SUPPLEMENTARY INFORMATION

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1 SUPPLEMENTARY INFORMATION DOI:./n Supplementry Figure Stroml ell senesene in mie with mesenhyml (RBP-Jk) eletion. () Skin o neworn (P) mouse with eletion o the (RBP-Jk) gene (KO), ierent rom the one shown in Fig., ws nlyze or SA-β-Gl tivity in prllel with immunoluoresene with nti-vimentin ntioies or irolst ientiition. () Two itionl skin lesions o months ol mutnt mie (mle), esies tht in Fig., were nlyze y oule immunoluoresene with ntioies ginst kertin (K) n Tensin C (upper pnels) n, in prllel setions, or SA-β-Gl tivity n nti-vimentin immunoluoresene (lower pnels). () Prllel setions o the skin lesions nlyze ove were stine with ntioies ginst vimentin F/ n phospho-histone (ph). Quntiition o prolierting (phospho-histone positive) irolsts (vimentin positive n F/ negtive) is shown in Fig.. Mmilln Pulishers Limite. All rights reserve

2 % SA-Gl pos. ells Signl / ell no o olonies No olonies / ish No olonies / ish % BrU positive ells Rel. Fluoresene Unit SUPPLEMENTARY INFORMATION h si# si# sh# sh# sh# IL μm sh# γ-tu strin # IL SERPINE DAPI/p e DR sh# sh# sh# sh# SERPINE DAPI/IL strin # p IL sh# sh# strin # si# si# IL IL PTGS TNC ACTA strin # i j sh# sh# g sh# sh# sh# sh# sh# sh# 9 ys HOF HBF HLF si# si# si# si# IL strin # IL SERPINE HKC HES HERP CDKNA MKI7 IL IL sh# sh# sh# sh# strin # si# si# IL SERPINE WI sh# sh# MMP MMP ACTA Supplementry Figure s negtive regultor o erml irolst senesene- n CAF-eterminnt genes. () s inete with two shrna lentiviruses ginst were nlyze, ys lter, or expression y immunolotting. Densitometri quntiition showe reution o to % n % o ontrol. Unproesse originl sns o lots re shown in Supplementry Fig. 9. () SA-ß gl n lonogeniity ssys o oreskin-erive s (strin #) plus/minus silening s shown in Fig., g or strin # ult-erive s; or SA--Gl tivity n=9 (), (sh), 7 (sh) ells ssesse rom, 9 n iels, respetively; men +/- s.., two-tile unpire t-test, p<.. () Clonogeniity ssys o nother ult-erive strin ( ) plus/minus silening; n= iologil replites/onition, two-tile unpire t-test, p<.. () s plus/minus silening were teste y -romo-`-eoxyuriine (BrU) inorportion ssy; n= (), 97 (sh), (sh) ells ssesse rom iels, men +/- s.., two-sie one smple t-test, p<.. (e) Cells s in () were teste or Almr lue luoresene ell ensity ssys; t re presente s luoresene intensity hnge over y. ( n g) Two strins ( n ) plus/minus silening y shrnas () n sirnas (g) exmine or senesene-eterminnt genes in Fig. h,i were nlyze y RT-qPCR or inite CAF mrker genes. (h) Immunoluoresene nlysis o s plus/minus silening y sirnas or p WAF/Cip n IL, with DAPI stining or ell ientiition. Shown re representtive imges n quntiition o luoresene signl intensity y Imge J sotwre nlysis. For p n= (), 9 (si), (si) ells, or n IL n= (), 9 (si), 97 (si) ells ssesse rom iels. Whisker oxes: min to mx, mein enter; two-tile unpire t-test, p<.. (i) Erly pssge orl (HOF), rest (HBF), lung (HLF) irolsts n WI iploi lung irolst line plus/minus shrna-meite silening s in Fig. k,l were teste y lonogeniity ssys; or WI n= iologil replites/onition, men +/- s.., two-tile unpire t-test, p<.. (j) Primry humn kertinoytes plus/minus sirna-meite silening were nlyze, ys ter trnsetion, y RT-qPCR or inite genes. Mmilln Pulishers Limite. All rights reserve

