The pathogenic role of MSI1 and MSI2 in myeloid malignancies
Hematology, Oncology
Final Report Abstract
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.
Publications
- 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
(See online at https://doi.org/10.7717/peerj.2619) - 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
(See online at https://doi.org/10.3324/haematol.2016.143891) - 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
(See online at https://doi.org/10.1074/jbc.RA118.002243) - 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
(See online at https://doi.org/10.1093/nar/gky1185) - Molecular approaches to treating pediatric leukemias. Front Pediatr 2019 Sep 6;7:368. eCollection 2019
Kuhlen M, Klusmann JH, Hoell JI
(See online at https://doi.org/10.3389/fped.2019.00368) - 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
(See online at https://doi.org/10.1136/gutjnl-2019-318215) - 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
(See online at https://doi.org/10.3390/ijms21103409) - 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
(See online at https://doi.org/10.3390/ijms21124453)
