Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Integrative copy number analysis of uveal melanoma reveals novel candidate genes involved in tumorigenesis including a tumor suppressor role for PHF10/ BAF45a

doi: 10.1158/1078-0432.CCR-18-3052

Figure Lengend Snippet: A. Enrichment analysis between copy number and expression at the cytogenetic band level. Results are presented for TCGA and CC cohorts where correlation coefficients were > 0.5. For each cytogenetic band the total number of genes analysed, and the frequency of the significantly correlated genes is shown, along with the P values and FDR P values. K is the number of genes in the set from MsigDB and k is the number of genes in the intersection of the query set with a set from MsigDB. The ratio of k/K in each cohort (CC and TCGA) is also provided.

Article Snippet: Established cell lines derived from primary uveal melanomas (Mel202 ( 22 ), 92–1 ( 23 ) and Mel290 ( 24 ) (described in Supplementary Table 1 ) were subjected to PHF10 knockdown with siRNA (Santa-cruz, sc-95343) or a siRNA control that consisted of scrambled sequence/non-silencing siRNA (Santa-cruz, sc-37007) (SiCtrl).

Techniques: Expressing, Amplification

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Integrative copy number analysis of uveal melanoma reveals novel candidate genes involved in tumorigenesis including a tumor suppressor role for PHF10/ BAF45a

doi: 10.1158/1078-0432.CCR-18-3052

Figure Lengend Snippet: The region of overlap that harbors PHF10, WDR27 and c6orf120 is shown. The location of the frameshift mutation identified in MM133 (a class 2 tumor) is also shown. The CC sample with the PHF10 HD was GSM1082739. The WU cohort sample with a PHF10 HD was MM016, a class 2 tumor in a female who was diagnosed with UM in her 20s, did not harbor a detectable mutation in BAP1, SF3B1 or EIF1AX and who died from metastasis.

Article Snippet: Established cell lines derived from primary uveal melanomas (Mel202 ( 22 ), 92–1 ( 23 ) and Mel290 ( 24 ) (described in Supplementary Table 1 ) were subjected to PHF10 knockdown with siRNA (Santa-cruz, sc-95343) or a siRNA control that consisted of scrambled sequence/non-silencing siRNA (Santa-cruz, sc-37007) (SiCtrl).

Techniques: Mutagenesis

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Integrative copy number analysis of uveal melanoma reveals novel candidate genes involved in tumorigenesis including a tumor suppressor role for PHF10/ BAF45a

doi: 10.1158/1078-0432.CCR-18-3052

Figure Lengend Snippet: A. GO analysis of differentially expressed transcripts. For RNA sequencing, three biological replicates were prepared for each condition. Transcripts with a fold change >2 and adjusted p-value < 0.5 following PHF10 kd were selected, and those shared by at least two cell lines were used for pathway analysis with g:Profiler (https://biit.cs.ut.ee/gprofiler/gost). GO redundant terms were removed with REVIGO (65); B. Venn diagram showing the number of differentially expressed transcripts unique to and shared by each cell line; C. Western blot analysis of some transcripts encoding chromatin remodelers that were differentially expressed in PHF10 mutant tumors. 30μg of whole cell lysate was loaded. Knockdown was confirmed with qRT-PCR, RNA-Seq and Knockdown was confirmed with Western blotting and an antibody to PHF10 at a concentration of 1:1000; D, E, F: Results of adhesion assays: ~105 cells (PHF10kd or siCtrl for 24h) were seeded on top of a collagen insert in serum-free media and medium containing 10% FBS and extracellular matrix proteins were added to the lower chamber. Cells were left to invade for 48h and then lysed and stained with CyQuant GR dye and fluorescence was measured at 480/520nm. The extracellular matrix proteins tested here were Col I, Col II and Col IV corresponding to Collagen 1, 2 and 4 respectively, FN (Fibronectin), LN (laminin), TN (tenascin), VN (vitronectin). Neg corresponds to the negative control. Three biological replicates were analysed and results are shown with error bars represent standard deviation of the mean * P-value <0.05. G: Result of migration assays performed as described elsewhere (27).

Article Snippet: Established cell lines derived from primary uveal melanomas (Mel202 ( 22 ), 92–1 ( 23 ) and Mel290 ( 24 ) (described in Supplementary Table 1 ) were subjected to PHF10 knockdown with siRNA (Santa-cruz, sc-95343) or a siRNA control that consisted of scrambled sequence/non-silencing siRNA (Santa-cruz, sc-37007) (SiCtrl).

Techniques: RNA Sequencing, Western Blot, Mutagenesis, Knockdown, Quantitative RT-PCR, Concentration Assay, Staining, CyQUANT Assay, Fluorescence, Negative Control, Standard Deviation, Migration