DOCSLIB.ORG

Genetic Assessment of Inbred Chicken Lines Indicates Genomic Signatures of Resistance to Marek’S Disease Lingyang Xu1,2,3*†, Yanghua He1†, Yi Ding1, George E

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genetic Assessment of Inbred Chicken Lines Indicates Genomic Signatures of Resistance to Marek’S Disease Lingyang Xu1,2,3*†, Yanghua He1†, Yi Ding1, George E Xu et al. Journal of Animal Science and Biotechnology (2018) 9:65 https://doi.org/10.1186/s40104-018-0281-x RESEARCH Open Access Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marek’s disease Lingyang Xu1,2,3*†, Yanghua He1†, Yi Ding1, George E. Liu2, Huanmin Zhang4, Hans H. Cheng4, Robert L. Taylor Jr.5 and Jiuzhou Song1* Abstract Background: Marek’s disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. However, the mechanisms of genetic resistance for MD are complex and not fully understood. MD-resistant line 63 and MD-susceptible line 72 are two highly inbred progenitor lines of White Leghorn. Recombinant Congenic Strains (RCS) were developed from these two lines, which show varied susceptibility to MD. Results: We investigated genetic structure and genomic signatures across the genome, including the line 63 and line 72, six RCSs, and two reciprocally crossed flocks between the lines 63 and 72 (F1 63 ×72 and F1 72 ×63)using Affymetrix® Axiom® HD 600 K genotyping array. We observed 18 chickens from RCS lines were specifically clustered into resistance sub-groups distributed around line 63. Additionally, homozygosity analysis was employed to explore potential genetic components related to MD resistance, while runs of homozygosity (ROH) are regions of the genome where the identical haplotypes are inherited from each parent. We found several genes including SIK, SOX1, LIG4, SIK1 and TNFSF13B were contained in ROH region identified in resistant group (line 63 and RCS), and these genes have been reported that are contribute to immunology and survival. Based on FST based population differential analysis, we also identified important genes related to cell death and anti-apoptosis, including AKT1, API5, CDH13, CFDP and USP15, which could be involved in divergent selection during inbreeding process. Conclusions: Our findings offer valuable insights for understanding the genetic mechanism of resistance to MD and the identified genes could be considered as candidate biomarkers in further evaluation. Keywords: Genetic structure, Genomic signature, Homozygosity, Marek’s disease, Recombinant Congenic Strains (RCS) Background worldwide, and interest for its economic importance to Poultry products are main components of our daily life. the commercial poultry industry. The complexity of food safety and quality issues facing MDV transforms mainly CD4+ T cells and causes vari- the poultry industry are rapidly escalating, and many ous clinical syndromes in chicken tissues, which include other critical issues (i.e., bioterrorism, environmental peripheral nerves, gonad, iris, muscle, viscera, and skin stewardship and global competitiveness) are emerging [2]. MDV is shed and transmitted between birds via epi- simultaneously. Marek’s disease (MD) is a T cell lymph- thelial cells of the feather follicle, dander, chicken house oma induced by the widespread and readily transmissible dust, feces and saliva. Vaccines were developed to con- Marek’s disease virus (MDV) [1]. MD is one of the main trol the disease but are not sterilizing allowing the virus chronic infectious diseases threatening the poultry to replicate and spread. Thus, in the last few decades, field strains of the virus have evolved resulting in new subtypes that the vaccines may not completely control * Correspondence: [email protected]; [email protected] † [3]. MDV has proven to be a valuable comparative bio- Lingyang Xu and Yanghua He contributed equally to this work. medical model organism for understanding the princi- 1Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA ples of human disease [4] and MD is a natural model for Full list of author information is available at the end of the article © The Author(s). 2018 Open Access 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. Xu et al. Journal of Animal Science and Biotechnology (2018) 9:65 Page 2 of 10 lymphomas overexpressing Hodgkin’s disease antigen carried out to explore potential genetic mechanism of [5]. However, there is a shortage of genetic information MD disease. Our studies revealed several genes related about the virus host and etiological process leading to to regulation of cell death and anti-apoptosis, which are MDV uptake, dissemination, latency and tumor probably related to the resistance to MD. formation. Currently, control strategies for MD predominantly rely Methods on vaccination of chickens. But the vaccination cannot Experimental population provide complete protection because of the changing na- In total, 30 chickens without treatments were selected ture of the disease itself and evolution of MDV with esca- and genotyped in this study. Among them, three were lated virulence [4]. Recently, studies using integrating from each of the line 72, line 63, reciprocal cross F1 hy- genomic approaches identified genes and molecular brid 72 ×63, F1 hybrid 63 ×72, and six recombinant con- markers associated with MD disease resistance [6]. genic strains (RCSs) [C, J, M, N, S and X] [11]. RCSs Genetic makers, quantitative trait loci (QTL) and genom- were developed using line 63 as the parental strain ics regions in a large reciprocal backcross (BC) were mated to line 72 and then backcrossed to line 63 twice discovered between two partially inbred commercial