Supplementary Data

Cyclophilin B Supports Myc and Mutant p53 Dependent Survival of Glioblastoma Multiforme Cells

Jae Won Choi, Mark A. Schroeder, Jann N. Sarkaria, and Richard J. Bram

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Figure S1. Pharmacological inhibition of Cyclophilin B reduces glioblastoma cell survival, Related to Figure 1 (A) Increased expression of CypB in individual biopsy samples (in blue) from patients with glioblastoma multiforme, compared to normal brain tissue (faint blue) (from www.Oncomine.org). (B) Mean expression of the Cyclophilin B (PPIB) in tumor and normal human brain samples, as indicated (from http://rembrandt.nci.nih.gov). Note that the lowest level of expression was found in the non-tumor samples. Both probes are specific for the Cyclophilin B transcript, and provide independent analyses of its expression. (C) Increased CypB expression in primary human GBM cells. (D) CsA dimer and compound 41 did not block PMA and ionomycin induced NFAT activation in Jurkat cells. (E) Morphology of U251 cells treated for 24 hours with compound 41. Bar = 200μm. (F-H) Cyclophilin inhibitors decreased the survival of T98G cells (E), Daoy (F) and D341 medulloblastoma cells (G), as measured by AlamarBlue.

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Figure S2. Inhibition of MAPK pathway prevents CypB knockdown-induced senescence (A-B) MEK inhibitor blocked cellular senescence in CypB-depleted U87 cells. Control or CypB knockdown U87 GBM cells were treated with MEK inhibitor (U0126). Cellular senescence was measured by SA beta-gal staining (A) and percentages of positive staining were quantified (B). (C) Treatment with MEK inhibitor suppressed Erk activation. Phospho-Erk levels were examined by westernblot. All errorbars show ± SD. ＊p<0.05.

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Figure S3. Cyclophilin B controls p53 expression. (A) CypB silencing in MCF7 cells ablated (wild type) p53 induction after treatment with DNA damaging drugs. (B) Reduced p21 induction following DNA damage (Etoposide) in CypB-depleted MCF7 cells. (C) Mutant p53 silencing reduced cell viability in U251 GBM cells. Bar = 50 μM. (D) Similar cell morphology in shCypB and shMYC U251 GBM cells. Large and flat morphology and binuclear cells were indicated with red arrow. Blue arrows indicate dying cells which have spindle shape morphology. Bar = 200 μm. All errorbars show ± SD. ＊p<0.05.

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Figure S4. Cyclosporine dimer treatment has a synergistic effect with ER stress- induced cell death. (A-B) A combination index for response to CsA-dimer combined with the ER stress inducer, Tg was calculated by using the Chou-Talalay method (www.compusyn.com). Treatment of cells with CsA-dimer and Tg showed a clear synergistic effect in the normalized isobologram (A) and Fa – CI plots (B). Combined treatment of CsA dimer with Tm also showed synergistic effects when applied to U251 and T98G GBM cells (data not shown).

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Figure S5. Several survival signals including JAK2, CHK1, mutant p53 are suppressed by CypB knockdown. (A) CypB depletion with additional knockdown constructs confirmed the major changes in cell signaling events reported in this study. U251 GBM cells were transduced with control or shCypB lentivirus, harvested and analyzed by western blotting with the indicated antibodies. (B) CypB silencing increased PERK expression and reduced p- Stat3 levels.

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Figure S6. Worse outcome in astrocytoma patients having higher CypB expression, Related to Figure 7. Kaplan-Meier curves showing that overall survival of patients with astrocytoma having higher PPIB (> 2.0; 38 cases) was significantly lower than those with a gene expression of 2.0 or below (67 cases). From http://rembrandt.nci.nih.gov.

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Figure S7. Better outcome in patients with tumors carrying deletions of PPIB, Related to Figure 7. Survival of patients with brain tumors, stratified into those with amplification of the gene for CypB (red) vs. those with deletion of the gene (green). Source: http://rembrandt.nci.nih.gov.

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Figure S8. Model for the proposed mechanism of cyclophilin B targeting in glioblastoma multiforme therapy

9 Table S1. Up-regulated in CypB depleted U251 GBM cells (>3 fold), Related to Figure 3

Gene symbol Fold Change p-value IL11 22.78 1.55E-06 SCG2 5.50 5.98E-06 GDF15 5.36 8.88E-06 SERPINE1 5.00 3.59E-05 NRP2 4.82 2.36E-05 DNAJC12 4.37 2.16E-06 SNORA62 4.11 0.000248345 SLC2A3 4.11 9.20E-06 BIK 4.06 9.09E-06 CPA4 4.04 6.81E-05 PGM2L1 4.02 9.07E-05 CLDN1 3.97 8.62E-05 LHB 3.97 5.64E-05 DUSP5 3.77 5.65E-06 IL8 3.75 0.00248549 CGB5 3.74 0.000254331 HBEGF 3.72 4.70E-06 SEL1L3 3.69 2.81E-05 ADM 3.56 1.62E-06 SCARNA13 3.53 3.70E-06 DCBLD2 3.50 1.18E-05 ASGR1 3.49 1.86E-06 CGB1 3.45 0.00010396 SNORA12 3.36 6.69E-05 PLAU 3.33 7.52E-06 SLC35D2 3.28 5.09E-05 PTHLH 3.19 1.69E-07 SNORA63 3.19 4.92E-05 STX1A 3.16 9.90E-05 DNM3 3.15 4.64E-05 SCARNA18 3.13 8.85E-06 TGFBR2 3.12 4.95E-06 HS.19193 3.07 0.000135658 SPRY2 3.06 8.84E-07 TSPAN6 3.00 5.50E-05

