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. 2018 Jun 12;5:180106.
doi: 10.1038/sdata.2018.106.

Pharmacological and Genomic Profiling of Neurofibromatosis Type 1 Plexiform Neurofibroma-Derived Schwann Cells

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Free PMC article

Pharmacological and Genomic Profiling of Neurofibromatosis Type 1 Plexiform Neurofibroma-Derived Schwann Cells

Marc Ferrer et al. Sci Data. .
Free PMC article

Abstract

Neurofibromatosis type I (NF1) is an autosomal dominant genetic condition characterized by peripheral nervous system tumors (PNSTs), including plexiform neurofibromas (pNFs) that cause nerve dysfunction, deformity, pain damage to adjacent structures, and can undergo malignant transformation. There are no effective therapies to prevent or treat pNFs. Drug discovery efforts are slowed by the 'benign' nature of the Schwann cells that are the progenitor cells of pNF. In this work we characterize a set of pNF-derived cell lines at the genomic level (via SNP Arrays, RNAseq, and Whole Exome- Sequencing), and carry out dose response-based quantitative high-throughput screening (qHTS) with a collection of 1,912 oncology-focused compounds in a 1536-well microplate cell proliferation assays. Through the characterization and screening of NF1-/-, NF1+/+ and NF1+/- Schwann cell lines, this resource introduces novel therapeutic avenues for the development for NF1 associated pNF as well as all solid tumors with NF1 somatic mutations. The integrated data sets are openly available for further analysis at http://www.synapse.org/pnfCellCulture.

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1. Schema of sample and data collection.
Figure 2
Figure 2. Distribution of (a) Log R Ratio values and (b) B Allele frequency values across the pNF cell lines.
Figure 3
Figure 3. Distribution of RNA-Seq counts.
(a) Boxplot representing normalized RNA-Seq counts across samples. (b) Principal component analysis (PCA) of samples.
Figure 4
Figure 4. Clustering of variants in Whole Exome Sequencing data (a) represents discordance between samples and (b) represents the number of shared sites between samples.
Figure 5
Figure 5. Growth rates for each cell line were determined in HTS microtiter well plate format.
(a) Cell growth plots in 384-well plates as determined by phase contrast using an Incucyte Zoom, at different cell seeding densities. Percentage cell confluence was calculated by the software from the Incucyte Zoom instrument from the phase contrast signal. (b) Cell density legend for panel a. (c) Doubling times for each cell in a 384-well calculated by fitting an exponential growth curve on the data points from time 0 h to 80% confluence, using Graphpad Prism 7. Values are for curves obtained from seeding 2000 cells/well. (d) Cell growth plots in 1536-well plates as determined by CellTiterGlo luminescence signal, at different cell seeding densities, at different time points. (e) Cell density legend for panel d. (f) Doubling times for each cell in a 1536-well calculated by fitting the RLU at each time point to an exponential growth curve, using Graphpad Prism 7. Values are for curves obtained from seeding 250 cells/well.
Figure 6
Figure 6. Quality control data for the dose response, quantitative high thoughput screen (qHTS) of the plexiform cells.
(a) Box plots of Z′-factor for all plates in each screen. (b) Median RLU signal for column 4 (100% viability) and column 2 (pharmacological inhibition with 9 μM Bortezomib) for each plate of each screen. Colors reflect individual cell lines, as describe in the inset legend. DMSO treated control wells and 9 μM Bortezomib treated control wells (c) Scatter plot and (d) heat map of an assay plate from one of the screens. For the scatter plot, the X-axis corresponds to column number, and the Y-axis corresponds to relative luminescence units (RLU). Dots are coloured by plate row. For the heat map plot, the X-axis corresponds to column number, and the Y-axis corresponds to row number, and the colour coding is red, black, and green for increase, no change, and decrease, respectively, in RLU signal. Column 1 are wells with media only as low signal control (0% viability); columns 2 and 3 are wells with cells and 9 μM Bortezomib as pharmacological control, and column 4 are wells with cells and DMSO, as high signal control (100% viability).

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References

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