DOCSLIB.ORG

Cellular Ciliary Phenotyping Indicates Pathogenicity of Novel Variants in IFT140 and Confrms a Mainzer–Saldino Syndrome Diagnosis Machteld M

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Cellular Ciliary Phenotyping Indicates Pathogenicity of Novel Variants in IFT140 and Confrms a Mainzer–Saldino Syndrome Diagnosis Machteld M Oud et al. Cilia (2018) 7:1 https://doi.org/10.1186/s13630-018-0055-2 Cilia SHORT REPORT Open Access Cellular ciliary phenotyping indicates pathogenicity of novel variants in IFT140 and confrms a Mainzer–Saldino syndrome diagnosis Machteld M. Oud1,2* , Brooke L. Latour1,2‡, Zeineb Bakey1,2‡, Stef J. Letteboer1,2, Dorien Lugtenberg1, Ka Man Wu1,2, Elisabeth A. M. Cornelissen3, Helger G. Yntema1,4, Miriam Schmidts1,2,5, Ronald Roepman1,2† and Ernie M. H. F. Bongers1† Abstract Background: Mainzer–Saldino syndrome (MZSDS) is a skeletal ciliopathy and part of the short-rib thoracic dysplasia (SRTD) group of ciliary disorders. The main characteristics of MZSDS are short limbs, mild narrow thorax, blindness, and renal failure. Thus far, variants in two genes are associated with MZSDS: IFT140, and IFT172. In this study, we describe a 1-year-old girl presenting with mild skeletal abnormalities, Leber congenital amaurosis, and bilateral hear- ing difculties. For establishing an accurate diagnosis, we combined clinical, molecular, and functional analyses. Methods: We performed diagnostic whole-exome sequencing (WES) analysis to determine the genetic cause of the disease and analyzed two gene panels, containing all currently known genes in vision disorders, and in hearing impairment. Upon detection of the likely causative variants, ciliary phenotyping was performed in patient urine- derived renal epithelial cells (URECs) and rescue experiments were performed in CRISPR/Cas9-derived Ift140 knock out cells to determine the pathogenicity of the detected variants in vitro. Cilium morphology, cilium length, and intrafa- gellar transport (IFT) were evaluated by immunocytochemistry. Results: Diagnostic WES revealed two novel compound heterozygous variants in IFT140, encoding IFT140. Thor- ough investigation of WES data did not reveal any variants in candidate genes associated with hearing impairment. Patient-derived URECs revealed an accumulation of IFT-B protein IFT88 at the ciliary tip in 41% of the cells indicative of impaired retrograde IFT, while this was absent in cilia from control URECs. Furthermore, transfection of CRISPR/ Cas9-derived Ift140 knock out cells with an IFT140 construct containing the patient mutation p.Tyr923Asp resulted in a signifcantly higher percentage of IFT88 tip accumulation than transfection with the wild-type IFT140 construct. Conclusions: By combining the clinical, genetic, and functional data from this study, we could conclude that the patient has SRTD9, also called Mainzer–Saldino syndrome, caused by variants in IFT140. We suggest the possibility that variants in IFT140 may underlie hearing impairment. Moreover, we show that urine provides an excellent source to obtain patient-derived cells in a non-invasive manner to study the pathogenicity of variants detected by genetic testing. Keywords: Mainzer–Saldino syndrome, MZSDS, SRTD9, UREC, IFT140 *Correspondence: [email protected] †Ronald Roepman and Ernie M. H. F. Bongers Senior authors contributed equally to this work ‡Brooke Latour and Zeinab Bakey contributed equally to this work 1 Department of Human Genetics (855), Radboud University Medical Centre, PO‑Box 9101, 6500 HB Nijmegen, The Netherlands Full list of author information is available at the end of the article © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Oud et al. Cilia (2018) 7:1 Page 2 of 9 Background phenotype. By showing defective retrograde transport in Short-rib thoracic dysplasia (SRTD) refers to a group of patient-derived URECs and mutant IFT140 transfected ciliopathies characterized by skeletal