SUPPLEMENTARY INFORMATION

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1 DOI:./n BJ RAS:ER Herrnz et l Supplementry Figure HFFF RAS:ER.. mrna Expression..... ILα ILβ IL IL CCL INH VEGF mrna Expression..... ILα ILβ IL IL CCL INH VEGF + OHT Torin NVP-BEZ + OHT shmtor. shmtor. mtor ILα ILα ILβ ILβ IL IL pebp T/T ps S/S pebp T/T ps S/S.. Intensity (.u.).... mrna Expression pebp T/T ps S/S mtor. mtor Intensity (.u.)..... IL IL! IL" Downregulte ftors Upregulte ftors Torin NVP-BEZ Common rugs 7 Common rugs 9 9 shmtor shmtor shmtor shmtor shmtor Supplementry Figure mtor inhiition regultes the SASP.. mtor inhiition regultes the SASP in ifferent firolsts strins. BJ ER:RAS n HFFF ER:RAS ells were generte n inue with OHT to tivte ER:RAS in the presene of nm rpmyin, nm Torin or. nm NVP-BEZ. Seven ys fter OHT inution, RNA ws ollete n qpcrs performe to etet the expression of selete SASP omponents. Dt re men ± s.. from n= inepenent experiments. Stuent s T-test ws performe to ompre the ifferent tretments to the ontrol (R+) with P <.. V, ells expressing n empty ; R, ells infete with plnc-er:ras.,. mtor inhiition () or mtor knokown () ereses phosphoryltion of S (ps S/S ) n eifebp (pebp T/T ) proteins n inhiits the inution of the SASP. Inite immunostinings were performe 7 ys fter OHT inution. Fol hnges of normlise vlues n representtive imges re shown. Error rs represent the ± s.. from n= inepenent experiments. Stuent s T-test ws performe to ompre trete/shmtor ells to the ontrol senesent ells. P <.. Sle r, mm.. Venn igrms representing the overlp n signifine for the SASP omponents ownregulte or upregulte y multiple mtor inhiitors n mtor knokown. The signifine of overlp ws ompute using hypergeometri test. P <.; P <.. For rw t, see Supplementry Tle 7. Mmilln Pulishers Limite. All rights reserve

2 . p INK p CIP Supplementry Figure Intensity (.u.).... V+ R+ R+ R+Torin R+NVP-BEZ Intensity % Positive (.u.) Cells. pink SA-β-Gl % Positive ells CDKNA BrU Intensity (.u.) p INK pink Dy p CIP CDKNA Dy - OHT Torin NVP-BEZ Torin NVP-BEZ OHT) Torin NVP-BEZ OHT CylinD) GAPDH) IMR9 ER:RAS e f Torin OHT 7 9 Torin +OHT, ps S/S, S, pebp T/T, EBP, GAPDH, Intensity (.u.) Intensity (.u.) IL IL! IL" pebp T/T ps S/S V+ R+ R+Torin Supplementry Figure mtor inhiition ontrols the senesene phenotype n ell prolifertion.. mtor inhiition ereses the levels of ell yle inhiitors involve in senesene. p INK n p CIP levels were mesure in the sme experimentl settings s in Supplementry Fig.. Error rs represent the ± s.. from n= inepenent experiments.. mtor knokown results in erese SA--Gl tivity, p INK n p CIP levels ut ells remin rreste. BrU inorportion n senesene mrkers were etermine fter 7 ys of inution with OHT. Dt re men ± s.. from n= (BrU) n n= (SA--Gl, p n p) inepenent experiments. Stuent s T-test ws performe to ompre the shmtor ells with the senesent ontrols (shct+oht). P <.; P <.: n.s, non signifint.. mtor inhiition ereses prolifertion of norml IMR9 humn firolsts n oes not resue OIS rrest. IMR9 ER:RAS ells ( x ) were trete s inite n prolifertion ws ssesse y CV stining fter ys in ulture. Imges re representtive of inepenent experiments.. Cylin D expression levels were ssesse y immunolot. IMR9 ER:RAS ells were left untrete or trete with OHT n the inite rugs for or ys. Dt re representtive of n= inepenent experiments. e-f. These figures re n extension of the experiment presente in Fig. -. Torin inhiition of mtor ownstrem trgets (ps S/S, pebp T/T ) n the SASP ws ssesse y immunolot (e) n IF (f) 7 ys fter OHT inution. Immunolots re representtive of n= inepenent experiments. Error rs represent the ± s.. from n= inepenent experiments. Stuent s T-test ws performe to ompre Torin trete ells to the ontrol. P <.. Unproesse originl sns of lots re shown in Supplementry Fig. 9. For rw t, see Supplementry Tle 7. Mmilln Pulishers Limite. All rights reserve

