Supplementary Figure 1!

Transcription

1 a!!gt-cre x Twist LoxP/LoxP!!GT-Cre x Twist LoxP/LoxP! x RosaLSLEYFP!!GT-Cre x Snail LoxP/LoxP!!GT-Cre x Snail LoxP/LoxP! x RosaLSLEYFP! Supplementary Figure!!GT-Cre x Twist LoxP/LoxP! x RosaLSLEYFP x "SMA-RFP! Cre - ; Twist LoxP/LoxP ()! Cre - ; Snail LoxP/LoxP ()! Cre + ; ; EYFP LoxP/wt! Cre + ; ; EYFP LoxP/wt ; "SMA-RFP! Cre + ; ; EYFP LoxP/wt! Cre + ; Twist LoxP/LoxP ( )! Cre + ;, EYFP LoxP/wt! Cre + ; Snail LoxP/LoxP ( )! Cre + ;, EYFP LoxP/wt! Cre + ;, EYFP LoxP/wt ; "SMA-RFP! b!! NTN! FA!!! Cre - ;, healthy! Cre + ;, healthy!, healthy!, healthy! FA! c!!! Cre - ;, healthy! Cre + ;, healthy!, healthy!, healthy! Pancreas! Liver! Sirius Red! Intestine! Lung! Heart! MTS! H&E! No. of healthy tubules /visual Þeld (!) 9 Cre - Cre + Percent of interstitial Þbrosis /visual Þeld (!) Cre - Cre + Percent of Sirius Red positive area/visual Þeld (!) Cre - Cre + d! Twist,!,! Snail,!,! e!, cont.!, cont.!, day!, day! Liver! Lung! Heart! Sirius red! MTS! H&E! Pancreas! Intestine! No. of healthy tubules /visual Þeld (!) day % interstitial Þbrosis /visula Þeld (!) day Percent of Sirius Red positive area/visual Þeld (!) day f! g!!g hydroxyproline /mg total protein lysate healthy "SMA!, contralat.!, contralat.!,!,! Percent of!sma + area /visual Þeld (") Nature Medicine: doi:./nm.9

2 Supplementary Figure! a!, healthy!, NTN!, NTN!, vehicle!,!,! b! c! f! Sirius red! Sirius red! MTS! MTS! H&E! H&E! d! H&E! MTS! Sirius red!!g hydroxyproline /mg total protein lysate No. of healthy tubules /visual Þeld (!) Sirius red! MTS! H&E! Healthy NTN, contralat.!, contralat.!,!,! healthy Percent of interstitial Þbrosis /visual Þeld (!) e! "SMA! Healthy NTN, contralat.! Percent of Sirius Red positive area/visual Þeld (!), vehicle!,!,! Healthy NTN, contralat.! No. of healthy tubules /visual Þeld (!) g! BUN (mg/dl) No. of healthy tubules /visual Þeld (!) No. of healthy tubules /visual Þeld (!) Percent of Sirius Red positive area/visual Þeld (!) 9,! Percent of interstitial Þbrosis /visual Þeld (!) Percent of interstitial Þbrosis /visual Þeld (!) Percent of interstitial Þbrosis /visual Þeld (!),! Percent Sirius Red positive area/visual Þeld (!) Percent of Sirius Red positive area/visual Þeld (!) Percent of!sma + area /visual Þeld (") Nature Medicine: doi:./nm.9

3 #GT Cre + ;! #GT Cre + ;! a!,!,! b! EYFP ßox/+! ; EYFP LoxP/wt! d! Supplementary Figure!,!,! DAPI! YFP! "SMA! c! e! Percent of YFP +!SMA + cells /YFP + tubular cells /visual Þeld (") #GT-Cre + EYFP LoxP/wt #GT-Cre + EYFP LoxP/wt No. of YFP + RFP + tubules /visual Þeld (!) "GT-Cre + EYFP LoxP/wt #SMA-RFP "GT-Cre + EYFP LoxP/wt #SMA-RFP DAPI/YFP/"SMA! "SMA! YFP! DAPI!!! DAPI! YFP! "SMA RFP! f! Percent of E-cad +!SMA + cells g!, contralat.!, contralat.!,!,! E cadherin APC! "SMA PE! h!, contralat.!, contralat.!,!,! E-cadherin APC! "SMA PE! Nature Medicine: doi:./nm.9

