Increasing the level of Peroxisome Proliferator-Activated Receptor Gamma. Supplement Figure 1. Regulation of PGC1α expression in cultured podocytes.

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Increasing the level of Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1 α in podocytes results in collapsing glomerulopathy Supplement Figure 1.

1 Increasing the level of Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1 α in podocytes results in collapsing glomerulopathy Supplement Figure 1. Regulation of PGC1α expression in cultured podocytes. Relative transcript levels of PGC1α in podocytes were measured by QRT PCR. Abbreviation: Tumor necrosis factor alpha (TNF), Vascular Endothelial Growth Factor A (VEGF-A), Lipopolysaccharides (LPS), Transforming Growth Factor Beta 1 (TGF-b). n=3 each group. *** q<0.001 compared to control, ANOVA post hoc test. 1

2 Supplement Figure 2. Restoring PGC1α in podocytes does not ameliorate albuminuria in DKD model. PGC1α transgene expression was titrated by doxycycline chow amount, after intensive-dose titration, we found a two-fold PGC1α is tolerable to podocytes and above that is toxic. In a 16 week STZ-induced DKD model, non-diabetic Nefta-PGC1α did not have more albuminuria if PGC1α expression is controlled in this window, but we did not observe a protective effect of diabetic albuminuria in Nefta-PGC1α mice. * p<0.05 compared to control group, ANOVA post hoc test, n=4 each group. 2

Supplement Figure 3. qpcr analysis of cultured podocytes infected with control (GFP) or adenoviral PGC1α (a) Notch pathway gene expression in control and PGC1α expressing cells.

(b) HIF pathway gene expression in control and PGC1α expressing cells.

3 Supplement Figure 3. qpcr analysis of cultured podocytes infected with control (GFP) or adenoviral PGC1α (a) Notch pathway gene expression in control and PGC1α expressing cells. Abbreviation: Hes Related Family BHLH Transcription Factor YRPW Motif 1 (Hey1), Hes Family BHLH Transcription Factor 1 (Hes1), Jagged 1 (Jag1). (b) HIF pathway gene expression in control and PGC1α expressing cells. Abbreviation: Hypoxia Inducible Factor 1 Alpha Subunit (Hif1a), Hypoxia Inducible Factor 2 Alpha Subunit (Hif2a), Twist Family BHLH Transcription Factor 1 (twist), Lysyl Oxidase (Lox), Lactate Dehydrogenase A (Ldha), Vascular Endothelial Growth Factor A (Vegfa). (c) PDGF pathway gene expression in control and PGC1α expressing cells. Abbreviation: Platelet Derived Growth Factor (Pdgf). (d) Tgf-β pathway gene expression in control and PGC1α expressing cells. Abbreviation: Transforming Growth Factor Beta 1 (Tgf-b), SMAD Family Member 7 (Smad-7), Snail Family Transcriptional Repressor 1 (Snail1), Snail Family Transcriptional Repressor 2 (Snail2). *q<0.05 compared to control, unpaired t test with Bonferroni correction. 3

4 Supplement figure 4. Block fatty acid utilization does not attenuate PGC1α induced podocytes proliferation and de-differentiation in vitro. p=ns p=ns relative expression (normalized to actin) p=ns ad-gfp + DMSO ad-gfp + etomoxir ad-pgc1a + DMSO ad-pgc1a + etomoxir 0 C-myc cyclin E Synpo Cultured podocytes were treated by CPT-1 specific inhibitor etomoxir (40uM) or DMSO before ad-gfp or ad-pgc1a infection. Etomoxir was not able to attenuate PGC1α induced proliferation (C-myc, cyclin E) and de-differentiation (Synpo). n=3 each group, t-test. 4

5 Supplement Figure 5. VEGF-a protein expression in Control and Nefta-PGC1α glomeruli p=ns 1.5 VEGF expression Control Nefta-PGC1a Glomeruli from control and Nefta-PGC1α mice were isolated by dynabeads perfusion, VEGF-a protein level was analyzed by western blot and quantified. N=6 each group, t-test. 5