abnormalities, that CRISPR/Cas9-derived Ift140 knockout cells, we confrm are classifed into 18 molecular subclasses; SRTD1-16, the clinical and molecular diagnosis of SRTD9/Mainzer– EVC, and EVC2. Te majority of genes mutated in SRTDs Saldino syndrome in this patient. encode intrafagellar transport (IFT) proteins, while a small subset encode proteins involved in hedgehog sign- Methods aling, ciliogenesis, or DNA damage response signaling Collection of samples [1–9]. IFT is required for cilium assembly, maintenance, Genomic DNA of patient II-3 was isolated from whole and disassembly. Two axonemal transport modules can blood and used for WES. Urine was collected from the be distinguished: the IFT-B complex, powered by the patient, her unafected parents, and three healthy con- kinesin-2 motor, for transport in anterograde direction trols to study the ciliary phenotype. (from ciliary base to tip), and the IFT-A complex, pow- ered by the dynein-2 motor, for retrograde transport Diagnostic whole-exome sequencing (from ciliary tip to base). Variants in genes encoding Diagnostic WES was performed as described previously subunits of the IFT-A particle are associated with SRTD [12]. In brief, we analyzed the vision disorder gene panel types 3–5, 7–9, 11, and 15 [1, 2, 4, 5, 8]. Te character- (version DG 2.3.2) and the hearing impairment gene istic skeletal fndings of SRTDs comprise short ribs and panel (version DG 2.3.2) [13, 14]. Exonic and intronic a narrow thorax and are often combined with short stat- positions − 20 till + 8 variants with a frequency < 5% ure, pelvic deformities, polydactyly, and brachydactyly. in dbSNP, < 1% in in-house database, and < 5% in the In addition to the skeletal abnormalities, other organ Exome Aggregation Consortium (ExAC) were evalu- systems can be involved including the kidneys, the liver, ated and classifed based on the guidelines for variant and the central nervous system [1]. Since the phenotypic classifcation determined by the Association for Clinical overlap between diferent SRTD subclasses is substan- Genetic Science (ACGS) [15]. Te same fltering strategy tial, the classifcation is based on the underlying genetic was used for the analysis of the complete WES dataset. defect and not on the clinical phenotype. Establishing an accurate diagnosis as early as possible is essential to Urine-derived renal epithelial cell isolation and culture provide the best-personalized care for the patient. For Te collection of urine, isolation of cells, and culturing example, monitoring renal function is likely to be more of URECs was performed as described previously [11]. important for patients carrying a pathogenic variant in In brief, midstream urine was collected and refriger- IFT140, TTC21B, or WDR19 than for patients who carry ated for up to 4 h. Cells were retrieved from the urine, DYNC2H1 or IFT80 variants, as the latter two are pri- washed once, and cultured in 1 ml primary UREC culture marily associated with a skeletal phenotype and IFT140, medium consisting of a 1:1 ratio Dulbecco’s Modifed TTC21B, and WDR19 are associated with a skeletal phe- Eagle’s medium (DMEM): Ham’s F12 Nutrient Mix con- notype accompanied by renal insufciency and retinal taining 10% FCS, 0.1 mg/ml Primocin (ant-pm-2, Invivo- degeneration [2, 10]. gen, Toulouse, France), and 1× REGM SingleQuots and Te efect of variants in ciliary genes can be studied at growth factors (CC-4127, Lonza; Basel, Switzerland) in a the protein level by analyzing the ciliary phenotype in 24-well plate. Cells were incubated at 37 °C with 5% CO2 patient-derived cells. Skin biopsies are commonly used and 0.5 ml primary UREC culture medium was added 24, to obtain patient-derived fbroblasts; however, this is an 48, and 72 h after cell isolation. At 96 h after cell isola- invasive and painful procedure. In 2015, Ajzenberg et al. tion, half of the culture medium was replaced by UREC reported on a non-invasive method to obtain