4 a c b, contralat.,, contralat., d, contralat., contralat.,, AQP AQP7 SLCA SLCA SLCA SLCA9 SLC7A9 SLCA SLC9A SLCA SLCA SLCA SLCA SLCA SLC7A SLCOA ATPA ATPB ATPA ATPVD TRPC AQP AQP7 SLCA SLCA SLCA SLCA9 SLC7A9 SLCA SLC9A SLCA SLCA SLCA SLCA SLCA SLC7A SLCOA ATPA ATPB ATPA ATPVD TRPC f Supplementary Figure g TIMP! MMP! MMP! COLA! COLA! SPARC! BMP! STEAP! SNAI! MMP9! ITGA! MSN! CALD! COLA! VIM! FOXC! GSC! TWIST! WNTA! TMEMA! AHNAK GNG! SNAI! TCF! VCAN! ITGAV! FN! SERPINE! CDH! SOX! SNAI! CAMKN! VPSA! IGFBP! WNTB! TMEFF! TIMP! MMP! MMP! COLA! COLA! SPARC! BMP! STEAP! SNAI! MMP9! ITGA! MSN! CALD! COLA! VIM! FOXC! GSC! TWIST! WNTA! TMEMA! AHNAK GNG! SNAI! TCF! VCAN! ITGAV! FN! SERPINE! CDH! SOX! SNAI! CAMKN! VPSA! IGFBP! WNTB! TMEFF! e, vs,, vs, NES=.779! p=.7! NES=.! p=.! NES=.9! p=.! NES=.! p=.! NES=.! p=.7! NES=.79! p=.! h, vs, contr., vs, i, vs, NES=.! p=.! NES= -.7! p=.! NES=.! p=.! NES=.! p=.! NES=.! p=.! NES=.7! p=.!, vs, contr., vs,, vs, NES=.9! p=.! NES= -.7! p=.! NES=.9! p=.! NES=.! p=.7! NES=.! p=.! Nature Medicine: doi:./nm.9

5 a! AQP! Na + /K + ATPase! SLCA! Cre - ;, healthyz! Cre + ;, healthy!, healthy!, healthy! No. of Na + /K + ATPase tubules /visual Þeld (!) No. of AQP + tubules /visual Þeld (!) No. of SLCA + tubules /visual Þeld (!) Supplementary Figure! Cre - Cre + Cre - Cre + Cre - Cre + b! AQP! Na + /K + ATPase!, contralat.!, contralat.!, day!, day! No. of Na + /K + ATPase + tubules /visual Þeld (!) No. of AQP + tubules /visual field (!) day day SLCA! No. of SLCA + tubules /visual Þeld (!) day c!, contralat.!, contralat.!,!,! d!, NTN!, NTN! SLCA! SLCA! No. of Na + /K + -ATPase + tubules /visual Þeld (!) AQP! AQP! Na + /K + -ATPase! Na + /K + -ATPase! No. of AQP + tubules /visual Þeld (!) No. of SLCA + tubules /visual Þeld (!) No. of Na + /K + -ATPase + tubules /visual Þeld (!) NTN No. of AQP + tubules /visual Þeld (!) NTN No. of SLCA + tubules /visual Þeld (!) NTN Nature Medicine: doi:./nm.9

6 a! Na + /K + ATPase! AQP!! GAPDH!! healthy!contr.!!!! contr.!!! healthy! contr.!!! contr.! AQP! GAPDH!! 7!! 7! SLCA! contr.,! healthy!! contr.!,!!!!! contr.! 7! VINCULIN!!!! contr.!!! contr.! 7! SLCA! VINCULIN!! Supplementary Figure! b! c! d! Aqp relative expression (/dct) Aqp relative expression (/dct) Aqp relative expression (/dct) Healthy NTN Slca relative expression (/dct) Slca relative expression (/dct) Slca relative expression (/dct), vehicle!,!,! e! f!.... Healthy NTN Atpb relative expression (/dct) Atpb relative expression (/dct) Atpb relative expression (/dct)..... p=. Healthy NTN, vehicle!,!,! SLCA! SLCA! AQP! Na + /K + ATPase! No. of Na + /K + -ATPase + tubules /visual Þeld (!) AQP! Na + /K + ATPase! No. of AQP + tubules /visual Þeld (!) No. of SLCA + tubules /visual Þeld (!) No. of Na + /K + -ATPase + tubules /visual Þeld (!) No. of AQP + tubules /visual Þeld (!) No. of SLCA + tubules /visual Þeld (!) Nature Medicine: doi:./nm.9

7 Supplementary Figure 7! healthy! contr.!!!!! contr.! Na + /K + ATPase! healthy! contr.!!!!! contr.! contr.,!,! AQP! GAPDH! healthy!! contr.!!!! contr.!! contr.!!!! contr.! Nature Medicine: doi:./nm.9

8 Supplementary Figure! a!, contralat.!, contralat.!,!,! DAPI/YFP/"SMA/AQP! "SMA! AQP! YFP! DAPI! b! c! d! Percent YFP +!SMA + cells /visual Þeld (!) Percent AQP + out of YFP + cells /visual Þeld (!) Percent!SMA + out of YFP + AQP + cells /visual Þeld (") Nature Medicine: doi:./nm.9

9 Supplementary Figure 9! a!, contralat.!, contralat.!,!,! DAPI/YFP/"SMA/AQP! "SMA! AQP! YFP! DAPI! b! c! d! Percent YFP +!SMA + cells /visual Þeld (") Percent AQP + out of YFP + cells /visual Þeld (!) Percent!SMA + out of YFP + AQP + cells /visual Þeld (") Nature Medicine: doi:./nm.9