3 +OHT EBP DN 7 Supplementry Figure EBP p-ebp T/ Intensity (.u.) EBP-DN. EBP pebp T/T mrna Expression Vetor EBP-DN Mok Gy Irrition Gy Irrition IL IL CCL ILβ IMR9 ER:RAS + OHT O.D. O.D. Torin Seimenttion O.D..... S S Mono Polysomes S 7 9 Frtion numer % EEF mrna % EEF mrna.%.% 7 9 Frtions Torin 9.% 7.7% 7 9 Frtions e % mrna in Polysomes InhiinA MMP Torin Torin MMP MMP Torin Torin Supplementry Figure Effet of mtor n EBP on the trnsltion of SASP omponents.. This is n extension of Figure -. Expression of n eifebp phospho-mutnt (EBP DN) results in erese phosphorylte EBP Thr/ levels. (right) Fol hnges of normlise intensity vlues otine from EBP n EBP Thr/ immunostinings Dt re men ± s.. from n= inepenent experiments. (left) Imges from representtive experiment re shown. Dt re men ± s.. from n= inepenent experiments. For ll grphs, stuent s T-test ws performe to ompre ells expressing EBP DN to the ontrol (+ ). P <.. Sle r, mm.. Expression of EBP DN impirs the SASP levels oserve in irrite IMR9 firolsts. RNA ws ollete ys fter irrition ( Gy). Dt re men ± s.. from n= inepenent experiments. Stuent s T-test ws performe to ompre the ells expressing EBP-DN to the ontrol ( irrite). P <.; P <.. Profile of mtor-regulte trnsltion in OIS. Representtive polysome profiles of IMR9 ER:RAS ells (inute for ys with OHT) trete with or nm Torin for h from n= inepenent experiments.. A shemti representtion of the position of frtions ( ), monosomes n polysomes is shown together with representtive profile for EEF mrna ( nonil mtor trget). Dt re representtive of inepenent experiments. e Polysome nlysis of mrnas for SASP omponents. Grphs show the perentge of the inite mrnas in tively trnslting polysomes uring OIS. Error rs represent the ± s.. from n= inepenent experiments. Stuent s T-test ws performe to ompre Torin trete ells to the -trete ontrols. P <.; P <.; P <.; N.S, non signifint. For rw t, see Supplementry Tle 7. Mmilln Pulishers Limite. All rights reserve