patient- proliferation medium consisting of REBM Basal Medium derived cells from urine [11]. Urine-derived renal epi- (CC-3191, Lonza; Basel, Switzerland) containing 1× thelial cells (URECs) can be used to study the ciliary REGM SingleQuots and growth factors, and 0.1 mg/ml phenotype and are an excellent alternative for fbroblasts. Primocin. Every day for up to 14 days, half of the cul- In addition, since the development of cystic kidneys is ture medium was replaced with fresh UREC proliferation one of the hallmarks of ciliopathies, it is benefcial to medium until the URECs were visible and at approxi- study the ciliary phenotype in cells that originate from mately 80% confuence. this afected organ. In this study, we describe the use of URECs and Ciliary phenotyping in URECs CRISPR/Cas9 knockout cell lines to determine the To determine the ciliary phenotype of the patient, pathogenicity of two novel missense variants in IFT140 healthy family members, and controls, URECs were in a 1-year-old girl clinically diagnosed with a SRTD analyzed for cilium morphology, length, and IFT. Oud et al. Cilia (2018) 7:1 Page 3 of 9 Immunocytochemistry was used to visualize the cilia as and genomic DNA was extracted to check for variants described previously [16]. In short, URECs were cultured in Ift140 by Sanger sequencing upon PCR amplifca- on glass coverslips until they reached ~ 80% confuence. tion of the region around the targeted sequence (Addi- After fxation, permeabilization, and blocking, the cov- tional fle 1: Figure S2). Immunoblotting was performed erslips were incubated with primary antibodies targeting to validate the knocking out of IFT140 on protein level. IFT88 at 1:100 dilution (rabbit, 13967-1-AP, Protein- Protein lysates were made from CRISPR/Cas9 negative tech Group, Manchester, UK), IFT140 at 1:100 dilution control cells and CRISPR/Cas9-derived Ift140 knockout (rabbit, 17460-1-AP, Proteintech Group), acetylated-α- cells with or without transfection of the IFT140-Myc- tubulin at 1:1000 (mouse, T6793, Sigma-Aldrich, Zwi- DDK construct (NM_014714, cat# RC207528, OriGene, jndrecht, Netherlands), and RPGRIP1L at 1:500 dilution Herford, Germany).
Load more

Recommended publications
  • PLATFORM ABSTRACTS Abstract Abstract Numbers Numbers Tuesday, November 6 41
    American Society of Human Genetics 62nd Annual Meeting November 6–10, 2012 San Francisco, California PLATFORM ABSTRACTS Abstract Abstract Numbers Numbers Tuesday, November 6 41. Genes Underlying Neurological Disease Room 134 #196–#204 2. 4:30–6:30pm: Plenary Abstract 42. Cancer Genetics III: Common Presentations Hall D #1–#6 Variants Ballroom 104 #205–#213 43. Genetics of Craniofacial and Wednesday, November 7 Musculoskeletal Disorders Room 124 #214–#222 10:30am–12:45 pm: Concurrent Platform Session A (11–19): 44. Tools for Phenotype Analysis Room 132 #223–#231 11. Genetics of Autism Spectrum 45. Therapy of Genetic Disorders Room 130 #232–#240 Disorders Hall D #7–#15 46. Pharmacogenetics: From Discovery 12. New Methods for Big Data Ballroom 103 #16–#24 to Implementation Room 123 #241–#249 13. Cancer Genetics I: Rare Variants Room 135 #25–#33 14. Quantitation and Measurement of Friday, November 9 Regulatory Oversight by the Cell Room 134 #34–#42 8:00am–10:15am: Concurrent Platform Session D (47–55): 15. New Loci for Obesity, Diabetes, and 47. Structural and Regulatory Genomic Related Traits Ballroom 104 #43–#51 Variation Hall D #250–#258 16. Neuromuscular Disease and 48. Neuropsychiatric Disorders Ballroom 103 #259–#267 Deafness Room 124 #52–#60 49. Common Variants, Rare Variants, 17. Chromosomes and Disease Room 132 #61–#69 and Everything in-Between Room 135 #268–#276 18. Prenatal and Perinatal Genetics Room 130 #70–#78 50. Population Genetics Genome-Wide Room 134 #277–#285 19. Vascular and Congenital Heart 51. Endless Forms Most Beautiful: Disease Room 123 #79–#87 Variant Discovery in Genomic Data Ballroom 104 #286–#294 52.