10 Twist Twist Twist c! ATPA a! SLCA (OAT) SLCA (OCT) g! i! ATPA SLCA (MCT) SA (FSP).... TEC TEC Biopsy ID! Histology! % Þbrosis! TEC culture!! normal! no! TEC!! normal! no! TEC!! diabetic nephropathy! <! "!! nephrosclerosis!! "!! nephrosclerosis!! "! S! mesangioproliferative GN!! TEC!! IgA nephritis!! "! S! diabetic nephropathy!! "! S! diabetic nephropathy! >! TEC7! S! nephrosclerosis! >9! "! S S S S S S S S S S S S SLC7A9 SLCA (OAT) SLCA (OCT) S S S S S S S S S S S S SLCA SLCA (OAT) SLCA (OCT) b! SA (FSP) ATPA X X TEC Normal TEC Normal S S TEC TEC7 TEC TEC TEC TEC7 TEC TEC7 Fibrosis S S S S Fibrosis SLC7A9 S S VIM 7 S S S S Normal S S S S S S S S e! f! up-regulated SLCA9 (MCT9) COLA.... TEC TEC TEC TEC TEC7 TEC TEC TEC TEC7 TEC TEC TEC7 diabetic nephropathy SLCA SLCA (MCT) Snai (Slug).... TEC TEC TEC TEC TEC TEC TEC TEC7 TEC TEC TEC7 TEC7 IgAN FSGS MCD ACTA X X X X X SA X X X X X COLA X X X TWIST X X X X SLUG X X X X SNAI X X VIM X X X X SCLA (MCT) X X X X X SCLA9 (MCT9) n.d. n.d. n.d. X SCLA (MCT) n.d. n.d. n.d. n.d. n.d. SLCA (OCTN) X X Normal Fibrosis S S S S SLCOC SLCA (OCT) VIM TEC TEC TEC TEC TEC TEC7 TEC TEC TEC TEC TEC7 TEC7 SLCA (OCTN) SLCA (OCT) ACTA (!SMA) TEC TEC TEC TEC TEC TEC TEC TEC TEC SLCOC SCLA (MCT) OCTN protein levels S S S S S S d! TEC7 TEC7 TEC7.... SLCA7 (OAT) SLCA (OCT) Fibrosis S S.... TEC TEC Snai (Slug) ACTA (!SMA) down-regulated S S S S S S S S S S S S TEC TEC7 SLCA (OCTN) SLCA9 (MCT9) SLC7A9 relative protein levels SLC7A9 protein levels Supplementary Figure! S S S S S S S S TEC TEC TEC TEC7 Cola CDH (ECad).... S S S S S S S S S S S S SLCOC relative protein levels.... SLCA7 (OAT) SLCA (MCT) SLCOC protein levels TEC TEC TEC TEC7 S S S S OCTN relative protein levels S S S S SLCOC X X X X X ATPB X X AQP!! X!! AQP X X X!! CDH (ECad) TEC TEC TEC TEC TEC7 TEC TEC TEC7 nephrosclerosis nephrosclerosis h SLCA (OAT).... TEC TEC diabetic nephropathy TEC TEC7 SLCA (OAT)..... TEC IgAN FSGS MCD CDH (ECAD) X X X X X SLCA (OCT) X X X SLCA (OCT) X X X SLCA (OCT) X X X SLCA (OAT) X X X X X SLCA7 (OAT) X X X SLCA (OAT) X X X X X SLCA (OAT) X X X X X SLCA (OAT) X X X X SLC7A9 X X X X X SLCA X X X X X TEC TEC TEC7 SLCA (OAT)..... S S S S S S S S S S S S TEC TEC TEC TEC7 TEC TEC TEC TEC7 Nature Medicine: doi:./nm.9

11 a! c! Relative expression (^ddct) Relative expression (^ddct) e! Relative expression (^ddct) L(+)-lactate (nm) h! i! SLCA (OAT) Control TGF! Control SLCA7 (OAT) Control SLCA (MCT) ACTA ("SMA) SA (FSP) TWIST SNAI (Snail) SNAI TGF! SLCA (OAT) SLCA (OAT) TGF! SLCA9 (MCT9) SLCA (MCT). Time (h) CD! CD! DAPI/F/! DAPI/F/! HK, untreated HK, TGF! ph 7. ph., contralat.!,!,!,! (Slug) VIM SLCA (OAT) Percent nuclear!-catenin /visual Þeld (!) COLA SLCA (OCT) d! f! SLC7A9 protein levels CDH (ECad) vh TGF! SLCA (OCT) SLCA (OCT)... Epithelial state! b! SLCA (OCT) BrightÞeld! Hoechst/! $ÐCatenin! Relative expression (^ddct).... SLCOC protein levels Control Control! SLC7A9... SLCA TGF! SLCOC SLCA protein levels TGF#! SLCA (OCTN) ATPA Mesenchymal state! Epithelial to Mesenchymal Transition!, contralat.!,!,!,! No. of CD + cells /visual Þeld(!) No. of F/ + cells /visual Þeld (!) No. of F/ + cells /visual Þeld(!) ATPB g! Supplementary Figure! LCN CXCL HAVCR CCL7 MMP AREG CD VCAM IGFBP MMP CXCL CCL SERPINE TNF TGFB CCL CSF ICAM TNFSFB PITX CXCL CCL CXCL CXCL CSF TGFB FGF7 IGFBP PDGFB CD ANXA WISP ILRN SPP IL7 FGF PDGFA IL SERPINF IL POSTN CHIL SELP TPO IL DKK CST TGFB FGF COLA HGF CXCL9 ENG FGF MMP9 CCL CD9 RARRES IL IL CCL9 DPP PRLC MPO LIF FGF7 CSF FGF IL7 FGF IL FGF FGF IL RBP FGF FGF GAS CCL FGF IL CCL PITX CCL ANGPTL FGF RAGE FGF FGF IL SELE IGFBP DLK LIX PCSK9 REGG ILA FGF HC AHSG FGF CFD LEP TYMP CXCL IFNG IGFBP LDLR RETN FGF IL IGFBP IL7A FGF FGF9 CD FGF ADIPOQ IL FGF EGF CXCL Row Z-Score! Nature Medicine: doi:./nm.9