3 Rel. hromtin ining % SA-Gl pos. ells Rel. hromtin ining No olonies / ish Rel. hromtin ining Rel. hromtin ining SUPPLEMENTARY INFORMATION neo rnert CDKNB CDKNA CDKNA ACTA A HM CDKNA pind-n - ox pind-n + ox pind pind-n e HOF strin Ctrl Jgge neo rnert CDKNB CDKNA CDKNA CDKNB CDKNA CDKNA DR ACTA strin strin A CS mir- A HM CDKNA mir- IL CDKNB pind + ox pind-n + ox CDKNA CDKNA DR strin Ctrl Jgge CDKNB CDKNA CDKNA DR ACTA ACTA 9 g site site site site site site HKm HK7A MMP A CS A HM hr: HKm HK7A FOSL A CS A HM hr: 9-7 Supplementry Figure Inution o irolst senesene n CAF mrkergene expression y inrese Noth tivity, n suppressive untion o. () s inete with retrovirus expressing the ytoplsmi tivte orm o Noth use to n ER omin (rnert) in prllel with empty vetor ontrol (neo) were trete with -hyroxy-tmoxien or hours to inue tivtion o the rnert protein, ollowe y etermintion o SA-ß Gl tivity; n= 7 (Neo) n (NERT) ells ssesse rom iels, men +/- s.., two-tile unpire t-test, p<.. () s inete with lentivirus or oxyyline-inuile expression o the ytoplsmi tivte orm o Noth (pind-n) in prllel with empty vetor ontrol (pind) were trete with oxyylin or ys, ollowe y lonogeniity ssy; n= iologil replites/onition, men +/- s.., two-tile unpire t-test, p<.. () s s in the previous two pnels were nlyze or expression o the inite genes y RT-qPCR. () Humn Orl Firolsts (HOF) stly inete with lentivirus or oxyylin-inuile expression o ytoplsmi Noth (pind-n), were trete or hours with oxyyline (+ox) or not (-ox) n nlyze or expression o inite genes y RT-qPCR. (e) Two strins ( n ) o inepenent origin were ulture or hours on ishes pre-ote with immunogloulin-ouple Jgge lign or immunogloulins lone (Ctrl), ollowe y RT-qPCR nlysis o the inite genes. () s o two ierent strins ( n ), esies the one showe in Figure ( ), were use or Chromtin Immuno-preipittion (Ch) ssys with two ierent ntioies ginst in prllel with non-immune ontrols, to ssess ining to the inite preite ining sites within eh o the genes. (g) Grphi illustrtion o the position o ining peks revele y Ch-seq nlysis with two ierent ntioies ginst (re n lue olors) or the inite genes, utilizing ENCODE inormtion or promoter n enhner loliztion, s inite y islns o Histone H moiitions (Km n K7A, respetively), long with the respetive position o Trnsription Strt Site (rrow) n oing exons (lk oxes). Mmilln Pulishers Limite. All rights reserve

4 F- NORM F- NORM F- NORM F- NORM SUPPLEMENTARY INFORMATION ining inity K = ±. nm nti- AB ining inity K =.7 ±. nm onentrtion [nm] nti- AB onentrtion [nm] BSA ining inity K = ± nm nti- AB ining inity K =. ±.9 nm BSA onentrtion [nm] nti- AB onentrtion [nm] Exp. Exp. p p p p h.. h.. Supplementry Figure Physil ining o the n proteins n isruption o -p ssoition. ( n ) s were immuno-preipitte with ntioies ginst () or () in prllel with non immune, s in Figure, ollowe y immuno-lotting with ntioies ginst the n proteins s inite. () Seon inepenent MST nlysis o puriie reominnt n proteins inute with eh other s in Figure e. Aitionlly, s positive ontrol o high ining inity, eh o the puriie reominnt n proteins ws lele with RED-NHS n mixe t onstnt onentrtion (9 nm or, nm or ) with two-ol seril ilutions o the orresponing speii ntioies (rom 9 mm to. nm), ollowe y MST nlysis. As negtive ontrol o speiiity, puriie reominnt ws mixe with two-ol seril ilutions o ovine serum lumin (rom 9 mm to. nm), ollowe y MST nlysis. Results re expresse s normlize thermophoresis-epenent luoresene units (F-Norm) s untion o unlele lign onentrtions s in Fig. e. () Two inepenent experiments, esies wht shown in Fig. i, with 9T ells o-trnsete with plus/minus expressing plsmis ( μg o eh in m ishes) ollowe, hours lter, y immuno-preipittion o p n immuno-lotting with ntioies ginst p n. For (-) n () unproesse originl sns o lots re shown in Supplementry Fig Mmilln Pulishers Limite. All rights reserve