6 Supplement Figure 6. A trend of increased PGC1α and its downstream gene expression in human CGN. a b lo g 2 m e d ia n -c e n te re d in te n s ity o f P P A R G C 1 A p = lo g 2 m e d ia n -c e n te re d in te n s ity o f N R F p = C o n tro l C G N 0.0 C o n tro l C G N c lo g 2 m e d ia n -c e n te re d intensity of C P T1B p = d lo g 2 m e d ia n -c e n te re d in te n s ity o f S L C 2 5 A p = C o n tro l C G N 0 C o n tro l C G N e 2.0 p = f 3.0 p = lo g 2 m e d ia n -c e n te re d in te n s ity o f N D U F A 4 L lo g 2 m e d ia n -c e n te re d in te n s ity o f U C P C o n tro l C G N 1.8 C o n tro l C G N Expression of PPARGC1A (a) and its downstream gene NRF1(b), CPT1B(c), SLC25A19(d), NDUFA4L2 (e), UCP2 (f) in human sample. n= 9 in control, n=6 in CGN. t test. 6

disease In podocytes, PGC1α increases mitochondrial

including (1) shifts mitochondrial fuel preference, (2)

electron transport chain subunits assembly, altogether,

7 Supplement Figure 7. Our model of PGC1α-induced podocytes dysfunction and kidney disease In podocytes, PGC1α increases mitochondrial biogenesis and alters mitochondrial intrinsic properties, including (1) shifts mitochondrial fuel preference, (2) increases mitochondrial fusion and size, and (3) alters electron transport chain subunits assembly, altogether, these changes reprogram cell fate and result in podocyte proliferation and dedifferentiation. Transcriptional factor (TF) 7

8 Supplement table 1. List of differentially expressed gene between Control and Nefta-PGC1α mouse glomeruli detected by RNAseq Gene Base Mean log2 Fold Change P value P adj Cox7a E E-72 Atp1a E E-67 Ndrg E E-62 Kirrel E E-61 Mthfd E E-47 Hcn E E-38 Cend E E-37 Ppargc1a E E-37 Tm6sf E E-30 Idh3a E E-24 Gpr E E-24 Got E-26 1E-22 Dsc E E-21 Chchd E E-21 Myl6b E E-21 Clec2l E E-19 Tmprss E E-19 Bcan E E-19 Slc41a E E-19 Asns E E-18 Tnfrsf12a E E-18 Fndc E E-17 Atf E E-17 Pcolce E E-16 Ndufa E E-16 Cs E E-16 Tmem E E-16 Trp53inp E E-16 Dlat E E-16 St8sia E E-15 Acot E E-14 Atp2b E E-14 Dok E E-14 Got E E-14 Slc25a E E-13 Stbd E E-13 Hspb E E-13 Acot E E-13 Aco E E-13 Cidea E E-12 Fuom E E-12 Ogdh E E-12 8

9 Mtfp E E-11 Ghitm E E-11 Map1b E E-11 Pdk E E-11 Tmem38a E E-10 Cox5a E E-10 Trib E E-10 Kcnn E E-10 Atp5o E E-10 H2-Q E E-10 Chd E E-10 Ndufab E E-09 Eno E E-09 Etfdh E E-09 Hpdl E E-09 Ndufb E E-09 Hspa E E-09 P4ha E E-09 Ndufb E E-09 Hk E E-08 Obscn E E-08 Ndufs E E-08 Ndufa E E-08 Abca E E-08 Atp5g E E-08 Spock E E-08 Syt E E-08 Eno1b E E-08 Mdh E E-08 Eef1a E E-08 Rin E E-08 Ifrd E E-08 Cox4i E E-08 Adssl E E-08 Atp5g E E-07 Lrfn E E-07 Ndufb E E-07 Ndufs E E-07 Sucla E E-07 Gfm E E-07 Nupr E E-07 Pkm E E-07 Slc25a E E-07 Uqcrb E E-07 Cox6b E E-07 9

10 Kcng E E-07 Tmem E E-07 Ndufb E E-07 Ndrg E E-07 Ndufv E E-07 Atp5j E E-07 Gars E E-07 Uqcrh E E-07 Cyc E E-07 Atp5b E E-07 Ndufb E E-07 Acadvl E E-07 Cox6a E E-07 Ndufs E E-07 Atp5k E E-06 Nol E E-06 Ndufv E E-06 Ndufaf E E-06 Cdsn E E-06 Ndufa E E-06 Cox7b E E-06 Atp5d E E-06 Hadha E E-06 Chchd E E-06 Hapln E E-06 Me E E-06 Osbpl1a E E-06 Matn E E-06 Slc26a E E-06 Cox5b E E-06 Ckb E E-06 Ndufa E E-05 Nceh E E-05 Plagl E E-05 Pigr E E-05 Mpc E E-05 Aldh1b E E-05 Uqcrq E E-05 Hadhb E E-05 Tnfaip E E-05 Sdhb E E-05 Hsdl E E-05 Frem E E-05 Pdhb E E-05 Mrm E E-05 10