12 a!, contralat.!, contralat.!,!,! Supplementary Figure! E cadherin APC! b! E cadherin APC! ph PE!, contralat.!, contralat.!,!,! c! ph! ph PE!, contralat.!, contralat.!,!,! No. of ph + tub. epithelial cells /visual Þeld (!) d! ph!, contralat.!, contralat.!,!,! No. of ph + tub. epithelial cells /visual Þeld (!) e! f! BrdU! Ki7!, contralat.!, contralat.!,!,! No. of Ki7 + tub. epithelial cells /visual Þeld (!) No. of BrdU + tub. epithelial cells /visual Þeld (!) Nature Medicine: doi:./nm.9

13 a!, contralat.!, contralat.!,!,! Supplementary Figure! "SMA! ph! YFP! DAPI! b! DAPI/YFP/! "SMA/pH! Percent YFP +!SMA + cells /visual Þeld (") c!, contralat.!, contralat.!,!,! YFP! DAPI! d! "SMA! ph! DAPI/YFP/! "SMA/pH! e! Percent YFP +!SMA + cells /visual Þeld (") Percent!SMA + out of YFP + ph + cells /visual Þeld (") Nature Medicine: doi:./nm.9

14 a! b! Relative expression (^ddct).... Acta Fn Hoechst! Twist Snai (Snail) Cola Cdh Ki7! T! ph! G! A! Hoechst/Ki7/pH! d! e! Supplementary Figure! Percent Ki7 + cells /visual Þeld (!) vh TGF! shscrbl vh TGF! shtwist Percent cells in M phase /visual Þeld (!) M! P! c! Hoechst! Ki7! ph! Hoechst/Ki7/pH! shtwist, TGF#! shtwist, vh.! shscrbl, TGF#$ shscrbl, vh.! vh TGF! shscrbl vh TGF! shtwist Nature Medicine: doi:./nm.9

15 a! Hoechst/! Hoechst/! Ki7/pH! $ Catenin! BrightÞeld! shscrbl, vh.! shscrbl, TGF#! shsnail, vh.! shsnail, TGF#! Snai relative Percent nuclear!-catenin /visual Þeld (!) Percent G + cells /visual Þeld (!) vh TGF! shscrbl vh TGF! shscrbl vh TGF! shscrbl Supplementary Figure! vh TGF! shsnail vh TGF! shsnail vh TGF! shsnail Percent Ki7 + cells /visual Þeld (!) vh TGF! shscrbl vh TGF! shsnail Percent cells in M phase /visual Þeld (!) vh TGF! shscrbl vh TGF! shsnail b! shscrbl! Empty vector! BrightÞeld! Hoechst/Ki7/pH! vehicle! TGF#! vehicle! TGF#! c! Percent G + cells /visual Þeld (!) shsnail! Empty vector! vh TGF! shscrbl Empty vector vh TGF! shsnail Empty vector vh TGF! shsnail OE Snail shsnail! OE Snail! g! Normal kidney! d! f! Fold change in absorbance (MTT assay).... sh scrbl, vh sh scrbl, TGF! shtwist, vh shtwist, TGF! Time (hrs) e! shscrbl,uv exposure! shscrbl, vh.! shscrbl, TGF#! shtwist, vh.! shtwist, TGF#! TEC injury! Cytokine/chemokine release! by injured TEC! Vasodilation, BM remodeling & initial inßux of immune cells! De-differentiation of surviving! TEC, proliferation & restoration! of TEC architecture and function! Macrophage! TGF# secretion! Hoechst/TUNEL!,!,! No. of Tunel + nuclei /visual Þeld (!) Inhibition! of TEC EMT program! TEC EMT program! Compromise of TEC function,! TEC cell cycle arrest! & pathological secretome! Enhanced immune inþltration! & myoþbroblast recruitment,! chronic Þbrosis! Nature Medicine: doi:./nm.9

