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Kaul 1 Kaul et al _Inventory of Supplemental Materials Supplemental Figures and Figure Legends Figure S1, related to Figure 1 Figure S2, related to Figure 2 Figure S3, related to Figure 3 Figure S4, related to Figure 4 Supplemental Materials and Methods Supplemental Tables Supplemental Table 1. Plasmids. Supplemental Table 2. Antibodies. Supplemental References

Kaul 2 Figure S1. f-braf and BRAF V600 activate mammalian target of rapamycin (mtor) in cerebellar NSCs. (A) Neurospheres generated from the cerebellum are positive for Sox2 (green) and Olig2 (red) expression, but negative for GFAP expression, and (B) can give rise to neurons (Tuj-1 + ), oligodendrocytes (O4 + ) and astrocytes (GFAP + ). Nuclei are counterstained with DAPI. (C) Following f-braf expression, fewer NSCs are required to generate individual neurospheres (limiting dilution assay), and there is increased (D) S6 and (E) S6-Kinase (S6K) phosphorylation. (F) BRAF V600 expression in cerebellar NSCs results in increased MAPK and mtor (phospho-s6) activation, as well as increased NSC proliferation. (G) Rapamycin treatment does not reduce f-braf-induced MAPK activation. pbabe, control virus; Veh, vehicle; Rap, rapamycin. Error bars denote mean ± SD. (*) p<0.01. Scale bars: 100 μm.

Kaul 3 Figure S2. mtor activation in human sporadic PAs. (A) Compared to pbabe-infected (control) NSCs, f-braf-expressing NSCs form 5-fold more colonies in soft agar. (B) Representative images of the injection site (dotted lines) at 2.5 months post-engraftment with mcherry + pbabeor f-braf-expressing NSCs reveal mild increase in cellularity (H&E) and GFAP immunoreactive

Kaul 4 cells. There are 3-fold increases in the numbers of Ki67 + (arrows and inset; C) and Iba1+ cells (arrows and inset; C) in the areas around the BRAF-expressing NSC injection sites. (D) Increased pmapk (arrows and inset; quantification, right) and ps6 (arrows and inset; quantification, right) immunoreactivity are observed in the areas around the BRAF-expressing NSC injection sites. (E) Immunofluorescence co-labeling of mcherry and GFAP shows distinct GFAP+ cell populations in the areas around the f-braf-expressing NSC injection sites, either co-labeling with both markers (yellow) or labeling with GFAP only (area within the dotted box). (F) Neither f-braf nor BRAF V600 expression increase the proliferation of cortical NSCs. While both f-braf and BRAF V600 expression increased MAPK phosphorylation, there are no changes in tuberin or S6 phosphorylation. (G) ps6 and pmapk are coordinately expressed in human sporadic PAs (p<0.0001, Chi-squared test). (H) Five representative f-braf-containing PA cases exhibit increased MAPK phosphorylation, mtor activation (S6 phosphorylation) and GFAP and Sox-2 immunoreactivity. Error bars denote mean ± SD. (**) p<0.005, (*) p< 0.05. Scale bars: 50μm. NS, not significant.

Kaul 5 Figure S3. f-braf expression does not increase astrocyte proliferation. (A) Constitutivelyactivate MEK (camek) and (B) BRAF V600 expression in cerebellar NSCs results in increased tuberin phosphorylation. (C) Cerebellar astrocytes are GFAP +, but Sox- and Olig2-negative. Nuclei are counterstained with DAPI. (D) No increase in cellular senescence (β-galactosidase (β-gal) cytochemistry; left) or apoptosis (TUNEL labeling; right) is observed following BRAF V600

Kaul 6 or f-braf expression in cerebellar astrocytes. Endogenous acidic β-gal activity serves as a positive control. (E) Both BRAF V600 and f-braf expression in forebrain astrocytes induce increased MAPK activation (phosphorylation), but no change in proliferation (thymidine incorporation; CPM). α-tubulin serves as an internal loading control. (F) Astrocyte proliferation following BRAF V600 and f-braf expression is not increased in response to epidermal growth factor (EGF), platelet-derived growth factor (PDGF), or pituitary adenylate cyclase-activating peptide (PACAP) exposure. (G) Increased MAPK phosphorylation induced by BRAF V600 and f- BRAF is reduced following treatment with the MEK inhibitor PD0325901 (PD901; 10nM). (H) camek expression in cerebellar astrocytes increases MAPK activation, with no change in proliferation. (I) Increased polycystin-1 expression is observed in astrocytes relative to NSCs. α- tubulin is included as an internal protein loading control. (J) Polycystin-1 knockdown in wild-type astrocytes, using two different shrna constructs, results in a 75% and 78% reduction in polycystin-1 expression, respectively (right), but does not change tuberin subcellular localization (left). (K) Polycystin-1 KD does not increase proliferation (ELISA-based BrdU incorporation) or tuberin phosphorylation in f-braf-expressing astrocytes. Error bars denote mean ± SD. NS, not significant. Scale bar: 100 μm.