    [Show full text]
  • Synergistic Genetic Interactions Between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models
    BASIC RESEARCH www.jasn.org Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models Rory J. Olson,1 Katharina Hopp ,2 Harrison Wells,3 Jessica M. Smith,3 Jessica Furtado,1,4 Megan M. Constans,3 Diana L. Escobar,3 Aron M. Geurts,5 Vicente E. Torres,3 and Peter C. Harris 1,3 Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Background Autosomal recessive polycystic kidney disease (ARPKD) and autosomal dominant polycystic kidney disease (ADPKD) are genetically distinct, with ADPKD usually caused by the genes PKD1 or PKD2 (encoding polycystin-1 and polycystin-2, respectively) and ARPKD caused by PKHD1 (encoding fibrocys- tin/polyductin [FPC]). Primary cilia have been considered central to PKD pathogenesis due to protein localization and common cystic phenotypes in syndromic ciliopathies, but their relevance is questioned in the simple PKDs. ARPKD’s mild phenotype in murine models versus in humans has hampered investi- gating its pathogenesis. Methods To study the interaction between Pkhd1 and Pkd1, including dosage effects on the phenotype, we generated digenic mouse and rat models and characterized and compared digenic, monogenic, and wild-type phenotypes. Results The genetic interaction was synergistic in both species, with digenic animals exhibiting pheno- types of rapidly progressive PKD and early lethality resembling classic ARPKD. Genetic interaction be- tween Pkhd1 and Pkd1 depended on dosage in the digenic murine models, with no significant enhancement of the monogenic phenotype until a threshold of reduced expression at the second locus was breached.
    [Show full text]
  • Evaluation of Variability in Human Kidney Organoids
    ARTICLES https://doi.org/10.1038/s41592-018-0253-2 Evaluation of variability in human kidney organoids Belinda Phipson 1, Pei X. Er1, Alexander N. Combes1,2, Thomas A. Forbes1,3,4, Sara E. Howden1,2, Luke Zappia1,5, Hsan-Jan Yen1, Kynan T. Lawlor1, Lorna J. Hale1,4, Jane Sun6, Ernst Wolvetang6, Minoru Takasato1,7, Alicia Oshlack1,5 and Melissa H. Little 1,2,4* The utility of human pluripotent stem cell–derived kidney organoids relies implicitly on the robustness and transferability of the protocol. Here we analyze the sources of transcriptional variation in a specific kidney organoid protocol. Although individ- ual organoids within a differentiation batch showed strong transcriptional correlation, we noted significant variation between experimental batches, particularly in genes associated with temporal maturation. Single-cell profiling revealed shifts in neph- ron patterning and proportions of component cells. Distinct induced pluripotent stem cell clones showed congruent transcrip- tional programs, with interexperimental and interclonal variation also strongly associated with nephron patterning. Epithelial cells isolated from organoids aligned with total organoids at the same day of differentiation, again implicating relative matura- tion as a confounder. This understanding of experimental variation facilitated an optimized analysis of organoid-based disease modeling, thereby increasing the utility of kidney organoids for personalized medicine and functional genomics. he ability to derive induced pluripotent stem cells (iPSCs) In this study, we provide a comprehensive transcriptional from the somatic cells of patients1, together with directed dif- and morphological evaluation of our kidney organoid protocol. Tferentiation protocols, provides a capacity to model the cell Applying RNA sequencing (RNA-seq) to 57 whole organoids and types affected by disease.
    [Show full text]
  • Blueprint Genetics Short Rib Dysplasia / Asphyxiating Thoracic Dysplasia Panel