16 !"#$%&'(&)$)+,$!%-./-)$+&$ Supplementary Figure legends Supplementary Figure. Genetic deletion of Twist and Snail in!gt expressing kidney tubular epithelial cells reduces renal fibrosis and improves tubular health (a) Schematic representation of the genetic crosses to genetically delete Twist and Snai in renal proximal tubules. The resulting progeny was subjected to unilateral ureter obstruction (), nephrotoxic serum induced nephritis (NTN) or (FA) to induce renal injury. (b) Representative H&E staining of heart, lung, liver, pancreas and intestine from the indicated experimental groups (healthy mice). Scale bar: µm. (c) Representative H&E, MTS and Sirius Red staining of kidneys from the indicated healthy mice and respective quantification of the number of healthy tubules per visual field, percent interstitial fibrosis, and percent Sirius red + area per visual field. Scale bar: µm. Cre ;, n = ; Cre + ;, n = ;, n = ;, n =. Data is represented as mean ± s.e.m. One way ANOVA with Tukey post hoc analysis was used and no statistical significant changes were noted. (d) Representative H&E staining of heart, lung, liver, pancreas and intestine from the indicated experimental groups (healthy mice). Scale bar: µm. (e) Representative H&E, MTS and Sirius Red staining of kidneys from the indicated experimental groups and respective quantification of the number of healthy tubules per visual field percent interstitial fibrosis, and percent Sirius red + area per visual field. Scale bar: µm. contralat., n = ; contralat, n = ;, n = ;, n =. (f) Hydroxyproline release measurement of collagen content in kidneys of the indicated experimental groups. healthy, n = ; contralat., n = ; contralat, n = ;, n = ;, n =. (g) Representative immunolabeling for!sma in the kidney of the indicated experimental groups and quantification of!sma positive interstitial area per visual field. Scale bar: µm. contralat., n = ; contralat, n = ;, n = ;, n =. Data is represented as mean ± s.e.m. One way ANOVA with Tukey post hoc analysis was used. P <., P <., P <., P <.. contralat.: contralateral kidney. Nature Medicine: doi:./nm.9

17 !"#$%&'(&)$)+,$!%-./-)$+&$ Supplementary Figure. Genetic targeting of EMT reduces NTN and FA induced renal fibrosis and improves tubular health (a) Representative H&E, MTS and Sirius Red staining of kidney from the indicated experimental groups and respective quantification of the number of healthy tubules, percent interstitial fibrosis, and percent Sirius red + area per visual field. Scale bar: µm. Insert scale bar: µm. healthy, n = ; NTN, n = 7; NTN, n = 7. (b) Representative H&E, MTS and Sirius Red staining of kidney from the indicated experimental groups and respective quantification of the number of healthy tubules, percent interstitial fibrosis, and percent Sirius red + area per visual field. Scale bar: µm. vehicle, n = ; folic acid, n = ; folic acid, n =. (c) Representative H&E, MTS and Sirius Red staining of kidney from the indicated experimental groups and respective quantification of the number of healthy tubules, percent interstitial fibrosis and percent Sirius red + area per visual field. Scale bar: µm. contralat., n = ; contralat, n = ;, n = 7;, n = 7. (d) Hydroxyproline release measurement of collagen content in kidneys of the indicated experimental groups. healthy, n = ; contralat., n = ; contralat, n = ;, n = ;, n =. (e) Representative immunolabeling for!sma in the kidney of the indicated experimental groups and respective quantification of!sma positive interstitial area per visual field. Scale bar: µm. contralat., n = ; contralat, n = ;, n = ;, n =. (f) Representative H&E, MTS and Sirius Red staining of kidney from the indicated experimental groups and respective quantification of the number of healthy tubules, percent interstitial fibrosis, and percent Sirius red + area per visual field. Scale bar: µm. vehicle, n = ; folic acid, n = ; folic acid, n =. (g) Blood Urea Nitrogen (BUN) levels. vehicle, n = ; folic acid, n = ; folic acid, n =. Data is represented as mean ± s.e.m. One way ANOVA with Tukey post hoc analysis was used, with the gray star indicating the use of unpaired two tailed t test. P <., P <., P <., P <.. Supplementary Figure. Genetic deletion of Twist and Snail in proximal TEC suppresses EMT Nature Medicine: doi:./nm.9