10 Table S2. Down-regulated genes in CypB depleted U251 GBM cells (>3 fold), Related to Figure 3

Gene symbol Fold Change p-value SERPINA3 -7.16 3.49E-06 TMEM85 -5.16 1.19E-05 HRCT1 -4.32 8.47E-06 FADS1 -4.17 4.60E-05 PI15 -4.02 2.81E-05 SLC7A5 -3.98 1.00E-06 KCTD12 -3.91 1.01E-05 FAM120AOS -3.55 9.50E-07 TMEM141 -3.50 6.57E-05 RNASEH2A -3.50 8.93E-06 NME4 -3.49 1.35E-05 BGN -3.44 5.60E-06 UCP2 -3.42 2.75E-05 RRBP1 -3.31 4.68E-05 C10ORF10 -3.28 2.30E-05 BCKDK -3.26 3.22E-06 C17ORF61 -3.25 4.46E-06 C10ORF81 -3.25 2.26E-05 EBNA1BP2 -3.23 3.04E-05 SPC24 -3.12 9.83E-06 HLA-A29.1 -3.11 2.31E-05 GLTP -3.07 1.50E-05 CLNS1A -3.05 4.28E-05 CRYAB -3.05 5.80E-05 GFAP -3.03 8.30E-05 COPS6 -3.02 4.68E-07 AURKB -3.01 2.13E-06 HCP5 -3.00 1.13E-05

11 Supplementary Material and Methods

shRNA-mediated silencing sequences

TRC 1.5 library,

Non-target control shRNA (5’-CAACAAGATGAAGAGCACCAA-3’),

CypB shRNA #48 (5’-TTCACCAGGGGAGATGGCACA-3’),

CypB shRNA #49 (5’-GTTCTTCATCACGACAGTCAA-3’),

STAT3 shRNA (5’-GCTGACCAACAATCCCAAGAA-3’),

MYC shRNA #1 (5’-CCTGAGACAGATCAGCAACAA-3’),

MYC shRNA #4 (5’-CAGTTGAAACACAAACTTGAA-3’), p53 shRNA #20 (5’-GTCCAGATGAAGCTCCCAGAA-3’), and p53 shRNA #33 (5’-CACCATCCACTACAACTACAT-3’) were used in this work.

TRC 2 library,

Non-target control shRNA (5’-CAACAAGATGAAGAGCACCAA-3’),

CypB shRNA #5 (5’-AGTCACCGTCAAGGTGTATTT-3’),

CypB shRNA #6 (5’-CCTACGAATTGGAGATGAAGA-3’),

CypB shRNA #7 (5’-CCGGGTGATCTTTGGTCTCTT-3’),

CypB shRNA #8 (5’-GCCTTAGCTACAGGAGAGAAA-3’), and

CypB shRNA #9 (5’-GTTCTTCATCACGACAGTCAA-3’) were used in this work.

Westernblot analysis antibody sources

Membranes (Millipore) were probed with the following antibodies: cyclophilin B (Affinity

BioReagents, PAI-027), beta- (Sigma), p21(Santa Cruz, C-19), c-Myc (Santa Cruz,

9E10), phospho-Stat3 (Upstate), Stat3 (Cell Signaling), Jak2 (Cell Signaling), PERK

(Cell signaling, D11A8), p53 (BD), (Sigma), p-Erk (Cell Signaling), H-ras (Santa

Cruz, C-20), p27 (BD), BiP (Calbochem), CHOP (Santa Cruz, R-20), Chk1 (Santa Cruz,

12 G-4), SERPIN A1 (R&D), SERPIN E1 (R&D) and Skp2 (Santa Cruz, H-435). Reactive bands were visualized with a secondary antibody conjugated with HRP (Zymed) and chemiluminescence (Thermo Scientific).

Catalog numbers of quantitative real-time PCR primers

Accession number of each TaqMAN® Gene Expression Assays (Applied Biosystems) is described: ACTIN (4333762F), CHK1 (Hs00967506_m1), GAPDH (4326317E), IL-11

(Hs00174148_m1*), JAK2 (Hs00234567_m1), c-Myc (Hs99999003_m1), p53

(Hs01034249_m1), and UCP2 (Hs01075227_m1).

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