4 S U P P L E M E N TA R Y I N F O R M AT I O N Herrnz et l Supplementry Figure + + Control Torin To rin IMR9&ER:RAS& BJs$ER:RAS$ IMR9&ER:RAS& ER:RAS inution (ys) BJ#ER:RAS# ER:RAS inution (ys) Dys% D pmapkapkt& MAPKAPK& MAPKAPK& MAPKAPK& pakts7& pakts7& pakts7& pakts& pakts& pakts& AKT& AKT& AKT& pss/s& pss/s& pss/s& S& S& S& pebpt/t& pebpt/t& pebpt/t& EBP& EBP& EBP& GAPDH&.. Dys mrna Expression D D D D D D Dys MK MK ps ps pebp pebp reltive intensity (.u.). HFFF ER:RAS MK ps pebp D GAPDH& HFFF ER:RAS HFFF ER:RAS. D D D D D D MK ps pebp D Dys D D D shct(-oht) shct(+oht) shmk. shmk... MK ps pebp.. Dys% IL IL ILα ILβ CCL Supplementry Figure MAPKAKP regultes the SASP.. Polysome istriution of MKK mrna. Error rs represent the ± s.. from n= inepenent experiments. Stuent s T-test ws performe to ompre Torin trete ells to the ontrol., non signifint.. Relte to Fig e. Smples were immunolotte with Streptviin-HRP to etet AHA-Biotin ontining proteins. Smples purifie y pull own with streptviin es (Strept. PD) were nlyse. Dt re representtive of inepenent experiments.. MAPKAPK protein levels orrelte with mtor signlling. IMR9 ER:RAS, BJ ER:RAS n HFFF ER:RAS ells were left untrete or trete with OHT for the inite times. (Top) Immunolots were performe with the inite ntioies. Dt re representtive of inepenent experiments. INHBA VEGFC shmk.' pmapkapkt& Reltive intensity (.u.) pmapkapkt& reltive intensity (.u.) Reltive intensity (.u.) reltive intensity (.u.) ZFPL&. ZFPL& GAPDH& ZFPL& HFFF ER:RAS Dys% shmk.' shctrl' HFFF$ER:RAS$ ER:RAS inution (ys) HFFF$ER:RAS$ Reltive intensity (.u.) Co nt ro l % mrna in Polysomes + Streptviin-HRP % mrna in Polysomes - CHX AHA-Biotin MKK Torin Strept. PD MAPKAPK' GAPDH' MK (Bottom) Quntifition of MK, pss/s n pebpt/t lots. Error rs represent the ± s.. from n= inepenent experiments.. MAPKAPK inhiition prevents SASP inution. IMR9 ER:RAS ells were infete with the inite hirpins n further trete with OHT. RNA n protein extrts were ollete t y fter inution. Expression of the SASP n MK were ssesse y qrt-pcr (left) or immunolotting (right). Immunolot imges re representtive of inepenent experiments. Error rs represent the ± s.. from n= inepenent experiments. Stuent s T-test ws performe to ompre ells efiient for MK to ontrol ells (shct + OHT ). P <.; P <.; P <.; N.S, non signifint. Unproesse originl sns of lots re shown in Supplementry Fig. 9. For rw t, see Supplementry Tle 7. Mmilln Pulishers Limite. All rights reserve

5 e g Averge Pek Are ZPL Ative: - Degre ARE mrnas - Unstle protein pzfpl Ser Rp + OHT RAS GV p-mk j S S9 S ZPL S! S9! S! ZFPL FPRRHSVTLPS RDRSFSEGGER LQHSFSFAGFP ZFPL FLRRHSASNLH RDRSFSENGDR LHHSLSFSGFP S7! S! S9! Intive: INACTIVE - Stilize y ining to -- S! S9! S! ZFPL FPRRHSVTLPS ----FSEGGER LQHSFSFAGFP TTP WGSSGPWSLSP PGFAPLAPRLG LRQSISFSGLP S! S! S7! mmttp TGRSTSLVEGR LRQSISFSGLP http PGRSTSLVEGR LRQSISFSGLP >> TTP Mut (SA,S S! S! h Vetor Chrterize+MK+ phosposites+ ZFPL WT MUT TTP Vetor WT MUT ZFPL GAPDH TTP GAPDH i -- ZFPL (long exp.) p-hsp7 S HSP7 GAPDH SASP omponents own in ll onitions NTD BOLA CCL CCL CSF CSF CXCL ERAP GROA OHT!!"! +! +! +! +! ZFPL (short exp.) p-zfpl A A9 A ZPL Mut Constitutively tive - Degre ARE mrnas - Cnnot e intivte y MK - Highly Unstle IL IL IL INHBA NAMPT POSTN TFPI TSP f l Density Herrnz et l Supplementry Figure MK inh. III.... k mtor inh. Up % mrna in Polyosome p u p u. Men ARE Sore ZFPL Control Upregulte ftors ZFPL Mut mtor inh Density Common Down in mtor inh. & ZFPL Mut..... Torin Vetor ZFPL Mut IL IL CCL ILβ IL IL ILα ILβ CCL INHBA Mok Gy Irrition Gy Irrition EV - OHT EV + OHT ZFPL WT ZFPL MUT ZFPL WT ZFPL MUT TTP WT TTP MUT Men ARE Sore Supplementry Figure ZFPL regultes the SASP.. Serine in ZFPL ws ientifie s n mtor inhiition-sensitive phosphosite y phosphoproteomis (n=).. Extension of Fig. Speifiity of MK inhiitor III is prove y the erese in the phosphoryltion of HSP7 (phsp7 S ) ownstrem trget of MK.. Shemti moel of ZFPL tivity n protein stility.. Perentge of ZFPL mrna in trnslting polysomes uring OIS (n=) e. IMR9 ER:RAS ells were infete s inite. Immunostinings were performe 7 ys fter OHT inution. Fol hnges of normlise intensity vlues re shown (n=). f. SASP genes expression ws mesure in IMR9 firolsts ys fter irrition ( Gy) (n=). g. Designe TTP n ZFPL phosphomutnts. Sine MK phosphosites for TTP n ZFPL hve not een esrie, we ligne their sequenes with tht of ZFPL iming to ientify puttive MK phosphosites. In the se of TTP, homology is low. However, the two known MK phosphosites in the murine form of TTP 9 re onserve in the humn form. h-i. IMR9 ER:RAS ells were infete with ZFPL wt/mut, ZFPL wt/mut or TTP wt/mut. OIS ws inue y OHT for 7 ys. (h) Protein levels were nlyse y immunolot in presene of MG ( mm, h). (i) Expression of SASP genes ws mesure y qrt-pcr (n=). j. SASP omponents etete in our proteomis nlysis tht re ownregulte y mtorinhiitors, shmtor n ZFPL Mut. k. Venn igrms representing the overlp etween SASP ftors upregulte y mtor inhiitors, shmtor n ZFPL Mut. l. ARE Sore for SASP ftors: (left) ommonly upregulte y shmtor n mtor inhiitors; (right) ommonly ownregulte y shmtor, mtor inhiitors n ZFPL Mut. Plots enote ARE sore istriution for rnom omintions of n 7 mrnas respetively. Sttistil signifine ws lulte y using: (,e,j n i: Stuent s t-test) (k: hypergeometri test), (l: permuttion tests). P <.; P <.; P <.; n.s, non signifint. Error rs represent mens ± s.. For n h t re representtive of inepenent experiments. n represents numer of inepenent experiments. For unproesse originl sns of lots, see Supplementry Fig. 9. For rw t, see Supplementry Tle 7. Mmilln Pulishers Limite. All rights reserve