18 !"#$%&'(&)$)+,$!%-./-)$+&$ (a) Individual channels for immunostaining data presented in Fig. h. (b) Representative images of kidneys immunolabeled for!sma and visualized for YFP expression (under the control of the "GT cre transgenic promoter) and (c) quantification of the YFP +!SMA + cells per total number of YFP + tubular epithelial cells per visual field., n = ;, n =. Scale bar: µm. White arrowheads: YFP +!SMA + cells. Two tailed student t-test was used. (d) Individual channels for immunostaining data presented in Fig. i. (e) Quantification of the number of YFP + RFP + tubules per visual field. YFP;!SMA RFP: n =, YFP;!SMA RFP; : n =. Two tailed student t-test. (f) Flow cytometry analysis of E cadherin +!SMA + cells on kidneys from the indicated experimental groups. contralat., n = ; contralat., n = ;, n = ;, n =. (g h) Representative scatter dot plot from flow cytometry analysis of E cadherin +!SMA + cells on kidneys from the indicated Twist (g) and Snail (h) experimental groups. Data is represented as mean ± s.e.m. f, data is presented as mean ± s.d. Unless otherwise specified, one way ANOVA with Tukey post hoc analysis was used. P <.. contralat.: contralateral kidney. Supplementary Figure. Gene expression profiling reveals an increase in genes associated with TEC function in and compared to kidneys (a,c) Heatmaps rendering of all significantly deregulated genes in the kidneys of the indicated experimental groups. (b,d) Heatmaps rendering of genes associated with tubular epithelial cell function in the kidneys of the indicated experimental groups. (e) Enrichment plots of gene datasets associated with tubular epithelial cell function in the kidneys of, compared to, (left) and, compared to, (right). (f g) Heatmaps rendering of genes associated with induction of EMT in the kidneys of the indicated experimental groups. (h) Enrichment plots of gene datasets associated with induction of EMT in the kidneys of the indicated experimental groups. (i) Enrichment plots of gene datasets associated with TEC survival in the kidneys of the indicated experimental groups. Nature Medicine: doi:./nm.9

19 !"#$%&'(&)$)+,$!%-./-)$+&$ Supplementary Figure. Suppression of EMT prevents loss of TEC associated solute and solvent transporters in kidney fibrosis ( and NTN) (a) Immunolabeling for Na + /K + ATPase, AQP, and SLCA in the kidney of the indicated experimental groups and respective quantification of the number of Na + /K + ATPase positive, AQP positive and SLCA positive tubules per visual field. Cre ;, n = ; Cre + ;, n = ;, n = ;, n =. Scale bar: µm. One way ANOVA with Tukey post hoc analysis was used and no statistically significant changes were noted. (b) Immunolabeling for Na + /K + ATPase, AQP, and SLCA in the kidney of the indicated experimental groups and respective quantification of the number of Na + /K + ATPase positive, AQP positive and SLCA positive tubules per visual field. contralat., n = ; contralat, n = ;, n = ;, n =. Scale bar: µm. (c) Immunolabeling for Na + /K + ATPase, AQP, and SLCA in the kidney of the indicated experimental groups and respective quantification of the number of Na + /K + ATPase positive, AQP positive and SLCA positive tubules per visual field. contralat., n = ; contralat., n = ;, n = ;, n =. Scale bar: µm. (d) Immunolabeling for Na + /K + ATPase, AQP, and SLCA in the kidney of the indicated experimental groups and relative quantification of the number of Na + /K + ATPase positive, AQP positive and SLCA positive tubules per visual field. NTN, n = ; NTN, n =. Scale bar: µm. Data is represented as mean ± s.e.m. One way ANOVA with Tukey post hoc analysis was used; in d: unpaired two tailed t-test was used. P <., P <., P <., P <.. contralat.: contralateral kidney. Supplementary Figure. Inhibition of EMT prevents loss of TEC associated solute and solvent transporters in kidney fibrosis (, NTN and ) (a) Western blot analysis of AQP, Na + /K + ATPase and SLCA protein expression level in kidneys of the indicated experimental groups (uncropped blot are shown in Supplementary Fig. 7). (b) Gene expression analysis (Q PCR) of AQP, Na + /K + ATPase and SLCA in kidneys of the indicated experimental groups. contralat., n = ; contralat, n = 7;, n = ;, n = 7. (c) Gene expression analysis of AQP, Na + /K + ATPase and SLCA in kidneys of the indicated Nature Medicine: doi:./nm.9

20 !"#$%&'(&)$)+,$!%-./-)$+&$ Snail experimental groups. contralat., n = ; contralat, n = ;, n = ;, n =. (d) Gene expression analysis of AQP, Na + /K + ATPase and SLCA in kidneys of the indicated experimental groups. healthy (NTN control), n =, NTN, n =, NTN, n =. Unpaired one tailed t-test was used and calculated using dct. (e f) Immunolabeling for Na + /K + ATPase, AQP, and SLCA in the kidney of the indicated experimental groups and respective quantification of the number of Na + /K + ATPase positive, AQP positive and SLCA positive tubules per visual field. Scale bar: µm. (e) vehicle, n = ; folic acid, n = ; folic acid, n =. (f) vehicle, n = ; folic acid, n = ; folic acid, n =. Data is represented as mean ± s.e.m. One way ANOVA with Tukey post hoc analysis was used with the gray star indicating unpaired two tailed t-test was used. P <., P <., P <., P <.. Supplementary Figure 7. Western blot expression analysis of AQP, Na+/K+ ATPase and SLCA Uncropped blots used to generate western blot panels presented in Supplementary Figure a. Supplementary Figure. Loss of AQP is associated with TEC exhibiting EMT program ( model) (a) Individual channels for individual markers used to generate the merged image presented in Fig. i. Scale bar: µm. (b) Quantification of the YFP +!SMA + cells per total number of YFP + tubular epithelial cells per visual field. (c) Quantification of the AQP + YFP + cells per total number of YFP + tubular epithelial cells per visual field. (d) Percent!SMA + cells out of the AQP + YFP + cells per visual field. contralat., n = ; contralat, n = ;, n = ;, n =. Data is represented as mean ± s.e.m. One way ANOVA with Tukey post hoc analysis was used. P <., P <., P <., P <.. contralat.: contralateral kidney. Supplementary Figure 9. Loss of AQP is associated with TEC exhibiting EMT program ( model) Nature Medicine: doi:./nm.9