followed by full-sib matings for about 20 generations. White Leghorn layer chicken [7] and in an F6 advanced Eventually, diverse RCSs were generated and they intercross population of commercial layer chickens [8]. contain 87.5% of line 63 and 12.5% of line 72 in the gen- Additionally, gene expression using transcript array [9, 10] etic background but with different MD resistance and allele-specific expression analysis using RNA sequen- (Additional file 1: Figure S1) [3, 13]. In this study, six cing [11] have been utilized to understand response to RCSs above were chosen to check their genetic back- MDV infection and MD genetic resistance. ground and reveal their particular resistant signatures. To determine the genetic components pertaining to disease resistance, the Avian Disease and Oncology La- Genotyping and quality control boratory (ADOL) has successfully developed inbred Genomic DNA from red blood cells was extracted using chicken lines resistant or susceptible to MD as a power- the DNeasy Blood & Tissue Mini Kit (QIAGEN). Geno- ful experimental model for investigation of host resist- typing for the 30 chickens was performed using the ance to this disease, the inbred lines 63 and 72. The Affymetrix® Axiom® Genome-Wide Chicken Genotyping percentage of chickens developing a tumor or tumors in- Array (600 K) by the Affymetrix service facility accord- duced by a partially attenuated vv + strain of MDV dif- ing to the manufacturer’s protocols [14]. Affymetrix fered significantly between the two lines of chickens. adopts a preliminary call rate of 90% that is used by de- Genetic resistance to MD in chickens is commonly eval- fault to pass arrays for further data analysis. Successfully uated with MD incidence post-MDV challenge, which passed arrays were clustered and final genotypes were had been descripted in previous study [12]. Only 0–3% generated using the Axiom GT1 algorithm. Quality con- of line 63 chickens developed tumors 8 wk post infection trol was assessed in Genotyping Console v4.1.3. All compared to 99%–100% of line 72 chickens. Importantly, chosen samples genotyped on Affymetrix SNP array met 19 recombinant congenic strains (RCS) have been devel- the 99% call rate. oped using the inbred lines 63 and 72 as progenitor lines. The tumor incidence differs among RCS either vacci- Multidimensional scaling and admixture analysis nated or unvaccinated. Thus, the varied resistance Quality control were considered using the following se- among the RCS can provide an ideal model to investi- lection criteria: MAF ≥ 0.01 (including SNPs with gate genomic components that play vital roles in genetic MAF ≥ 0.01), geno ≥0.1 (including only SNPs with a resistance to MD. Although a previous study has dem- 90% genotyping rate or higher), and P value of x2 test − onstrated some genetic variability among the RCSs by for Hardy-Weinberg equilibrium ≥10 6. To avoid link- microsatellite fingerprinting [2], genetic variations age distortion for the population structure analysis, underlying varied susceptibility to MD in the RCS lines SNPs were pruned for linkage disequilibrium (LD) remains poorly understood. using pair-wise genotype correction (r2 >0.2)in50SNP In this study, we hypothesized that differential gen- sliding widows with a step of 10 SNPs across the gen- omic signatures contribute to MD resistance in the RCS. ome. To look for evidence of population substructure, Using ten lines, including line 63 and line 72, two hybrid we carried out Multidimensional Scaling (MDS) ana- F1 (F1 63–72 and F1 72–63) and six RCSs representing lysis using 5,064 LD filtered SNPs among all 30 chick- various capacity in resistance/susceptibility to MD,
Load more

Recommended publications
  • Gene Family: Gene Duplication and Retrotransposon Insertion
    21 Bucentaur (Bcnt)1 Gene Family: Gene Duplication and Retrotransposon Insertion Shintaro Iwashita and Naoki Osada Iwaki Meisei University / National Institute of Genetics Japan 1. Introduction Members of multiple gene families in higher organisms allow for more refined cellular signaling networks and structural organization toward more stable physiological homeostasis. Gene duplication is one the most powerful ways of providing an opportunity to create a novel gene(s) because a novel function might be acquired without the loss of the original gene function (Ohno, 1970). Gene duplication can result from unequal crossing over by recombination, retroposition of cDNA, or whole-genome duplication. Furthermore, a replication-based mechanism of change in gene copy number has been proposed recently (Hastings et al., 2009). Gene duplication generated by retroposition is frequently accompanied by deleterious effects because the insertion of cDNA into the genome is nearly random or unlinks the original gene location resulting in an alteration of the original vital functions of the target genes. Thus retroelements such as transposable elements and endogenous retroviruses have been thought of as “selfish”. On the other hand, gene duplication caused by unequal crossing over generally results in tandem alignment, which less frequently disrupts the functions of other genes. Recent genome-wide studies have demonstrated that retroelements can definitely contribute to the creation of individual novel genes and the modulation of gene expression, which allows for the dynamic diversity of biological systems, such as placental evolution (Rawn & Cross, 2008). It is now recognized that tandem duplication and retroposition are among the key factors that initiate the creation of novel gene family members (Brosius, 2005; Sorek, 2007; Kaessmann, 2010).
