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Supporting Information Supporting Information Collin et al. 10.1073/pnas.1220864110 SI Materials and Methods Mutation Analysis of PASK and ZNF408. The two candidate variants Human Subjects. A detailed clinical description of familial exudative that were left after linkage and exome analysis were analyzed in vitreoretinopathy (FEVR) family W05-215 has been reported family W05-215 with Sanger sequencing of exon 6 of proline- previously (1), and clinical details of the affected individuals alanine-rich ste20-related kinase (PASK) and exon 5 of zinc studied using next-generation sequencing (NGS) (III:5 and V:2) finger protein 408 (ZNF408). Primer sequences are available are summarized below. Eight affected individuals, three un- on request. The presence of these two changes in additional affected individuals, and three spouses participated in the ge- Dutch FEVR probands and 110 control individuals was ana- netic analysis (Fig. S1A). After linkage and exome sequencing lyzed via restriction fragment length polymorphism analysis, analysis were performed, three additional affected relatives using AflIII for the c.791dup change in PASK and SfaNI for the (IV:10, IV:11, and V:7) were sampled. Clinical details of the c.1363C>T change in ZNF408. All exons and intron–exon two individuals with FEVR from family W05-220 (IV:3 and boundaries of ZNF408 were amplified under standard PCR V:2) are summarized below. Furthermore, 132 individuals with conditions using primers that are available on request. Sanger FEVR (8 from The Netherlands, 64 from the United Kingdom, sequence analysis was performed with the ABI PRISM Big Dye 55 from Japan, and 5 from Switzerland) participated in this Terminator Cycle Sequencing V2.0 Ready Reaction Kit and study, along with 110 ethnically matched Dutch and 191 eth- an ABI PRISM 3730 DNA analyzer (Applied Biosystems). nically matched Japanese controls. Written informed consent The occurrence of the c.377G>A (p.Ser126Asn) variant in was obtained from all participants, and the study was approved 191 Japanese controls was assessed via Sanger sequencing by the local Ethics Committee, adhering to the tenets of the analysis. All PASK exons were analyzed using DNA of indi- Declaration of Helsinki. viduals IV:3 and V:2 of family W05-220 by Sanger sequencing, as described above. Linkage Analysis. Genomic DNA from all participating individuals of family W05-215 was extracted from peripheral blood lympho- Generation of Plasmids. An Image clone containing the full ORF cytes according to standard protocols (2), except for DNA of in- of ZNF408 (ImaGenes; accession no. NM_024741.2) was used dividuals IV-10, IV-11, and V-7 of family W05-215, which was as a template to amplify a cDNA molecule encoding the full- extracted from saliva using Oragene containers (DNA Genotek) length WT ZNF408 protein but lacking the start methionine according to the protocol supplied by the manufacturer. Eight to generate an N-terminally tagged fusion construct. PCR analysis affected individuals of family W05-215 were genotyped using was performed using the following primers: forward, 5′-GGGG- the Infinium II HumanLinkage-12 Panel (HumanOmniExpress; ACAAGTTTGTACAAAAAAGCAGGCTTCGAGGAGGCG- Illumina), which contains 733,202 SNP markers. Multipoint link- GAGGAGCTG-3′; reverse, 5′-GGGGACCACTTTGTACAA- age analysis was performed with the GeneHunter 2.1r5 program GAAAGCTGGGTTCAGGTGCCCATCTCCACC-3′ (attB1- and in the easyLinkage v5.052beta software package (3) using the attB2- sites for Gateway cloning are underlined). Using Gateway MarshfieldSNPmapandCaucasianallelefrequencies.Forthe technology (Invitrogen), the cDNA encoding human full-length microsatellite markers, two-point logarithm of the odds (LOD) ZNF408 was cloned into the pDONR201 vector as described scores were calculated using the SuperLink v1.6 program in the previously (6). To introduce the missense variants that were easyLinkage software. For each calculation, an autosomal dom- identified in this study, site-directed mutagenesis was performed inant mode of inheritance was assumed with a penetrance of by PCR with Phusion Taq (Finnzymes) and corresponding 0.75, and the disease allele frequency was estimated at 0.0001. primers (available on request). The DNA constructs after site- directed mutagenesis were validated by Sanger sequencing of Exome Sequencing Analysis and Variant Filtering. The exomes of the entire coding regions of the WT and mutant ZNF408 cDNAs. individuals III:3 and V:2 of family W05-215 (Fig. S1A) were The cDNAs were subsequently cloned into either the HA-tagged enriched using the SureSelect Human Exome Enrichment Kit or enhanced cyan fluorescent protein (eCFP)-tagged destina- V1 (Agilent) and sequenced using one-quarter of a SOLiD se- tion vectors (pcDNA3-HA/DEST and pcDNA3-eCFP/DEST; quencing