21 !"#$%&'(&)$)+,$!%-./-)$+&$ (a) Immunolabeling for YFP, AQP and!sma in the indicated experimental groups. Scale bar: µm. (b) Quantification of the YFP +!SMA + cells per total number of YFP + tubular epithelial cells per visual field. (c) Quantification of the AQP + YFP + cells per total number of YFP + tubular epithelial cells per visual field. (d) Percent of!sma + cells out of the AQP + YFP + cells per visual field. contralat., n = ; contralat, n = ;, n = ;, n =. Data is represented as mean ± s.e.m. One way ANOVA with Tukey post hoc analysis was used. P <., P <., P <., P <.. contralat.: contralateral kidney. Supplementary Figure. Gene and protein expression profiles in biopsies and biopsy derived primary TECs isolated from subjects with chronic kidney diseases (a) List of human renal biopsies with various histology and relative renal fibrosis and primary tubular epithelial cell culture (TEC culture) established from indicated biopsies. (b c) Relative expression of the indicated genes in human renal biopsies with various histology and relative renal fibrosis. (d) Relative protein levels for the indicated proteins in human renal biopsies with various histology and relative renal fibrosis. (e f) Selected list of up and down regulated genes in subjects kidney biopsies in MCD: minimal change disease. (g) Relative expression of the indicated tubular transporter encoded genes in tubular epithelial cells isolated from human renal biopsies with various histology and relative renal fibrosis. (h) Relative protein levels for the indicated proteins in tubular epithelial cells isolated from human renal biopsies with various histology and relative renal fibrosis. (i) Relative expression of the indicated EMT related genes in tubular epithelial cells isolated from human renal biopsies with various histology and relative renal fibrosis. Supplementary Figure. EMT program reduces TEC expression of solute and solvent transporters and suppression of EMT decreases immune infiltrate in fibrotic kidneys (a) Relative expression of the indicated genes in human HK renal tubular epithelial cells subjected to TGF-# for 7 hours and compared to untreated control cells, n =. (b) Brightfield images of human renal tubular epithelial cell line HK treated with vehicle or Nature Medicine: doi:./nm.9

22 !"#$%&'(&)$)+,$!%-./-)$+&$ TGF-# and representative images of vehicle or TGF-# treated HK cells immunolabeled for! catenin and respective quantification of the percentage of HK displaying nuclear accumulation of! catenin following treatment with vehicle compared to TGF-#. (c) Relative expression of the indicated genes in human renal tubular epithelial cells subjected to TGF-# and compared to untreated control cells. (d) Relative protein levels for the indicated proteins in HK cells subjected to TGF-# and compared to untreated control cells. (e) Measurement of lactate secretion by HK cells over time, comparing untreated with TGF-# treated cells. The ph of the media is listed. (f) Schematic representation of the inverse correlation between acquisition of EMT features and loss of expression of transporters. (g) Representative heatmaps of select cytokines in the indicated experimental groups. (h) Immunolabelling for CD in the indicated experimental groups and quantification of the number of CD positive cells per visual field in the indicated experimental groups. Scale bar: µm. contralat., n = ; contralat., n = ;, n = ;, n =. (i) Immunolabelling for F/ in the indicated experimental groups and quantification of the number of F/ positive cells per visual field in the indicated experimental groups. Scale bar: µm. ( control), n = ;, n = ; ( control), n = ;, n =. Data is represented as mean ± s.e.m. (vh) and TGF-# treatment were conducted for 7 hours, n =. Unpaired two tailed (b, d, e, i) or one tailed (a, c) t-test was used. For h, one way ANOVA with Tukey post hoc analysis was used. P <., P <., P <., P <.. contralat.: contralateral kidney. Supplementary Figure. EMT program arrests TECs in G phase (a b) Representative scatter dot plot from FC analysis of E cadherin + p $ + cells on kidneys from the indicated Twist (a) and Snail (b) experimental groups. (c d) Representative image of phospho histone H (ph) immunolabeled kidneys from the indicated experimental groups and respective quantification of the number of ph + tubular epithelial cells per visual field. Scale bar: µm. (c) contralat., n = 9; contralat., n = 9;, n = ;, n =. (d) contralat., n = Nature Medicine: doi:./nm.9

