Die pathogenetische Rolle der beiden Proteine MSI1 und MSI2 in Erkrankungen des blutbildenden Systems

• Antragstellerin: Privatdozentin Dr. Jessica Höll
• Fachliche Zuordnung: Kinder- und Jugendmedizin ; Hämatologie, Onkologie
• Förderung: Förderung von 2015 bis 2019
• Projektkennung: Deutsche Forschungsgemeinschaft (DFG) - Projektnummer 281781283

• Erstellungsjahr: 2020

Zusammenfassung der Projektergebnisse

The role of post-transcriptional gene regulation through RNA-binding proteins (RBP) has recently become a prime focus of leukemia research. This proposal focused on MSI2, which is not only highly expressed in acute myeloid leukemia (AML) but can also be used as prognostic marker in acute leukemias. We performed PAR-CLIP to identify the transcriptome-wide targets of MSI2. Through analyzing the most frequently sequenced PAR-CLIP clusters, we described and validated the RNA-binding motif of MSI2, which consists of the four nucleotides TTAG. Following RNA-Seq of MSI2 knockdown samples, we integrated PAR-CLIP data of MSI2 to identify physically bound and differentially regulated genes. Most of the identified genes showed a negative regulation by MSI2 including IL6ST. The IL6ST/MSI2 regulation affects the phosphorylation of STAT3 and ERK1/2 proteins, which in turn affects JAK/STAT and MAPK signaling pathways. Correlation analysis of MSI2 expression with IL6ST expression in AML patients confirmed a significant reciprocal expression. We thus revealed another mechanism of MSI2 downstream target regulation, which will be important to consider when targeting this protein therapeutically. In parallel to working on MSI2, we also strove to improve CLIP analysis, in particular PAR-CLIP analysis. We developed the PARA-suite, which takes the distinctive properties of short CLIP read sequences into account. The PARA-suite was a key element in the analysis of all our RBP-centered manuscripts. In general, the sequencing error profiles of RNA-Seq datasets, including PAR-CLIP data, can vary between different sequencing runs, depending on the sequencing machine, the experimental conditions, and the biological properties of the sample. Thus, we established (and subsequently put to use several times) the PARA-suite package, which includes a read simulator, an error estimation tool for CLIP datasets and an alignment pipeline for RBP binding site detection. The PARA-suite thus represents a resource for all those who wish to analyze RBP function through performing (PAR-)CLIP experiments.

Projektbezogene Publikationen (Auswahl)

• The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PeerJ. 2016 Oct 27;4:e2619
  Kloetgen A, Borkhardt A, Hoell JI, McHardy AC
  
• Alterations of miRNAs and miRNA-regulated mRNA expression in GC B cell lymphomas determined by integrative sequencing analysis. Haematologica. 2016 Nov;101(11):1380-1389
  Hezaveh K, Kloetgen A, Bernhart SH, Mahapatra KD, Lenze D, Richter J, Haake A, Bergmann AK, Brors B, Burkhardt B, Claviez A, Drexler HG, Eils R, Haas S, Hoffmann S, Karsch D, Klapper W, Kleinheinz K, Korbel J, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Leich E, Loeffler M, Mantovani-Loeffler L, López C, McHardy AC, Möller P, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schlesner M, Scholz I, Stadler PF, Stilgenbauer S, Sungalee S, Szczepanowski M, Trümper L, Weniger MA, Siebert R, Borkhardt A, Hummel M, Hoell JI
  
• Transcriptome-wide analysis uncovers the targets of the RNA-binding protein MSI2 and effects of MSI2’s RNA-binding activity on IL-6 signaling. J Biol Chem. 2018 Oct 5;293(40):15359-15369
  Duggimpudi S, Kloetgen A, Kumar Maney S, Münch PC, Hezaveh K, Shaykhalishahi H, Hoyer W, McHardy AC, Lang PA, Borkhardt A, Hoell JI
  
• Deciphering human ribonucleoprotein regulatory networks. Nucleic Acids Res. 2019 Jan 25;47(2):570-581
  Mukherjee N, Wessels HH, Lebedeva S, Sajek M, Ghanbari M, Garzia A, Munteanu A, Yusuf D, Farazi T, Hoell JI, Akat KM, Akalin A, Tuschl T, Ohler U
  
• Molecular approaches to treating pediatric leukemias. Front Pediatr 2019 Sep 6;7:368. eCollection 2019
  Kuhlen M, Klusmann JH, Hoell JI
  
• Fragile X mental retardation protein protects against tumour necrosis factor-mediated cell death and liver injury. Gut. 2020 Jan;69(1):133-145
  Zhuang Y, Xu HC, Shinde PV, Warfsmann J, Vasilevska J, Sundaram B, Behnke K, Huang J, Hoell JI, Borkhardt A, Pfeffer K, Taha MS, Herebian D, Mayatepek E, Brenner D, Ahmadian MR, Keitel V, Wieczorek D, Häussinger D, Pandyra AA, Lang KS, Lang PA
  
• RNA-binding proteins in acute leukemias. Int J Mol Sci. 2020 May 12;21(10):E3409
  Schuschel K, Helwig M, Hüttelmaier S, Heckl D, Klusmann JH, Hoell JI
  
• YBX1 indirectly targets heterochromatin-repressed inflammatory response-related apoptosis genes through regulating CBX5 mRNA. Int J Mol Sci. 2020 Jun 23;21(12):E4453
  Kloetgen A, Duggimpudi S, Schuschel K, Hezaveh K, Picard D, Schaal H, Remke M, Klusmann JH, Borkhardt A, McHardy AC, Hoell JI