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Supplementary Materials and Methods Truncating mutations in YIF1B cause a progressive encephalopathy with various degrees of mixed movement disorder, microcephaly, and epilepsy. Item Type Article Authors AlMuhaizea, Mohammed; AlMass, Rawan; AlHargan, Aljouhra; AlBader, Anoud; Medico Salsench, Eva; Howaidi, Jude; Ihinger, Jacie; Karachunski, Peter; Begtrup, Amber; Segura Castell, Monica; Bauer, Peter; Bertoli-Avella, Aida; Kaya, Ibrahim H; AlSufayan, Jumanah; AlQuait, Laila; Chedrawi, Aziza; Arold, Stefan T.; Colak, Dilek; Barakat, Tahsin Stefan; Kaya, Namik Citation AlMuhaizea, M., AlMass, R., AlHargan, A., AlBader, A., Medico Salsench, E., Howaidi, J., … Kaya, N. (2020). Truncating mutations in YIF1B cause a progressive encephalopathy with various degrees of mixed movement disorder, microcephaly, and epilepsy. Acta Neuropathologica. doi:10.1007/ s00401-020-02128-8 Eprint version Post-print DOI 10.1007/s00401-020-02128-8 Publisher Springer Nature Journal Acta neuropathologica Rights Archived with thanks to Acta neuropathologica Download date 06/10/2021 17:47:21 Link to Item http://hdl.handle.net/10754/661480 SUPPLEMENTARY MATERIALS AND METHODS Human Subjects The study was approved by institutional review boards (RAC# 2120022) at King Faisal Specialist Hospital and Research Centre and written informed consents were taken from the participants. Nucleic Acid Extraction, PCR, and Sanger Sequencing Peripheral blood samples were used for DNA extraction using Gentra’s Puregene Blood Kit, and QIAamp Venlo, Netherlands. Nucleic acid quality and quantity were determined using NanoDrop ND-1000 (ThermoFisher Scientific, Inc., Waltham, MA, US) and 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, US) equipment. Primers were designed using Primer 3 and tested on human control DNA. PCRs were performed according to standard protocols and successfully amplified PCR products were directly used for Sanger sequencing using one of the PCR primers tagged with M13 universal site. Autozygosity Mapping DNA was also used for genome-wide SNP interrogation using GeneChip axiom arrays. SNP calls were extracted using Affymetrix’s Genotyping Console and transferred to AutoSNPa software for autozygome analysis. Runs of homozygosity (ROH) across the autozygome of the affected individuals were determined as previously described [1, 2, 8]. Whole Exome Sequencing (WES), Variant Calls and Filtering Case 1-4: TruSeq Exome Enrichment kit (Illumina, San Diego, CA, USA) was used to capture exomic sequences for library preparation and enrichment. The established libraries were run and sequenced on Illumina HiSeq 2000 Sequencer. WES data analysis and filtering were performed as previously published [1, 2, 4, 8]. Case 5: Whole exome sequencing was performed at CENTOGENE AG, as previously described [12]. Case 6: Using genomic DNA from the proband and parents, the exonic regions and flanking splice junctions of the genome were captured using the Clinical Research Exome kit (Agilent Technologies, Santa Clara, CA). Massively parallel (NextGen) sequencing was done on an Illumina system with 100bp or greater paired-end reads. Reads were aligned to human genome build GRCh37/UCSC hg19, and analyzed for sequence variants using a custom-developed analysis tool. Additional sequencing technology and variant interpretation protocol has been previously described [9]. The general assertion