1 SUPPLEMENTARY INFORMATION wt and 2657+5G>A mutant CFTR splicing minigene sequence CTTTGGCATTAGGAGCTTGAGCCCAGACGGCCCTAGCAGGGACCCCAGCGCCCGAGAGACCATGCAGAGGTCGCCTCT GGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAGCTGGACCAGACCAATTTTGAGGAAAGGATACAGACAGCGCCT GGAATTGTCAGACATATACCAAATCCCTTCTGTTGATTCTGCTGACAATCTATCTGAAAAATTGGAAAGAGAATGGGA TAGAGAGCTGGCTTCAAAGAAAAATCCTAAACTCATTAATGCCCTTCGGCGATGTTTTTTCTGGAGATTTATGTTCTA TGGAATCTTTTTATATTTAGGGGAAGTCACCAAAGCAGTACAGCCTCTCTTACTGGGAAGAATCATAGCTTCCTATGA CCCGGATAACAAGGAGGAACGCTCTATCGCGATTTATCTAGGCATAGGCTTATGCCTTCTCTTTATTGTGAGGACACT GCTCCTACACCCAGCCATTTTTGGCCTTCATCACATTGGAATGCAGATGAGAATAGCTATGTTTAGTTTGATTTATAA GAAGACTTTAAAGCTGTCAAGCCGTGTTCTAGATAAAATAAGTATTGGACAACTTGTTAGTCTCCTTTCCAACAACCT GAACAAATTTGATGAAGGACTTGCATTGGCACATTTCGTGTGGATCGCTCCTTTGCAAGTGGCACTCCTCATGGGGCT AATCTGGGAGTTGTTACAGGCGTCTGCCTTCTGTGGACTTGGTTTCCTGATAGTCCTTGCCCTTTTTCAGGCTGGGCT AGGGAGAATGATGATGAAGTACAGAGATCAGAGAGCTGGGAAGATCAGTGAAAGACTTGTGATTACCTCAGAAATGAT CGAGAACATCCAATCTGTTAAGGCATACTGCTGGGAAGAAGCAATGGAAAAAATGATTGAAAACTTAAGACAAACAGA ACTGAAACTGACTCGGAAGGCAGCCTATGTGAGATACTTCAATAGCTCAGCCTTCTTCTTCTCAGGGTTCTTTGTGGT GTTTTTATCTGTGCTTCCCTATGCACTAATCAAAGGAATCATCCTCCGGAAAATATTCACCACCATCTCATTCTGCAT TGTTCTGCGCATGGCGGTCACTCGGCAATTTCCCTGGGCTGTACAAACATGGTATGACTCTCTTGGAGCAATAAACAA AATACAGGATTTCTTACAAAAGCAAGAATATAAGACATTGGAATATAACTTAACGACTACAGAAGTAGTGATGGAGAA TGTAACAGCCTTCTGGGAGGAGGGATTTGGGGAATTATTTGAGAAAGCAAAACAAAACAATAACAATAGAAAAACTTC TAATGGTGATGACAGCCTCTTCTTCAGTAATTTCTCACTTCTTGGTACTCCTGTCCTGAAAGATATTAATTTCAAGAT AGAAAGAGGACAGTTGTTGGCGGTTGCTGGATCCACTGGAGCAGGCAAGACTTCACTTCTAATGATGATTATGGGAGA ACTGGAGCCTTCAGAGGGTAAAATTAAGCACAGTGGAAGAATTTCATTCTGTTCTCAGTTTTCCTGGATTATGCCTGG CACCATTAAAGAAAATATCATCTTTGGTGTTTCCTATGATGAATATAGATACAGAAGCGTCATCAAAGCATGCCAACT AGAAGAGGACATCTCCAAGTTTGCAGAGAAAGACAATATAGTTCTTGGAGAAGGTGGAATCACACTGAGTGGAGGTCA ACGAGCAAGAATTTCTTTAGCAAGAGCAGTATACAAAGATGCTGATTTGTATTTATTAGACTCTCCTTTTGGATACCT AGATGTTTTAACAGAAAAAGAAATATTTGAAAGCTGTGTCTGTAAACTGATGGCTAACAAAACTAGGATTTTGGTCAC TTCTAAAATGGAACATTTAAAGAAAGCTGACAAAATATTAATTTTGAATGAAGGTAGCAGCTATTTTTATGGGACATT TTCAGAACTCCAAAATCTACAGCCAGACTTTAGCTCAAAACTCATGGGATGTGATTCTTTCGACCAATTTAGTGCAGA AAGAAGAAATTCAATCCTAACTGAGACCTTACACCGTTTCTCATTAGAAGGAGATGCTCCTGTCTCCTGGACAGAAAC AAAAAAACAATCTTTTAAACAGACTGGAGAGTTTGGGGAAAAAAGGAAGAATTCTATTCTCAATCCAATCAACTCTAT ACGAAAATTTTCCATTGTGCAAAAGACTCCCTTACAAATGAATGGCATCGAAGAGGATTCTGATGAGCCTTTAGAGAG AAGGCTGTCCTTAGTACCAGATTCTGAGCAGGGAGAGGCGATACTGCCTCGCATCAGCGTGATCAGCACTGGCCCCAC GCTTCAGGCACGAAGGAGGCAGTCTGTCCTGAACCTGATGACACACTCAGTTAACCAAGGTCAGAACATTCACCGAAA GACAACAGCATCCACACGAAAAGTGTCACTGGCCCCTCAGGCAAACTTGACTGAACTGGATATATATTCAAGAAGGTT