    Short Rib Dysplasia / Asphyxiating Thoracic Dysplasia Panel Test code: MA1101 Is a 18 gene panel that includes assessment of non-coding variants. Is ideal for patients with a clinical suspicion of asphyxiating thoracic dystrophy or short-rib dysplasia with or without polydactyly. The genes on this panel are included in the Comprehensive Growth Disorders / Skeletal Dysplasias and Disorders Panel. About Short Rib Dysplasia / Asphyxiating Thoracic Dysplasia Short-rib dysplasia (SRD) with or without polydactyly refers to a group of autosomal recessive skeletal ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a trident aspect of the acetabular roof. SRD encompasses Ellis-van Creveld syndrome (EVC), Jeune syndrome or asphyxiating thoracic dystrophy (ATD), short rib- polydactyly syndromes (SRPS, Beemer-Langer type, Majewski type, Saldino-Noonan type, Verma-Naumoff type), and Mainzer-Saldino syndrome (MZSDS). Polydactyly is variably present, and there is phenotypic overlap in the various forms of SRDs, which differ by visceral malformation and metaphyseal appearance. Nonskeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Availability 4 weeks Gene Set Description Genes in the Short Rib Dysplasia / Asphyxiating Thoracic Dysplasia Panel and their clinical significance Gene Associated phenotypes Inheritance ClinVar HGMD CSPP1 Jeune asphyxiating thoracic dystrophy, Joubert
    [Show full text]
  • Gene Ontology Functional Annotations and Pleiotropy
    Network based analysis of genetic disease associations Sarah Gilman Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2013 Sarah Gilman All Rights Reserved ABSTRACT Network based analysis of genetic disease associations Sarah Gilman Despite extensive efforts and many promising early findings, genome-wide association studies have explained only a small fraction of the genetic factors contributing to common human diseases. There are many theories about where this “missing heritability” might lie, but increasingly the prevailing view is that common variants, the target of GWAS, are not solely responsible for susceptibility to common diseases and a substantial portion of human disease risk will be found among rare variants. Relatively new, such variants have not been subject to purifying selection, and therefore may be particularly pertinent for neuropsychiatric disorders and other diseases with greatly reduced fecundity. Recently, several researchers have made great progress towards uncovering the genetics behind autism and schizophrenia. By sequencing families, they have found hundreds of de novo variants occurring only in affected individuals, both large structural copy number variants and single nucleotide variants. Despite studying large cohorts there has been little recurrence among the genes implicated suggesting that many hundreds of genes may underlie these complex phenotypes. The question
    [Show full text]
  • Partial Uniparental Isodisomy of Chromosome 16 Unmasks a Deleterious Biallelic Mutation in IFT140 That Causes Mainzer-Saldino Syndrome Benjamin M
    Helm et al. Human Genomics (2017) 11:16 DOI 10.1186/s40246-017-0111-9 PRIMARY RESEARCH Open Access Partial uniparental isodisomy of chromosome 16 unmasks a deleterious biallelic mutation in IFT140 that causes Mainzer-Saldino syndrome Benjamin M. Helm1,2, Jason R. Willer3, Azita Sadeghpour3, Christelle Golzio3,4, Eric Crouch5, Samantha Schrier Vergano1,6, Nicholas Katsanis3* and Erica E. Davis3* Abstract Background: The ciliopathies represent an umbrella group of >50 clinical entities that share both clinical features and molecular etiology underscored by structural and functional defects of the primary cilium. Despite the advances in gene discovery, this group of entities continues to pose a diagnostic challenge, in part due to significant genetic and phenotypic heterogeneity and variability. We consulted a pediatric case from asymptomatic, non-consanguineous parents who presented as a suspected ciliopathy due to a constellation of retinal, renal, and skeletal findings. Results: Although clinical panel sequencing of genes implicated in nephrotic syndromes yielded no likely causal mutation, an oligo-SNP microarray identified a ~20-Mb region of homozygosity, with no altered gene dosage, on chromosome 16p13. Intersection of the proband’s phenotypes with known disease genes within the homozygous region yielded a single candidate, IFT140, encoding a retrograde intraflagellar transport protein implicated previously in several ciliopathies, including the phenotypically overlapping Mainzer-Saldino syndrome (MZSDS). Sanger sequencing yielded a maternally inherited homozygous c.634G>A; p.Gly212Arg mutation altering the exon 6 splice donor site. Functional studies in cells from the proband showed that the locus produced two transcripts: a majority message containing a mis-splicing event that caused a premature termination codon and a minority message homozygous for the p.Gly212Arg allele.