11 Vegfb E E-05 Ndufb E E-05 Slc25a E E-05 Dld E E-05 Tfrc E E-05 Cox6c E E-05 Spata E E-05 Fam134b E E-05 Tlr E E-05 Atp5a E E-05 Ppm1l E E-05 Trak E E-05 Lypd E E-05 Hccs E E E04Rik E E-05 Gm E E-05 Slc25a E E-05 Pdha E E-05 Comp E E-05 Cox E E-05 Grin2d E E-05 Ndufc E E-05 Cxcr E E-05 Immt E E-05 Esrra E E-05 Mycl E E-05 Fh E Gdpd E Ndufa E Pamr E Neurl1a E Coq E Sdhd E Bdh E Atp5c E Fam129a E Mpnd E Btnl E Tmc E Slc7a E Pdhx E Zim E Stac E Gapdh E Dlst E

12 Lfng E Syt E Ddit E Hoxd E Retsat E Cox7a E Dnajc E Oxct E Mdh E Pfkp E Uqcr E Mrpl E Eif4ebp E Thsd7a E Aqp E Snx E Idh3g E Myof E Minos E Slc16a E Ppfia E Uqcr E Ndufa E Pm20d E Ndufb E mt-tp E Msrb E Srxn E Uqcrc E Ak E F05Rik E Gbas E Slmo E Idh3b E Mtx E Tomm E Ptprv E Ppp1r14b E Ndufaf E Ndufs E Fbxo E Slc37a E Ndufc E Pgm E Tpi E

13 Sars E Cox6a E Ndufa E Cycs E Ndufa E Tnfrsf E Tmem E Atp5j E Rab E Mrpl E Sec16b E Rsad E Gm E Sfrp E Calr E Ndc E Prdx E Pnpla E Tuba1a E Sod E Vdac E Sema3g E Atp5h E Ptgds E M20Ri k E Ppp3cc E Lrpprc E Myo E J03Rik E Lypd E Ptprc E Pfkm E Gpr E C430049B03Rik E Sec14l E Srrm E Cyp2d E Prdx E Coq E Maff E Cox8a E Aars E Fam162a E Wnt E Pptc E

14 Bola E Mrpl E Pacsin E Nars E Tmem E Arhgef E Adamts E Zfp E Sdsl E Uqcrc E Fastkd E Itgal E Gde E Synm E Prr E Meis E Ltbp E Uqcrfs Kcnj Myh Ndufa Slc41a Letm Tbc1d Crct Aldoa Iars Atp1b Scn4b Igfbp Mrps Atp5f Tmx Atp5e Ppa Mef2c A230052G05Rik Ndufa Krt Dll Mfn RP24-358M Ptges Cdkn1a Mrpl

15 Ccbe Ndufs Slc25a Vwf Atp6v1b Cx3cl Sptbn Ndufs Them Fbln Fam73b Hdac Slc13a Grsf Gale Esm Mrps18a Mrpl Ushbp Mt Foxc Cers Cyp26b Mrpl S100g Ighg2b Timm17a E2f Adamts Afg3l Slc39a Masp Calb Rasgrf Ung Ptcd Sdha Sirt Ackr Agl Slc19a Kctd Tmco Hspa1b Pde4b

16 Fam131c Cars Cluh Endog Timm Mrpl Lace Rpp Alkbh Nudt C09Rik Cldn Cxcl Tril Coq Clcnkb Cmc Tmem106b Phb Tarsl Ppp1r13l Nfkb Cldn Icam Coa Macrod Filip Slc25a Pi4ka Slit Ndufs Fa2h Ube2m Man2a Ano Adamtsl Foxred St8sia Fdx Magi Tiam Hpd Nrg Tmem Gpnmb

17 Elovl Ren Gm Pla2g4b Slc38a mt-tc Cryab Smpd Tbcel Pnpt Zfp Fitm Samm Ptcd Lmo Fars Pik3c2b Cep RP23-349J Mrpl Gpx Arl4c B4galt Slc25a Fbxo Letmd Dchs Mrpl Adamts Ndufb Ngb Cers St6gal E14Rik Ndufb mt-tl Tyro Oaf Tufm Hgd Clic Ccr Alox12b Crim Stab

