Bohlander S, and Greif P (2020 Jan 2) The clinical mutatome of core binding factor leukemia. Leukemia. doi: 10.1038/s41375-019-0697-0
Leubolt G, Redondo Monte E, Greif PA (2020) GATA2 mutations in myeloid malignancies: Two zinc fingers in many pies. IUBMB Life. Jan;72(1):151-158. doi:10.1002/iub.2204. Epub 2019 Nov 29. Review. PubMed PMID: 31785092.
2019
Kerbs P, Nazeer Batcha AM, Vosberg S, Metzler D, Herold T, Greif PA (2019) Gene Fusion Detection By RNA-Seq in Acute Myeloid Leukemia (AML) Blood (2019) 134 (Supplement_1): 4655. https://doi.org/10.1182/blood-2019-125869
Sadafi A, Koehler N, Makhro A, Bogdanova A, Navab N, Marr C, Peng T (2019) Multiclass Deep Active Learning for Detecting Red Blood Cell Subtypes in Brightfield Microscopy. In: Shen D. et al. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2019. MICCAI 2019. Lecture Notes in Computer Science, vol 11764. Springer, Cham. https://doi.org/10.1007/978-3-030-32239-7_76
Kasper M-A, Gerlach M, Schneider AFL, Groneberg C, Ochtrop P, Boldt S, Schumacher D, Helma J, Leonhardt H, Christmann M and Hackenberger CPR (in press) NHS-modified ethynylphosphonamidates enable the synthesis of configurationally defined protein conjugates. ChemBioChem 10.1002/cbic.201900587. http://dx.doi.org/10.1002/cbic.201900587
Grunwald VV, Hentrich M, Schiel X, Dufour A, Schneider S, Neusser M, Subklewe M, Fiegl M, Hiddemann W, Spiekermann K, Rothenberg-Thurley M, & Metzeler KH (2019). Patients with spontaneous remission of high-risk MDS and AML show persistent preleukemic clonal hematopoiesis. Blood Advances, 3(18), 2696-2699. doi: https://doi.org/10.1182/bloodadvances.2019000265
Vosberg S, Greif PA. Clonal evolution of acute myeloid leukemia from diagnosis to relapse. (2019 Sep 3) Genes Chromosomes Cancer. DOI:10.1002/gcc.22806
Tirier SM, Park J, Preußer F, Amrhein L, Gu Z, Steiger S, Mallm JP, Waschow M, Eismann B, Gu M, Gut IG, Rippe K, Schlesner M, Theis F, Fuchs C, Ball CR, Glimm H, Eils R, Conrad C. pheno-seq – linking morphological features to gene expression in 3D cell culture systems. (2019 Aug 26) Scientific Reports 9:12367. doi.org/10.1038/s41598-019-48771-4
Liu WL, Mrozek-Gorska P, Herold T, Schwarzkopf L, Pich D, Völse K, Wirth AK, Melo-Narváez MC, Carlet M, Hammerschmidt W, Jeremias I. KLF4 acts as a tumor suppressor in human B-cells and patients' B-cell leukemias growing in mice. (2019 August 16) bioRxiv https://www.biorxiv.org/content/biorxiv/early/2019/08/16/737726.full.pdf
Vaikari VP, Du Y, Wu S, Zhang T, Metzeler K, Batcha AMN, Herold T, Hiddemann W, Akhtari M, Alachkar H. Clinical and Preclinical characterization of CD99 Isoforms in Acute Myeloid Leukemia. (2019 August) Haematologica. doi:10.3324/haematol.2018.207001
Vieth B, Parekh S, Ziegenhain C, Enard W, Hellmann I. A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines: Library preparation and normalisation methods have the biggest impact on the performance of scRNA-seq studies (08 Aug 2019) accepted Nature Communications. biorxiv https://www.biorxiv.org/content/10.1101/583013v2
Batcha AMN, Bamopoulos SA, Kerbs P, Kumar A, Jurinovic V, Rothenberg-Thurley M, Ksienzyk B, Philippou-Massier J, Krebs S, Blum H, Schneider S, Konstandin N, Bohlander SK, Heckman C, Kontro M, Hiddemann W, Spiekermann K, Braess J, Metzeler KH, Greif PA, Mansmann U, Herold T. Allelic imbalance of recurrently mutated genes in Acute Myeloid Leukaemia (13 Aug 2019). Scientific Reports 9: 11796. doi: 10.1038/s41598-019-48167-4
Vincent-Fabert, C., Roland, L., Zimber-Strobl, U., Feuillard, J., and Faumont, N. Pre-clinical blocking of PD-L1 molecule, which expression is down regulated by NF-kappaB, JAK1/JAK2 and BTK inhibitors, induces regression of activated B-cell lymphoma. (2019). Cell Commun Signal 17, 89. doi: 10.1186/s12964-019-0391-x.