23 !"#$%&'(&)$)+,$!%-./-)$+&$ 7; contralat., n = 7;, n = 7;, n = 7. (e f) Representative image of Ki7 (e) and BrdU (f) immunolabeled kidneys from the indicated experimental groups, and respective quantification of the number of Ki7 + and BrdU + tubular epithelial cells per visual field. Scale bar: µm. (e) contralat., n = ; contralat., n = ;, n = ;, n =. (f) contralat., n = ; contralat., n = ;, n = ;, n =. Data is represented as mean ± s.e.m. For c f: one way ANOVA with Tukey post hoc analysis was used; for g and grey stars in d, unpaired two tailed t-test was used. P <., P <., P <., P <.. contralat.: contralateral kidney. Supplementary Figure. Inhibition of EMT decreases ph accumulation in TEC (a) Individual channel for individual markers and merged images used to generate the image presented in Fig. b. Scale bar: µm. (b) Quantification of the YFP +!SMA + cells per total number of YFP + tubular epithelial cells per visual field. contralat., n = ; contralat, n = ;, n = ;, n =. (c) Immunolabeling for YFP, ph and!sma in, contralateral and and, contralateral and kidneys. Scale bar: µm. (d) Quantification of the YFP +!SMA + cells per total number of YFP + tubular epithelial cells per visual field. contralat., n = ; contralat, n = ;, n = ;, n =. (e) Percent!SMA + cells out of the ph + YFP + cells per visual field (%). contralat., n = ; contralat, n = ;, n = ;, n =. Data is represented as mean ± s.e.m. One way ANOVA with Tukey post hoc analysis was used. For b: unpaired two tailed t-test was used. P <., P <., P <., P <.. contralat.: contralateral kidney. Supplementary Figure. EMT is associated with cell cycle arrest specifically in the G phase (a) Relative expression of the indicated genes in mouse MCT renal tubular epithelial cells subjected to TGF-# and compared to untreated control cells. (b) Representative images of MCT cells immunolabeled for Ki7 and ph. Scale bar: µm. Arrowheads: cells in prophase (P), metaphase (M), anaphase (A) telophase (T), and G phase (G). (c) Nature Medicine: doi:./nm.9

24 !"#$%&'(&)$)+,$!%-./-)$+&$ Individual channel for individual Ki7 and ph markers used to generate the merged image presented in Fig. f. (d) Relative percentage of Ki7 + vehicle or TGF- #&treated MCT shscrbl and MCT shtwist cells. (e) Relative percentage of vehicle or TGF-#&treated MCT shscrbl and MCT shtwist in the M phase of the cell cycle (combining cells in either A, P, M or T). Data is represented as mean ± s.e.m. One way ANOVA with Tukey post hoc analysis was used. In a, unpaired one tailed t-test was used. In d e, One way ANOVA with Tukey post hoc analysis was used and no statistically significant changes were noted. P <., P <., P <., P <.. Supplementary Figure. EMT program via induction of Twist and Snail arrests TEC in G phase (a) Phase contrast light microscopy images and relative expression of Snai in MCT shscrbl and MCT shsnail cells treated with vehicle or TGF-#. Representative images of vehicle or TGF-# treated MCT shscrbl and shsnail cells immunolabeled for! catenin and respective quantification of the percentage of MCT shscrbl and MCT shsnail cells displaying nuclear accumulation of! catenin following treatment with vehicle compared to TGF-#, n =. Representative images of vehicle or TGF-# treated MCT shscrbl and shsnail cells immunolabeled for Ki7 and ph and respective quantification of the percentage of MCT shscrbl and MCT shsnail cells in G phase and in the M phase (combining cells in either A, P, M or T) of the cell cycle and the relative percentage of Ki7 + MCT shscrbl and MCT shsnail cells, comparing cells treated with vehicle or TGF- #, n =. Hoechst: nucleus. Scale bar: µm. (b) Phase contrast light microscopy and immunolabeling for Ki7 and ph of MCT shscrbl and MCT shsnail cells transfected with empty or Snail overexpression (OE Snail) plasmids and treated with vehicle or TGF- #. Scale bar: µm. (c) Quantification of the percentage of empty or Snail OE transfected MCT shscrbl and MCT shsnail cells in G phase of the cell cycle comparing cells treated with vehicle or TGF-#, n =. (d) Relative fold change in absorbance readings from MTT assay of the indicated cells and treatment groups. (e) Representative images of comet assay performed on MCT shscrbl and MCT shtwist cells treated with vehicle or TGF-#. (f) Representative images of TUNEL assay on and Nature Medicine: doi:./nm.9

25 !"#$%&'(&)$)+,$!%-./-)$+&$ kidneys and number of positive nuclei per visual field., n = ;, n =. (g) Schematic of progression of kidney fibrosis and role of EMT in tubular parenchyma sustained damage. Data is represented as mean ± s.e.m. (vh) and TGF-# treatment were conducted for hours, n =. Hoechst: nucleus. One way ANOVA with Tukey post hoc analysis was used. P <., P <., P <., P <.. OE: overexpression.! Nature Medicine: doi:./nm.9