5 % o ells rtio (lesione / norml) signl (AU) SUPPLEMENTARY INFORMATION iel iel e CD Vimentin DAPI Vimentin+ CD- Vimentin+ CD+ j Beore IR n UV Cutting Phse ontrst PDGFR AK# μm μm P AK# μm iel iel # # μm μm P P P P P Selet Ares or IR n UV PDGFR PI μm. vimentin. PDGFRα CD CD In situ SCCs μm μm # #.... Ater IR n UV Cutting Phse ontrst PDGFR μm SCCs μm μm # # g LPS + % + % + % LPS + % LPS. + LPS + % + % + % LPS + % LPS. vimentin. PDGFRα.. + LPS + % + % + % LPS + % LPS CD HUVEC + % HUVEC + % HUVEC. CD.. Cpture ells on the p Phse ontrst PDGFR μm mm mm. MDF MDF + % MDF + % eno + % eno + % eno. MDF MDF + % MDF + % eno + % eno + % eno MDF MDF + % MDF + %. MDF eno MDF + % eno MDF + % eno μm Vimentin CD h. CD p=.. CD p=.7. CD p=. i. CD p=. k p=. Vimentin Vimentin In situ SCC# μm..... NS AK..... NS SCC... NS SCC mthe... lesion #A # # # #B #A #B NS SCC NS CD Vimentin NS SCC CD Vimentin μm SCC Supplementry Figure Anlysis o stroml ell senesene n gene expression in AKs, in situ n invsive skin SCCs. (-) SA--Gl stining o two itionl AKs (), our in situ SCCs () n two invsive SCCs () esies those shown in Fig.. () Lrger iels n higher mgniition imges o in situ SCC (Fig. ) immune-luoresene or vimentin n CD mrophge mrker. CD positive ells were only eeply lolize. (e) AKs o Fig. (Ptients -) were nlyze y IF or vimentin n CD. Representtive imge (P lesion) n quntiition o vimentin-positive ells CD-positive/negtive; n(ells)=, 7,, 9, (P-P) ssesse rom (P-P), (P, P) n (P) iels. () RNA smples rom r pssge s, humn THP monoytes ter TPA-inue mrophge ierentition (MF) plus/minus LPS-triggere tivtion, n HUVEC enothelil ells, were nlyze iniviully n mixe in inite mounts y RT-qPCR. (g) RNA smples rom n pssge mouse erml irolsts, primry mouse mrophges (MF) n enothelil ells (eno) were nlyze iniviully n mixe in inite mounts y RT-qPCR. (h n i) Sme LCM/RNA smples o Fig. n e-g were exmine y RTqPCR or leukoyte/mrophge CD mrker. (h) n= AKs n mthe NS regions, men+/-s.e.m., two-tile pire t-test; n= SCC n NS regions rom ierent iniviuls, men+/-s.e.m., two-tile unpire t-test; n= SCC regions (two per SCC) n mthe NS, men+/-s.e.m., two-tile pire t-test; (i) n= ete n unete regions, rtio (ete/unete), two-sie one smple t-test. No signl ws otine or enothelil CD mrker. (j) Representtive imges o in situ SCCs n norml skin setions proesse or luoresene-guie LCM utilizing nti- PDGR-FITC-onjugte ntioies n Propiium ioie (PI) stining or nulei ientiition. Shown re stine setions, selete ells prior to LCM (y InrRe n UV utting), orresponing empty spes n pture mteril on LCM p. (k) Quntiition o immunoluoresene signl in vimentin-positive n CD-negtive ells in strom unerlying three skin SCCs versus norml skin rom ierent iniviuls n representtive imges o triple immuno-luoresene nlysis; n(vimentin-positive/cd- negtive ells)=7, 7, (NS) n 7,, 7 (AK), men o signl intensity +/-s.e.m., two tile unpire t-test. Mmilln Pulishers Limite. All rights reserve