Kasper MA, Stengl A, Ochtrop P, Gerlach M, Stoschek T, Schumacher D, Helma J, Penkert M, Krause E, Leonhardt H, Hackenberger CPR. Ethynylphosphonamidates for the rapid and cysteine selective generation of efficacious Antibody-Drug-Conjugates. (2019) Angew. Chem. Int. Ed. 10.1002/anie.201904193
Ebinger S, Zeller C, Carlet M, Senft D, Liu WH, Rothenberg-Thurley M, Metzeler KH, Spiekermann K, Vick B and Jeremias I. Functional plasticity and reversible growth behavior of patients’ acute myeloid leukemia stem cells growing in mice. (19 Jul 2019) bioRxiv: 707935. doi: http://dx.doi.org/10.1101/707935
Stief S, Hanneforth AL, Weser S, Mattes R, Carlet M, Liu WH, Bartoschek MD, Domínguez Moreno H, Oettle M, Kempf J, Vick B, Ksienzyk B, Tizazu B, Rothenberg-Thurley M, Quentmeier H, Hiddemann W, Vosberg S, Greif PA, Metzeler KH, Schotta G, Bultmann S, Jeremias I, Leonhardt H and Spiekermann K. Loss of KDM6A confers drug resistance in acute myeloid leukemia. Leukemia (2019 Jun 14). [Epub ahead of print] doi.org/10.1038/s41375-019-0497-6)
Bastidas-Ponce A, Tritschler S, Dony L, Scheibner K, Tarquis-Medina M, Salinno C, Schirge S, Burtscher I, Böttcher A, Theis FJ, Lickert H, Bakhti M . Massive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis (17 June 2019, 146: dev173849) Development. doi: 10.1242/dev.173849
Amrhein L, Harsha K, Fuchs C. A mechanistic model for the negative binomial distributions of single-cell mRNA counts. (2019) BioRxiv, doi: https://doi.org/10.1101/657619.
Tepper S, Mortusewicz O, Czlonka E, Bello A, Schmidt A. Jeschke J, Fischbach A, Pfeil I, Petersen-Mahrt SK, Mangerich A, Helleday T, Leonhardt H and Jungnickel B (2019). Restriction of AID activity and somatic hypermutation by PARP-1. Nucleic Acids Res., 2019 May 25. doi.org/10.1093/nar/gkz466
Danese A, Richter ML, Fischer DS, Theis FJ, Colomé-Tatché M. EpiScanpy: integrated single-cell epigenomic analysis (2019) doi: https://doi.org/10.1101/648097
Sandner AS, Weggel R, Mehraein Y, Schneider S, Hiddemann W, Spiekermann K. Frequency of hematologic and solid malignancies in the family history of 50 patients with acute myeloid leukemia – a single center analysis. (2019) PloS One 14(4):e0215453. doi: 10.1371/journal.pone.0215453
Sperling SA, Fiedler P, Lechner M, Pollithy A, Ehrenberg S, Schiefer AI, Kenner L, Feuchtinger A, Kühn R, Swinerd G, Schmidt-Supprian M, Strobl LJ, Zimber-Strobl U. Chronic CD30-signaling in B cells results in lymphomagenesis by driving the expansion of plasmablasts and B1 cells. Blood (2019 Apr 8) DOI: https://doi.org/10.1182/blood.2018880138. [Epub ahead of print]
Vincent-Fabert C, Saintamand A, David A, Alizadeh M, Boyer F, Arnaud N, Zimber-Strobl U, Feuillard J, Faumont N. Reproducing indolent B-cell lymphoma transformation with T-cell immunosuppression in LMP1/CD40-expressing mice. Cell Mol Immunol. (2019 Apr 16) 4:412-414. DOI: https://doi.org/10.1038/s41423-018-0197-6.