18 Cmtm Tmem74b Cbx Nrtn Atp13a Oxnad Mrps Eif Abca Uqcc Igdcc Kctd Sdpr

19 Supplement Table 2. qpcr primer sequences Gene Forward Backward Ppargc1a AGTCCCATACACAACCGCAG CCCTTGGGGTCATTTGGTGA Esrra CACTACGGTGTGGCATCCTG ACAGCTGTACTCGATGCTCC Nrf1 CTCGCTGGAAAAAGAAGTG CCGTCCAGGAGTTCAGAGG Nrf2 AAGTGCCCGAAGCCCTCCCT GCCCTTCTGGCGCCGGTTAC Tfam GAGCAGCTAACTCCAAGTCAG GAGCCGAATCATCCTTTGCCT Ndufa10 ACCTTTCACTACCTGCGGATG GTACCCAGGGGCATACTTGC Atp5a1 TCTCCATGCCTCTAACACTCG CCAGGTCAACAGACGTGTCAG Atp5b TCCTGCCAGAGACTATGCG GATGACTGCCACGATTCGC Maoa GCCCAGTATCACAGGCCAC GTCCCACATAAGCTCCACCA Ucp2 CAG CCA GCG CCC AGT ACC CAATGCGGACGGAGGCAAAGC Sod2 GGCCAAGGGAGATGTTACAA GAACCTTGGACTCCCACA Opa1 TGGAAAATGGTTCGAGAGTCAG CATTCCGTCTCTAGGTTAAAGCG Mfn1 ACCTGGAGCAAGAGTTCCAA TGGTGTTTTCAGTGCCAGAG Mfn2 ATGTTACCACGGAGCTGGAC ACTGCTTCTCCGTCTGCAT Drp1 GCGCTGATCCCGCGTCAT CCGCACCCACTGTGTTGA Fis1 TTACCCACTTGCCCCTTTCTT TTGCCCTTCCAGAACTTGGA Slc2a1 ACACTCACCACGCTTTGGTC ACACACCGATGATGAAGCGG Slc2a4 CGTGGCCATCTTCTCTGTGG GCATAGACTCCAAGCCCAGC Hk1 CGGAATGGGGAGCCTTTGG GCCTTCCTTATCCGTTTCAATGG Hk2 TGATCGCCTGCTTATTCACGG AACCGCCTAGAAATCTCCAGA Pkm2 GCCGCCTGGACATTGACTC CCATGAGAGAAATTCAGCCGAG Ldha GCTGCCCCTGCAGAAAATT CACTGGAGTCACAGTTTTCAACGT Pdk4 AAAAAGCGACAACAAACTCCA AACGCAAATCCACCAAGATA Acox1 CTTGGATGGTAGTCCGGAGA TGGCTTCGAGTGAGGAAGTT Acox2 TACCAACGCCTGTTTGAGTG TTTCCAGCTTTGCATCAGTG Acox3 GTGACACGAAGACCCTGCTT TGAACATGGCGAATCCATTA Ldl GGGAGTTTGGCTCCAGAGTTT TGTGTCTTCAGGGGTCCTTAG Acadl TCACCACACAGAATGGGAGA TTTCTCTGCGATGTTGATGC Acadvl GCATCTTGCTCTATGGCACA CACTCGAGGGCTCTGTTAGG Cpt1 CAGGATTTTGCTGTCAACCTC GAGCATCTCCATGGCGTAG Cpt2 CAGCACAGCATCGTACCCA TCCCAATGCCGTTCTCAAAAT Slc1a5 CATCAACGACTCTGTTGTAGACC CGCTGGATACAGGATTGCGG Gls GGGAATTCACTTTTGTCACGA GACTTCACCCTTTGATCACC Glud1 CCCAACTTCTTCAAGATGGTGG AGAGGCTCAACACATGGTTGC Got1 GCGCCTCCATCAGTCTTTG ATTCATCTGTGCGGTACGCTC 19

20 Got2 GGACCTCCAGATCCCATCCT GGTTTTCCGTTATCATCCCGGTA c-myc CAACGACAGCAGCTCGCCCA CCGTGGGGAGGACTCGGAGG Ccnd1 TGGTGGCTGCGATGCA TGCGTTGTGCGGTAGCA Ccne GCGGACACAGCTTCGGGTCT GCGGACTGAAAGGTCGGAGCC Ccna CCCATCGACCGCAGCAAGCA AGGCGGCTCCATGAGGGACA Pcna CACGTATATGCCGAGACCTTAGC CTCCACTTGCAGAAAACTTCACC Wt1 CGGCGGAGTGCTTAGATGAG CTCGCTTCCGTTCCTTCTGT Synpo GGCAGAGGGTGAACGAGTTC GGGCCTCTTGGTTGAGCTTT Nphs1 AGCGTGAGCCCTCACTCGGT CTCCGCCAGAGGAGTCCCCC Nphs2 CACAAGGTTGATCTCCGTCTC GCAGACAGCGTCTATCTCCATT Col1a1 GCCAAGAAGACATCCCTGAA GTTTCCACGTCTCACCATTG Col3a1 ACAGCTGGTGAACCTGGAAG ACCAGGAGATCCATCTCGAC Fn ACAAGGTTCGGGAAGAGGTT CCGTGTAAGGGTCAAAGCAT 20

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