OLFR1248 NEFM IMPG2 JAK1 NGFRAP1 NKRF MRGPRX2 KIF26B IL17RD MAP3K15 GM263 MED22 MRPL47 LYPLA1 LYRM4 DMSO ATF5. perk ERK TUBULIN.

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1 A genome-wide RNA interference screen reveals an essential //MCL1 survival pathway in malignant glioma with therapeutic implications Zhi Sheng, Li Li, Lihua J. Zhu, Thomas W. Smith, Andrea Demers, Alonzo H. Ross, Richard P. Moser & Michael R. Green Supplementary Figure 1 DT (nm):.1.2 GL261 DT (nm):.25.5 GL261/ p-dtr/ pcmv- f a c Relative Frs sirna: R elative C reb3l2 expressio n sirna: Luc FRS2 Luc Relative Pak1 FRS2 PAK sirna: g Luc PAK1 TUBULIN Relative Creb3l sirna: b Fold Atf5 PD shrna: Luc CL387,785 NS ACCN5 BST1 DPYS d Relative Atf5 Manumycin A Sorafenib h EFNA2 EPM2AIP1 FAM38B FRS2 FSTL5 R elative C reb3l2 expressio n PD17374 CL-387,785 Manumycin A LY2942 GDAP2 GM263 GM4873 GM5444 IL17RD IMPG2 JAK1 KIF26B LYRM4 e perk ERK TUBULIN i Relative caspase activity LYPLA1 MAP3K15 MED22 MRGPRX2 MRPL47 NEFM NGFRAP1 NKRF OLFR1248 OLFR745 PADI6 PD17374 PD17374 CL387,785 Manumycin A CL-387,785 Manumycin A SKINT11 PAK1 PLA2G12B PUS7 RIPK3 RPL31 SDPR SETBP1 SKIL Sorafenib LY2942 Flag Flag- SLC9A5 SMS SPRED1 TALDO1 TCTN2 TEX21 TMEM189 TOX V1RD12 V1RE1 V1RE8 VPS13C XRCC4 ZFP6 ZFP6 ZMYND A4RIK 1725B11RIK 312H9RIK E3RIK L6RIK C3323M2RIK LOC29917 LOC Supplementary Figure 1 A genome-wide RNAi screen reveals a signaling pathway required for. (a) Generation of a GL261/p-DTR/pCMV- cell line that is resistant to DT. Parental GL261 cells (top) or GL261/p-DTR/pCMV- (bottom) cells were plated in a 6-well plate, and different concentrations of DT were added to the media, as indicated. Five days later, cells were stained with crystal violet. (b) Validation of candidate shrnas for their ability to inhibit endogenous Atf5. GL261 cells were transiently transfected with a plasmid expressing an individual shrna identified from primary screen. Expression of endogenous Atf5 upon treatment of each shrna was normalized to that obtained with the control non-silencing (NS) shrna. Those shrnas that inhibited Atf5 2.5 fold, indicated by the red line, were considered positive.(c) Analysis of Frs2, Pak1 and Creb3l2 following sirna-mediated knockdown. GL261 cells were transiently transfected with sirnas against FRS2, PAK1 or, or as a control luciferase (Luc), and target gene was monitored by qrt-pcr. (d,e) Atf5 is reduced by treatment with an inhibitor of FGFR, EGFR or RAS. (d) qrt-pcr analysis monitoring Atf5 in GL261 cells treated with, the FGFR inhibitor PD17374 (4 µm), the EGFR inhibitor CL-387,785 (8 µm) or the farnesyl transferase inhibitor manumycin A (2.5 µm). (e) Immunoblot analysis monitoring the levels of, perk and ERK in GL261 cells treated with, PD17374, CL387,765, manumycin A or sorafenib. Tubulin was monitored as a loading control. (f-h) is substantially reduced by treatment with an sirna against FRS2 or PAK1 or with an inhibitor of MAPK or PI3K. (f) qrt-pcr analysis monitoring Creb3l2 in GL261 cells transiently transfected with an sirna against luciferase (Luc), FRS2 or PAK1. (g) Immunoblot analysis monitoring levels in GL261 cells treated with, the FGFR inhibitor PD17374 (4 µm), the EGFR inhibitor CL-387,785 (8 µm), the farnesyl transferase inhibitor manumycin A (2.5 µm) or sorafenib (1 µm). Tubulin was monitored as a loading control. (h) qrt-pcr analysis monitoring Creb3l2 in GL261 cells treated with or the PI3K inhibitor LY2942 (2 µm). (i) Over- of antagonizes apoptosis induced by inhibitors of FGFR, EGFR, RAS or PI3K. Caspase 3/7 activity assay in GL261 cells expressing Flag or Flag- and treated with, the FGFR inhibitor PD17374 (4 µm), the EGFR inhibitor CL-387,785 (8 µm), the farnesyl transferase inhibitor manumycin A (5 µm) or the PI3K inhibitor LY2942 (2 µm). Nature Medicine: doi:1.138/nm.2158