Jilg S, Hauch RT, Kauschinger J, Buschhorn L, Odinius TO, Dill V, Müller-Thomas C, Herold T, Prodinger PM, Schmidt B, Hempel D, Bassermann F, Peschel C, Götze KS, Höckendorf U, Haferlach T, Jost PJ. Venetoclax with azacitidine targets refractory MDS but spares health hematopoiesis at tailored dose (2019 Apr 6) Exp Hematol Oncol 8:9. doi: 10.1186/s40164-019-0133-1
Köhnke T, Bücklein V, Rechkemmer S, Schneider S, Rothenberg-Thurley M, Metzeler KH, Sauerland MC, Hiddemann W, Spiekermann K, Subklewe M. Response assessment in acute myeloid leukemia by flow cytometry supersedes cytomorphology at time of aplasia, amends cases without molecular residual disease marker and serves as an independent prognostic marker at time of aplasia and post-induction. Haematologica (2019 Apr 4) doi: 10.3324/haematol.2018.215236. [Epub ahead of print]
Hartmann L and Metzeler KH. Clonal hematopoiesis and pre‐leukemia – genetics, biology and clinical implications. Genes Chromosomes Cancer (2019) Accepted Author Manuscript. doi:10.1002/gcc.22756
Bagnoli JW, Wange LE, Janjic A, and Enard W. Studying Cancer Heterogeneity by Single-Cell RNA Sequencing. Methods in Molecular Biology (2019) 1956: 305–19. DOI: 10.1007/978-1-4939-9151-8_14
Fischer DS, Fiedler AK, Kernfeld EM, Genga RMJ, Bastidas-Ponce A, Bakhti M, Lickert H, Hasenauer J, Maehr R, Theis FJ. Inferring population dynamics from single-cell RNA-sequencing time series data. Nature Biotechnology(2019) volume 37, 461–468. DOI: https://doi.org/10.1038/s41587-019-0088-0
Stengl A, Gerlach M, Kasper MA, Hackenberger CPR, Leonhardt H, Schumacher D, and Helma J (2019). TuPPL: Tub-tag mediated C-terminal protein-protein-ligation using complementary click-chemistry handles. Org Biomol Chem., (Apr 1, 2019) [Epub ahead of print] DOI: 10.1039/c9ob00508k
Weber J, de la Rosa J, Grove CS, Schick M, Rad L, Baranov O, Strong A, Pfaus A, Friedrich MJ, Engleitner T, Lersch R, Öllinger R, Grau M, Menendez IG, Martella M, Kohlhofer U, Banerjee R, Turchaninova MA, Scherger A, Hoffman GJ, Hess J, Kuhn LB, Ammon T, Kim J, Schneider G, Unger K, Zimber-Strobl U, Heikenwälder M, Schmidt-Supprian M, Yang F, Saur D, Liu P, Steiger K, Chudakov DM, Lenz G, Quintanilla-Martinez L, Keller U, Vassiliou GS, Cadiñanos J, Bradley A, Rad R. PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice. Nature Communications (2019 Mar 29) 10(1):1415. doi: 10.1038/s41467-019-09180-3
Matek C, Schwarz S, Spiekermann K, Marr C. Human-level recognition of blast cells in acute myeloid leukemia with convolutional neural networks. (2019, Feb 28) bioRXiv doi: https://doi.org/10.1101/564039. Accepted in Nature Machine Intelligence
Alig S, Jurinovic V, Pastore A, Haebe S, Schmidt C, Zoellner AK, Dreyling M, Unterhalt M, Hoster E, Hiddemann W, Weigert O. Impact of age on clinical risk scores in follicular lymphoma. Blood Advances (2019 Feb 24) 3: 1033-1038 doi: https://doi.org/10.1182/bloodadvances.2019032136
Effenberger M, Stengl A, Schober K, Gerget M, Kampick M, Müller TR, Schumacher D, Helma J, Leonhardt H, Busch DH. FLEXamers: A double tag for universal generation of versatile peptide-MHC multimers. J Immunol (13 Feb 2019) 202 (7): . doi:10.4049/jimmunol.1801435
Garg G, Mushaweckh A, Moreno H, Vasanthakumar A, Floess S, Lepennetier G, Oellinger R, Zhan Y, Regen T, Hilentsperger M, Peter C, Aly L, Knier B, Palam LR, Kapur R, Kaplan MH, Waismann A, Rad R, Schotta G, Huehn J, Kallies A, Korn T. Blimp1 prevents methylation of Foxp3 and loss of regulatory T cell identity at sites of inflammation. Cell Reports (Feb 12, 2019). 26 (7): 1854-1868. doi: 10.1016/j.celrep.2019.01.070
Wolf FA, Hamey FK, Plass M, Solana J, Dahlin JS, Göttgens B, Rajewsky N, Simon L, Theis FJ. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biology (2019)20:59. https://doi.org/10.1186/s13059-019-1663-x
Krautenbacher N, Flach N, Böck A, Laubhahn K, Laimighofer M, Theis FJ, Ankerst DP, Fuchs C, Schaub B. A strategy for high-dimensional multivariable analysis classifies childhood asthma phenotypes from genetic, immunological, and environmental factors. Allergy. 2019 Feb 9. doi: 10.1111/all.13745.
