SFB 1243 Cancer Evolution
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SFB 1243 Publications

2018

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)

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. https://academic.oup.com/bfg/advance-article/doi/10.1093/bfgp/ely009/4951519

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, e44799. *equal contribution/last authorship

Herold T, Jurinovic V, Batcha AMN, Bamopoulos SA, Rothenberg-Thurley M, Ksienzyk B, Harmann L, Greif PA, Phillippou-Massier J, Krebs S, Blum H, Amler S, Schneider S, Konstandin N, Sauerland MC, Görlich D, Berdel WE, Wörmann BJ, Tischer J, Sublkewe M, Bohlander SK, Braess J, Hiddemann W, Metzeler KH, Mansmann U, Spiekermann K  A 29-gene and cytogenetic score for the prediction of resistance to indcution treatment in acute myeloid leukemia. Haematologica (2018 Mar) 103:456-465. doi: 10.3324/haematol.2017.178442

Cusan M, Cai SF, Mohammad HP, Krivtsov A, Chramiec A, Loizou E, Witkin MD, Smitheman KN, Tenen DG, Ye M, Will B, Steidl U, Kruger RG, Levine RL, Rienhoff Jr. HY, Koche RP, Amrstrong SA LSD1 inhibition exerts its anti-leukemic effect by recommissioning PU.1- and C/EBPa-dependent enhancers in AML. Blood 2018 :blood-2017-09-807024; doi: https://doi.org/10.1182/blood-2017-09-807024

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.

Greif PA, Hartmann L, Vosberg S, Stief SM, Mattes R, Hellmann I, Metzeler KH, Herold T, Bamopoulos SA, Kerbs P, Jurinovic V, Schumacher D, Pastore F, Bräundl K, Zellmeier E, Ksienzyk B, Konstandin NP, Schneider S, Graf A, Krebs S, Blum H, Neumann M, Baldus CD, Bohlander SK, Wolf S, Görlich D, Berdel WE, Wörmann BJ, Hiddemann W, Spiekermann K Evolution of cytogenetically normal Acute Myeloid Leukemia during therapy and relapse: An exome sequencing study of 50 patients. Clinical Cancer Research (2018) 1-11. DOI: 10.1158/1078-0432.CCR-17-2344. http://clincancerres.aacrjournals.org/content/early/2018/02/25/1078-0432.CCR-17-2344

Mueller S, Engleitner T, Maresch R, Zukowska M, Lange S, Kaltenbacher T, Konukiewitz B, Öllinger R, Zwiebel M, Strong A, Yen HY, Banerjee R, Louzada S, Fu B, Seidler B, Götzfried J, Schuck K, Hassan Z, Arbeiter A, Schönhuber N, Klein S, Veltkamp C, Friedrich M, Rad L, Barenboim M, Ziegenhain C, Hess J, Dovey OM, Eser S, Parekh S, Constantino-Casas F, de la Rosa J, Sierra MI, Fraga M, Mayerle J, Klöppel G, Caninaños J, Liu P, Vassiliou G, Weichert W, Steiger K, Enard W, Schmid RM, Yang F, Unger K, Schneider G, Varela I, Bradley A, Saur D, Rad R  Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes. Nature (2018) 554:62-68. doi:10.1038/nature25459. https://www.nature.com/articles/nature25459

Rehage N, Davydova E, Conrad C, Behrens G, Maiser A, Stehklein JE, Brenner S, Klein J, Jeridi A, Hoffmann A, Lee E, Dianzani U, Willemsen R, Feederle R, Reiche K, Hackermüller J, Leonhardt H, Sharma S, Niessing D, Heissmeyer V Binding of NUFIP2 to Rophin promotes recognition and regulation of ICOS mRNA. Nature Communications (2018) 9:299. DOI: 10.1038/s41467-017-02582-1.

2017

Essig K, Hu D, Guimaraes JC, Alterauge D, Edelmann S, Raj T, Kranich J, Behrens G, Helseke A, Floess S, Klein J, Maiser A, Marschall S, Hrabe de Angelis M, Leonhardt H, Calkhoven CF, Noessner E, Brocker T, Huehn J, Krug AB,  Zavolan M, Baumjohann D, Heissmeyer V Roquin suppresses the PI3K-mTOR Signaling Pathway to inhibit T helper cell differentiation and conversion of Treg to Tfr cellsImmunity 47, 1067-1082 (2017 Dec 19) https://doi.org/10.1016/j.immuni.2017.11.008

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; Epub ahead of print)

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 K 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.
https://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.

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 (2017 Aug 14). doi: 10.1038/leu.2017.257. [Epub ahead of print]
http://www.nature.com/leu/journal/vaop/ncurrent/full/leu2017257a.html?foxtrotcallback=true

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: 631-643. http://dx.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 (2017)

Guinney J, Wang T, Laajala T, Fuchs C, ..., Costello J, Prostate Cancer Challenge DREAM Community Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. The Lancet Oncology (2017):18, 132-142. DOI: 10.1016/S1470-2045(16)30560-5

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

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

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. PubMed PMID: 27926740

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. eCollection 2016. PubMed PMID: 27658049; PubMed Central PMCID: PMC5033393.

Diesch J, Zwick A, Garz AK, Palau A, Buschbeck, Götze K A clinical-molecular update on azanucleoside-based therapy for the treatment of hematologic cancers. Clinical Epigenetics (2016) Jun 21; 8:71. doi: 10.1186/s13148-016-0237-y

Engel K, Rudelius M, Slawska J, Ahangarian Abhari B, Altmann B, Kurutz J, Brunner A, Targosz BS, Loewecke F, Knorn AM, Gloeckner CJ, Ueffing M, Fernandez-Sáiz V, Baumann U, Fulda S, Pfreundschuh M, Trümper L, Klapper W, Keller U, Jost PJ, Rosenwald A, Peschel C, Bassermann F  USP9X stabilizes XIAP to regulate mitotic cell death and mediate resistance to anti-tubulin chemotherapeutics in aggressive B-cell lymphoma. EMBO Mol. Med. (2016) 8, 851-62. DOI 10.15252/emmm.201506047

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

Ponce LP, Fenn NC, Mortiz N, Krupka C, Kozik JH, Lauber K, Sublewe M, Hopfner KPSIRTα-antibody fusion proteins stimulate phagocytosis and promote elimination of acute myeloid leukemia cells. Oncotarget, Advance Publications (2016) 1-18. www.impactjournals.com/oncotarget

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. http://dx.doi.org/10.1016/j.ccell.2016.11.002

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 www.nature.com/scientificreports/

Kondofersky I, Theis F, Fuchs C Inferring catalysis in biological systems. IET Systems Biology (2016):10,210-218. 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) www.impactjournals.com/oncotarget

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.