Role of hnRNP K and Interacting mRNAs in Pathogenesis of AML with 9q Deletion

Introduction: Acute myeloid leukemia (AML) is characterized by heterogeneous cytogenetic and molecular aberrations. Deletions on the long arm of chromosome 9 (del(9q)) are observed in 2% of AML patients. In about 24% of the cases, del(9q) is observed as sole karyotypic abnormality, while in the remaining 76%, it is associated with a t(8;21) translocation or other aberrations. Among all del(9q) AML cases, 36%-50% exhibit an additional t(8;21), whereas 7%-14% of AML cases with t(8;21) show del(9q) as an additional aberration. A commonly deleted region (CDR) of del(9q) was defined and further analysis specified a minimally deleted region (MDR) composed of seven annotated genes (GKAP1, KIF27, C9ORF64, HNRNPK, RMI1, SLC28A3 and NTRK2) (Kronke J et al. Blood. 2013). However, the function of these genes and their impact on the pathogenesis of AML remain elusive. A recent study demonstrated that reduced expression of the HNRNPK gene product can contribute to leukemogenesis in AML (Gallardo M, Cancer Cell. 2015). The multifunctional protein hnRNP K interacts with other proteins, DNA and RNA, to modulate gene activity and gene expression on different levels. For example, hnRNP K not only regulates SRC gene transcription, but as well SRC mRNA translation and the activity of c-Src kinase. In the context of AML, hnRNP K was shown to interact with the mRNAs encoding C/EBPa (CEBPA) and p21 (CDKN1A). We analyzed a cohort of 31 del(9q) AML patients in order to further analyze the deleted region and to analyze the impact of HNRNPK deletion on leukemogenesis.

Methods: 31 del(9q) patients were used for the characterization of the deleted region. mRNA level (determined by RT-qPCR analysis) and clinical parameters were compared with a cohort of 24 normal karyotype (NK) AML patients. HnRNP K immunoprecipitation was combined with RNA-Seq, a whole transcriptome shotgun sequencing application based on next generation sequencing and validated by RT-qPCR analysis. CRISPR-Cas9 genome editing has been applied to functionally characterize the impact of post-transcriptional control by hnRNP K in pathogenesis of AML.

Results: Our analysis confirmed the MDR in a cohort of 31 AML del(9q) patients. Survival of patients and clinical parameters were not correlated with deletion size, further supporting the importance of the MDR, while other deleted genes seem to be less important for leukemogenesis. As demonstrated by qPCR analysis, the mRNA level of HNRNPK and other genes located in the MDR was reduced in patients carrying a del(9q) compared to NK patients. To further dissect a potential function of hnRNP K in AML del(9q), we characterized hnRNP K interacting mRNAs in the AML cell line KG-1a. Therefore, hnRNP K was immunoprecipitated from cytoplasmic extracts of KG-1a cells and interacting RNAs were identified by RNA-Seq analysis. This analysis revealed that 1076 RNAs are potentially associated with hnRNP K, among them the C/EBPa mRNA. Panther Protein Class analysis identified a high number of transcripts encoding nucleic acid binding proteins, mainly transcription factors. KG-1a cell lines harboring either a complete knock out of hnRNP K or a deletion of the RNA-binding KH-domain are currently generated by CRISPR-Cas9 genome editing to functionally analyze the impact of hnRNP K-mediated post-transcriptional control in AML.

Conclusion and Outlook: The deletion of seven genes (GKAP1, KIF27, C9ORF64, HNRNPK, RMI1, SLC28A3 and NTRK2) in the MDR is indispensable, indicating a crucial function for the development of AML del(9q). Among them HNRNPK seems to be a particularly important factor in this process. The identification of hnRNP K interacting RNAs provides the basis to further improve our insight in molecular mechanisms, which drive the pathogenesis of AML del(9q). HNRNPK knock out cell lines will be used to analyze the effect of HNRNPK deletion on post-transcriptional control of identified target genes.