    [Show full text]
  • HSP90-Incorporating Chaperome Networks As Biosensor for Disease-Related Pathways in Patient- Specific Midbrain Dopamine Neurons
    ARTICLE DOI: 10.1038/s41467-018-06486-6 OPEN HSP90-incorporating chaperome networks as biosensor for disease-related pathways in patient- specific midbrain dopamine neurons Sarah Kishinevsky1,2,3,4, Tai Wang3, Anna Rodina3, Sun Young Chung1,2, Chao Xu3, John Philip5, Tony Taldone3, Suhasini Joshi3, Mary L. Alpaugh3,14, Alexander Bolaender3, Simon Gutbier6, Davinder Sandhu7, Faranak Fattahi1,2, Bastian Zimmer1,2, Smit K. Shah3, Elizabeth Chang5, Carmen Inda3,15, John Koren 3rd3,16, Nathalie G. Saurat1,2, Marcel Leist 6, Steven S. Gross7, Venkatraman E. Seshan8, Christine Klein9, Mark J. Tomishima1,2,10, Hediye Erdjument-Bromage11,12, Thomas A. Neubert 11,12, Ronald C. Henrickson5, 1234567890():,; Gabriela Chiosis3,13 & Lorenz Studer1,2 Environmental and genetic risk factors contribute to Parkinson’s Disease (PD) pathogenesis and the associated midbrain dopamine (mDA) neuron loss. Here, we identify early PD pathogenic events by developing methodology that utilizes recent innovations in human pluripotent stem cells (hPSC) and chemical sensors of HSP90-incorporating chaperome networks. We show that events triggered by PD-related genetic or toxic stimuli alter the neuronal proteome, thereby altering the stress-specific chaperome networks, which produce changes detected by chemical sensors. Through this method we identify STAT3 and NF-κB signaling activation as examples of genetic stress, and phospho-tyrosine hydroxylase (TH) activation as an example of toxic stress-induced pathways in PD neurons. Importantly, pharmacological inhibition of the stress chaperome network reversed abnormal phospho- STAT3 signaling and phospho-TH-related dopamine levels and rescued PD neuron viability. The use of chemical sensors of chaperome networks on hPSC-derived lineages may present a general strategy to identify molecular events associated with neurodegenerative diseases.
    [Show full text]
  • IFT Trains in Different Stages of Assembly Queue at the Ciliary Base
    RESEARCH ARTICLE IFT trains in different stages of assembly queue at the ciliary base for consecutive release into the cilium Jenna L Wingfield1, Ilaria Mengoni1, Heather Bomberger1,2†, Yu-Yang Jiang1, Jonathon D Walsh3, Jason M Brown4,5, Tyler Picariello4, Deborah A Cochran4, Bing Zhu6, Junmin Pan6,7, Jonathan Eggenschwiler3, Jacek Gaertig1, George B Witman4, Peter Kner2, Karl Lechtreck1* 1Department of Cellular Biology, University of Georgia, Athens, United States; 2College of Engineering, University of Georgia, Athens, United States; 3Department of Genetics, University of Georgia, Athens, United States; 4Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, United States; 5Department of Biology, Salem State University, Salem, United States; 6MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China; 7Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China Abstract Intraflagellar transport (IFT) trains, multimegadalton assemblies of IFT proteins and motors, traffic proteins in cilia. To study how trains assemble, we employed fluorescence protein- *For correspondence: lechtrek@ tagged IFT proteins in Chlamydomonas reinhardtii. IFT-A and motor proteins are recruited from uga.edu the cell body to the basal body pool, assembled into trains, move through the cilium, and disperse Present address: †Department back into the cell body. In contrast to this ‘open’ system, IFT-B proteins from retrograde trains of Biomedical Engineering, reenter the pool and a portion is reused directly in anterograde trains indicating a ‘semi-open’ University of Minnesota, system. Similar IFT systems were also observed in Tetrahymena thermophila and IMCD3 cells.
    [Show full text]
  • Variation in Protein Coding Genes Identifies Information Flow
    bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number.
    [Show full text]
  • LCA) Anna Skorczyk‑Werner1* , Zuzanna Niedziela1,2, Marcin Stopa2 and Maciej Robert Krawczyński1,3
    Skorczyk‑Werner et al. Orphanet J Rare Dis (2020) 15:345 https://doi.org/10.1186/s13023‑020‑01634‑y RESEARCH Open Access Novel gene variants in Polish patients with Leber congenital amaurosis (LCA) Anna Skorczyk‑Werner1* , Zuzanna Niedziela1,2, Marcin Stopa2 and Maciej Robert Krawczyński1,3 Abstract Background: Leber congenital amaurosis (LCA) is a rare retinal disease that is the most frequent cause of congenital blindness in children and the most severe form of inherited retinal dystrophies. To date, 25 genes have been impli‑ cated in the pathogenesis of LCA. As gene therapy is becoming available, the identifcation of potential treatment candidates is crucial. The aim of the study was to report the molecular basis of Leber congenital amaurosis in 22 Polish families. Methods: Single Nucleotide Polymorphism‑microarray for LCA genes or Next Generation Sequencing diagnostic panel for LCA genes (or both tests) were performed to identify potentially pathogenic variants. Bidirectional Sanger sequencing was carried out for validation and segregation analysis of the variants identifed within the families. Results: The molecular background was established in 22 families. From a total of 24 identifed variants, 23 were pre‑ dicted to afect protein‑coding or splicing, including 10 novel variants. The variants were identifed in 7 genes: CEP290, GUCY2D, RPE65, NMNAT1, CRB1, RPGRIP1, and CRX. More than one‑third of the patients, with clinical LCA diagnosis con‑ frmed by the results of molecular analysis, appeared to be afected with a severe form of the disease: LCA10 caused by the CEP290 gene variants. Intronic mutation c.2991 1655A>G in the CEP290 gene was the most frequent variant identifed in the studied group.