2 Supplementary Figure 2 Relative Mcl Flag Flag- Supplementary Figure 2 Over- of induces Mcl1 transcription. qrt- PCR analysis monitoring Mcl1 in GL261 cells stably transfected with plasmids encoding either Flag or Flag-. Nature Medicine: doi:1.138/nm.2158

3 Supplementary Figure 3 a FRS2 3. MCL1 Normalized units Sub Class Class T-test: P-value: 6.5E T-test: P-value: 1.6E-7-2. T-test: P-value: 1.1E T-test: P-value: 1.6E-7 b Copy number EGFR KRAS Normal brain Glioblastoma MCL1 c Sample Staining perk MCL1 All 4 d Normal brain (n = 4) Malignant glioma (n = 38) Comparison perk vs perk vs perk vs MCL1 vs vs MCL1 vs MCL1 Positive Negative Positive Negative % 1% 74% 26% % 1% 55% 45% Phi Correlation Coefficient % 1% 71% 29% P-value % 1% 5% 5% % 1% 42% 13% Supplementary Figure 3 Expression of pathway components in human malignant glioma (a) Up-regulation of, FRS2, PAK1 and MCL1 in human glioblastoma. Brain tumor array datasets were accessed using the Oncomine Cancer Profiling Database ( The dataset includes 23 normal brain samples from epilepsy patients (class 1; blue) and 77 human glioblastoma multiforme samples (class 2; red). Box-plots depicting gene in each sample, as well as Student s t-tests and P-values comparing gene between the groups, were obtained directly through the Oncomine 3. software. (b) Components of the -mediated survival pathway are amplified in human glioblastoma. The copy number of,, EGFR, KRAS and MCL1 was retrieved from the focal copy number dataset (table S5) from Parsons et al. 3. The copy number was averaged from two normal brain samples and 16 glioblastoma samples and plotted. To perform the copy number analysis, Parsons et al. evaluated tumors for copy number alterations through genomic hybridization of DNA samples to Illumina SNP arrays containing ~1 million probes. (c) Summary of immunohistochemical results for four normal individuals and 38 glioblastoma patients. Staining intensity was empirically scored on a scale of to 3; negative staining was defined as or 1, whereas positive staining was defined as 2 or 3. The percentage of samples staining positively or negatively for each protein, or all four proteins (right), is stated. (d) Statistical analysis of the immunohistochemical results. Pair-wise combinations were analyzed for correlation coefficients phi and P-value. The phi coefficient was calculated to determine the strength of the correlation between all pair-wise combinations of the four protein status that are all dichotomous variables. Because most of the 2-by-2 contingency table contains cells with an expected frequency less than 5, Chi-squared can be unreliable. Therefore, Fisher's exact test was performed to determine the significance of each correlation. Nature Medicine: doi:1.138/nm.2158

4 Supplementary Figure 4 a Relative level 1,2 1, U87MG SF295 b Percentage viability Sorafenib (µm) TMZ + TMZ (1 µm) + TMZ (4 µm) 1. Supplementary Figure 4 Sorafenib does not synergistically inhibit SF295 glioblastoma cell viability in combination with temozolomide. (a) Expression of and in U87MG and SF295 human glioblastoma cells. The original data were obtained from the BioGPS database ( (b) SF295 cells were treated with combinations of sorafenib and temozolomide (TMZ) at different concentrations. Cell viability was monitored by MTT assay. Nature Medicine: doi:1.138/nm.2158

