In search of new biomarkers suitable for the diagnosis and treatment of prostate cancer, genome-wide transcriptome sequencing was carried out with tissue specimens from 40 prostate cancer (PCa) and 8 benign prostate hyperplasia patients. We identified two intergenic long non-coding transcripts, located in close genomic proximity, which are highly expressed in PCa. Microarray studies on a larger cohort comprising 155 patients showed a profound diagnostic potential of these transcripts (AUC~0.94), which we designated as tumor associated prostate cancer increased lncRNA (TAPIR-1 and -2). To test their therapeutic potential, knockdown experiments with siRNA were carried out. The knockdown caused an increase in the p53/TP53 tumor suppressor protein level followed by downregulation of a large number of cell cycle- and DNA-damage repair key regulators. Furthermore, in radiation therapy resistant tumor cells, the knockdown leads to a renewed sensitization of these cells to radiation treatment. Accordingly, in a preclinical PCa xenograft model in mice, the systemic application of nanoparticles loaded with siRNA targeting TAPIR-1 significantly reduced tumor growth. These findings point to a crucial role of TAPIR-1 and -2 in PCa.

Background: The survival of INA-6 human multiple myeloma cells is strictly dependent upon the Interleukin-6activated transcription factor STAT3. Although transcriptional analyses have revealed many genes regulated by STAT3, to date no protein-coding STAT3 target gene is known to mediate survival in INA-6 cells. Therefore, the aim here was to identify and analyze non-protein-coding STAT3 target genes. In addition to the oncogenic microRNA-21, we previously described five long noncoding RNAs (lncRNAs) induced by STAT3, named STAiRs. Here, we focus on STAT3-induced RNA 18 (STAiR18), an mRNA-like, long ncRNA that is duplicated in the human lineage. One STAiR18 locus is annotated as the already well described LINC00152/CYTOR, however, the other harbors the MIR4435-2HG gene and is, up to now, barely described.Methods: CAPTURE-RNA-sequencing was used to analyze STAiR18 transcript architecture. To identify the STAiR18 and STAT3 phenotype, siRNA-based knockdowns were performed and microarrays were applied to identify their target genes. RNA-binding partners of STAiR18 were determined by Chromatin-Isolation-by-RNA-Purification (ChIRP) and subsequent sequencing. STAT3 expression in dependence of STAiR18 was investigated by immunoblots, chromatin-and RNA-immunoprecipitations. Results: As identified by CAPTURE-RNA sequencing, a complex splice pattern originates from both STAiR18 loci, generating different transcripts. Knockdown of the most abundant STAiR18 isoforms dramatically decreased INA-6 cell vitality, suggesting a functional role in myeloma cells. Additionally, STAiR18 and STAT3 knockdowns yielded overlapping changes of transcription patterns in INA-6 cells, suggesting a close functional interplay between the two factors. Moreover, Chromatin isolation by RNA purification (ChIRP), followed by genome-wide RNA sequencing showed that STAiR18 associates specifically with the STAT3 primary transcript. Furthermore, the knockdown of STAiR18 reduced STAT3 levels on both the RNA and protein levels, suggesting a positive feedback between both molecules. Furthermore, STAiR18 knockdown changes the histone methylation status of the STAT3 locus, which explains the positive feedback and indicates that STAiR18 is an epigenetic modulator.

Glioblastoma multiforme (GBM) is an extremely aggressive brain tumor, characterized by its high genetic heterogeneity. In search of novel putative therapeutic RNA targets we investigated the role of the oncogenic long noncoding RNA LINC00152 (CYTOR, and STAiR18) in A172 glioblastoma cells. Here, we are the first to describe, that LINC00152 unexpectedly acts in a tumor suppressive manner in this cell line. SiRNA-based knockdown of LINC00152 enhanced malignant tumor behaviors including proliferation, cell cycle entry, migration, and invasion, contradicting previous studies using U87-MG and LN229 glioblastoma cells. Furthermore, LINC00152 knockdown had no influence on survival of A172 glioblastoma cells. In a genome wide transcription analysis of A172 and U87-MG glioblastoma cells, we identified 70 LINC00152 target genes involved in locomotion, cell migration, and motility in A172 cells, whereas in U87-MG cells only 40 target genes were detected. The LINC00152-regulated genes found in A172 differed from those identified in U87-MG glioblastoma cells, none of them being regulated in both cell lines. These findings underline the strong genetic heterogeneity of glioblastoma and point to a potential, yet unknown risk addressing LINC00152 lncRNA as a prospective therapeutic target in GBM.

ZusammenfassungHintergrundDer histogenetische Ursprung des atypischen Fibroxanthoms (AFX) und pleomorphen dermalen Sarkoms (PDS) ist nicht abschließend geklärt. Neben einem fibroblastären Ursprung wird aufgrund starker klinischer, histomorphologischer und molekulargenetischer Ähnlichkeiten zum entdifferenzierten Plattenepithelkarzinom der Haut (cutaneous squamous cell carcinoma, cSCC) eine keratinozytäre Differenzierung diskutiert.Patienten und Methodik56 Fälle (36 AFX, 8 PDS, 12 entdifferenzierte cSCC) wurden hinsichtlich ihrer klinischen, histomorphologischen und immunhistochemischen Charakteristika untersucht. An 18 Fällen (6 AFX/PDS, 6 entdifferenzierte cSCC, 6 differenzierte cSCC) wurde eine RNA‐Transkriptomanalyse durchgeführt.ErgebnisseKlinisch bestätigten sich starke Gemeinsamkeiten hinsichtlich Alter, Geschlecht und Lokalisation der Tumoren. Histomorphologisch ist es häufig ohne weiterführende immunhistochemische Färbungen nicht möglich AFX/PDS und entdifferenzierte cSCC voneinander abzugrenzen. In der Hauptkomponentenanalyse der RNA‐Transkriptomanalyse konnte gezeigt werden, dass AFX/PDS und differenzierte cSCC jeweils ein eigenes Cluster bildeten, während sich die entdifferenzierten cSCC dazwischen einordneten, ohne ein eigenes Cluster zu bilden. Bei der Betrachtung differenziell exprimierter Gene (DEG) verdeutlichten die Heat Maps, dass es innerhalb der entdifferenzierten cSCC‐Fälle gab, welche vom Expressionsprofil eher den AFX/PDS als den differenzierten cSCC zuzuordnen waren.SchlussfolgerungenDie Ergebnisse der Gesamtuntersuchungen geben Hinweise auf molekulare Ähnlichkeiten zwischen AFX/PDS und entdifferenzierten cSCC und lassen einen gemeinsamen histogenetischen Ursprung vermuten.