ATCTCAAGAAACTGGCTTGGAAATAAGTGAAGAAATTAACGAAGAAGACTTAAAGgtaggtatacatcgcttgggggt atttcaccccacagaatgcattgagtagaatgcaatatgtagcatgtaacaaaatttactaaaatcataggattagga taaggtgtatcttaaaactcagaaagtatgaagttcattaattatacaagcaacgttaaaatgtaaaataacaaatga tttctttttgcaatggacatatctcttcccataaaatgggaaaggatttagtttttggtcctctactaagccagtgat aactgtgactataagttagaaagcatttgctttattaccatcttgaaccctctgtgggaagaggtgcagtataaataa ctgtataaataaatagtagctttcattatttatagctcgcaaaataatctgtatggaagtagcatatataaggtatat aaacatttagcctcttgataggactaactcacattctggtttgtatatcagtcttgcctgaatttagctagtgtgggc ttttttttatcttgtgagtttgctttatacattgggtttctgaaaagatttcttttagagaatgtatataagcttaac atgtactagtgccaatcttcagacagaaattttgttctattaggttttaagaataaaagcattttatttttaaaacag gaaataatataaaaaggagagtttttgttgttttagtagaaaacttaatgccttggatgaaatgagccatgggcaggg ttgtaatgaattgatatgtttaatagtatagatcatttgtgaataatatgacctttgacaagacacaagccattaaca tctgtaggcagaagtttccttctttgtaaaatgagggaataaaatagatccctaaagtgtgtaattttagtatttcta aactttatgaaggtttcctaaatgataattcatctatatagtgtttttttgtgtgtttgtttgtttgtttgtttgaga tggagtctcgctctgtcacctaggctggagtgcaatggtgcaacctcggctcactgcaacctctgcctcctgggttca agctaatctcctgcctcagcctcctgagtagctgagattacaggcatgcaccaccatgccgagctaatttttgtattt ttagtagagaaggggtttcatcatgttgaccaggctggtcttgaactcctgaccttgtgatccacccacctcagcctc ccaaagtgctggtattacaggcgtgtgccaccacgtccagcctgagccactgcgcccagcccatctatatagtttaat atcaatctaaatgaatttctcagtcctgagcctaaaaatttagttgtaaagaatgatatccttgactaataatagttt ctattaatggattgcatctagtgctaggtggcatatatttagtccccacaactaccctggaaggtatttaaaattttt cacatttgcagataaggaaactaaagttcagagttcggcaacatgcttgaattcaagcagctcctaggatgttaatgg tggaggttgggttcaaatccagatctgtctgactcaaaaaatgcatactcctaaccagtgcactatatcccaattcca taggagcccttctttgtgattcatagcactttcccatgagttttgttgattttgtgagaaacaaaactctttttcctt 2 tggactgtctggaatctctcttttacaaatttttgaaatgtatttctatgccaaaagacaaagatttctagaggaata tgcctaggatgagaattatgtaatttaaatcacagctggaaagagagaaagtcctaagttactaagaaatgttcaaac acaaatgggctttcagtctattggaagacctttatagctagaagtatactgaactgtacttgtccatggacccctgaa gaaacaggttaaatcaaagagagttctgggaaacttcatttagatggtatcattcatttgataaaaggtatgccactg ttaagcctttaatggtaaaattgtccaataataatacagttatataatcagtgatacatttttagaattttgaaaaat tacgatgtttctcatttttaataaagctgtgttgctccagtagacattattctggctatagaatgacatcatacatgg catttataatgatttatatttgttaaaatacacttagattcaagtaatactattcttttattttcatatattaaaaat aaaaccacaatggtggcatgaaactgtactgtcttattgtaatagccataattcttttattcagGAGTGCCTTTTTGA TGATATGGAGAGCATACCAGCAGTGACTACATGGAACACATACCTTCGATATATTACTGTCCACAAGAGCTTAATTTT TGTGCTAATTTGGTGCTTAGTAATTTTTCTGGCAGAGgtaagaatgttctattgtaaagtattactggatttaaagtt aaattaagatagtttggggatgtatacatatatatgcacacacataaatatgtatatatacacatgtatacatgtata agtatgcatatatacacacatatatcactatatgtatatatgtatatattacatatatttgtgattttacagtatata