Truncating PREX2 Mutations Activate Its GEF Activity and Alter Gene Expression Regulation in NRAS-Mutant Melanoma

Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma Item Type Article Authors Lissanu Deribe, Yonathan; Shi, Yanxia; Rai, Kunal; Nezi, Luigi; Amin, Samir B.; Wu, Chia-Chin; Akdemir, Kadir C.; Mahdavi, Mozhdeh; Peng, Qian; Chang, Qing Edward; Hornigold, Kirsti; Arold, Stefan T.; Welch, Heidi C. E.; Garraway, Levi A.; Chin, Lynda Citation Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma 2016, 113 (9):E1296 Proceedings of the National Academy of Sciences Eprint version Post-print DOI 10.1073/pnas.1513801113 Publisher Proceedings of the National Academy of Sciences Journal Proceedings of the National Academy of Sciences Rights Archived with thanks to Proceedings of the National Academy of Sciences Download date 25/09/2021 13:20:05 Link to Item http://hdl.handle.net/10754/600889 Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma Yonathan Lissanu Deribe1#*, Yanxia Shi1,2#, Kunal Rai1, Luigi Nezi1, Samir B. Amin1, Chia-Chin Wu1, Kadir C. Akdemir1, Mozhdeh Mahdavi1, Qian Peng1,Q. Edward Chang3 ,Kirsti Hornigold4, Stefan T. Arold5, Heidi Welch4, Levi Garraway6, and Lynda Chin1,3* 1. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA 2. Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborate Center for Cancer Medicine, Guangzhou 510060, China 3. Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA 4. The Babraham Institute, Babraham Research Campus, Cambridge, UK 5. King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900 Saudi Arabia 6. Broad Institute of MIT and Harvard, Boston, MA 02141, USA *Corresponding authors: Email: [email protected] and [email protected] # These authors contributed equally to this work. Classification: BIOLOGICAL SCIENCES; Medical Sciences Short title: PREX2 melanoma mutations activate its GEF activity Keywords: melanoma, PREX2, GEF, Akt, mouse models of cancer, p57, Rac1 1 Supplementary Materials and Methods: Supplementary Methods Cell culture and generation of mouse embryonic fibroblasts The generation of human primary melanocytes (PMEL/hTERT/CDK4(R24C)/P53DD with either NRASG12D or BRAFV600E have been described previously (1). These cells were grown in Ham’s F10 medium (Invitrogen), containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. 293FT cells were grown in DMEM (Invitrogen) containing 10% FBS. We generated MEFs from embryonic day 13.5 (E13.5) embryos using standard methods following PTENL/L, Rosa26-CreERT2 mouse intercrosses. MEFs were grown in DMEM (Invitrogen) containing 10% FBS and 1% penicillin/streptomycin. All cells were grown at 37oC in a humidified 5% CO2 incubator. The Rac1 inhibitor EHT1864 was purchased from Selleckchem and dissolved to 10mM in DMSO. In vitro GEF assay PREX2 GEF assays were conducted as previously described in detail (2, 3). Briefly, assays were performed for 10 min at 300C, liposomes consisting of PC, PS and PI, cold and radioactive GTPgammaS, and purified proteins (no PIP3 or Gbetagamma in any of these assays). As substrate, we used 100 nM GDP-loaded human recombinant Rac protein, purified from Sf9 cells, throughout. Recombinant human P-Rex proteins (full length and iDHPH2 M1 to R363) were purified from Sf9-cells and used at 50 nM in the assay. Rac1 activation assay Rac1 activation assays were performed using Rac1 pull-down activation assay biochemical kit according to the manufacturer’s detailed protocol (Cytoskeleton Inc, Denver, CO, USA). 2 Plasmids, lentiviral and adenoviral transduction PREX2 plasmids have been previously described (4). Lentiviral stocks were prepared by co-transfecting 293FT cells with pLenti6.3-PREX2 expression constructs and standard viral packaging systems. 48 and 72 hours later viral supernatants were collected and used to transduce PMEL cells. All the PTEN expression constructs were in pSG5L vector [described previously (5)] and received from Addgene. PTEN plasmids were transfected into 293T cells using Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions. Rac1 wt or Q61L mutant were cloned into the pLenti6.3 vector system, lentivirus prepared and used to transduce PMEL cells. Xenograft studies All animal studies were approved by MD Anderson Cancer Center Internal Animal Care and Use Committee (IACUC). Cells were subcutaneously implanted (1106 cells) in female NCR-NUDE mice (Taconic). Animals were monitored for tumors formation and were sacrificed when tumor diameter approached 1.5 cm. Log- rank statistical test was performed using Prism 5 (Graphpad). Tumors were dissected and snap frozen in liquid Nitrogen for protein, RNA and