criteria for variant classification are publicly available on the GeneDx ClinVar submission page. (http://www.ncbi.nlm.nih.gov/clinvar/submitters/26957/)" Age of Mutation Calculation The border of ROH among the affected individuals (Supplementary Figure 1A) was determined using AutoSNPa software (Chr19:35,473,940-39,941,310) using the UCSC Genome Browser on Human Feb. 2009 (GRCh37/hg19) Assembly. Sex-average recombination rates (RR) were taken from DECODE. The sum of the RR in the region is 5.35 centiMorgan. Age of the mutation is therefore approximately 37 generations, corresponding to 925 years (assuming one generation is 25 years) [1]. Pathway and Gene Network Analysis of YIF1B-Co-expressed genes It has been reported that co-expressed genes are likely to be functionally related and may provide important information on gene function and its possible regulation [10, 15]. We used publicly available datasets with over 46,000 human RNAseq to identity genes that are co-expressed with YIF1B [2]. We selected the most strongly associated genes with YIF1B with Pearson correlation (r) > 0.9 (171 genes). We then performed gene ontology enrichment and interaction network analyses using Ingenuity Pathways Analysis (IPA) 6.4 (Ingenuity Systems, Mountain View, CA). Computational structural analysis RaptorX [7] was used to predict protein structural disorder and secondary structure. iTasser [16] was used to build an initial model for the structured region of the protein (residues 69-314), whereas RaptorX was used to build a model for the flexible N-terminal 65 residues. SWISS-MODEL [3] was used combined both models. Models were manually inspected, and mutations evaluated, using the PyMOL program (pymol.org). SUPLEMENTARY FIGURE LEGENDS Supplementary Figure 1. A. Extended large ROH (black region) shared among the index cases (F1, F2, and F3) is framed with red lines. Blue line points location of YIF1B on chromosome 19 and red arrows show beginning and end of the run. Right panel presents selected non-affected individuals from the same families. Based on the shared ROH regions, the age of this founder mutation can be estimated to be 925 years. B. Multiple sequence alignment of all three YIF1B variants indicating high conservation of the amino acids in the regions among various species. Supplementary Figure 2. Protein and mRNA expressions of YIF1B, from the Protein Atlas (http://www.proteinatlas.org) and FANTOM5 [5, 6, 11, 13, 14]. According to FANTOM5 mRNA expression levels of the gene are the highest in different brain regions in comparison to other organs except for lymph node and liver. Supplementary Figure 3. Immunocytochemistry in three different cells lines (HPA039328: U-251 MG; HPA039328: U-2 OS; HPA039328: A549) revealed location of YIF1B mainly in vesicles and localized to the Golgi apparatus. Green labeled molecules are YIF1B. Data is taken from The Human Protein Atlas [11, 13, 14]. Supplementary Figure 4. Immunohistochemistry on normal brain tissue using two different primary antibodies targeting YIF1B. A. IHH results from cerebral cortex of a male brain. B. IHH results were obtained using a different antibody in the same region of another male at different age. Data is taken from The Human Protein Atlas.