atggtatagattcatatagttcttagcttctgaaaaatcaacaagtagaaccactactgatagccagcagtctgagat tagtttctttaaaaaatgtttattatttaaaacattcagctgtgatcttggctttcttgtgaggttcaatagtttcta ttgagtaaaggagagaaatggcagagaatttacttcagtgaaatttgaattccattaacttaatgtggtctcatcaca aataatagtacttagaacacctagtacagctgctggacccaggaacacaaagcaaaggaagatgaaattgtgtgtacc ttgatattggtacacacatcaaatggtgtgatgtgaatttagatgtgggcatgggaggaataggtgaagatgttagaa aaaaaatcaactgtgtcttgttccattccagGTGGCTGCTTCTTTGGTTGTGCTGTGGCTCCTTGGAAAgtgagtatt ccatgtcctattgtgtagattgtgttttatttctgttgattaaatattgtaatccactatgtttgtatgtattgtaat ccactttgtttcatttctcccaagcattatggtagtggaaagataaggttttttgtttaaatgatgaccattagttgg gtgaggtgacacattcctgtagtcctagctcctccacaggctgacgcaggaggatcacttgagcccaggagttcaggg ctgtagtgttgtatcattgtgagtagccaccgcactccagcctggacaatatagtgagatcctatatctaaaataaaa taaaataaaatgaataaattgtgagcatgtgcagctcctgcagtttctaaagaatatagttctgttcagtttctgtga aacacaataaaaatatttgaaataacattacatatttagggttttcttcaaattttttaatttaataaagaacaactc aatctctatcaatagtgagaaaacatatctattttcttgcaataatagtatgattttgaggttaagggtgcatgctct tctaatgcaaaatattgtatttatttagactcaagtttagttccatttacatgtattggaaattcagtaagtaacttt ggctgccaaataacgatttcctatttgctttacagCACTCCTCTTCAAGACAAAGGGAATAGTACTCATAGTAGAAAT AACAGCTATGCAGTGATTATCACCAGCACCAGTTCGTATTATGTGTTTTACATTTACGTGGGAGTAGCCGACACTTTG CTTGCTATGGGATTCTTCAGAGGTCTACCACTGGTGCATACTCTAATCACAGTGTCGAAAATTTTACACCACAAAATG TTACATTCTGTTCTTCAAGCACCTATGTCAACCCTCAACACGTTGAAAGCAGGTGGGATTCTTAATAGATTCTCCAAA GATATAGCAATTTTGGATGACCTTCTGCCTCTTACCATATTTGACTTCATCCAGTTGTTATTAATTGTGATTGGAGCT ATAGCAGTTGTCGCAGTTTTACAACCCTACATCTTTGTTGCAACAGTGCCAGTGATAGTGGCTTTTATTATGTTGAGA GCATATTTCCTCCAAACCTCACAGCAACTCAAACAACTGGAATCTGAAGGCAGGAGTCCAATTTTCACTCATCTTGTT ACAAGCTTAAAAGGACTATGGACACTTCGTGCCTTCGGACGGCAGCCTTACTTTGAAACTCTGTTCCACAAAGCTCTG AATTTACATACTGCCAACTGGTTCTTGTACCTGTCAACACTGCGCTGGTTCCAAATGAGAATAGAAATGATTTTTGTC ATCTTCTTCATTGCTGTTACCTTCATTTCCATTTTAACAACAGGAGAAGGAGAAGGAAGAGTTGGTATTATCCTGACT TTAGCCATGAATATCATGAGTACATTGCAGTGGGCTGTAAACTCCAGCATAGATGTGGATAGCTTGATGCGATCTGTG AGCCGAGTCTTTAAGTTCATTGACATGCCAACAGAAGGTAAACCTACCAAGTCAACCAAACCATACAAGAATGGCCAA CTCTCGAAAGTTATGATTATTGAGAATTCACACGTGAAGAAAGATGACATCTGGCCCTCAGGGGGCCAAATGACTGTC AAAGATCTCACAGCAAAATACACAGAAGGTGGAAATGCCATATTAGAGAACATTTCCTTCTCAATAAGTCCTGGCCAG AGGGTGGGCCTCTTGGGAAGAACTGGATCAGGGAAGAGTACTTTGTTATCAGCTTTTTTGAGACTACTGAACACTGAA GGAGAAATCCAGATCGATGGTGTGTCTTGGGATTCAATAACTTTGCAACAGTGGAGGAAAGCCTTTGGAGTGATACCA CAGAAAGTATTTATTTTTTCTGGAACATTTAGAAAAAACTTGGATCCCTATGAACAGTGGAGTGATCAAGAAATATGG AAAGTTGCAGATGAGGTTGGGCTCAGATCTGTGATAGAACAGTTTCCTGGGAAGCTTGACTTTGTCCTTGTGGATGGG GGCTGTGTCCTAAGCCATGGCCACAAGCAGTTGATGTGCTTGGCTAGATCTGTTCTCAGTAAGGCGAAGATCTTGCTG