Kaul 7 Figure S4. f-braf regulation of NSC proliferation requires Rheb-mediated mtor/s6k activation and p27 degradation. (A) Rheb overexpression in cerebellar NSCs, following Ad5Cre (Cre) infection, results in increased S6 phosphorylation. Ad5LacZ (LacZ) infection generates wild-type control cells. (B) Rheb overexpression induces increased cerebellar NSC proliferation, as assessed by both direct cell counting and secondary neurosphere diameters. (C) Rheb knockdown using a second shrna construct similarly inhibits S6 phosphorylation and f-brafinduced cerebellar NSC proliferation, as assessed by both secondary neurosphere diameters and direct cell counting. (D) f-braf expression in cerebellar NSCs results in increased p27 phosphorylation and decreased p27 expression, which is attenuated following PD901 (2 nm)

Kaul 8 and rapamycin (0.2 nm Rap) treatment. (E) hs6k1 overexpression in cerebellar NSCs results in increased mtor activation (S6 phosphorylation), increased p27 phosphorylation, and decreased p27 levels. (F) hs6k1 overexpression increases cerebellar NSC proliferation as assessed by direct cell counting and secondary neurosphere diameters. MSCV-GFP was used as control. (G) S6k1 knockdown using a second shrna construct similarly inhibits f-brafinduced S6 and p27 phosphorylation, and restores p27 to wild-type levels. α-tubulin was included as an internal protein loading control. (H) Treatment of f-braf-expressing cerebellar NSCs with the cdk2 inhibitor (PurA) reduces proliferation (cell number) to wild-type levels. Veh, vehicle. Error bars denote mean ± SD. (*) p<0.01, (**) p<0.05.

Kaul 9 Supplemental Materials and Methods Adenovirus and retroviral infections. Ad5-LacZ and Ad5-Cre (University of Iowa Gene Transfer Core, Iowa City, IA) infection was used to generate wild-type and Rheb-overexpressing NSCs, respectively. Control and hs6k1-overexpressing NSCs were generated following infection with MSCV-GFP or MSCV-hS6K1 retrovirus, respectively, as previously described (Uhlmann et al., 2004). Multi-lineage differentiation and limiting dilution assay. NSC differentiation and limiting dilution analyses were performed as previously described (Dasgupta and Gutmann, 2005; Lee et al., 2010) Soft agar colony forming assay. Neural stem cell media was mixed with melted agarose in water (0.6% agar), which was layered into 6 well plates to form the bottom agar. Neurospheres were trypsinized, mixed with soft agarose/neural stem cells media mixture (0.3%) and plated at 20,000 cells per well. The top agar, containing the NSCs was allowed to polymerize and 2 mls of normal NSC growth media was then layered on top of the polymerized agar. Cultures were incubated for 4 weeks and viable colonies visualized by incubating with 5% MTT in PBS for 1hr at 37 o C. Analysis of TMA tumors. Sporadic PAs were analyzed using a previously-generated tissue microarray (TMA;(Tibbetts et al., 2009). Tumors were scored as negative when <25% cells were immunopositive and positive when >50% of the tumor cells were immunopositive. Scored tumor samples were analyzed using the chi-square test of association.

Kaul 10 Senescence assay and TUNEL labeling. The senescence-associated β-galactosidase (SAβgal) assay was performed as previously reported (Debacq-Chainiaux et al., 2009) following fixation in 4% paraformaldehyde. Terminal deoxynucleotidyl transferase mediated dutp nick end labeling (TUNEL) labeling was performed using a fluorescence-based in situ cell death detection kit (Roche Diagnostics). Cell proliferation using BrdU ELISA. Astrocyte proliferation (8000 cells/well in a 96-well plate) was assessed using the BrdU Cell Proliferation ELISA kit (Roche), following the manufacturer s instructions. Briefly, cells were labeled with BrdU for 16 hrs in serum free medium, and proliferating cells identified using a peroxidase-conjugated Anti-BrdU antibody by colorimetric substrate reaction measured at 450nm using a spectrophotometer.

