SUPPLEMENTARY INFORMATION doi:1.138/nature1458 Grosso et al. Barbosa et al. 74 72 45 33 47 7 51 Rappsilber et al. Supplementary Figure 1 a, Venn-Diagram of identified splice factors in the work of Barbossa et al., Grosso et al. and Rappsilber et al. A total number of 329 genes were indentified. 1 2 3A 4 5 6 7 8 3C Supplementary Figure 2 Schematic representation of KHK pre-mrna. Alternative spliced exons 3A and 3C leading to expression of either KHK-A or KHK-C protein are highlighted in blue (exon 3A) and red (exon 3C). www.nature.com/nature 1
RESEARCH SUPPLEMENTARY INFORMATION a Rel. mrna levels Rel. mrna levels 2 15 1 5 3 2 1 sham 1K1C 15 1 5 ** b Nppa Nppb αmhc βmhc sk. αactin sham 2 ** TAC c Rel. mrna levels d Rel. mrna levels 16 14 12 1 8 6 4 2 sk. αactin Nppb αmhc βmhc NaCl ISO ** ** ** sk. αactin Nppb αmhc βmhc NPPA Ctrl HCM NPPB Rel. mrna levels 12 1 8 6 4 2 NPPA Ctrl sten. * * NPPB Supplementary Figure 3 Gene expression of hypertrophic markers in mouse models of cardiac hypertrophy or heart disease patients and their corresponding controls, presented in Extended Data Fig. 1. a, b, Probes from left ventricles of 1K1C, TAC or ISO-treated mice and their corresponding controls were analyzed for mrna hypertrophic markers. All values were presented in relation to sham-operated controls set as 1. (n = 6; shown is mean ± SEM; *p<.5; **p<.1; p <.1; two-tailed unpaired t-test). c, d, Leftventricular biopsies of hypertrophic cardiomyopathy (HCM) patients and healthy controls were analysed for mrna expression hypertrophic markers (t). All values are presented in relation to healthy controls set as 1. (n = 6 for controls and n = 16 for patient samples; shown is mean ± SEM; *p<.5; p<.1; two-tailed unpaired t-test). 2 WWW.NATURE.COM/NATURE
SUPPLEMENTARY INFORMATION RESEARCH Rel. mrna levels 4 3.5 3 2.5 2 1.5 1.5 Sf3a3 Sf3b2 Sf3b3 Sf3b1 ** ** * ** ** shsf3a3 shsf3b2 shsf3b3 shsf3a3 shsf3b2 shsf3b3 ** HIF1αΔODD Supplementary Figure 4 Depletion of U2-snRNP components in NMC in the presence or absence of HIF1αΔODD. NMC were transduced with either scrambled shrna or shsf3a3, shsf3b2 or shsf3b3 were co-transduced with vector or HIF1αΔODD. Gene expression was evaluated by qrt-pcr. Values were normalised to / infected NMC (n = 3; shown is mean ± SD; *p <.5; **p <.1; p <.1; one-way ANOVA followed by Dunnett s multiple comparison post-test). www.nature.com/nature 3