6 No olonies / ish SUPPLEMENTARY INFORMATION. strin.... PDGF-BB CTGF SHH HGF FGF tivin PF IL ILB TGFB IL IL CCL SDFα nm nm nm μm μm μm CDKNA Pontini mir 7 nm nm nm μm μm μm Pontini Imtini Pontini Imtini Pontini Imtini 7 nm nm nm μm μm μm β tin β tin nm nm nm Imtini μm μm μm % SA-Gl pos. ells Pontini Imtini μm e Pontini Imtini Pontini Imtini Pontini Imtini Pontini Imtini μm % SA-Gl pos. ells nm nm um Supplementry Figure Impt o vrious growth tors n TK inhiitors on irolst gene expression n tivity. () s o inepenent origin rom those teste in Fig. were similrly trete with the inite growth tors / ytokines (t the onentrtions speiie in online methos) ollowe, 7 hours lter, y RT-qPCR nlysis o expression. ( n ) s o ierent strin rom tht teste in Fig. were similrly trete with the Pontini or Imtini inhiitors t the inite onentrtions ollowe, 7 hours lter, y RT-qPCR nlysis o, CDKNA n mir expression () or immunolotting (). Unproesse originl sns o lots re shown in Supplementry Fig. 9. () s ulture in the presene or sene o Pontini ( nm) or Imtini (mm) or 7 ys were ssye or SA-ß-gl tivity or lonogeniity in triplite ishes. For SA-ß-gl n=77 (), (Pontini), (Imtini) ells ssesse rom iels; or lonogeniity ssy n= iologil replites/onition, men +/- s... Shown re representtive imges o ells ter SA-ß-gl stining s well s quntiition o the t (let n right pnels, respetively). (e) Similr CAF ultures s in Fig.,g (strin #) were ulture in the presene or sene o Pontini or Imtini ollowe y ssy or SA-ß-gl tivity; n= (), (Pontini nm), 7 (Pontini nm), (Imtini) ells ssesse rom,, 7 n iels, respetively. Shown is men +/- s.. Mmilln Pulishers Limite. All rights reserve

7 SUPPLEMENTARY INFORMATION WT CRISPR β-tin Rel. mrna levels.. WT CRISPR.. CDKNA mir- MDM % SA-Gl pos. ells sh# sh# No olonies / ish sh# sh# PTGS.. 9. Rel. mrna levels sh sh. sh sh sh sh# sh# e % SA-Gl pos. ells si# si# si# si# PTGS No olonies / ish Rel. mrna levels shp sip sip sip Supplementry Figure 7 Arogtion o senesene with enhnement o CAF mrker expression y onomitnt n silening or gene isruption. () Erly pssge s were inete with CRISPR lentivirus ginst, ollowe y seletion or the virlly-trnsue ntiioti resistne gene (puromyin). Resulting olonies (>) were poole n nlyze (CRISPR), in prllel with prentl ontrol ells (WT), or protein levels y immuno-lotting, n or expression o trget genes (p WAF/Cip, mir-, MDM) y RT-qPCR (let n right pnels, respetively). Similr results were otine with two other strin o s o inepenent origin. Unproesse originl sns o lots re shown in Supplementry Fig. 9. () s ( seon strin esies tht teste in Figure 7) were inete with ontrol versus silening retroviruses, ollowe y inetion with ontrol versus silening lentiviruses. Numer o ells positive or SA-ß-Gl tivity ws etermine week lter (let pnel); rom let to right n (ells)=,,,,, ssesse rom,,,, 9 n iels, respetively. The sme ells were lso plte uner sprse onitions, ollowe y etermintion o olony ormtion ys lter (right pnel); n= iologil replites/onition. () Prllel ultures o ells s in the previous pnel were nlyze y RT-qPCR or expression o the inite genes. () s were inete with ontrol versus CDKNA silening retroviruses, ollowe y inetion with either ontrol or silening lentiviruses n testing y lonogeniity ssys s in other experiments; n= iologil replites/onition. (e) s were trnsete with sirnas ginst with or without sirnas or CDKNA, ollowe, ys lter, y repete trnsetion. SA-ß-Gl tivity ws ssesse t y seven; rom let to right, n(ells) =,,,,, ssesse rom,,,,, n 9 iels, respetively. () Prllel ultures o ells s in the previous pnel were nlyze y RT-qPCR or expression o the inite genes, with or normliztion. For () n (-e) men +/- s.., two-tile unpire t-test is shown; p< Mmilln Pulishers Limite. All rights reserve