5 Supplementary Figure 5 Sorafenib MCL1 Control Supplementary Figure 5 Expression of, and MCL1 in a mouse xenograft of human glioblastoma. The human glioblastoma xenografts shown in Figure 5a were stained with an antibody against, or MCL1. Nature Medicine: doi:1.138/nm.2158

6 Supplementary Table 1 List of 12 validated genes required for Atf5 in GL261 cells. Mouse gene symbol Name Accn5 amiloride-sensitive cation channel 5, intestinal Creb3l2 camp responsive element binding protein 3-like 2 Frs2 fibroblast growth factor receptor substrate 2 Jak1 Janus kinase 1 Mrgprx2 MAS-related GPR, member X2 Pak1 p21 protein (Cdc42/Rac)-activated kinase 1 Pla2g12b phospholipase A2, group XIIB Ripk3 receptor-interacting serine-threonine kinase 3 Sdpr serum deprivation response Tex21 testis expressed gene 21 Tox thymocyte selection-associated high mobility group box C3323M2Rik RIKEN cdna C3323M2 gene Nature Medicine: doi:1.138/nm.2158

7 Supplementary Table 2 is elevated in a wide range of tumors relative to normal tissue. The Oncomine 4 database was used to query level and copy number in a variety of human tumors. Study Name Tissue Sample Size Log e of Median Expression Unit P-value Storz Lymphoma Skin Cutaneous follicular lymphoma E-5 Basso Lymphoma B-lymphocyte 5.44 Diffuse large B-cell lymphoma E-9 Bhattacharjee Lung Lung 17.7 Small cell lung carcinoma E-4 Hao Esophagus Esophagus Esophageal adenocarcinoma E-5 Bredel Brain Brain Glioblastoma E-4 Detwiller Sarcoma Mixed normal samples Round cell liposarcoma E-4 FriersonHF Salivary-gland Salivary gland Salivary gland adenoid cystic E-5 Radvanyi Breast carcinoma Breast Invasive mixed breast carcinoma Zhan Myeloma 3 Bone marrow Monoclonal gammopathy of E-6 Boer Renal undetermined Kidney significance Chromophobe renal cell carcinoma E-4 Basso Lymphoma B-lymphocyte 5.44 Chronic lymphocytic leukemia E-4 Hendrix Ovarian Ovary Ovarian serous adenocarcinoma E-7 Talantov Melanoma Skin Cutaneous melanoma E-7 Dyrskjot Bladder 3 Bladder Superficial bladder cancer E-6 Toruner Head-Neck Squamous cell Oral cavity squamous cell carcinoma Pyeon Multi-cancer Cervix uteri Cervical cancer E-5 Chen Gastric Gastric mucosa Gastric intestinal type adenocarcinoma Kaiser Colon Colon Rectal adenocarcinoma Wallace Prostate Prostate gland Prostate adenocarcinoma Buchholz Pancreas Pancreatic duct Pancreatic ductal adenocarcinoma Chen Liver Liver Hepatocellular carcinoma E-9 TCGA Brain 2 (copy number) Brain (DNA copy number) Glioblastoma E-7 Nature Medicine: doi:1.138/nm.2158