6 ARE Sore Rnom Set Enrihment sore FRIDMAN_SENESCENCE_UP NES =-.7 FDR q=. ZFPL Mut vs ER:RAS Enrihment sore SASP_COMPONENTS NES =-.97 FDR q=. ZFPL Mut vs ER:RAS ARE sore FC < FC < FC <. FC < FC <. < < - < -. < - < -. log (mut/ras) 9. Expression +OHT.... h h TIMP h h 7h ng/ml Dox. ng/ml Dox. TRE-ZFPL Mut ng/ml Dox. % Positive ells h h BrU BrU BrU h h 7h 7h nm Dox. nm Dox. nm Dox. e BrU BrU f +'OHT' Vetor' Vetor' p' % Positive ells % Positive ells Vetor Vetor p + OHT Vetor ZFPLMut Vetor' ZFPL Mut' 9%# %# 7%# 7#%# #%# %# SA-β-Gl Supplementry Figure Further hrteriztion of the role of ZFPL in the regultion of the SASP.. GSEAs of signture ssoite with senesen n (left) SASP omponents upregulte in OIS (right) in the gene expression profile (GEP) of IMR9 ER:RAS ells expressing ZFPL Mut versus ontrol IMR9 ER:RAS, oth OHT-trete. NES, normlize enrihment sore; FDR, flse isovery rte. GEPs were otine y performing trnsriptome sequening (RNA-Seq) of the forementione onitions in n= inepenent experiments. RNAs were ollete 7 ys fter inution with OHT.. Men ARE sore of genes own regulte (t the inite log of fol hnges) when ompring IMR9 ER:RAS ells expressing ZFPL Mut versus ontrol IMR9 ER:RAS, re shown in lue. The istriution of men ARE sores erive from simultions of rnom genes with equl smple size re shown in re.. This is n extension of Figure. The expression of TIMP ws monitore y qrt-pcr t the inite times. Dt re for representtive experiment of n= inepenent experiments. Bru inorportion ws mesure y IF t the inite times. Error rs represent the ± s.. from n= inepenent experiments. Stuent s T-test ws performe to ompre ZFPL Mut expressing ells (ng/ml oxyyline) to the ontrol senesent ells (, +OHT). P <..e-f. IMR9 ER:RAS expressing TRE-FLAG-ZFPL Mut (or empty ) n the reverse trnstivtor (rtta-m) were further infete with enoing the oing sequene of p. After ys of inution with OHT, the expression of ZFPL Mut ws inue with ng/ml oxyyline for 7h n (e) the % of BrU positive ells or (f) SA--Gl positive ells ws quntifie. Error rs represent the ± s.. from n= inepenent experiments. SA--Gl stinings re representtive of n= inepenent experiments. Stuent s T-test ws performe to ompre the inite onitions P<.;, non signifint. For rw t, see Supplementry Tle 7. Mmilln Pulishers Limite. All rights reserve