RESEARCH SUPPLEMENTARY INFORMATION OCR/ECAR [pmol/mph] ECAR [mph/min] 2 15 1 5 1 8 6 4 2 OA shsf3b1 8 17 34 42 51 59 68 76 85 93 12 11 119 shns shsf3b1 Time (min) OCR [pmol/min] 3 2 1 FCCP OA FCCP Supplementary Figure 5 Assessment of extracellular acidification rate (ECAR), and oleic acid and FCCP-induced oxygen consumption rate (OCR) in NMC transduced with and shsf3b1 lentiviruses. Highlighted ECAR measurements were done at baseline. All data are compared to -transduced NMC. (n = 9 per condition) 4 WWW.NATURE.COM/NATURE
SUPPLEMENTARY INFORMATION RESEARCH mm Glc 2.5 mm Glc 1 mm Glc µm Frc µm Frc 5 µm Frc a KHK-A KHK-C KHK-A KHK-C KHK-A KHK-C KHK-A KHK-C KHK-A KHK-C KHK-A KHK-C Khk-A/C Khk-C α-actinin Rel. lipid accumulation e Rel. [ 3 H] count in lipid fraction 3 2 1 8 6 4 2 / /HIF1αΔODD ** shsf3b1 -A -C shglut5 5 4 3 2 1 shsf3b1 21% O 2 3% O 2 b c d g OCR/ECAR [pmol/mph/min] ECAR [mph/min] 2 15 1 5 1 8 6 4 2 -A -C OA OCR [pmol/min] FCCP -A 8 17 34 42 51 59 68 76 85 93 12 11 119 Time (min) -A 2 15 1 5 OA FCCP Rel. lipid accumulation -A -C HIF1αΔODD h OCR/ECAR [pmol/mph/min] ECAR [mph/min] 2 15 1 5 1 8 6 4 2 -A -C shglut5 B d, NMC transduced and treated as indicated were incubated overnight with OA and stained with Nile Red. Stainings were quantified using a plate reader with 485/5 nm excitation/emission filters. Values were compared to control set as 1.. (n = 3; shown is mean ± SD; p >.1; one-way ANOVA followed by Dunnett s multiple comparison post-test).e, NMC infected as denoted were incubated with oleic acid (OA) and [ 3 H]fructose. A lipid extraction was done to assess incorporation of [ 3 H] into lipids (n = 4; shown is mean ± SD; p >.1; one-way ANOVA followed by Dunnett s multiple comparison post-test). f, shrna against Glut5 was evaluated by qpcr for its potential to inhibit Glut5 expression. Data are shown in relation to NMC (set to 1.), (n = 3; shown is mean ± SD; p >.1; two-tailed unpaired t-test). g, h, Assessment of ECAR and OA and FCCP-induced OCR in NMC infected with or -A lentiviruses (g) and or -C lentiviruses (h), Highlighted ECAR measurements were done at baseline. All data are compared to transduced NMC (n = 9; shown is mean ± SEM; p >.1; two-tailed unpaired t-test). KHK-A KHK-C OA Rel. lipid accumulation f Glut5 (Rel. mrna levels) 8 17 34 42 51 59 68 76 85 93 12 11 119 -C Time (min) OCR [pmol/min] 2 15 1 5 FCCP -C OA FCCP 6 4 2 1.2 1.8.6.4.2 mock PE shglut5 shsf3b1 -A -C Supplementary Figure 6 Downstream metabolic effects of fructose metabolism in NMC. a, Lysates of NMC transduced with or and coinfected with vector or KHK-A or KHK-C overexpression lentiviruses, respectively and cultured in media with different fructose and glucose concentrations as indicated were probed for protein expression of KHK-A, KHK-C and sarcomeric α-actinin by immunoblotting. www.nature.com/nature 5