Haubner S, Perna F, Köhnke T, Schmidt C, Berman S, Augsberger C, Schnorfeil FM, Krupka C, Lichtenegger FS, Liu X, Kerbs P, Schneider S, Metzeler KH, Spiekermann K, Hiddemann W, Greif PA, Herold T, Sadelain M, Subklewe M. Coexpression profile of leukemic stem cell markers for combinatorial targeted therapy in AML. Leukemia (Jan 2019) 33 (1): 64-74. doi: 10.1038/s41375-018-0180-3
Senft D and Jeremias I. A rare subgroup of leukemia stem cells harbors relapse-inducing potential in acute lymphoblastic leukemia (Jan 2019) Exp Hematol 69: 1-10. DOI: https://doi.org/10.1016/j.exphem.2018.09.006
Eraslan G, Simon LM, Mircea M, Mueller NS, Theis FJ. Single-cell RNA-seq denoising using a deep count autoencoder. Nature Communications (2019) volume 10, Article number: 390. DOI: https://doi.org/10.1038/s41467-018-07931-2
Büttner M, Miao Z, Wolf FA, Teichmann SA, Theis FJ. A test metric for assessing single-cell RNA-seq batch correction. Nature Methods (2019) volume 16:43–49. DOI: https://doi.org/10.1038/s41592-018-0254-1
2018
Lotfollahi, Wolf FA, Theis FJ. Generative modeling and latent space arithmetics3predict single-cell perturbation response across4cell types, studies and species56M. bioRxiv (2018) http://dx.doi.org/10.1101/478503doi: bioRxiv
Bast L, Calzolari F, Strasser MK, Hasenauer J, Theis FJ, Ninkovic J, Marr C. Increasing Neural Stem Cell Division Asymmetry and Quiescence Are Predicted to Contribute to the Age-Related Decline in Neurogenesis. Cell Rep. 2018 Dec 18;25(12):3231-3240.e8. doi: 10.1016/j.celrep.2018.11.088.
Herrmann M, Krupka C, Deiser K, Brauchle B, Marcinek A, Ogrinc Wagner A, Rataj F, Mocikat R, Metzeler KH, Spiekermann K, Kobold S, Fenn NC, Hopfner KP, Subklewe M. Bifunctional PD-1 x αCD3 x αCD33 fusion protein reverses adaptive immune escape in acute myeloid leukemia. Blood (2018, Dec 6) 132(23): 2484-2494. doi: 10.1182/blood-2018-05-849802.
Jeremias I and Schewe DM . Characteristics and Therapeutic Targeting of Minimal Residual Disease in Childhood Acute Lymphoblastic Leukemia. (Nov 2018) In: Aguirre-Ghiso J (eds.) "Biological Mechanisms of Minimal Residual Disease and Systemic Cancer". Adv Exp Med Biol 1100: 127-139. Springer, Cham. DOI https://doi.org/10.1007/978-3-319-97746-1_8
Neschen S, Wu M, Fuchs C, Kondofersky I, Theis FJ, de Angelis MH, Häring HU, Sartorius T. Impact of Brain Fatty Acid Signaling on Peripheral Insulin Action in Mice. Exp Clin Endocrinol Diabetes. (2018 Nov 5) doi: 10.1055/a-0735-9533.
Wenk C, Garz AK, Grath S, Huberle C, Witham D, Weickert M, Malinverni R, Niggemeyer J, Kyncl M, Hecker J, Pagel C, Mulholland CB, Müller-Thomas C, Leonhardt H, Bassermann F, Oostendorp RAJ, Metzeler KH, Buschbeck M and Götze KS. Direct modulation of the bone marrow mesenchymal stromal cell compartment by azacitidine enhances healthy hematopoiesis. Blood Adv. (Nov 2018) 2, 3447-3461. doi: https://doi.org/10.1182/bloodadvances.2018022053.
Konstandin NP, Pastore F, Herold T, Dufour A, Rothenberg-Thurley M, HinrichsenT, Ksienzyk B, Tschuri S, Schneider S, Hoster E, Berdel WE, Woermann BJ, Sauerland MC, Braess J, Bohlander SK, Klein HG, Hiddemann W, Metzeler KH, Spiekermann K. Genetic heterogeneity of cytogenetically normal AML with mutations of CEBPA. Blood Adv (2018 Oct 23) 2(20):2724-2731. doi:10.1182/bloodadvances.2018016840.
Heckl BC, Carlet M, Vick B, Roolf C, Alsadeq A, Grunert M, Liu WH, Liebl A, Hiddemann W, Marschalek R, Schewe DM, Spiekermann K, Junghanss C and Jeremias I. Frequent and reliable engraftment of certain adult primary acute lymphoblastic leukemias in mice. (20 Sep 2018) Leuk Lymphoma 60(3):848-851. https://doi.org/10.1080/10428194.2018.1509314
Hellmuth JC, Louissant A, Szczepanowski M, Haebe S, Pastore A, Alig S, Staiger AM, Hartmann S, Kridel R, Ducar MD, Koch P, Dreyling M, Hansmann M-L, Ott G, Rosenwald A, Gascoyne RD, Weinstock DM, Hiddemann W, Klapper W, Weigert O. Duodenal type and nodal follicular lympohoma differ by their immune microenvironment rahter than their mutation profiles. Blood. Aug 2018. pii: blood-2018-03-837252. doi: 10.1182/blood-2018-03-837252. [Epub ahead of print].