7 Herrnz et l Supplementry Figure 7 EMT inution CM IMR9 ER:RAS -/+ mtorinh. T7D EMT CM: + OHT Torin NVP-BEZ. E-herin Brightfiel IF:E-herin Intensity (.u.)..... Rpm. Torin NVP +OHT 9 SNAIL 9 ZEB SNAIL ZEB SNAIL ZEB SNAIL ZEB +$OHT%.. -OHT Vetor / Vetor Vetor / Vetor Vetor / p +OHT ZFPL Mut / Vetor ZFPL Mut / p E-herin TRE&EV$/$EV$ TRE&EV$/$EV$ TRE&EV$/$CDKNA&CDS$ TRE&ZFPL Mut$ /$EV$ TRE&ZFPL Mut$ /$CDKNA$CDS$ Fol Chnge... IF:$E&CADHERIN$. Supplementry Figure 7 The prrine protumorigeni effets of senesent ells re sensitive to mtor inhiition n ZFPL tivity.. mtor inhiition prevents the EMT inue y the CM of senesent ells. IMR9 ER:RAS ells were trete s inite in the sheme. CM ws ollete 7 ys fter OHT inution (mtor inhiitors were remove from the mei t y, see methos for etils) n T7D ells ulture in tht CM. h fter, E-Cherin expression ws monitore y IF. Fol hnges of normlise intensity vlues (top) n representtive pitures re shown (ottom). Dt re men ± s.. from n= inepenent experiments. Stuent s T-test ws performe to ompre trete ells to the ontrol. P <.. Sle r, mm.. Both inhiition of mtor signlling n expression of ZFPL Mut prevent the upregultion of EMT-speifi trnsription ftors y the CM of senesent ells. IMR9 ER:RAS ells were trete s inite in the sheme in (). CM ws ollete fter 7 ys. T7D ells were ulture in tht CM for the inite times n proesse for RNA extrtion. Snil n Ze levels were mesure y qrt-pcr. In the se of the CM of IMR9 ER:RAS trete with mtor inhiitors, t re men ± s.. from n= inepenent experiments. For the rest of the experiments t re from representtive experiment of n= inepenent experiments.. CM of oth proliferting n rreste ZFPL Mut expressing ells is unle to trigger omplete EMT. The inite ells were trete with OHT for 9 ys. Expression of TRE-ZFPL Mut ws tivte for the lst 7h. CM ws then ollete n T7D ells were ulture in tht CM for h. E-Cherin expression ws monitore y IF. Fol hnges of normlise intensity vlues (right) n representtive pitures re shown (left). Dt re men ± s.. from n= inepenent experiments.. Stuent s T-test ws performe to ompre ZFPL Mut ells to the ontrol (Vetor/ Vetor). P <.. Sle r, mm. For rw t, see Supplementry Tle Mmilln Pulishers Limite. All rights reserve

