Characterization of non-coding RNAs in cancer

While originally though to only code for proteins, it now stands clear that RNA is a multifunctional molecule involved in a great variety of molecular processes. Recent advances in genome-wide platforms have revealed underappreciated roles of non-protein coding RNAs (ncRNAs). Thousands of ncRNAs have been characterized using these novel techniques but functional investigations are still very limited. Pseudogenes constitute one group of non-coding DNA. These genes represent duplications of protein-coding genes that have lost their protein-coding potential through various molecular events. Pseudogenes litter the human genome and it was not until recently it was found that many pseudogenes are actively transcribed. One of those is the PTEN pseudogene, PTENpg1. PTEN is a tumor suppressor gene, which is frequently dysregulated in cancers by epigenetic inactivation. In paper I, we characterized a previously unknown long ncRNA, PTENpg1 antisense RNA (asRNA). We identified two different isoforms that are involved in regulating expression of PTEN at both the transcriptional and post-transcriptional level. While one isoform recruits the chromatin remodelers DNMT3a and EZH2 to the PTEN promoter, the other isoform is involved in microRNA-mediated regulation of PTEN mRNA. In paper II, we investigated the role of PTENpg1 asRNA in drug resistance mechanisms to the BRAF inhibitor vemurafenib in melanoma. BRAF is a proto-oncogene commonly mutated in melanoma, resulting in its constitutive activation. Therapies that specifically target the mutated BRAF have been developed and vemurafenib is one of those drugs. However, the development of resistance during treatment is a major problem. We found that the PTENpg1 asRNA is involved in resistance to vemurafenib and that gain in expression of PTENpg1 asRNA promotes silencing of PTEN in melanoma cells. Moreover, we revealed that the expression of PTENpg1 asRNA is a promising marker for clinical outcome in melanoma patients. In paper III, we investigated the expression of microRNAs in Swedish and Egyptian patients with ABC DLBCL (Acute B-cell diffuse large B-cell lymphoma). We found that differences in environmental exposure alter the expression of microRNAs and that miR-1234 targets the proto-oncogene STAT3. The expression of miR-1234 was elevated in the Egyptian patients and STAT3 was consequently suppressed in these patients. Additionally, we also showed that ectopic expression of miR-1234 in cell line models mediates suppression of STAT3. Taken together, the findings in this thesis reveal intriguing molecular functions of ncRNAs, which are relevant for cancer development. The characterization of PTENpg1 asRNA and miR-1234 may prove important for the development of therapies and for predicting clinical outcome in various cancers.

List of scientific papers

I. Johnsson, P., Ackley, A., Vidarsdottir, L., Lui, W.O., Corcoran, M., Grandér, D., and Morris, K.V. (2013). A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nature Structural & Molecular Biology. 20(4), 440-6.
https://doi.org/10.1038/nsmb.2516.

II. Johnsson P., Vidarsdottir, L., Azimi, A., Serviss, A., Ingvar, C., Jönsson, G., Olsson, H., Frostvik Stolt, M., Hansson, J., Egyházi Brage, S., and Grandér, D. PTENpg1 antisense RNA mediates PTEN suppression in vemurafenib resistance and predicts clinical outcome in melanoma patients. [Manuscript]

III. Hogfeldt, T., Johnsson, P., Grandér, D., Bahnassy, A.A., Porwit, A., Eid, S., Osterborg, A., Zekri, A.R., Lundahl, J., Khaled, M.H., Mellstedt, H., and Moshfegh, A. (2014). Expression of microRNA-1234 related signal transducer and activator of transcription 3 in patients with diffuse large B-cell lymphoma of activated B-cell like type from high and low infectious disease areas. Leukemia & Lymphoma. 55, 1158-1165.
https://doi.org/10.3109/10428194.2013.824077.