Abstract
Neuroblastoma is the most common extra-cranial solid tumor of early childhood. Standard therapies are not effective in case of poor prognosis and chemotherapy resistance. To improve drug therapy, it is imperative to discover new targets that play a substantial role in tumorigenesis of neuroblastoma. The mitotic machinery is an attractive target for therapeutic interventions and inhibitors can be developed to target mitotic entry, spindle apparatus, spindle activation checkpoint, and mitotic exit. We present an elaborate analysis pipeline to determine cancer specific therapeutic targets by first performing a focused gene expression analysis to select genes followed by a gene knockdown screening assay of live cells. We interrogated gene expression studies of neuroblastoma tumors and selected 240 genes relevant for tumorigenesis and cell cycle. With these genes we performed time-lapse screening of gene knockdowns in neuroblastoma cells. We classified cellular phenotypes and used the temporal context of the perturbation effect to determine the sequence of events, particularly the mitotic entry preceding cell death. Based upon this phenotype kinetics from the gene knockdown screening, we inferred dynamic gene functions in mitosis and cell proliferation. We identified six genes (DLGAP5, DSCC1, SMO, SNRPD1, SSBP1, and UBE2C) with a vital role in mitosis and these are promising therapeutic targets for neuroblastoma. Images and movies of every time point of all screened genes are available at https://ichip.bioquant.uni-heidelberg.de.
Highlights
Neuroblastoma is an embryonal tumor arising in the sympathetic nervous system, mostly in adrenal glands
Based on gene expression analysis, we selected genes involved in the malignant progression of neuroblastomas
By automated image processing and machine learning using Support Vector Machines (SVMs), a quantitative description of phenotypic classes and cell nuclei were obtained from raw bitmaps
Summary
Neuroblastoma is an embryonal tumor arising in the sympathetic nervous system, mostly in adrenal glands. Some tumors undergo spontaneous regression without therapy, whereas, highrisk neuroblastoma patients are often resistant to available therapies and undergo a fatal clinical outcome [1]. These different clinical courses depend on age of the patient, stage of the disease and genetic abnormalities, most prominently the amplification of the transcription factor MYCN [2]. Given the high degree of heterogeneity in response to anti-mitotic drugs in different tumor cells, [11] identification of target proteins that are substantial for the etiology of neuroblastoma is a challenging task
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