RESEARCH SUPPLEMENTARY INFORMATION a b Ad lacz Ad Cre Ad-lacZ / AAV9-fl/fl- GFP 1 x 1 x Ad-lacZ / AAV9-fl/fl-shSf3b1#1 GFP 1 x 1 x Ad-lacZ / AAV9-fl/fl-shSf3b1#2 1 x GFP 1 x shsf3b1#1 shsf3b1#2 shsf3b1#1 shsf3b1#2 GFP Ad-Cre / AAV9-fl/fl- Ad-Cre/ AAV9-fl/fl-shSf3b1#1 Ad-Cre/ AAV9-fl/fl-shSf3b1#2 Cre Sf3b1 Sf3b1 (Rel. mrna levels) Sf3b1 (Rel. mrna Levels) c 1.5.5 d 1 1.5 1.5 Mlc2v-cre Mlc2v-cre+ LV Liver Spleen Pancreas sk. Muscle * LV Liver Spleen Pancreas sk. Muscle * AAV9-fl/fl-shSf3b1#1 α-actinin WAT Intestine Gut right Kidney left Kidney Brain BAT Lungs AAV9-fl/fl-shSf3b1#1 WAT Intestine Gut right Kidney left Kidney Brain BAT Lungs Supplementary Figure 7 In vitro and in vivo validation of modified AAV9. a, b, NMC transduced with AAV9-fl/fl, AAV9-fl/fl-shSf3b1#1 and AAV9-fl/fl-shSf3b1#2 viruses in NMC were investigated for removal of the CMV-GFP/ stop reporter cassette by Adeno-Cre-mediated recombination using immunofluorescent microscopy (a) and immunoblot detection for indicated proteins (b) As a control served transductions with Adeno-lacZ viruses, where the GFP/stop reporter cassette is retained. c, d, Sf3b1 mrna expression was assessed using qpcr in different organs of Mlc2v-cre and Mlc2v-cre+ mice injected as in m. Data represent mean ± SEM; (n = 4 for Mlc2v-cre AAV9-fl/fl-shSf3b1#1 or Mlc2vcre+ AAV9-fl/fl-shSf3b1#1 mice and n = 3 for for Mlc2v-cre AAV9-fl/fl-shSf3b1#2 or Mlc2v-cre+ AAV9-fl/fl-shSf3b1#2 mice; shown is mean ± SEM; p <.1; two-tailed unpaired t-test). 6 WWW.NATURE.COM/NATURE
SUPPLEMENTARY INFORMATION RESEARCH Sample ID LV 1J LV 2J LV 3J LV 26 LV 29 LV 3 LV 34 LV 39 LV 41 LV 43 LV 48 LV 33 LV 61 LV 62 LV 9 LV 92 LV11 Sample ID Sex Type age AVA (cm 2 ) male male male male male male Sex Type Age PCWP (mmhg) MPG (mmhg) PWD (mm) IVSD (mm) Antihyp. Drugs EF (%) Type 2 Diabetes.8.8 54 yes yes.6.6 45 yes 75 no.7.7 52 yes 74 yes 8 47 14 yes 6 yes 74.8 47 yes 75 no 77.77 44 12 13 yes 55 no 58 n.a. yes 65 yes 72.9 43 15 16 yes 7 yes 83.7 5 12 13 yes 7 yes 77.6 67 14 16 yes 6 77.6 7 15 17 yes 6 no 77.9 43 15 15 yes 6 79.5 5 17 15 yes 6 74.7 38 19 19 yes 6 57.6 52 yes 6 78.4 53 17 21 yes 6 52.7 74 14 19 yes 6 CI (l/min/ m 3 ) pmean (mmhg) IVSD (mm) Hyperte nsion EF (%) LVEDD (mm) LV 77 HCM 77.7 4 4 yes 65 LV 91 HCM 5 yes 3 LV115 HCM 56 68 68 26 yes 6 LV496 male HCM 42 16 1.8 2 yes 6 76 LV5 male HCM 45 19 1.98 13 yes 18 61 LV552 HCM 55 12 1.67 2 yes 46 43 LV624 HCM 66 1.56 31 yes 65 LV679 HCM 53 11 2.3 2 yes 39 4 LV73 male HCM 48 23 2. yes 3 LV712 HCM 55 14 2. LV7 male HCM 33 1.37 17 yes 4 53 yes 2 Supplementary Table 4 Demographic and clinical data of patients with and hypertrophic cardiomyopathy. LV = left ventricle; AVA = aortic valve area; MPG = mean pressure gradient; PWD = posterior wall diameter; IVSD = interventricular septum diameter; EF = ejection fraction; PCWP = pulmonary capillary wedge pressure; CI = cardiac index; pmean = mean pressure; LVEDD = left ventricular end-diastolic diameter. www.nature.com/nature 7