Kaul 11 Supplemental Table 1. Plasmids. Construct KIAA1549-BRAF(16-9)pBABEpuro MEKQ56PpBABEpuro BRAFV600EpBABEpuro mcherryfuw shrhebnm_053075.2, TRCN0000075607 shrhebnm_053075.2, TRCN0000075605 shs6k1 NM_028259.1, TRCN0000022905 shs6k1 NM_028259.1, TRCN0000022904 shpolycystin-1 NM_013630.2, TRCN00000304612 shpolycystin-1 NM_013630.2, TRCN000003046664 plko.1 p5r_iresgfp (MSCV vector) Source Dr. Peter Collins, University of Cambridge Dr. Jason Weber, Washington University Dr. Graeme Hodgson, University of California, San Francisco Dr. Josh Rubin, Washington University Dr. Jason Weber, Washington University

Kaul 12 Supplemental Table 2. Antibodies. Antibody Host Source Dilution BRAF Rabbit Abcam 1:500 Calnexin Rabbit Enzo 1:5000 GFAP (IHC, ICC) Rat Invitrogen 1:200 GFAP (IHC) Mouse Millipore 1:500 Hamartin Mouse Invitrogen 1:1000 Iba1 (IHC) Rabbit Wako 1:1000 Ki67 (IHC) Mouse BD Pharmingen 1:500 MAPK Rabbit Cell Signaling 1:2000 MEK1/2 Rabbit Cell Signaling 1:1000 O4(ICC) Mouse Chemicon 1:1000 Olig2(ICC) Rabbit Gift from Prof. Charles Stiles, 1:10,000 Dana Farber Cancer Institute, Boston, MA p27 Rabbit Cell Signaling 1:2000 p70s6-kinase Rabbit Cell Signaling 1:1000 Rabbit Cell Signaling 1:5000 (WB and IHC) phospho-p27 Thr187 Rabbit Abcam 1:500 phospho-mapk Thr202/Tyr204 phospho-p70s6-kinase Rabbit Cell Signaling 1:1000 phospho-rsk Thr573 Rabbit Cell Signaling 1:1000 phospho-s6 Ser235/236 Rabbit Cell Signaling 1:1000 Rabbit Cell Signaling 1:5000 (WB and IHC) phospho-tuberin Ser939 Rabbit Cell Signaling 1:1000 phospho-s6 Ser240/244 Polycystin-1 Mouse Abcam 1:500 Rheb Rabbit Cell Signaling 1:500 RSK (p90-rsk) Rabbit Cell Signaling 1:1000 S6 Rabbit Cell Signaling 1:2000 Sox2(ICC) Mouse Abcam 1:10,000 Sox2(IHC) Mouse Cell Signaling 1:20 Tuberin Rabbit Cell Signaling 1:1000 Tuj-1(ICC) Mouse Covance 1:1000 α-tubulin Mouse 1:20,000 WB: Western Blot, IHC: Immunohistochemistry, ICC: Immunocytochemistry

Kaul 13 Supplemental References Dasgupta, B., and Gutmann, D. H. (2005). Neurofibromin regulates neural stem cell proliferation, survival, and astroglial differentiation in vitro and in vivo. J Neurosci 25, 5584-5594. Debacq-Chainiaux, F., Erusalimsky, J. D., Campisi, J., and Toussaint, O. (2009). Protocols to detect senescence-associated beta-galactosidase (SA-betagal) activity, a biomarker of senescent cells in culture and in vivo. Nat Protoc 4, 1798-1806. Lee, D. Y., Yeh, T. H., Emnett, R. J., White, C. R., and Gutmann, D. H. (2010). Neurofibromatosis-1 regulates neuroglial progenitor proliferation and glial differentiation in a brain region-specific manner. Genes Dev 24, 2317-2329. Tibbetts, K. M., Emnett, R. J., Gao, F., Perry, A., Gutmann, D. H., and Leonard, J. R. (2009). Histopathologic predictors of pilocytic astrocytoma event-free survival. Acta Neuropathol 117, 657-665. Uhlmann, E. J., Li, W., Scheidenhelm, D. K., Gau, C. L., Tamanoi, F., and Gutmann, D. H. (2004). Loss of tuberous sclerosis complex 1 (Tsc1) expression results in increased Rheb/S6K pathway signaling important for astrocyte cell size regulation. Glia 47, 180-188.

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