Jan Korbel and Andreas Kulozik
MMPU Faculty collaborator: Martina Muckenthaler
Our research interest
Our group aims to unravel biological mechanisms that govern the transition from treatment sensitivity to treatment resistance in T-cell acute lymphoblastic leukaemia.
Background
T-cell acute lymphoblastic leukaemia (T-ALL) is an aggressive malignancy of thymocytes, which accounts for about 15% of paediatric ALL. A variety of genetic events affecting cellular processes, such as the cell cycle, differentiation, and survival, have been identified in T-ALL and result in developmental arrest, uncontrolled cell growth, and clonal expansion of T cells.
At the time of first diagnosis, most patients with T-ALL can be treated successfully, with long-term survival rates of approximately 80%. In stark contrast, in patients with T-ALL relapses, the disease is mostly treatment resistant with only a minority of patients surviving. This particularly poor prognosis of relapsed T-ALL also contrasts with relapsed precursor B-ALL, which, even at the time of relapse, can be eliminated in more than 50% of patients. Our group focuses on deciphering the molecular mechanisms governing the exquisite treatment sensitivity of relapsed T-ALL, aiming to eventually identify pathways that are targetable by novel treatment strategies. We have recently focused on genomic and epigenomic analyses (Richter-Pechańska et al., Blood Cancer J 2017; Richter-Pechańska et al., EMBO Mol Med 2018; Erarslan-Uysal et al., EMBO Mol Med 2020), and have more recently employed new technology for single-cell analyses of structural variants, developed in the Korbel group, to analyse primary leukaemia cells (Sanders et al., Nat Biotechnol 2020).
Goals
It is of particular biological interest, of medical relevance, and is our general thrust to unravel the mechanisms that govern the transition from treatment sensitivity to treatment resistance in this entity. As resistance typically initiates itself in small subclones of the clinical disease, it is essential to appreciate the molecular mechanisms against the background of the subclonal architecture of the leukaemia.
In our specific projects, we aim to understand patterns of somatic mosaicism at single-cell resolution. Whole-genome sequencing (WGS) has been demonstrated to be insensitive towards subclonal structural variations (SVs), which escape detection unless they rise to a high clonal fraction. Our recently developed single-cell tri-channel processing (scTRIP) method enables the direct detection of SV mutational processes in single cells, and as such can be used to obtain insights into pathomechanisms acting in human tissues. scTRIP leverages strand-specific sequencing (Strand-seq) to computationally integrate read depth, DNA strand, and haplotype phase, in order to enable the scalable discovery of SVs in single cells, including copy-number variations, inversions, translocations, and complex DNA rearrangements such as chromothripsis events (Sanders et al., Nat Biotechnol 2020). In addition, we aim to uncover the epigenetic landscape of T-ALL relapses by using new single cell methodologies developed in the Korbel group.
Important publications
Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution.
Richter-Pechańska P, Kunz JB, Rausch T, Erarslan-Uysal B, Bornhauser B, Frismantas V, Assenov Y, Zimmermann M, Happich M, von Knebel-Doeberitz C, von Neuhoff N, Köhler R, Stanulla M, Schrappe M, Cario G, Escherich G, Kirschner-Schwabe R, Eckert C, Avigad S, Pfister SM, Muckenthaler MU, Bourquin JP, Korbel JO, Kulozik AE.
Leukemia. 2022 May 18. doi: 10.1038/s41375-022-01587-0. Online ahead of print. PMID: 35585141
Differential Analysis of the Nuclear and the Cytoplasmic RNA Interactomes in Living Cells.
Backlund M, Kulozik AE.
Methods Mol Biol. 2022;2428:291-304. doi: 10.1007/978-1-0716-1975-9_18. PMID: 35171487
Constitutional PIGA mutations cause a novel subtype of hemochromatosis in patients with neurologic dysfunction.
Muckenthaler L, Marques O, Colucci S, Kunz J, Fabrowski P, Bast T, Altamura S, Höchsmann B, Schrezenmeier H, Langlotz M, Richter-Pechanska P, Rausch T, Hofmeister-Mielke N, Gunkel N, Hentze MW, Kulozik AE, Muckenthaler MU.
Blood. 2022 Mar 3;139(9):1418-1422. doi: 10.1182/blood.2021013519. PMID: 34875027
Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA.
Powers KT, Stevenson-Jones F, Yadav SKN, Amthor B, Bufton JC, Borucu U, Shen D, Becker JP, Lavysh D, Hentze MW, Kulozik AE, Neu-Yilik G, Schaffitzel C.
Nucleic Acids Res. 2021 Jul 21;49(13):7665-7679. doi: 10.1093/nar/gkab532. PMID: 34157102
NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes.
