title: Time-lapse imaging of neuroblastoma cells to determine cell fate upon gene knockdown.
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.
authors.affiliation: Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Germany.
authors.forename: Richa
authors.initials: R
authors.lastname: Batra
authors.forename: Nathalie
authors.initials: N
authors.lastname: Harder
authors.forename: Sina
authors.initials: S
authors.lastname: Gogolin
authors.forename: Nicolle
authors.initials: N
authors.lastname: Diessl
authors.forename: Zita
authors.initials: Z
authors.lastname: Soons
authors.forename: Christina
authors.initials: C
authors.lastname: Jäger-Schmidt
authors.forename: Christian
authors.initials: C
authors.lastname: Lawerenz
authors.forename: Roland
authors.initials: R
authors.lastname: Eils
authors.forename: Karl
authors.initials: K
authors.lastname: Rohr
authors.forename: Frank
authors.initials: F
authors.lastname: Westermann
authors.forename: Rainer
authors.initials: R
authors.lastname: König
mesh_terms: D002453:Cell Cycle / Q000235:genetics; D045744:Cell Line, Tumor; D002471:Cell Transformation, Neoplastic / Q000235:genetics* / Q000378:metabolism; D055785:Gene Knockdown Techniques; D006801:Humans; D009447:Neuroblastoma / Q000235:genetics* / Q000378:metabolism; D008941:Spindle Apparatus / Q000235:genetics* / Q000378:metabolism; D059008:Time-Lapse Imaging / Q000379:methods*