Rothenberg-Thurley M, Amler S, Goerlich D, Köhnke T, Konstandin NP, Schneider S, Sauerland MC, Herold T, Hubmann M, Ksienzyk B, Zellmeier E, Bohlander SK, Subklewe M, Faldum A, Hiddemann W, Braess J, Spiekermann K, Metzeler KH. Persistence of pre-leukemic clones during first remission and risk of relapse in acute myeloid leukemia. Leukemia. 2018 Jul;32(7):1598-1608. doi: 10.1038/s41375-018-0034-z.
Braciak TA, Roskopf CC, Wildenhain S, Fenn NC, Schiller CB, Schubert IA, Jacob U, Honegger A, Krupka C, Subklewe M, Spiekermann K, Hopfner KP, Fey GH, Aigner M, Krause S, Mackensen A, Oduncu FS. Dual-targeting triplebody 33-16-123 (SPM-2) mediates effective redirected lysis of primary blasts from patients with a broad range of AML subtypes in combination with natural killer cells. Oncoimmunology (2018 Jul 30) 7(9):e1472195. doi: 0.1080/2162402X.2018.1472195
Stosch JM, Heumüller A, Niemöller C, Bleul S, Rothenberg-Thurley M, Riba J, Renz N, Szarc Vel Szic K, Pfeifer D, Follo M, Pahl HL, Zimmermann S, Duyster J, Wehrle J, Lübbert M, Metzeler KH, Claus R, Becker H. Gene mutations and clonal architecture in myelodysplastic syndromes and changes upon progression to acute myeloid leukaemia and under treatment. Br J Haematol. 2018 Jul 5. doi: 10.1111/bjh.15461.
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Parekh S, Ziegenhain C, Vieth B, Enard W, Hellmann I. zUMIs - A Fast and Flexible Pipeline to Process RNA Sequencing Data with UMIs. GigaScience 2018 7 (6). https://doi.org/10.1093/gigascience/giy059.
Bagnoli JW, Ziegenhain C, Janjic A, Wange LE, Vieth B, Parekh S, Geuder J, Hellmann I, Enard W Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq. Nature Communications (2018) 9: 2937. DOI: 10.1038/s41467-018-05347-6
Reidel V, Kauschinger J, Hauch RT, Müller-Thomas C, Nadarajah N, Burgkart R, Schmidt B, Hempel D, Jacob A, Slotta-Huspenina J, Höckendorf U, Peschel C, Kern W, Haferlach T, Götze KS, Jilg S, Jost PJ. Selective inhibition of BCL-2 is a promising target in patients with high-risk myelodysplastic syndromes and adverse mutational profile. Oncotarget (2018) Apr. 3; 9 (25): 17270-17281. doi:10.18632/oncotarget.24775.
Bultmann S, Stricker SH Entering the post-epigenomic age: back to epigenetics Open Biology (2018 Mar 28) 8: 180013. DOI: 10.1098/rsob.180013
Jurinovic V, Metzner B, Pfreundschuh M, Schmitz N, Wandt H, Keller U, Dreger P, Dreyling M, Hiddemann W, Unterhalt M, Hoster E*, Weigert O* Autologous Stem Cell Transplantation for Patients with Early Progression of Follicular Lymphoma: A Follow-up Study of Two Randomized Trials from the German Low Grade Lymphoma Study Group. Biol Blood Marrow Transplant (2018, accepted on March 23) Jun; 24(6):1172-1179. doi: 10.1016/j.bbmt.2018.03.022.
Ziegenhain C, Vieth B, Parekh S, Hellmann I and Enard W Quantitative single-cell transcriptomics. Briefings in Functional Genomics (2018) 1-13. doi: 10.1093/bfgp/ely009.