Becker JP, Helm D, Rettel M, Stein F, Hernandez-Sanchez A, Urban K, Gebert J, Kloor M, Neu-Yilik G, von Knebel Doeberitz M, Hentze MW, Kulozik AE.
iScience. 2021 Apr 1;24(4):102389. doi: 10.1016/j.isci.2021.102389. eCollection 2021 Apr 23. PMID: 33981976
Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia.
Roels J, Thénoz M, Szarzyńska B, Landfors M, De Coninck S, Demoen L, Provez L, Kuchmiy A, Strubbe S, Reunes L, Pieters T, Matthijssens F, Van Loocke W, Erarslan-Uysal B, Richter-Pechańska P, Declerck K, Lammens T, De Moerloose B, Deforce D, Van Nieuwerburgh F, Cheung LC, Kotecha RS, Mansour MR, Ghesquière B, Van Camp G, Berghe WV, Kowalczyk JR, Szczepański T, Davé UP, Kulozik AE, Goossens S, Curtis DJ, Taghon T, Dawidowska M, Degerman S, Van Vlierberghe P.
Blood Cancer Discov. 2020 Nov;1(3):274-289. doi: 10.1158/2643-3230.BCD-20-0059. Epub 2020 Sep 23. PMID: 33179015
Chromatin accessibility landscape of pediatric T-lymphoblastic leukemia and human T-cell precursors.
Erarslan-Uysal B, Kunz JB, Rausch T, Richter-Pechańska P, van Belzen IA, Frismantas V, Bornhauser B, Ordoñez-Rueada D, Paulsen M, Benes V, Stanulla M, Schrappe M, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Loukanov T, Gorenflo M, Waszak SM, Bourquin JP, Muckenthaler MU, Korbel JO, Kulozik AE.
EMBO Mol Med. 2020 Aug 5:e12104. doi: 10.15252/emmm.202012104. Online ahead of print. PMID: 32755029
Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.
Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechańska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Benes V, Schrappe M, Mardin BR, Kulozik AE, Bornhauser B, Bourquin JP, Marschall T, Korbel JO.
Nat Biotechnol. 2020 Mar;38(3):343-354. doi: 10.1038/s41587-019-0366-x. Epub 2019 Dec 23. PMID: 31873213
Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files.
Rausch T, Fritz MH, Untergasser A, Benes V.
BMC Genomics. 2020 Mar 14;21(1):230. doi: 10.1186/s12864-020-6635-8. PMID: 32171249
PTEN abnormalities predict poor outcome in children with T-cell acute lymphoblastic leukemia treated according to ALL IC-BFM protocols.
Szarzyńska-Zawadzka B, Kunz JB, Sędek Ł, Kosmalska M, Zdon K, Biecek P, Bandapalli OR, Kraszewska-Hamilton M, Jaksik R, Drobna M, Kowalczyk JR, Szczepański T, Van Vlierberghe P, Kulozik AE, Witt M, Dawidowska M.
Am J Hematol. 2019 Apr;94(4):E93-E96. doi: 10.1002/ajh.25396. Epub 2019 Jan 24. No abstract available. PMID: 30614545
Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation.
Erkek S, Johann PD, Finetti MA, Drosos Y, Chou HC, Zapatka M, Sturm D, Jones DTW, Korshunov A, Rhyzova M, Wolf S, Mallm JP, Beck K, Witt O, Kulozik AE, Frühwald MC, Northcott PA, Korbel JO, Lichter P, Eils R, Gajjar A, Roberts CWM, Williamson D, Hasselblatt M, Chavez L, Pfister SM, Kool M.
Cancer Cell. 2019 Jan 14;35(1):95-110.e8. doi: 10.1016/j.ccell.2018.11.014. Epub 2018 Dec 27. PMID: 30595504
PDX models recapitulate the genetic and epigenetic landscape of pediatric T-cell leukemia.
Richter-Pechańska P, Kunz JB, Bornhauser B, von Knebel Doeberitz C, Rausch T, Erarslan-Uysal B, Assenov Y, Frismantas V, Marovca B, Waszak SM, Zimmermann M, Seemann J, Happich M, Stanulla M, Schrappe M, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Muckenthaler MU, Korbel JO, Bourquin JP, Kulozik AE.
EMBO Mol Med. 2018 Nov 2. pii: e9443. doi: 10.15252/emmm.201809443. [Epub ahead of print] PMID:30389682
The landscape of genomic alterations across childhood cancers.