8 SUPPLEMENTARY INFORMATION Supplementry Figure Tumor n stroml ell expnsion s untion o n stroml expression. () DsRe expressing SCC ells were mixe with GFP expressing s with shrna-meite silening o or iniviully or in omintion, ollowe y prllel injetions into mouse ers n imging every - ys uner luoresene issetion mirosope s in Figure. Shown re imges rom nother pir o mouse er injetions o SCC ells mixe with s with omine n silening versus silening lone, t the inite times ter injetion. () Immunohistohemil nlysis o the inite mrkers in lesions rom nother pir o mouse er injetions, esies tht shown in Figure, o SCC ells mixe with s with omine silening o n versus lone. () Let Pnel: He/Nek Cl7 SCC ells expressing DsRe were mixe with PKH7-green lele s with silene iniviully or in omintion with, ollowe y prllel injetions into mouse ers n imging every - ys uner luoresene issetion mirosope. Shown re representtive imges rom one pir o mouse ers t the eginning n en o the experiment ( ys ter injetion). Right pnel: Quntiition o igitl imges or re (SCC ells) luoresene intensity vlues (intensity x sure re) or the two omintion o ells throughout the experiment with NOD/SCID Ilrg-/- -weeks-ol mle mie/er pirs per onition. To tke into ount iniviul niml vritions, or eh mouse pir, the signl inrese in the er injete with ontrol ells ws set to. Quntiition ws one y sotwre (ImgeJ) nlysis o the igitlly quire imges; n= lesions per onition, men +/- s.e.m., one-tile pire t-test t y, p>. () Histologil imges o one pir o mouse ers t the en o the experiment t low (upper) n high (lower) mgniition. (e) Doule immunoluoresene nlysis with ntivimentin n phospho-histone ntioies, showing inrese proliertion in oth vimentin negtive n positive ells. Mmilln Pulishers Limite. All rights reserve

9 SUPPLEMENTARY INFORMATION Figure j si# si# si# si# si# si# p si# si# Figure s CAFs H H H H H C C C C CC CC C C C C Figure pind pind--my pind pind--my pind pind--my CAF# CAF# CAF# IL -my p γ-tu β-tin γ-tu α-sma α-sma Figure trl OE γ-tu γ-tu trl trl OE trl trl OE trl trl OE my-tgge my h.. i p p Figure s CAFs H H H H H C C C C C C C C C α-sma β tin e Pontini nm nm trl CTGF FGF HGF nm β tin CAF# CAF# Pontini Pontini nm nm Imtini um um um nm nm h.. β-tin β tin WT mt WT Figure 7 si# si# si si# si# si# si# si si# si# si# si# si si# si# Figure 7 WT sh# sh# CRSP sh# sh# WT sh# sh# CRSP sh# sh# p γ-tu β-tin p Suppl Fig Suppl Fig sh# sh# Suppl Fig Pontini nm nm nm Imtini um um um Exp. p p Exp. p γ-tu Suppl Fig 7 WT CRSP β tin p p β-tin h.. h.. Supplementry Figure 9 Un-proesse originl sns o immunolots. 9 Mmilln Pulishers Limite. All rights reserve

10 SUPPLEMENTARY INFORMATION Supplementry Tle legens Supplementry Tle Relte to Fig. g. List o gene onorntly/isorntly moulte y knok-own rom RNA-Seq experiment n skin/orl CAFs rom puli tses; Gene Ontology o the moulte genes. Supplementry Tle Relte to Fig. n. Ch-Seq peks in s ientiie y Cell-Signlling n Home-Me ntioies; CAF-relte genes ientiie rom literture serh n iret trgets o. Light lue highlighte genes re ierentilly expresse upon si- knok-own (rom RNA-Seq experiment). Supplementry Tle List o primers use in this stuy. Liste re primers use or RT-qPCR, Ch-PCR, sirna n iotinylte oligos. Supplementry Tle List o ntioies use in this stuy. Mmilln Pulishers Limite. All rights reserve

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