Alig S, Jurinovic V, Pastore A, Bararia D, Häbe S, Hellmuth JC, Kridel R, Gascoyne R, Schmidt C, Zöllner A, Buske C, Dreyling M, Unterhalt M, Hiddemann W, Hoster E, Weigert O Impact of age on genetics and treatment efficacy in follicular lymphoma. Haematologica. (2018) Epub ahead of print, doi: 10.3324/haematol.2018.187773
Fung E, Richter C, Yang HB, Schäffer I, Fischer R, Kessler BM, Bassermann F*, D'Angiolella V* FBXL13 directs the proteolysis of CEP192 to regulate centrosome homeostasis and cell migration. EMBO Rep. (2018) 19, pii: e44799. doi: 10.15252/embr.201744799. *equal contribution/last authorship
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Reiter K, Polzer H, Krupka C, Maiser A, Vick B, Rothenberg-Thurley M, Metzeler KH, Dörfel D, Salih HR, Jung G, Nößner E, Jeremias I, Hiddemann W, Leonhardt H, Spiekermann K, Subklewe M, Greif PA. Tyrosine kinase inhibition increases the cell surface localization of FLT3-ITD and enhances FLT3-directed immunotherapy of acute myeloid leukemia. Leukemia (2018 Feb) 32(2):313-322. doi: 10.1038/leu.2017.257.
Colomé-Tatché M, Theis FJ. Statistical single cell multi-omics integration. Current Opinion in Systems Biology (Feb 2018) Volume 7: 54-59. https://doi.org/10.1016/j.coisb.2018.01.003
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2017
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Palau A, Garz AK, Diesch J, Zwick A, Malinverni R, Valero V, Lappin K, Casquero R, Lennartsson A, Zuber J, Navarro T, Mills KI, Götze KS, Buschbeck M Polycomb protein RING1A limits hematopoietic differentiation in myelodysplastic syndromes. Oncotarget (2017 Dec 1) 8(70):115002-115017. doi: 10.18632/oncotarget.22839
Klaeger S, Heinzlmeir A, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B The target landscape of clinical kinase drugs. Science (2017 Dec 01) 358:6367. doi: 10.1126/science.aan4368
Mottok A, Jurinovic V, Farinha P, Rosenwald A, Leich E, Ott G, Horn H, Klapper W, Boesl M, Hiddemann W, Steidl C, Connors JM, Sehn LH, Gascoyne RD, Hoster E, Weigert O, Kridel R FOXP1 expression is a prognostic biomarker in follicular lymphoma treated with Rituximab-containing regimens. Blood (2017, accepted Oct 27) Jan 11; 131(2):226-235. doi: 10.1182/blood-2017-08-799080.
Chlis NK, Wolf FA, Theis FJ. Model-based branching point detection in single-cell data by K-branches clustering. Bioinformatics. 2017 Oct 15;33(20):3211-3219. doi: 10.1093/bioinformatics/btx325.
Garz AK, Wolf S, Grath S, Gaidzik V, Habringer S, Vick B, Rudelius M, Ziegenhain C, Herold S, Weickert M, Smets M, Peschel C, Oostendorp R, Bultmann S, Jeremias I, Thiede C, Döhner K, Keller U, Götze KS. Azacitidine combined with the selective FLT3 kinase inhibitor crenolanib disrupts stromal protection and inhibits expansion of residual leukemia-initiating cells in FLT3-ITD AML with concurrent epigenetic mutations. Oncotarget (2017 Oct 16). Online ISSN: 1949-2553. doi.org/10.18632/oncotarget.21877
Weigert O, Weinstock DM The promises and challenes of using gene mutations for patient stratification in follicular lympohma. Blood (2017 Sept 28) 130(13): 1491-1498. doi: 10.1182/blood-2017-07-737353.
Vieth B, Ziegenhain C, Parekh S, Enard W, Hellmann I. powsimR: Power analysis for bulk and single cell RNA-seq experiments. Bioinformatics (2017). https://doi.org/10.1093/bioinformatics/btx435
Krautenbacher N, Theis F, Fuchs C Correcting classifiers for sample selection bias in two-phase case-control studies. Computational and Mathematical Methods in Medicine (2017) Article ID 7847531. DOI:10.1155/2017/7847531
Schlenker R, Olguín-Contreras LF, Leisegang M, Schnappinger J, Disovic A, Rühland S, Nelson PJ, Leonhardt H, Harz H, Wilde S, Schendel DJ, Uckert W, Willimsky G, Noessner E. Chimeric PD-1:28 Receptor Upgrades Low-Avidity T cells and Restores Effector Function of Tumor-Infiltrating Lymphocytes for Adoptive Cell Therapy. Cancer Research (2017) 11(13): 3577-3590. DOI: 10.1158/0008-5472.CAN-16-1922