Gröbner SN, Worst BC, Weischenfeldt J, Buchhalter I, Kleinheinz K, Rudneva VA, Johann PD, Balasubramanian GP, Segura-Wang M, Brabetz S, Bender S, Hutter B, Sturm D, Pfaff E, Hübschmann D, Zipprich G, Heinold M, Eils J, Lawerenz C, Erkek S, Lambo S, Waszak S, Blattmann C, Borkhardt A, Kuhlen M, Eggert A, Fulda S, Gessler M, Wegert J, Kappler R, Baumhoer D, Burdach S, Kirschner-Schwabe R, Kontny U, Kulozik AE, Lohmann D, Hettmer S, Eckert C, Bielack S, Nathrath M, Niemeyer C, Richter GH, Schulte J, Siebert R, Westermann F, Molenaar JJ, Vassal G, Witt H; ICGC PedBrain-Seq Project; ICGC MMML-Seq Project, Burkhardt B, Kratz CP, Witt O, van Tilburg CM, Kramm CM, Fleischhack G, Dirksen U, Rutkowski S, Frühwald M, von Hoff K, Wolf S, Klingebiel T, Koscielniak E, Landgraf P, Koster J, Resnick AC, Zhang J, Liu Y, Zhou X, Waanders AJ, Zwijnenburg DA, Raman P, Brors B, Weber UD, Northcott PA, Pajtler KW, Kool M, Piro RM, Korbel JO, Schlesner M, Eils R, Jones DTW, Lichter P, Chavez L, Zapatka M, Pfister SM.
Nature. 2018 Mar 15;555(7696):321-327. doi: 10.1038/nature25480. Epub 2018 Feb 28. Erratum in: Nature. 2018 Jul;559(7714):E10. PMID:29489754
MAP3K7 is recurrently deleted in pediatric T-lymphoblastic leukemia and affects cell proliferation independently of NF-κB.
Cordas Dos Santos DM, Eilers J, Sosa Vizcaino A, Orlova E, Zimmermann M, Stanulla M, Schrappe M, Börner K, Grimm D, Muckenthaler MU, Kulozik AE, Kunz JB.
BMC Cancer. 2018 Jun 18;18(1):663. doi: 10.1186/s12885-018-4525-0. PMID: 29914415
Genomic profiling of Acute lymphoblastic leukemia in ataxia telangiectasia patients reveals tight link between ATM mutations and chromothripsis. Ratnaparkhe M, Hlevnjak M, Kolb T, Jauch A, Maass KK, Devens F, Rode A, Hovestadt V, Korshunov A, Pastorczak A, Mlynarski W, Sungalee S, Korbel J, Hoell J, Fischer U, Milde T, Kramm C, Nathrath M, Chrzanowska K, Tausch E, Takagi M, Taga T, Constantini S, Loeffen J, Meijerink J, Zielen S, Gohring G, Schlegelberger B, Maass E, Siebert R, Kunz J, Kulozik AE, Worst B, Jones DT, Pfister SM, Zapatka M, Lichter P, Ernst A.
Leukemia. 2017 Oct;31(10):2048-2056. doi: 10.1038/leu.2017.55. Epub 2017 Feb 15. PMID: 28196983
Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia.
Richter-Pechańska P, Kunz JB, Hof J, Zimmermann M, Rausch T, Bandapalli OR, Orlova E, Scapinello G, Sagi JC, Stanulla M, Schrappe M, Cario G, Kirschner-Schwabe R, Eckert C, Benes V, Korbel JO, Muckenthaler MU, Kulozik AE.
Blood Cancer J. 2017 Feb 3;7(2):e523. doi: 10.1038/bcj.2017.3. PMID: 28157215
Ex vivo drug response profiling detects recurrent sensitivity patterns in drug resistant ALL.
Frismantas V, Dobay MP, Rinaldi A, Tchinda J, Dunn SH, Kunz J, Richter-Pechanska P, Marovca B, Pail O, Jenni S, Diaz-Flores E, Chang BH, Brown TJ, Collins RH, Uhrig S, Balasubramanian GP, Bandapalli OR, Higi S, Eugster S, Voegeli P, Delorenzi M, Cario G, Loh ML, Schrappe M, Stanulla M, Kulozik AE, Muckenthaler MU, Saha V, Irving JA, Meisel R, Radimerski T, Von Stackelberg A, Eckert C, Tyner JW, Horvath P, Bornhauser BC, Bourquin JP.
Blood. 2017 Jan 25. pii: blood-2016-09-738070. doi: 10.1182/blood-2016-09-738070. [Epub ahead of print]
PMID: 28122742
Mutating heme oxygenase-1 into a peroxidase causes a defect in bilirubin synthesis associated with microcytic anemia and severe hyperinflammation.
Greil J, Verga-Falzacappa MV, Echner NE, Behnisch W, Bandapalli OR, Pechanska P, Immenschuh S, Vijayan V, Balla J, Tsukahara H, Schneider M, Janka G, Claus M, Longerich T, Muckenthaler MU, Kulozik AE.