RESEARCH SUPPLEMENTARY INFORMATION The protein coding sequence of (mouse) codon optimised Sf3b1 atggcgaagatcgccaagactcacgaagatatcgaagcacagattcgagaaattcaaggcaagaaggcagctcttgatga! agcccaaggagtgggccttgattccacaggttattatgaccaagaaatttatggtggaagtgatagcagatttgctggat! atgtgacatcaattgctgcaactgaacttgaagatgatgacgatgactactcatcatccacgagcttgctcggtcagaag! aagcctggatatcatgcccccgtggcgttgcttaatgatataccacagtcaacagagcagtatgatccatttgctgagca! tcgtcctccaaagattgccgatcgggaagatgaatacaaaaagcataggcggaccatgataatttccccagagcgtcttg! atccttttgcagatggagggaagactcccgatcctaaaatgaatgctagaacctacatggatgttatgcgagaacaacat! ttgactaaggaagagagagaaattaggcaacaactagcagaaaaagctaaagctggagaactaaaagtcgtcaatggagc! agcagcatcccagcctccctcaaaacgaaaacggcgctgggatcagaccgctgaccagactcctggtgccactcccaaaa! agctatcgagttgggatcaggcagagacccctgggcataccccatctttaagatgggatgagacaccgggtcgtgcaaaa! ggaagtgaaacacctggcgcaaccccaggctcaaaaatatgggaccctacaccgagtcatacacctgcgggagctgctac! tcctgggcgaggcgacacaccaggccatgcaaccccgggccatggtggtgcaacttccagtgctcgtaaaaacagatggg! atgagacccccaaaacagaaagagatactcctgggcatggaagtggatgggctgagactcctcgaacagatcgaggtgga! gactctattggtgaaacaccaactcctggagcaagtaaaagaaagtctcgttgggatgaaacgccggcgagtcaaatggg! tggaagcactcctgttctgactccaggaaaaacaccaattggcacaccagccatgaacatggctaccccgactccaggtc! acataatgagcatgacacctgaacagcttcaggcgtggcggtgggagagagaaattgatgaacgaaaccgcccactttct! gatgaagaattagatgctatgttcccagaaggatataaggtacttccccctccagctggttatgttcctattcgaactcc! agctcgaaagctgacagcaactcctacacctttgggtggtatgactggtttccacatgcaaactgaagacagaactatga! aaagtgtcaatgaccagccatctgggaatcttccatttttaaaacctgatgacattcagtactttgataaactattggtt! gatgtagatgaatcaacacttagtccagaagaacaaaaagaaagaaaaataatgaagttgcttttaaaaattaagaatgg! tacacctccaatgagaaaggctgccttacgtcagattactgataaagctcgagaatttggagccggaccactgttcaacc! agattctgccactgctgatgtcacctacactggaagaccaggagagacacctgctggtgaaggtcatcgaccggattctg! tataaactggacgatctggtgagaccatacgtccataaaatcctggtggtcattgagcccctgctgatcgacgaagatta! ctatgccagggtggagggcagagaaatcatttcaaacctggctaaggccgctggactggcaacaatgatcagcactatgc! ggcccgacattgataacatggatgagtatgtgagaaataccacagcacgggccttcgctgtggtcgcaagtgccctgggc! atcccctcactgctgccttttctgaaggccgtgtgcaaatctaagaaaagttggcaggcacggcacactgggatcaagat! tgtgcagcagatcgccattctgatgggctgtgctatcctgcctcacctgcgcagtctggtggagatcattgaacatggcc! tggtggacgagcagcagaaggtcaggactatctcagctctggcaattgcagccctggctgaggctgcaaccccttatgga! atcgaatcattcgatagcgtgctgaagccactgtggaaaggaattcgacagcataggggcaagggactggccgcttttct! gaaagccatcggctatctgattccactgatggacgccgagtacgctaactactatacacgggaagtgatgctgatcctga! ttcgcgagttccagagccccgacgaggaaatgaagaaaatcgtgctgaaggtggtcaaacagtgctgtggcacagatgga! gtggaggccaattatatcaaaactgaaattctgccccctttctttaagcacttttggcagcatcgcatggccctggacag! gagaaactaccgacagctggtggatactaccgtcgaactggctaataaggtcggagcagccgagatcattagcagaatcg! tcgacgatctgaaggatgaggccgaacagtaccggaaaatggtcatggagaccatcgaaaagattatggggaacctgggc! gctgcagacatcgatcacaagctggaggaacagctgatcgacgggattctgtatgccttccaggagcagacaactgaaga! ttccgtgatgctgaacgggtttggcaccgtggtcaatgctctgggaaagcgcgtgaaaccttacctgccacagatctgcg! ggacagtcctgtggcggctgaacaataagtctgcaaaagtgcgccagcaggccgctgacctgatcagtaggactgctgtg! gtcatgaagacctgtcaggaggaaaaactgatgggacacctgggggtggtcctgtacgaatatctgggggaggaataccc! agaggtgctggggtctatcctgggcgcgttaaaggccatcgtgaacgtcattggcatgcacaagatgaccccacccatca! aagatctgctgccacgactgacacccattctgaagaacaggcatgagaaagtgcaggaaaattgcattgacctggtggga! agaattgctgatcgcggagctgagtatgtgagtgcccgagaatggatgaggatctgtttcgagctgctggaactgctgaa! ggcacacaagaaagccattcggcgcgctactgtgaatacctttgggtacatcgccaaagctattggacctcatgacgtgc! tggccaccctgctgaacaatctgaaggtccaggagagacagaaccgggtgtgcaccacagtcgcaatcgccattgtggcc! gagacctgttcccctttcacagtcctgccagctctgatgaatgagtatagagtgcctgaactgaacgtgcagaatggcgt! cctgaaaagcctgtccttcctgtttgagtacatcggcgaaatgggaaaggactacatctacgcagtgacaccactgctgg! aggatgccctgatggaccgcgatctggtgcaccgacagactgctagcgcagtggtccagcatatgtccctgggagtgtat! ggattcgggtgcgaggactccctgaaccacctgctgaattacgtgtggcccaacgtctttgaaacctctcctcatgtgat! ccaggcagtcatgggagccctggagggactgagggtggccattggaccctgcagaatgctgcagtattgtctgcaggggc! tgttccaccctgctcgcaaggtgcgagacgtgtactggaagatctataactccatctacatcggctctcaggatgctctg! attgcacattaccctcgaatctacaatgacgacaagaacacttacatccgctatgaactggactacatcctgtga! Translation of the protein coding sequence of (mouse) codon optimised Sf3b1 MAKIAKTHEDIEAQIREIQGKKAALDEAQGVGLDSTGYYDQEIYGGSDSRFAGYVTSIAATELEDDDDDYSSSTSLLGQKKPGYHAPVAL LNDIPQSTEQYDPFAEHRPPKIADREDEYKKHRRTMIISPERLDPFADGGKTPDPKMNARTYMDVMREQHLTKEEREIRQQLAEKAKAGE LKVVNGAAASQPPSKRKRRWDQTADQTPGATPKKLSSWDQAETPGHTPSLRWDETPGRAKGSETPGATPGSKIWDPTPSHTPAGAATPGR GDTPGHATPGHGGATSSARKNRWDETPKTERDTPGHGSGWAETPRTDRGGDSIGETPTPGASKRKSRWDETPASQMGGSTPVLTPGKTPI GTPAMNMATPTPGHIMSMTPEQLQAWRWEREIDERNRPLSDEELDAMFPEGYKVLPPPAGYVPIRTPARKLTATPTPLGGMTGFHMQTED RTMKSVNDQPSGNLPFLKPDDIQYFDKLLVDVDESTLSPEEQKERKIMKLLLKIKNGTPPMRKAALRQITDKAREFGAGPLFNQILPLLM SPTLEDQERHLLVKVIDRILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIISNLAKAAGLATMISTMRPDIDNMDEYVRNTTAR