RNA sequencing of drug combinations for SL-176 and GSK-J4 in neuroblastoma cell lines
High-risk neuroblastoma remains a deadly disease with a survival rate of only 50-60 %. Prognosis is particularly poor in children who relapse after chemotherapy. In light of this, increasing attention has been directed toward the development of targeted therapies for neuroblastoma. Drug combination screening and follow-up experiments have shown that the WIP1 inhibitor SL-176 and the H3K27 demethylase inhibitor GSK-J4 act synergistically against neuroblastoma cells. To understand the mechanisms behind this synergism, we have treated cells of neuroblastoma cell lines IMR-32 and SK-N-BE(2) with either vehicle, SL-176, GSK-J4, or the combination of both drugs for 72 hours and performed RNA sequencing (Illumina NextSeq 550). Total RNA was subjected to quality control with the Agilent TapeStation (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions. To construct libraries suitable for Illumina sequencing, the Illumina TruSeq Stranded mRNA sample preparation protocol which includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries was used. The yield and quality of the amplified libraries was analyzed using Qubit by ThermoFisher and the Agilent TapeStation. The indexed cDNA libraries were normalized and combined, and the pools were sequenced on the Illumina NextSeq 550 (Illumina, San Diego, CA, USA) for a 75-cycle v2 sequencing run generating 75 bp single-end reads. Basecalling and demultiplexing was performed using CASAVA software (Illumina) with default settings generating Fastq files for further downstream mapping and analysis. Raw data was adapter and quality trimmed using Cutadapt, and aligned to the human genome build (Gene reference: Ensembl Homo_sapiens.GRCh38.104.gtf) using STAR. Gene assignment was performed using FeatureCounts. Differential gene expression was determined using DEseq2.
Treis, D., Lundberg, K.I., Bell, N. et al. Targeted inhibition of WIP1 and histone H3K27 demethylase activity synergistically suppresses neuroblastoma growth. Cell Death Dis 16, 318 (2025). https://doi.org/10.1038/s41419-025-07658-1
Department of Women's and Children's Health
A common neoplasm of early childhood arising from neural crest cells in the sympathetic nervous system, and characterized by diverse clinical behavior, ranging from spontaneous remission to rapid metastatic progression and death. This tumor is the most common intraabdominal malignancy of childhood, but it may also arise from thorax, neck, or rarely occur in the central nervous system. Histologic features include uniform round cells with hyperchromatic nuclei arranged in nests and separated by fibrovascular septa. Neuroblastomas may be associated with the opsoclonus-myoclonus syndrome. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, pp2099-2101; Curr Opin Oncol 1998 Jan;10(1):43-51)
A medical specialty concerned with maintaining health and providing medical care to children from birth to adolescence.
The study of the origin, nature, properties, and actions of drugs and their effects on living organisms.