    [Show full text]
  • Seq2pathway Vignette
    seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway.
    [Show full text]
  • Universidade Nova De Lisboa Instituto De Higiene E Medicina Tropical
    Universidade Nova de Lisboa Instituto de Higiene e Medicina Tropical Regulation of the apoptosis pathway in Rhipicephalus annulatus ticks by the protozoan Babesia bigemina Catarina Sofia Bento Monteiro DISSERTAÇÃO PARA A OBTENÇÃO DO GRAU DE MESTRE EM PARASITOLOGIA MÉDICA JANEIRO, 2018 Universidade Nova de Lisboa Instituto de Higiene e Medicina Tropical Regulation of the apoptosis pathway in Rhipicephalus annulatus ticks by the protozoan Babesia bigemina Autor: Catarina Sofia Bento Monteiro Orientador: Doutora Ana Isabel Amaro Gonçalves Domingos (IHMT, UNL) Coorientador: Doutora Sandra Isabel da Conceição Antunes (IHMT, UNL) Dissertação apresentada para cumprimento dos requisitos necessários à obtenção do grau de mestre em parasitologia médica The results obtained during the development of this master project were reported at two international conferences: Monteiro, C, Domingos, A, and Antunes, S 2017, ´Regulation of the apoptosis pathway in Rhipicephalus annulatus ticks by the protozoan Babesia bigemina´, COST action: EuroNegVec, 11-13 September, Crete, Greece. Monteiro, C, Domingos, A, and Antunes, S 2017 ´Is the apoptosis pathway in Rhipicephalus annulatus ticks regulated by the protozoan Babesia bigemina?´ Conference: Biotecnología Habana 2017: ´La Biotecnología Agropecuaria en el siglo XXI´, 3-6 December, Varadero, Cuba. i Acknowledgments Quero, desde já, agradecer à Doutora Ana Domingos por se ter disponibilizado a orientar-me e por não ter desistido de mim. À Doutora Sandra Antunes, pelo apoio constante e compreensão durante toda esta longa jornada. Admiro a simplicidade com que encaras a vida. À Joana Couto pela boa disposição e prontidão em ajudar. És das pessoas mais genuínas que já conheci. À Joana Ferrolho com quem partilho o mesmo gosto pela medicina veterinária.
    [Show full text]
  • Master Biomedizin 2018 1) UCSC & Uniprot 2) Homology 3) MSA 4) Phylogeny
    Master Biomedizin 2018 1) UCSC & UniProt 2) Homology 3) MSA 4) Phylogeny Pablo Mier 1 [email protected] Genomics *Images from: Wikipedia 1 a. Get the fasta sequence of the human (Homo sapiens) protein P53 from UniProt (https://www.uniprot.org/). Which one of all the isoforms should you download? P04637 b. Find the P53 protein from mouse (Mus musculus). As you see, there is more than one entry for mouse. Which UniProt entry should you select? P02340 c. BLAT the human P53 using “hg38” as database (in UCSC, http://genome.ucsc.edu/cgi-bin/hgBlat), and answer: How many amino acids has the query sequence? 393 aa And how many nucleotides? 1179 nt Is it a perfect alignment? No Which is the genomic locus of the target? Chr17 7669612-7676594 d. Visualize and navigate through the P53 genome region, and answer: Which genes are around? ATP1B2 and WRAP53 How many exons does it have? 9 exons e. BLAT the mouse P53 against the human genome “hg38”. What do you observe? The result is worse (85%) Human Mouse (Homo sapiens) (Mus musculus) Pablo Mier 2 [email protected] Genomics *Images from: UniProt 1 a. P04637 (P53_HUMAN). The canonical. b. P02340 (P53_MOUSE). Pablo Mier 3 [email protected] Genomics *Images from: UCSC 1 c. 393 amino acids Not a perfect alignment chr17 393*3 = 1179 nucleotides (“lpennvl”) 7669612-7676594 d. ATP1B2 and WRAP53. 9 exons (9 blocks). 9 8 7 6 5 4 3 2 1 e. The result is worse (85%). Pablo Mier 4 [email protected] UniProt database 2 a.
