A Highly Sensitive XNA-Based RT-qPCR Assay for the Identification of ALK, RET, and ROS1 Fusions in Lung Cancer.

Lung cancer is often triggered by genetic alterations that result in the expression of oncogenic tyrosine kinases. Specifically, ALK, RET, and ROS1 chimeric receptor tyrosine kinases are observed in approximately 5-7%, 1-2%, and 1-2% of NSCLC patients, respectively. The presence of these fusion genes determines the response to tyrosine kinase inhibitors. Thus, accurate detection of these gene fusions is essential in cancer research and precision oncology. To address this need, we have developed a multiplexed RT-qPCR assay using xeno nucleic acid (XNA) molecular clamping technology to detect lung cancer fusions. This assay can quantitatively detect thirteen ALK, seven ROS1, and seven RET gene fusions in FFPE samples. The sensitivity of the assay was established at a limit of detection of 50 copies of the synthetic template. Our assay has successfully identified all fusion transcripts using 50 ng of RNA from both reference FFPE samples and cell lines. After validation, a total of 77 lung cancer patient FFPE samples were tested, demonstrating the effectiveness of the XNA-based fusion gene assay with clinical samples. Importantly, this assay is adaptable to highly degraded RNA samples with low input amounts. Future steps involve expanding the testing to include a broader range of clinical samples as well as cell-free RNAs to further validate its applicability and reliability.

miRNA-211 maintains metabolic homeostasis in medulloblastoma through its target gene long-chain acyl-CoA synthetase 4.

The prognosis of childhood medulloblastoma (MB) is often poor, and it usually requires aggressive therapy that adversely affects quality of life. microRNA-211 (miR-211) was previously identified as an important regulator of cells that descend from neural cells. Since medulloblastomas primarily affect cells with similar ontogeny, we investigated the role and mechanism of miR-211 in MB. Here we showed that miR-211 expression was highly downregulated in cell lines, PDXs, and clinical samples of different MB subgroups (SHH, Group 3, and Group 4) compared to normal cerebellum. miR-211 gene was ectopically expressed in transgenic cells from MB subgroups, and they were subjected to molecular and phenotypic investigations. Monoclonal cells stably expressing miR-211 were injected into the mouse cerebellum. miR-211 forced expression acts as a tumor suppressor in MB both in vitro and in vivo, attenuating growth, promoting apoptosis, and inhibiting invasion. In support of emerging regulatory roles of metabolism in various forms of cancer, we identified the acyl-CoA synthetase long-chain family member (ACSL4) as a direct miR-211 target. Furthermore, lipid nanoparticle-coated, dendrimer-coated, and cerium oxide-coated miR-211 nanoparticles were applied to deliver synthetic miR-211 into MB cell lines and cellular responses were assayed. Synthesizing nanoparticle-miR-211 conjugates can suppress MB cell viability and invasion in vitro. Our findings reveal miR-211 as a tumor suppressor and a potential therapeutic agent in MB. This proof-of-concept paves the way for further pre-clinical and clinical development.

GADD45α MODULATES DNA METHYLATION INDUCED BY DNA DAMAGE DURING HOMOLOGOUS RECOMBINATION / GADD45α MODULA LA METILACIÓN DEL ADN INDUCIDO POR EL DAÑO DEL ADN DURANTE LA RECOMBINACIÓN HOMÓLOGA

Homologous recombination is one of the major pathways for repairing DNA double strand breaks, the most deleterious of DNA lesions. Recent studies suggest that DNA methylation events target homologous recombination segments; however, the underlying mechanism of DNA methylation during homologous recombination is not understood. In this work, we show that GADD45α, a protein involved in cell cycle control, growth arrest, and apoptosis, plays some role in the epigenetic of homologous recombination. Specifically, it is suggested that dimerization of GADD45α monomers is required. Several point mutants of GADD45α were constructed and analyzed to show defects in self-association. Among them, the GADD45α mutant, CE83AA, lacked the ability to dimerize or oligomerize, which suppressed DNA methylation at homologous recombination sites in vivo. Based on this, we propose a model in which the dimerization (or oligomerization) of GADD45α is involved in strand specific DNA methylation that attends homologous recombination.

La recombinación homóloga es una de las principales vías para la reparación de la ruptura de doble cadena del ADN, la más grave de las lesiones del ADN. Estudios recientes sugieren que la metilación del ADN apunta hacia segmentos de recombinación homóloga; sin embargo, el mecanismo de metilación del ADN durante la recombinación homóloga no es claro. En este estudio, mostramos que GADD45α, una proteína que se encuentra relacionada con el control del ciclo celular, el ceso del crecimiento y la apoptosis, juega un papel en la epigenética de la recombinación homóloga. Específicamente, se ha sugerido que es requerido un dímero de monómeros de GADD45α. Varios puntos mutantes de GADD45α fueron construidos y analizados para mostrar defectos en la libre asociación. Entre ellos, el mutante GADD45α, CE83AA, carecía de la habilidad de dimerización u oligomerización, lo cual suprimió in vivo la metilación del ADN en los sitios de recombinación homóloga. Con base en esto, proponemos un modelo en el cual la dimerización (u oligomerización) de GADD45α está involucrada en la cadena específica de metilación del ADN que lleva a la recombinación homóloga.