slide (Life Technologies). The SureSelect Human Invitrogen), as described previously (6, 7). Exome Enrichment Kit V1 covers 1.22% of human genomic re- gions corresponding to the National Center for Biotechnology Transient Transfection of COS-1 Cells. HA-tagged or eCFP-tagged Information’s Consensus Coding DNA Sequence Database WT and mutant ZNF408 were expressed using the mammalian (CCDS), including >700 human miRNAs from the Sanger v13 expression vector pcDNA3-HA/DEST or pcDNA3-eCFP/DEST, database and >300 additional human noncoding RNAs, such both driven by a cytomegalovirus (CMV) promoter. COS-1 cells as small nucleolar RNAs (snoRNAs) and small Cajal body- were transiently transfected using Effectene (Qiagen), according specific RNAs (scaRNAs). This design covers >37 Mb of the to the manufacturer’s instructions. At 24 h after transfection, cells human genome. Color space reads were mapped to the hg19 were washed with PBS and then prepared for (immuno)fluores- reference genome with SOLiD BioScope version 1.3, which used cence analysis. an iterative mapping approach. Single-nucleotide variants were subsequently called by the diBayes algorithm with conservative Subcellular Localization of WT and Mutant ZNF408 in COS-1 Cells. To call stringency. Small insertions and deletions were detected using determine the subcellular localization of the HA- or eCFP-tagged the SOLiD Small InDel Tool. Called SNP variants and indels WT and mutant ZNF408 proteins, transiently transfected cells were combined and annotated using a custom analysis pipeline, were fixed with 4% paraformaldehyde and either directly mounted with information concerning the effect of the variants on the (in case of eCFP fusion proteins) or incubated with primary anti- amino acid translation, overlap of variants with polymorphisms HA and secondary goat anti-mouse Alexa Fluor 680 antibodies from dbSNP132, overlap with variants from our own in-house before mounting with Vectashield containing DAPI (Vector database, and evolutionary conservation scores for the affected Laboratories). Images were obtained with a Zeiss AxioImager nucleotide (4, 5). Z1 upright fluorescent microscope and processed with a Zeiss Collin et al. www.pnas.org/cgi/content/short/1220864110 1of8 ApoTome slider module. All experiments were performed in Left eye: 20/125; refraction: sphere, −12/cylinder, −1.0 × 0°. duplicate. Anterior segments: Slight cortical cataract in both eyes. Fundi. Evolutionary Conservation of ZNF408. To assess the evolutionary Stretched course of the temporal retinal vessels; some conservation of the mutated amino acids, amino acid sequences of temporal ectopia of the macula. Local areas of atrophy of choroid orthologous ZNF408 proteins were aligned with the protein se- and retinal pigment epithelium (RPE) (posterior pole). Avascular quence of human ZNF408 using the Align program in Vector NTI peripheral retina temporally anterior to the equator. Left eye with version 11 (Invitrogen). Protein identification numbers, derived large pigmented scars of choroid and retina in the inferotemporal from GenBank and/or Uniprot, were as follows: human ZNF408: quadrant (secondary to surgical procedures). No retinal exudates, Q9H9D4; bovine ZNF408: NP_001180086; canine ZNF408: F1:00 defects, or detachment. PMD3; mouse Znf408/Zfp408: NP_001028623; zebrafish ZNF408: Patient V:2. NP_001002305. Family D, daughter of V-12 of van Nouhuys (1). History. No history of premature birth. Eye examination at age 3 y Morpholinos and Zebrafish Embryo Manipulations. Tg(fli1:eGFP) fi because of family history; visual impairment and FEVR diagnosed. zebra sh were bred and raised under standard conditions (8), Support at school age because of a considerable visual handicap. in accordance with international and institutional guidelines. Examination at age 15 y; best corrected visual acuities: Zebrafish eggs were obtained from natural spawning. Trans- lation (5′-TCCCAGTGACTGTAGACATCAGGGC-3′)and Right eye: Finger counting; poor fixation. splice-blocking (5′-GCAACCCCTGAAAAATAACAACACA-3′) Left eye: 20/100; pseudoexotropia due to a large positive morpholinos (MOs) for znf408 were designed by Gene Tools kappa angle. and diluted in deionized, sterile water supplemented with 0.5% phenol red. To determine the most effective dose of the znf408 Anterior segments: No abnormalities. MOs, 1 nL of diluted MO (containing 2, 6, and 10 ng) was injected Fundi. Right eye: Prominent falciform retinal fold running from into the yolk of one- to two-cell stage embryos using a Pneumatic the optic nerve head across the center of the posterior pole in the PicoPump pv280 (World Precision Instruments). For in vivo rescue inferotemporal direction. Marked chorioretinal atrophy and ret- experiments, human ZNF408 and mutant p.His455Tyr ZNF408 inal
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