CTTGATGAACCCAGTGCTCATTTGGATCCAGTAACATACCAAATAATTAGAAGAACTCTAAAACAAGCATTTGCTGAT TGCACAGTAATTCTCTGTGAACACAGGATAGAAGCAATGCTGGAATGCCAACAATTTTTGGTCATAGAAGAGAACAAA GTGCGGCAGTACGATTCCATCCAGAAACTGCTGAACGAGAGGAGCCTCTTCCGGCAAGCCATCAGCCCCTCCGACAGG GTGAAGCTCTTTCCCCACCGGAACTCAAGCAAGTGCAAGTCTAAGCCCCAGATTGCTGCTCTGAAAGAGGAGACAGAA GAAGAGGTGCAAGATACAAGGCTTTAGAGAGCAGCATAAATGTTGACATGGGACATTTGCTCATGGAATTGGAGCTCG TGGGACAGTCACCTCATGGAATTGGAGCTCGTGGAACAGTTACCTCTGCCTCAGAAAACAAGGATGAATTAAGTTTTT TTTTAAAAAAGAAACATTTGG Supp. Figure S1 wild-type and 2657+5G>A mutant CFTR cDNA sequence plus IVS 14, IVS 15 and IVS 16. CFTR minigenes were produced by inserting the complete wt-CFTR cDNA and relevant intronic regions into the pCDNA5/FRT/CFTR mammalian expression vector, as described previously (Masvidal, et al, 2014). Thus, the full sequence of the minigenes contains 3 full-length CFTR cDNA, relevant intronic regions and part of the 3’UTR region. The ATGtranslation initiation codon and the termination codon are highlighted in bold. Exons are represented in capital letters and introns (IVS14, IVS15 and IVS16) in small letters. Exon 16 is highlighted in grey. The 2657+5G>A mutation is underlined in bold and grey. The 2657+5G>A mutant minigene sequence is the same as the wt sequence, as the former was produced from the pCDNA5/FRT/wt-CFTR backbone by site-directed mutagenesis. 2657+5G>A CFTR splicing minigene intronic region targeted by AONs and their sequence 3’ss 15 5’ss 16 +5 +10 IVS16 +28 GTGAGTATTCCATGTCCTATTGTGTAGATTGTGTTTT GGUACAGGAUAACACAUCU AGGUACAGGAUAACACAUC AG 17 CFTR pre-mRNA Anti-AON1 Anti-AON2 Supp. Figure S2 Antisense oligonucleotide design and diagram showing an inset of CFTR IVS 16, which contains the 2657+5G>A splicing mutation, highlighted in bold (position +5). The region targeted by the antisense oligonucleotides AON1 (+10 to +28) and AON2 and their aligned sequences are represented below. As the 2657+5G>A mutation is located at the 5’ end of IVS 16, 5 nucleotides downstream the intron, a region that is conserved among mammals and harbours the canonical base-pairing region for U1 snRNA, a key component of U1 snRNP required for correct splicing, the AONs were designed a few nucleotides downstream from the U1 snRNA binding region. Nucleotides involved in base pairing with U1 snRNA are depicted in the grey box. AON2 was designed targeting the same sequence as AON1 but shifted by one nucleotide upstream (+9 to +27). 