AFAVVASALGIPSLLPFLKAVCKSKKSWQARHTGIKIVQQIAILMGCAILPHLRSLVEIIEHGLVDEQQKVRTISALAIAALAEAATPYG IESFDSVLKPLWKGIRQHRGKGLAAFLKAIGYLIPLMDAEYANYYTREVMLILIREFQSPDEEMKKIVLKVVKQCCGTDGVEANYIKTEI LPPFFKHFWQHRMALDRRNYRQLVDTTVELANKVGAAEIISRIVDDLKDEAEQYRKMVMETIEKIMGNLGAADIDHKLEEQLIDGILYAF QEQTTEDSVMLNGFGTVVNALGKRVKPYLPQICGTVLWRLNNKSAKVRQQAADLISRTAVVMKTCQEEKLMGHLGVVLYEYLGEEYPEVL GSILGALKAIVNVIGMHKMTPPIKDLLPRLTPILKNRHEKVQENCIDLVGRIADRGAEYVSAREWMRICFELLELLKAHKKAIRRATVNT FGYIAKAIGPHDVLATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTVLPALMNEYRVPELNVQNGVLKSLSFLFEYIGEMGKDYIYAVT PLLEDALMDRDLVHRQTASAVVQHMSLGVYGFGCEDSLNHLLNYVWPNVFETSPHVIQAVMGALEGLRVAIGPCRMLQYCLQGLFHPARK VRDVYWKIYNSIYIGSQDALIAHYPRIYNDDKNTYIRYELDYIL*! Supplementary Data 1 Coding and amino acid sequence of (mouse) codon optimised Sf3b1. 8 WWW.NATURE.COM/NATURE
SUPPLEMENTARY INFORMATION RESEARCH Agarose gel referring to Fig. 1c Agarose gel referring to Fig. 1d HIF1αΔODD shns shsf3b1 shns shsf3b1 sham 1K1C 1 bp 5 bp 4 bp 3 bp 2 bp 1 bp 1.5 % agarose gel, Gene Ruler 1 bp DNA Ladder 1 bp 5 bp 4 bp 3 bp 2 bp 1 bp 1.5 % agarose gel, Gene Ruler 1 bp DNA Ladder Agarose gels referring to Fig. 1g Primer set 1 Primer set 1 1 bp 5 bp 3 bp 2 bp 1 bp 5 bp 3 bp 2 bp 1.5 % agarose gel, Gene Ruler 1 bp DNA Ladder Primer set 2 1.5 % agarose gel, Gene Ruler 1 bp DNA Ladder Primer set 2 1 bp 5 bp 3 bp 2 bp 5 bp 3 bp 2 bp 1.5 % agarose gel, Gene Ruler 1 bp DNA Ladder 1.5 % agarose gel, Gene Ruler 1 bp DNA Ladder www.nature.com/nature 9
RESEARCH SUPPLEMENTARY INFORMATION Immunoblots Figure 1e 15 1 75 Anti-HIF1α 15 13 5 Anti-Sf3b1 Anti-Khk-A/C (l. E.) 13 1 Anti-Khk-A/C 75 Anti-αActinin 1 WWW.NATURE.COM/NATURE
SUPPLEMENTARY INFORMATION RESEARCH Immunoblots Figure 1h 13 1 15 7 1 Anti-SF3B1 Anti-HIF1α Anti-KHK-A/C 13 Anti-KHK-C 1 7 Anti-cardiac αactinin www.nature.com/nature 11
RESEARCH SUPPLEMENTARY INFORMATION ChIP Fig. 2b 2 bp 1 bp 21% O 2 HIF1αΔODD 3% O 2 21% O 2 HIF1αΔODD shhif1α 3% O 2 shhif1α 5 bp 4 bp 3 bp 2 bp 1 bp 12 WWW.NATURE.COM/NATURE
SUPPLEMENTARY INFORMATION RESEARCH Immunoblots Figure 4e 13 1 7 Anti-Hif1α 15 13 Anti-Sf3b1 15 Anti-GFP Anti-Khk-A/C Anti-Khk-C 13 1 Anti-αActinin www.nature.com/nature 13
RESEARCH SUPPLEMENTARY INFORMATION Immunoblots Figure 4h 13 1 7 Anti-Hif1α 15 13 Anti-Sf3b1 5 Anti-GFP Anti-Khk-A/C 13 Anti-Khk-C 1 Anti-αActinin 14 WWW.NATURE.COM/NATURE
SUPPLEMENTARY INFORMATION RESEARCH Immunoblots Figure 5d 13 1 7 Anti-HIF1α 15 13 Anti-Sf3b1 Anti-Khk-A/C Anti-Khk-C 1 75 5 Anti-αActinin www.nature.com/nature 15
RESEARCH SUPPLEMENTARY INFORMATION Immunoblots Figure 5h 13 1 Anti-HIF1α 15 Anti-Sf3b1 Anti-Khk-A/C Anti-Khk-C 1 75 5 Anti-αActinin 16 WWW.NATURE.COM/NATURE