8 % % Positive positive ells mrna reltive expression (fol) IMR9 ER:RAS CM -/+ TRE-ZFPL Mut (-/+ CDKNA CDS)..... P=. Prrine senesene BrU IL IL P=. P=.9 IMR9 P=.9 -OHT +OHT Senesene Vetor / Vetor Vetor / Vetor Vetor / p ZFPL Mut / Vetor ZFPL Mut / p Herrnz et l Supplementry Figure Prrine senesene Co-ulture & IMR9 BrU IMR9 ER:RAS +/- shmtor + IMR9 & Conitione IMR9 ER:RAS: mei -OHT +OHT shmtor. shmtor. MAPKAPK& pebp T/T& EBP& GAPDH& e. tretment MCP RANTES CXCL CTACK NRsGV - 9 Nrs Nrs+ ells NRs g NRs GV NRs tretment p Cip Nrs+ ells p+ ells p+ ells Nrs NRs% p Cip p Ink p Ink f. mrna Reltive expression (fol)... P=. P=. P=. P=.. CD B CD KlrD Supplementry Figure mtor inhiition lunts the tumour suppressive effets of the SASP.. CMs of IMR9 ER:RAS expressing TRE- ZFPL Mut (or empty ) n p (or empty ) were ollete 7h fter inution of ZFPL Mut n 9 ys fter OHT ition. The effet CMs h on BrU inorportion n SASP inution in IMR9 wt ells ws evlute y IF. Grphs show t from n= inepenent experiments. IMR9 wt ells were o-ulture with the inite IMR9 ER:RAS ells with or without OHT. BrU inorportion ws monitore y IF. Dt re representtive of n= inepenent experiments.. This figure is relte to Fig.. Expression of the inite trnsripts ws quntifie y qrt-pcr., n= mie;, n= mie. P vlues re inlue.. Expression of MAPKAPK, EBP n phosphoryltion of EBP were nlyse y immunolot. Quntifition is presente in Fig. e. Nrs GV trnsposons were oelivere into mouse livers through hyroynmi injetion (Dy ). Mie were srifie ys lter n Nrs+ ells were ounte (n= mie per onition) Mie were trete with rrier or rugs from ys prior Nrs GV injetion. Representtive imges of the setions quntifie re shown (x). Sle r, mm. f. Quntifition of the expression of immune ell mrkers y qrt- PCR in livers of the inite mie ys fter NrsGV injetion., n= mie; rpmyin, n = mie. CD, T ell mrker; B, B ell mrker; CD, mrophge mrker; KlrD, NK ell mrker. P vlues re inlue. g. Nrs GV trnsposons were o-elivere into mie s expline efore. Mie were srifie ys lter. Mie were only trete with rrier or rpmyin ys post-injetion Nrs+ (left), p Cip + (entre) n p Ink + (right) ells on liver setions were ounte (n= mie per onition). Representtive imges of setions quntifie in the top pnel re shown in the ottom. Sle r, mm. Sttistil signifine ws lulte using Stuent s t-test, P <.; P <.; P <.; n.s, non signifint. Error rs represent mens ± s.. For unproesse originl sns of lots, see Supplementry Fig. 9. For rw t, see Supplementry Tle 7. Mmilln Pulishers Limite. All rights reserve

9 S U P P L E M E N TA R Y I N F O R M AT I O N Full sns of immunolots use in figures (I) Fig. / Fig. e GAPDH HSP7 S Fig./S EBP Fig. f Fig. Fig. i GAPDH HSP7 Supplementry Figure 9 Full sns of immunolots use in figures. 9 Mmilln Pulishers Limite. All rights reserve

10 S U P P L E M E N TA R Y I N F O R M AT I O N Full sns of immunolots use in figures (II) Fig. S Fig. Fig. S (IMR9) Fig. Se Fig. S (BJ) Supplementry Figure 9 ontinue Mmilln Pulishers Limite. All rights reserve

11 S U P P L E M E N TA R Y I N F O R M AT I O N Full sns of immunolots use in figures (III) Fig. S (HFFF) Fig. S pakts7 MK Fig. Fig. e Fig. Sg Supplementry Figure 9 ontinue Mmilln Pulishers Limite. All rights reserve

12 Supplementry Tles Legens Tle S Effet of the hemil ompouns in the levels of key SASP omponents. Tle S Seretome proteomis t for mtor inhiitors (normlise vlues). Tle S Phosphoproteomi t. Tle S Chemil ompouns use in the rug sreen. Tle S Primers, Tqmn proes n RNAi sequenes use in this stuy. Tle S Antioies use in this stuy. Tle S7 Rw t. Mmilln Pulishers Limite. All rights reserve

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