    [Show full text]
  • Leber Congenital Amaurosis/Early-Onset Severe
    BJO Online First, published on July 8, 2017 as 10.1136/bjophthalmol-2016-309975 Review Br J Ophthalmol: first published as 10.1136/bjophthalmol-2016-309975 on 8 July 2017. Downloaded from Leber congenital amaurosis/early-onset severe retinal dystrophy: clinical features, molecular genetics and therapeutic interventions Neruban Kumaran,1,2 Anthony T Moore,1,2,3 Richard G Weleber,4 Michel Michaelides1,2 1UCL Institute of ABSTRACT EOSRD, severe early childhood-onset retinal Ophthalmology, University Leber congenital amaurosis (LCA) and early-onset dystrophy (SECORD)7 and early-onset retinitis College London, London, UK 2Moorfields Eye Hospital NHS severe retinal dystrophy (EOSRD) are both genetically pigmentosa. Whereas LCA is congenital or pres- Foundation Trust, London, UK and phenotypically heterogeneous, and characterised ents within the first few months of life, is asso- 3University of California San clinically by severe congenital/early infancy visual loss, ciated with nystagmus, poor pupil responses Francisco, San Francisco CA, nystagmus, amaurotic pupils and markedly reduced/ and in most instances an undetectable full-field California, USA absent full-field electroretinograms. The vast genetic electroretinogram (ERG); EOSRD/SECORD is 4Casey Eye Institute, Oregon Health and Science University, heterogeneity of inherited retinal disease has been defined as a severe retinal dystrophy presenting Portland, Oregon, USA established over the last 10 - 20 years, with disease- after infancy and usually before the age of 5 causing variants identified in 25 genes to date associated years. Other distinguishing features of EOSRD/ Correspondence to with LCA/EOSRD, accounting for 70–80% of cases, SECORD include better residual visual func- Professor Michel Michaelides, with thereby more genes yet to be identified.
    [Show full text]
  • Statistical and Bioinformatic Analysis of Hemimethylation Patterns in Non-Small Cell Lung Cancer Shuying Sun1* , Austin Zane2, Carolyn Fulton3 and Jasmine Philipoom4
    Sun et al. BMC Cancer (2021) 21:268 https://doi.org/10.1186/s12885-021-07990-7 RESEARCH ARTICLE Open Access Statistical and bioinformatic analysis of hemimethylation patterns in non-small cell lung cancer Shuying Sun1* , Austin Zane2, Carolyn Fulton3 and Jasmine Philipoom4 Abstract Background: DNA methylation is an epigenetic event involving the addition of a methyl-group to a cytosine- guanine base pair (i.e., CpG site). It is associated with different cancers. Our research focuses on studying non-small cell lung cancer hemimethylation, which refers to methylation occurring on only one of the two DNA strands. Many studies often assume that methylation occurs on both DNA strands at a CpG site. However, recent publications show the existence of hemimethylation and its significant impact. Therefore, it is important to identify cancer hemimethylation patterns. Methods: In this paper, we use the Wilcoxon signed rank test to identify hemimethylated CpG sites based on publicly available non-small cell lung cancer methylation sequencing data. We then identify two types of hemimethylated CpG clusters, regular and polarity clusters, and genes with large numbers of hemimethylated sites. Highly hemimethylated genes are then studied for their biological interactions using available bioinformatics tools. Results: In this paper, we have conducted the first-ever investigation of hemimethylation in lung cancer. Our results show that hemimethylation does exist in lung cells either as singletons or clusters. Most clusters contain only two or three CpG sites. Polarity clusters are much shorter than regular clusters and appear less frequently. The majority of clusters found in tumor samples have no overlap with clusters found in normal samples, and vice versa.
    [Show full text]