8 Supplementary Table 3 Primer sequences for RT-PCR, qrt-pcr and qpcr analysis; oligo ID numbers and clone locations for shrnas obtained from Open Biosystems; sequences of synthesized sirnas; source of antibodies used; and source and concentration of chemical inhibitors used. Application Gene symbol Forward primer Reverse primer RT-PCR Atf5 5 -CTTCACCCAGCTGAACAATCTT-3 5 -AGAGGAAGGAGAGCTGTGAAGTC-3 Gapdh 5 -ACCACAGTCCATGCCATCAC-3 5 -TCCACCACCCTGTTGCTGTA-3 5 -ATTTGTGCCCATAACCCCTAGA-3 qrt-pcr Atf5 5 - GGGTCATTTTAGCTCTGTGAGAGAA- 3 qpcr/chip RNAi (shrnas) RNAi (sirnas) Creb3l2 5 -GGGCTGGAGTTGGTCATTTTT-3 5 -TGCAAAGTATCCAAACCTGACTGT-3 Frs2 5 -GCCTGCGGGATAGGTTATCTT-3 5 -ACTGCCTGCCGATGACTGA-3 Hprt1 5 - GTCAAGGGCATATCCAACAACAAAC GTTCTTTGCTGACCTGCTGGATTAC- 3 Mcl1 5 -CTGGCTTTTGCGGGTGTT-3 5 -TTGGTGGCTGGAGCTTTAAGA-3 Pak1 5 -CAAATAACGGCGTAGACATCCA-3 5 -TTTAGGGTTCCAGTGTCTTTGCT-3 5 -CCGGGTGCAGTGGCTTAT-3 5 -CTATGTTGCCCAGGCTGGTATT-3 CD GCATTGGCATCTTCTATGGTT-3 5 -CGCCTTGTCCTTGGTAGTGT-3 5 -CCCCCACCGTGGTTCTTT-3 5 -CTGCAGCCTTTCATTTACAATATCC- 3 GFAP 5 -GGCCCGCCACTTGCA-3 5 -CGGTTCTCCTCGCCCTCTAG-3 MCL1 5 -CGGGCAAATCCTCCAAAAG-3 5 -CCCTGAGAGAAGCGTAAGACAAA-3 NES 5 -CAGCGTTGGAACAGAGGTTGG-3 5 -TGGCACAGGTGTCTCAAGGGTAG-3 Atf5 ( ) Atf5 ( ) Mcl1 ( ) Mcl1 ( ) Mcl1 (13-274) 5 -CTTGTTCCCTAGCACTGTGTG-3 5 -AGGTGGGACACACAGAACGAT-3 5 -TAACCCTGGCTGATGGGCGCT-3 5 -TCAGGTCTTTAGGGCTGGGTT-3 5 -CTGGGCTATGCAGAGTTCCAG-3 5 -CCTAGGAGCTCAGAATCTGGT-3 5 -TGTGGTGGTCAGAGGAGATCG-3 5 -CCCGTTTGAGTTCCTGTCCTG-3 5 -GCTGGAATTAAAGGCGTGCCC-3 5 -GCGAGGACTTCCCGTAAAAGG-3 Oligo ID Catalog number V2MM_ RMM FRS2 V2MM_9453 RMM PAK1 V2MM_897 RMM Sequence (sense strand) Atf5 5 -GTCAGCTGCTCTCAGGTAC-3 Creb3l2 Frs2 Pak1 Luciferase 5 -GGAGAAAGATCAAGAATAA-3 5 -GTATAAATGTGGTGGAAGA-3 5 -GCGTAGACATCCAGGACAA-3 5 -TGATCAAATACAAGGGATA-3 5 -GTCGGCGGCTCTGAGGTAC-3 Nature Medicine: doi:1.138/nm.2158

9 Protein Antibody source symbol ChIP Aviva Systems Biology Santa Cruz Biotechnology, Inc. Immunoblot GeneTex, Inc. β-actin Sigma BCL2 Santa Cruz Biotechnology, Inc. BCL2L1/ Cell Signaling Technology BCL-XL BIRC3/ Cell Signaling Technology ciap2 c-casp3 Cell Signaling Technology Aviva Systems Biology ERK Cell Signaling Technology MCL1 Santa Cruz Biotechnology, Inc. p-erk Cell Signaling Technology Tubulin Sigma Immunohisto Abnova Corporation chemistry Aviva Systems Biology ERK Cell Signaling Technology GFAP DakoCytomation MCL1 Santa Cruz Biotechnology, Inc. Inhibitor Concentration Source Chemical CL-387,785 8 µm Calbiochem inhibition FR µm Calbiochem JNK inhibitor 2 µm Calbiochem I LY µm Cayman Chemical manumycin A 2.5 or 5 µm Calbiochem PD µm Calbiochem SB µm Calbiochem sorafenib tosylate 1 or 2 µm Bayer HealthCare Bayer Schering Pharma U126 2 µm Cell Signaling Technology Nature Medicine: doi:1.138/nm.2158