Ziegenhain C, Vieth B, Parekh S, Reinius B, Guillaumet-Adkins A, Smets M, Leonhardt H, Heyn H, Hellmann I, Enard W. Comparative Analysis of Single-Cell RNA Sequencing Methods. Molecular Cell (2017) 65(4): 631-643. DOI:https://doi.org/10.1016/j.molcel.2017.01.023
Seyednasrollah F, Koestler D, Wang T, Piccolo S, Vega R, Greiner R, Fuchs C, ..., Costello J, Prostate Cancer DREAM Challenge Community A DREAM challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer. Journal of Clinical Oncology Clinical Cancer Informatics(Nov 2017). DOI: 10.1200/CCI.17.00018 JCO Clinical Cancer Informatics - published online August 4, 2017
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Jacobsen C, Kopp N, Layer JV, Redd RA, Tschuri S, Haebe S, van BodegomD, Bird L, Christie AL, Christodoulou A, Saur A, Tivey T, Zapf S, Deepak B, Zimber-Strobl U, Rodig SJ, Weigert O, Weinstock DM. HSP90 inhibition overcomes ibrutinib resistance in mantel cell lymphoma. Blood (2017) 128 (21): 2517-2526. DOI 10.1182/blood-2016-04-711176
de la Rosa J, Weber J, Friedrich MJ, Li Y, Rad L, Ponstingl H, Liang Q, Bernaldo de Quirós S, Noorani I, Metzakopian E, Strong A, Li MA, Astudillo A, Fernández-García MT, Fernández-García MS, Hoffman GJ, Fuente R, Vassiliou GS, Rad R, López-Otín C, Bradley A, Cadiñanos J. A single-copy Sleeping Beauty transposon mutagenesis screen identifies new PTEN-cooperating tumor suppressor genes. Nature Genetics (2017) 49(5): 730-743. doi:10.1038/ng.3817
Buggenthin F, Buettner F, Hoppe PS, Endele M, Kroiss, M, Strasser, M, Schwarzfischer M, Loeffler D, Kookaliaris KD, Hilsenbeck O, Schroeder T, Theis FJ, Marr C. Prospective identification of hematopoietic lineage choice by deep learning. Nature Methods (2017) 14: 403-406. doi:10.1038/nmeth.4182
Kronke J, Kuchenbauer F, Kull M, Teleanu V, Bullinger L, Bunjes D, Greiner A, Kolmus S, Kopff S, Schreder M, Mügge LO, Straka C, Engelhardt M, Döhner H, Einsele H, Bassermann F, Bargou R, Knop S, Langer C IKZF1 expression is a prognostic marker in newly diagnosed standard-risk multiple myeloma treated with lenalidomide and intensive chemotherapy: a study of the German Myeloma Study Group (DSMM). Leukemia (2017) 31, 1363-1367. doi:10.1038/leu.2016.384
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Haebe S, Weigert O. It's a long way to the top (if you want to personalize immunotherapy). J Immunother Cancer. (2017 Jan 17) 5:6. doi: 10.1186/s40425-016-0207-0
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2016
Ng SW, Mitchell A, Kennedy JA, Chen WC, McLeod J, Ibrahimova N, Arruda A, Popescu A, Gupta V, Schimmer AD, Schuh AC, Yee KW, Bullinger L, Herold T, Görlich D, Büchner T, Hiddemann W, Berdel WE, Wörmann B, Cheok M, Preudhomme C, Dombret H, Metzeler K, Buske C, Löwenberg B, Valk PJ, Zandstra PW, Minden MD, Dick JE, Wang JC. A 17-gene stemness score for rapid determination of risk in acute leukaemia. Nature. (2016) Dec 15;540(7633):433-437. doi: 10.1038/nature20598. Epub 2016 Dec 7.
Jacobson C, Kopp N, Layer JV, Redd RA, Tschuri S, Haebe S, van Bodegom D, Bird L, Christie AL, Christodoulou A, Saur A, Tivey T, Zapf S, Bararia D, Zimber-Strobl U, Rodig SJ, Weigert O, Weinstock DM. HSP90 inhibition overcomes ibrutinib resistance in mantle cell lymphoma. Blood (2016 Nov 24) 128(21):2517-2526. DOI:10.1182/blood-2016-04-711176
Riba J, Renz N, Niemöller C, Bleul S, Pfeifer D, Stosch JM, Metzeler KH, Hackanson B, Lübbert M, Duyster J, Koltay P, Zengerle R, Claus R, Zimmermann S, Becker H. Molecular Genetic Characterization of Individual Cancer Cells Isolated via Single-Cell Printing. PLoS One. (2016) Sep 22;11(9):e0163455. doi: 10.1371/journal.pone.0163455.
