Figure 5 from The Proteogenomics of Prostate Cancer Radioresistance
Authors: Haas Roni , Frame Gavin , Khan Shahbaz , Neilsen Beth K. , Hong Boon Hao , Yeo Celestia P.X. , Yamaguchi Takafumi N. , Ong Enya H.W. , Zhao Wenyan , Carlin Benjamin , Yeo Eugenia L.L. , Tan Kah Min , Bugh Yuan Zhe , Zhu Chenghao , Hugh-White Rupert , Livingstone Julie , Poon Dennis J.J. , Chu Pek Lim , Patel Yash , Tao Shu , Ignatchenko Vladimir , Kurganovs Natalie J. , Higgins Geoff S. , Downes Michelle R. , Loblaw Andrew , Vesprini Danny , Kishan Amar U. , Chua Melvin L.K. , Kislinger Thomas , Boutros Paul C. , Liu Stanley K. 
Published: September 2024

<p>The proteome signature upon <i>POLQ</i> inhibition. <b>A,</b> Experimental design schematic. <b>B,</b> Genetic <i>POLQ</i> inhibition. The parental, CF-resistant, and HF-resistant cells were treated with either <i>POLQ</i> siRNA or scramble siRNA as the control. Significant radiosensitization was observed in all cell lines upon <i>POLQ</i> knockdown (<i>P</i> = 0.01, 0.002, and 0.02 for the parental, CF-resistant, and HF-resistant cells, respectively; paired <i>t</i> test). Three biological replicas of 4,000 cells per well and three of 6,000 cells per well were considered for each sample. <b>C,</b> Pharmacologic POLQ inhibition. CF-resistant, HF-resistant, and the parental cells were treated with 100 μmol/L novobiocin to achieve POLQ inhibition (Nvb 100 µmol/L). Significant radiosensitization was observed in all DU145 cell lines upon POLQ inhibition (<i>P</i> = 0.04, 0.02 and 0.01, for the parental, CF-resistant, and HF-resistant cells; paired <i>t</i> test). In <b>B</b> and <b>C,</b> both the control and the treated cells were irradiated with 0 or 4 Gy in two fractions. The surviving fraction of the treated cells (<i>POLQ</i> siRNA or Nvb 100 µmol/L) was normalized to the surviving fraction of the corresponding control of each cell line (black dots). <b>D,</b> The (top) 10 activated and suppressed biological processes at the protein level following <i>POLQ</i> depletion, in CF-resistant cells and the parental. The dot size represents the enrichment score, and the dot color is the directionality: orange shows upregulation toward <i>POLQ</i>-treated cells. <b>E,</b><i>POLQ</i> genetic inhibition creates a proteomic signature, involving 12 affected genes in CF-resistant cells. Three replicates from each cell type were used for the analysis. Left: signature genes whose protein abundances were changed between <i>POLQ</i>-depleted cells and the control, in CF-resistant cells and the parental cells. The dot size represents the Cohen’s d effect size, and the dot color is the directionality: magenta, upregulation, and green, downregulation toward <i>POLQ</i>-treated cells. Middle: changes in protein abundances of signature genes, between CF-resistant cells and the parental. The dot size represents the Cohen’s d effect size, and the dot color is the directionality: magenta, upregulation, and green, downregulation toward CF-resistant cells. Right: changes in RNA abundances of signature genes between CF-resistant cells and the parental. The dot size represents the log<sub>2</sub> (fold change) values. The dot color represents the directionality: red shows upregulation toward CF-resistant cells. <b>F,</b> Investigating signature genes (that were affected by <i>POLQ</i> inhibition in cell lines) in primary patient data. Left: RNA-RNA Pearson correlations between <i>POLQ</i> and signature genes. Middle, Pearson correlation between the abundances of <i>POLQ</i> RNA and proteins of signature genes. Right: Abundance of signature genes in normal vs. tumor samples at the RNA and protein levels. For all panels, datasets refer to the cohort names used for analysis and the data type for the type of molecule tested for signature genes (i.e., RNA or protein).</p>