5′ ss: splicing donor site, 3’ ss: splicing acceptor site. 4 AON1 effect on the 2562T>G and 2657+5G>A CFTR variants assessed by sqRT-PCR in HEK293 and CFBE cells HEK293 CFBE AON1 wt % exon 16 100 inclusion SNP 100 Mut 55 Double Mut 43 SNP 100 Mut 94 AON1 Double Mut 94 wt 100 SNP 100 Mut 75 Double Mut 68 SNP 100 Mut 94 Double Mut 14 15 16 14 15 17 14 17 17 93 Supp. Figure S3 AON1 effect on the 2562T>G and 2657+5G>A CFTR variants using splicing minigenes. The c.2562T>G is a common single nucleotide polymorphism (SNP) in exon 15 which we have previously found in patient samples to be in linkage disequilibrium with the c.2657+5G>A mutation (Mut) (Masvidal L, et al, 2014). HEK293 and CF bronchial epithelial (CFBE41o-; from herein CFBE) cells were transiently transfected for 24 h with wt or mutant CFTR splicing minigenes alone or cotransfected with AON1. The AON1 effect on the SNP, both alone (SNP) and in combination with the 2657+5G>A splicing mutation (double Mut) was assessed by semi-quantitative (sq) RT-PCR. Left panel, sqRT-PCR analysis of wt, SNP, Mut, double Mut and the AON1 effect on these variants in HEK293 cells. The same for the right hand panel but in CFBE cells. Result from agarose gel electrophoretic analysis where the upper band corresponds to correctly spliced products and lower band corresponds to alternatively spliced products, i.e. exon 16 skipping. A lower band lacking exon 15 and 16 is detected, as previously (Masvidal L, et al, 2014). Numbers shown below correspond to the average percentage levels of exon 16 inclusion. 5 wt and alternative transcripts after AON1 correction confirmed by PCR-band sequencing wt transcript- upper band Mut AON1 Mut AON1 Mut AON1 GAGTGCTTTTTTGATGATATGGAGAGCATACCAGCAGTGACTACATGGAACACATACCTTCGATATATTACTGTCCACAAGAGC |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GAGTGCTTTTTTGATGATATGGAGAGCATACCAGCAGTGACTACATGGAACACATACCTTCGATATATTACTGTCCACAAGAGC TTAATTTTTGTGCTAATTTGGTGCTTAGTAATTTTTCTGGCAGAGGTGGCTGCTTCTTTGGTTGTGCTGTGGCTCCTTGGAAAC |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| TTAATTTTTGTGCTAATTTGGTGCTTAGTAATTTTTCTGGCAGAGGTGGCTGCTTCTTTGGTTGTGCTGTGGCTCCTTGGAAAC ACTCCTCTTCAAGACAAAGGGAATAGTACTCATAGTAGAAATAAC ||||||||||||||||||||||||||||||||||||||||||||| ACTCCTCTTCAAGACAAAGGGAATAGTACTCATAGTAGAAATAAC Alternative transcript- lower band (no ex16) Mut AON1 Mut AON1 Mut AON1 GAGTGCTTTTTTGATGATATGGAGAGCATACCAGCAGTGACTACATGGAACACATACCTTCGATATATTACTGTCCACAAGAGC |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GAGTGCTTTTTTGATGATATGGAGAGCATACCAGCAGTGACTACATGGAACACATACCTTCGATATATTACTGTCCACAAGAGC TTAATTTTTGTGCTAATTTGGTGCTTAGTAATTTTTCTGGCAGAGCACTCCTCTTCAAGACAAAGGGAATAGTACTCATAGTAG |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| TTAATTTTTGTGCTAATTTGGTGCTTAGTAATTTTTCTGGCAGAGCACTCCTCTTCAAGACAAAGGGAATAGTACTCATAGTAG AAATAACAGCTATGCAGTGATTATCACCAGCAC ||||||||||||||||||||||||||||||||| AAATAACAGCTATGCAGTGATTATCACCAGCAC Supp. Figure S4 Alignment of wt and alternatively spliced transcripts after AON1 correction. PCR products from upper (wt) and lower (no exon 16) bands were PCR re-amplified and sequenced to confirm the presence of complete exon 16 inclusion after AON1 treatment. Upper panel shows the alignment of wt transcripts from upper mutant PCR band vs upper mutant-AON1 treated PCR band, showing exon 15, exon 16 (highlighted in bold) and part of exon 17. Lower panel shows the alignment of alternatively spliced products from the lower mutant PCR band vs lower mutant-AON1 treated PCR band showing exon 15 and part of exon 17 with exon 16 missing. 6 Alternative splicing analysis by sqRT-PCR after kinetin and EGCG treatment Mut DMSO K EGCG 14 15 16 14 15 17 17 Supp. Figure S5 Small-molecule compound treatment of HEK293 Flp-In cells stably expressing the 2657+5G>A CFTR splicing minigene. RT-PCR analysis of mutant (Mut) minigene transcripts treated for 24 h with dimethyl sulfoxide (DMSO) used as control, kinetin (K; 200 μM) and epigallocatechin gallate (EGCG; 50 μM). Other compounds have also been tested (data not shown). These compounds have been previously shown to improve exon inclusion in other disorders (Hims, et al, 2007; Anderson, et al, 2003; Sumanasekera, et al, 2008). Supp. Table S1 Primer sequences for mCherry insertion upstream of CFTR minigenes and Flagtag insertion on IVS 17. Oligonucleotide Sequence (5’-3’) mCherry-Fusion-CFTR fw CGGATCCACTAGTAACGGCCATGGTGAGCAAGGGCGAGGAG mCherry-Fusion-CFTR rv GGCCTTTTCCAGAGGCGACCTCTGCATGGTGGGCCCGCGGTACCGTCGACT Flag-tag fw AAAGGGAATAGTACTCATAGTAGAAATAACGATTACAAAGATGATGATGAT AAAAGCTATGCAGTG Flag-tag rv CACTGCATAGCTTTTATCATCATCATCTTTGTAATCGTTATTTCTACTATGAG TACTATTCCCTTT References Anderson SL, Qiu J, Rubin BY. 2003. EGCG corrects aberrant splicing of IKAP mRNA in cells from patients with familial dysautonomia. Biochem Biophys Res Commun 310(2):62733. Hims MM, Ibrahim EC, Leyne M, Mull J, Liu L, Lazaro C, Shetty RS, Gill S, Gusella JF, Reed R, Slaugenhaupt SA. 2007. Therapeutic potential and mechanism of kinetin as a treatment for the human splicing disease familial dysautonomia. J Mol Med 85(2):149-61. Masvidal L, Igreja S, Ramos MD, Alvarez A, de Gracia J, Ramalho A, Amaral MD, Larriba S, Casals T. 2014. Assessing the residual CFTR gene expression in human nasal epithelium cells bearing CFTR splicing mutations causing cystic fibrosis. Eur J Hum Genet 22(6):784-91. Sumanasekera C, Watt DS, Stamm S. 2008. Substances that can change alternative splice-site selection. Biochem Soc Trans 36(Pt 3):483-90.