Haematologica. 2016 Nov;101(11):e436-e439. No abstract available.
A novel autosomal recessive TERT T1129P mutation in a dyskeratosis congenita family leads to cellular senescence and loss of CD34+ hematopoietic stem cells not reversible by mTOR-inhibition.
Stockklausner C, Raffel S, Klermund J, Bandapalli OR, Beier F, Brümmendorf TH, Bürger F, Sauer SW, Hoffmann GF, Lorenz H, Tagliaferri L, Nowak D, Hofmann WK, Buergermeister R, Kerber C, Rausch T, Korbel JO, Luke B, Trumpp A, Kulozik AE.
Aging (Albany NY). 2015 Nov;7(11):911-27. PMID:26546739
Pediatric T-lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation.
Kunz JB, Rausch T, Bandapalli OR, Eilers J, Pechanska P, Schuessele S, Assenov Y, Stütz AM, Kirschner-Schwabe R, Hof J, Eckert C, von Stackelberg A, Schrappe M, Stanulla M, Koehler R, Avigad S, Elitzur S, Handgretinger R, Benes V, Weischenfeldt J, Korbel JO, Muckenthaler MU, Kulozik AE.
Haematologica. 2015 Aug 20. pii: haematol.2015.129692. [Epub ahead of print] PMID: 26294725
The activating STAT5B N642H mutation is a common abnormality in pediatric T-cell acute lymphoblastic leukemia and confers a higher risk of relapse.
Bandapalli OR, Schuessele S, Kunz JB, Rausch T, Stütz AM, Tal N, Geron I, Gershman N, Izraeli S, Eilers J, Vaezipour N, Kirschner-Schwabe R, Hof J, von Stackelberg A, Schrappe M, Stanulla M, Zimmermann M, Koehler R, Avigad S, Handgretinger R, Frismantas V, Bourquin JP, Bornhauser B, Korbel JO, Muckenthaler MU, Kulozik AE.
Haematologica. 2014 Oct;99(10):e188-92. doi: 10.3324/haematol.2014.104992. Epub 2014 Jun 27. PMID:24972766
Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.
Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, Shih DJ, Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, Cavalli FM, Zuyderduyn S, Bader GD, VandenBerg S, Esparza LA, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfister SM.
Nature. 2014 Jul 24;511(7510):428-34. doi: 10.1038/nature13379. Epub 2014 Jun 22. PMID:25043047
Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition.
Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM; ICGC PedBrain Tumor Project.
Cancer Cell. 2014 Mar 17;25(3):393-405. doi:10.1016/j.ccr.2014.02.004.PMID:24651015
NOTCH1 activation clinically antagonizes the unfavorable effect of PTEN inactivation in BFM-treated children with precursor T-cell acute lymphoblastic leukemia.
Bandapalli OR, Zimmermann M, Kox C, Stanulla M, Schrappe M, Ludwig WD, Koehler R, Muckenthaler MU, Kulozik AE.
Haematologica. 2013 Jun;98(6):928-36. doi: 10.3324/haematol.2012.073585. Epub 2013 Jan 24. PMID:23349303
ALL can be separated from NOTCH pathway activation by FBXW7 loss of function.
Kox, C, M. Zimmermann, M. Stanulla, M. S. Leible, M. Schrappe, W.-D. Ludwig, M. Muckenthaler, A.E. Kulozik. Leukemia. 2010 Dec;24(12):2005-13. Epub 2010 Oct 14
High-resolution genomic profiling of childhood T-ALL reveals frequent copy-number alterations affecting the TGF-beta and PI3K-AKT pathways and deletions at 6q15-16.1 as a genomic marker for unfavorable early treatment response.
Remke M, Pfister S, Kox C, Toedt G, Becker N, Benner A, Werft W, Breit S, Liu S, Engel F, Wittmann A, Zimmermann M, Stanulla M, Schrappe M, Ludwig WD, Bartram CR, Radlwimmer B, Muckenthaler MU, Lichter P, Kulozik AE.
Blood. 2009 Jul 30;114(5):1053-62. doi: 10.1182/blood-2008-10-186536. Epub 2009 Apr 30. PMID:19406988
Activating NOTCH1 mutations predict favorable early treatment response and long-term outcome in childhood precursor T-cell lymphoblastic leukemia.
Breit S, Stanulla M, Flohr T, Schrappe M, Ludwig WD, Tolle G, Happich M, Muckenthaler MU, Kulozik AE.
Blood. 2006 Aug 15;108(4):1151-7. Epub 2006 Apr 13. PMID:16614245