other molecular profiling experiments. Immunoprecipitation, western blotting and antibodies Cells were lysed in lysis buffer (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% NP40) containing protease and phosphatase inhibitor cocktail tablets (Roche) on ice. For phosphorylation of Akt we lysed cells in RIPA buffer. Lysates were subjected to immunoprecipitation using the respective antibodies (usually 1:100 dilution) for 1 to 3 several hours. In case of V5, we used V5-coupled beads (Sigma-Aldrich). An equal mixture of Protein A and G beads were then added and incubated for an additional hour rotating in a cold room. Beads were washed in lysis buffer at least three times and bound proteins were eluted by boiling in SDS-loading buffer (BioRad). Lysates or IPs were then loaded on SDS-PAGE gels (BioRad) and transferred using BioRad Turbo semidry transfer system to nitrocellulose membranes which were probed with respective antibodies: V5 (1:5000), PREX2 antibodies (1:1000, Sigma-Aldrich or monoclonal antibody from Abcam), HA (1:1000, Santa-Cruz), PTEN (1:1000), phospho-Akt S475 (1:1000, Cell Signaling), phospho-Akt T308 (1:1000 Cell Signaling). Immunohistochemistry and Ki67 quantification Tumors were fixed in formalin for 24 hours, paraffin embedded and sectioned. After antigen retrieval, slides were stained using Ki67 antibody (1:200, Dako) using standard methods. NuclearQuant 1.15.1 software (3DHISTECH) was used for Ki67 quantitation. Experienced pathologist set up the algorithm. Three non-necrotic tumor areas were selected for analysis on each slide. The software automatically generated quantitative results based on H-Score formula. Reverse phase protein array (RPPA) Cellular proteins were denatured by 1% SDS (with beta-mercaptoethanol) and diluted in five 2-fold serial dilutions in dilution buffer (lysis buffer containing 1% SDS). Serial diluted lysates were arrayed on nitrocellulose-coated slides (Grace Biolab) by Aushon 2470 Arrayer (Aushon BioSystems). Total 5808 array spots were arranged on each slide including the spots corresponding to positive and negative controls prepared from mixed cell lysates or dilution buffer, respectively. 4 Each slide was probed with a validated primary antibody plus a biotin-conjugated secondary antibody. Only antibodies with a Pearson correlation coefficient between RPPA and western blotting of greater than 0.7 were used in reverse phase protein array study. Antibodies with a single or dominant band on western blotting were further assessed by direct comparison to RPPA using cell lines with differential protein expression or modulated with ligands/inhibitors or siRNA for phospho- or structural proteins, respectively. The signal obtained was amplified using a Dako Cytomation–catalyzed system (Dako) and visualized by DAB colorimetric reaction. The slides were scanned, analyzed, and quantified using a customized-software, Microvigene (VigeneTech Inc.), to generate spot intensity. Each dilution curve was fitted with a logistic model (“Supercurve Fitting” developed by the Department of Bioinformatics and Computational Biology in MD Anderson Cancer Center, “http://bioinformatics.mdanderson.org/OOMPA”). This fits a single curve using all the samples (i.e., dilution series) on a slide with the signal intensity as the response variable and the dilution steps as the independent variable. The fitted curve is plotted with the signal intensities – both observed and fitted - on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes. The protein concentrations of each set of slides were then normalized by median polish, which was corrected across samples by the linear expression values using the median expression levels of all antibody experiments to calculate a loading correction factor for each sample. 5 mRNA expression profiling Total RNA isolation was performed with the Qiagen RNeasy kit, according to the manufacturer’s instructions. Affmetrix GeneChip Mouse genome 430 2.0 or Human Genome U133 plus 2 arrays containing probe sets for >45,000 characterized genes and expressed sequence tags, were used. Sample labeling and processing, hybridization, and scanning were performed according to Affymetrix protocols. Briefly, double- stranded cDNA was synthesized from total RNA with GeneChip 3’ IVT express kit (Affmetrix), with a T7 RNA polymerase promoter site added to its 3′ end (Genset, La Jolla, CA). Biotinylated cRNAs were generated from cDNAs in vitro and amplified by using GeneChip 3’ IVT express kit. After purification of cRNAs by the RNeasy mini kit (Qiagen, Hilden, Germany),

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