[11, 13, 14] Supplementary Figure 5. Gene interaction network analysis of YIF1B co-expressed genes. Genes in the network are co-expressed with YIF1B in over 46,000 human RNASeq data (with Pearson correlation > 0.9). Nodes represent genes with their shape representing the functional class of the gene product, and edges indicate biological relationship between the nodes. YIF1B co-expressed genes are significantly associated with neurological disease and developmental disorders (p <0.01) (indicated in purple). Supplementary Figure 6. A) Secondary structure prediction for wild type (left) and mutant YIF1B (right). B) Protein structural disorder prediction for wild type (left) and mutant YIF1B (right). C) Sequences from YIF1B wild-type and both mutants are compared. Color-coding corresponds to Figure 1, with the amino acid sequence resulting from the frame-shifts shown in bold (these residues are not shown in Figure 1). SUPPLEMENTARY FIGURE 6 A B C SUPLEMENTARY TABLES Supplementary Table 1. Clinical descriptions of the patients from the families. FAMILY II:2; Family 1 II:3; Family 1 II:2; Family 2 II:2; Family 3 II:3; family 4 II:6; Family 5 GENDER F F F F M F AGE AT PRESENTATION 6-MONTH BIRTH 8-MONTH 6-MONTH NA 6-MONTH AGE AT FIRST EVALUATION 7 YEARS 17-MONTH 4 YEARS 2 YEARS NA 23 MONTH AGE AT LAST EVALUATION 9 YEARS 4 YEARS 11 YEARS 11 YEARS NA 7 YEARS OUTCOME (ALIVE OR DEAD) ALIVE ALIVE ALIVE ALIVE NA ALIVE ETHNICITY ARAB ARAB ARAB ARAB NA SOMALI PRENATAL AND BIRTH NA PRENATAL COMPLIACTIONS (E.G. IUGR) NO NO NO possible IUGR NA NO GESTATIONAL AGE TERM TERM TERM FULL TERM NA FULL TERM BIRTH WEIGHT (SGA) NORMAL NORMAL NORMAL 2.16 KG NA UNKNOWN BIRTH LENGTH NORMAL NORMAL NORMAL 50 CM NA UNKNOWN BIRTH HEAD CIRCUMFERENCE NORMAL NORMAL NORMAL 32 CM NA UNKNOWN (MICROCEPHALY) GROWTH NA FTT (CURRENT WEIGHT) YES YES YES 10% PERCENTILE NA NO SHORT STATURE (CURRENT HEIGHT) YES YES YES 10% NA NO MICROCEPHALY YES YES YES YES NA NO DEVELOPMENT AND BEHAVIOR NA GLOBAL DEVELOPMENTAL DELAY YES YES YES - PROFOUND YES NA YES HYPOTONIA AXIAL HYPOTONIA AXIAL HYPOTONIA AXIAL HYPOTONIA AXIAL HYPOTONIA NA YES BEST GROSS MOTOR MILESTONE 1/2 ROLL ROLL OVER NOT ROLLING NOT ROLLING NA NOT ROLLING BEST FINE MOTOR MILESTONE REACH AND HOLD HOLD -IMMATURE HOLD -IMMATURE HOLD OBJECT NA REACH FOR OBJECTS OBJECT BEST LANGUAGE MILESTONE CHOOING LIKE SOUNDS BABBLES SOUNDS SOUNDS NA VOCALISATION SOCIAL DEVELOPMENT SOCIAL SMILE SOCIAL SMILE SMILE SOCIAL SMILE NA SOCIAL SMILE IRRITABILITY YES, INTERMITTENT YES, MORE WITH STRESS YES MORE ON OCCASIONAL NA YES AND TRAVEL LEVETIRACETAM VISUAL ABNORMALITY NO NO NO NO NA CORTICAL BLINDNESS, HYPERMETROPIA, ASTIGMATISM HEARING IMPAIRMENT NO NO NO NO NA NO AURISTIC FEATURES NO NO NO NO NA ? N/A MOVEMENT DISORDER NA DYSTONIA UPPER AND LOWER LIMB DYSTONIA LIMB DYSTONIA LIMB UPPER MORE NA NO DYSTONIA LIMBS THAN LOWER SPASTICITY LIMB LIMB SEVERE LIMB SPASTICITY MILD LIMB SPASTICITY NA SPASTIC QAUDRIPLEGIA DYSKINESIA LIMB AND FACE CHOREA WITH DYSTONIA LIMB FACE AND DISTAL NA ND LIMBS RESPONSE TO LEVODOPA/CARBIDOPA NO NO N/D NO RESPONSE NA ND RESPONSE TO BACLOFEN PARTIAL NOT USED NOT USED NA ND RESPONSE TO TRIHEXPHENYDIL PARTIAL PARTIAL IMPROVEMENT ND PARTIAL NA ND IMPROVEMENT SEIZURES NO NO YES NO NA YES EEG ABNORMAL 1: EXCESSIVE NORMAL/AWAKE ABNORMAL III (AWAKE ND NA DIFFUSE HIGH FAST ACTIVITY AND SLEEP). AMPLITUDE SLOWING BACKGROUND SLOW WITH SUPERIMPOSED ACTIVITY. SLOW SPIKE FREQUENT AND WAVE COMPLEX, GENERALIZED AND GENERALIZED. SPIKES, MULTIFOCAL MULTIREGIONAL. PAROXYSMAL INTERMITTENT SLOW EPILEPTIFORM ACTIVITY, GENERALIZED.
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