Höckendorf U, Yabal M, Herold T, Munkhbaatar E, Rott S, Jilg S, Kauschinger J, Magnani G, Reisinger F, Heuser M, Kreipe H, Sotlar K, Engleitner T, Rad R, Weichert W, Peschel C, Ruland J, Heikenwalder M, Spiekermann K, Slotta-Huspenina J, Groß O, Jost PJ. RIPK3 Restricts Myeloid Leukemogenesis by Promoting Cell Death and Differentiation of Leukemia Initiating Cells. (2016 July 11) Cancer Cell 30:1, P75-91. DOI:https://doi.org/10.1016/j.ccell.2016.06.002
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Eichner R, Heider M, Fernández-Sáiz V, van Bebber F, Garz AK, Lemeer S, Rudelius M, Targosz BS, Jacobs L, Knorn AM, Slawska J, Platzbecker U, Germing U, Langer C, Knop S, Einsele H, Peschel C, Haass C, Keller U, Schmid B, Götze KS, Kuster B, and Bassermann F Immunomodulatory drugs disrupt the CRBN-CD147/MCT1 axis to exert anti-tumor activity and teratogenicity. Nature Medicine (2016) 22, 735-743. doi:10.1038/nm.4128
Ebinger S, Özdemir EZ, Ziegenhain C, Tiedt S, Castro Alves C, Grunert M, Dworzak M, Lutz C, Turati VA, Enver T, Horny HP, Sotlar K, Parekh S, Spiekermann K, Hiddemann W, Schepers A, Polzer B, Kirsch S, Hoffmann M, Knapp B, Hasenauer J, Pfeifer H, Panzer-Grümayer R, Enard W, Gires O, Jeremias I. Characterization of Rare, Dormant and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia. Cancer Cell (2016) 30: 849-862. DOI:https://doi.org/10.1016/j.ccell.2016.11.002
Haghverdi L, Büttner M, Wolf FA, Buettner F, Theis FJ. Diffusion pseudotime robustly reconstructs lineage branching. Nature Methods(2016) volume 13:845–848. DOI: https://doi.org/10.1038/nmeth.3971
Kondofersky I, Laimighofer M, Kurz C, Krautenbacher N, Söllner J, Dargatz P, Scherb H, Ankerst D, Fuchs C Three general concepts to improve risk prediction: good data, wisdom of the crowd, recalibration. F1000Research (2016):5(2671). DOI: 10.12688/f1000research.8680.1.
Jurinovic v, Kridel R, Staiger AM, Szczepanowski M, Horn H, Dreyling MH, Rosenwald A, Ott G, Klapper W, Zelenetz AD, Barr PM, Friedberg JW, Ansell S, Sehn LH, Connors JM, Gascoyne RD, Hiddemann W, Unterhalt M, Wenstock DM, Weigert O. Clinicogenetic risk models predict early progression of follicular lymphoma after first-line immunochemotherapy. Blood (2016) 128(8): 1112-1120. doi:10.1182/blood-2016-05-717355
Metzeler KH, Herold T, Rothenberg-Thurley M, Amler S, Sauerland MC, Görlich D, Schneider S, Konstandin NP, Dufour A, Bräundl K, Ksienzyk B, Zellmeier E, Harmann L, Greif PA, Fiegl M, Subklewe M, Bohlander SK, Krug U, Faldum A, Berdel WE, Wörmann B, Büchner T, Hiddemann W, Braess J, Spiekermann K, on behalf of the AMLCG Study Group. Spectrum and prognostic relevance of driver gene mutations in acute myeloid leukemia. Blood (2016) 128(5): 686-698. DOI 10.1182/blood-2016-01- 693879
Parekh S, Ziegenhain C, Vieth B, Enard W, Hellmann I. The impact of amplification on differential expression analyses by RNA-seq. Nature Scientific Reports (2016) 6:25533. DOI: 10.1038/srep25533
Kondofersky I, Theis F, Fuchs C Inferring catalysis in biological systems. IET Systems Biology (2016):10(6)210-218. DOI: 10.1049/iet-syb.2015.0087.
Melchardt T, Hufnagl C, Weinstock DM, Kopp N, Neureiter D, Tränkenschuh W, Hackl H, Weiss L, Rinnerthaler G, Hartmann TN, Greil R, Weigert O, Egle A. Clonal evolution in relapsed and refractory diffuse large B-cell lymphoma is characterized by high dynamics of subclones. Oncotarget, Advanced Publications. (2016) 7: 51494-51502. https://doi.org/10.18632/oncotarget.9860
Hartmann L, Dutta S, Opatz S, Vosberg S, Reiter K, Leubolt G, Metzeler KH, Herold T, Bamopoulos SA, Bräundl K, Zellmeier E, Ksienzyk B, Konstandin NP, Schneider S, Hopfner KP, Graf A, Krebs S, Blum H, Middeke JM, Stölzel F, Thiede C, Wolf S, Bohlander SK, Preiss C, Chen-Wichmann L, Wichmann C, Sauerland MC, Büchner T, Berdel WE, Wörmann BJ, Braess J, Hiddemann W, Spiekermann K, Greif PA. ZBTB7A mutations in acute myeloid leukaemia with t(8;21) translocation. Nature Communications (2016) 7:11733. doi: 10.1038/ncomms11733.