Objective: Neurogenic tumors are highly heterogeneous, causing difficulties in finding a universal therapeutic target. In glioblastoma and neuroblastoma, MYCN oncogene copy-number disruption, gene transcription disruption and overall high transcriptional deregulation are found. We analyzed changes in cell survival and changes in expression of MYCN, HAND2, PHOX2A, PHOX2B oncogenes after exposure to senexin B in combination with the potential therapeutic agent 10058-F4 and temozolomide. Methods: Resazurin assay and MTT assay, as well as real-time PCR were used. Results and Discussion: Glioblastoma did not respond with a change in viability after incubation with 10058-F4, growth of one cell line of neuroblastoma was suppressed. One glioblastoma cell line was resistant to the tested concentrations of temozolomide, with the maximum inhibitory effect on the other cell line starting at 250 μM. Neuroblastoma did not respond with decreased survival following exposure to temozolomide. In the Kelly neuroblastoma line, we observed PHOX2B activation and decreased PHOX2A expression after drug exposure. Incubation of cells with 10058-F4 was accompanied by a significant decrease in MYCN mRNA levels. In the IMR-32 line, MYCN expression was reduced only upon simultaneous exposure to senexin B and 10058-F4. Co-incubation of temazolomide and senexin B resulted in the significant activation of all genes examined except PHOX2A. In the glioblastoma cell line T98G, only the basal level of PHOX2A mRNA was detected, which fell after exposure to all combinations tested. Meanwhile, the expression of other genes increased from exposure. MYCN and PHOX2A transcripts were detected in the U87MG cell line. Compound 10058-F4 decreased the expression of both genes and increased PHOX2B expression. Other combinations of substances also decreased MYCN and PHOX2A expression. The Kelly line responded with a statistically significant decrease in survival after incubation with senexin B in combination with 10058-F4, but less than after 10058-F4 alone. There was no cytotoxic effect for the IMR-32 cell line, but we observed increased cell survival after incubation with temazolomide and its combination with senexin B. In glioblastoma cell lines, we observed decreased cell survival after exposure to senexin B and 10058-F4. In the U87MG cell line, viability was decreased by 25–35% after incubation with temozolomide, as well as with the combination of senexin B and temozolomide. Conclusions: Our work shows the substance 10058-F4 is not effective against glioblastoma. In neuroblastoma cell lines, PHOX2B and MYCN respond most strongly to changes in expression; in glioblastoma cell lines, it is difficult to detect unambiguous changes in gene expression, except for a decrease in PHOX2A (also MYCN for U87MG) in both cell lines after any drug treatment. In summary, the expression of transcription factors involved in tumor progression and survival requires further investigation.