    [Show full text]
  • Supplementary Materials
    Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine
    [Show full text]
  • Product Sheet CA1009
    API5 Antibody Applications: WB, IHC Detected MW: 51 kDa Cat. No. CA1009 Species & Reactivity: Human, Rat Isotype: Rabbit IgG BACKGROUND APPLICATIONS The apoptosis inhibitor-5 [API5; antiapoptosis Application: *Dilution: clone 11 (AAC-11); fibroblast growth factor-2 WB 1:1000 (FGF2)-interacting factor (FIF)] is a 504-aa IP n/d nuclear protein whose expression has been shown IHC 1:50-200 to prevent apoptosis after growth factor ICC n/d deprivation. It was shown that its antiapoptotic action seems to be mediated, at least in part, by FACS n/d *Optimal dilutions must be determined by end user. the suppression of the transcription factor E2F1- induced apoptosis. Moreover, it was also reported that API5 interacts with, and negatively regulates Acinus, a protein involved in apoptotic DNA QUALITY CONTROL DATA fragmentation. API5 can form homo-oligomers, through a leucine-zipper (LZ) motif, and oligomerization-deficient mutants of AAC-11 can no longer inhibit apoptosis nor interact with Acinus.1 The API5gene has been shown to be highly expressed in multiple cancer cell lines as well as in some metastatic lymph node tissues and in B-cell chronic lymphoid leukemia. API5 expression seems to confer a poor outcome in subgroups of patients with non-small cell lung carcinoma, whereas its depletion seems to be tumor cell lethal under condition of low-serum stress. Interestingly, API5 overexpression has been reported to promote both cervical cancer cells growth and invasiveness. Combined, these observations implicate API5as a putative metastatic oncogene and suggest that API5 could constitute a therapeutic target in cancer.2 References: 1.
    [Show full text]
  • Identifying Genetic Risk Factors for Coronary Artery Angiographic Stenosis in a Genetically Diverse Population
    Please do not remove this page Identifying Genetic Risk Factors for Coronary Artery Angiographic Stenosis in a Genetically Diverse Population Liu, Zhi https://scholarship.miami.edu/discovery/delivery/01UOML_INST:ResearchRepository/12355224170002976?l#13355497430002976 Liu, Z. (2016). Identifying Genetic Risk Factors for Coronary Artery Angiographic Stenosis in a Genetically Diverse Population [University of Miami]. https://scholarship.miami.edu/discovery/fulldisplay/alma991031447280502976/01UOML_INST:ResearchR epository Embargo Downloaded On 2021/09/26 20:05:11 -0400 Please do not remove this page UNIVERSITY OF MIAMI IDENTIFYING GENETIC RISK FACTORS FOR CORONARY ARTERY ANGIOGRAPHIC STENOSIS IN A GENETICALLY DIVERSE POPULATION By Zhi Liu A DISSERTATION Submitted to the Faculty of the University of Miami in partial fulfillment of the requirements for the degree of Doctor of Philosophy Coral Gables, Florida August 2016 ©2016 Zhi Liu All Rights Reserved UNIVERSITY OF MIAMI A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy IDENTIFYING GENETIC RISK FACTORS FOR CORONARY ARTERY ANGIOGRAPHIC STENOSIS IN A GENETICALLY DIVERSE POPULATION Zhi Liu Approved: ________________ _________________ Gary W. Beecham, Ph.D. Liyong Wang, Ph.D. Assistant Professor of Human Associate Professor of Human Genetics Genetics ________________ _________________ Eden R. Martin, Ph.D. Guillermo Prado, Ph.D. Professor of Human Genetics Dean of the Graduate School ________________ Tatjana Rundek, M.D., Ph.D. Professor of Neurology LIU, ZHI (Ph.D., Human Genetics and Genomics) Identifying Genetic Risk Factors for Coronary Artery (August 2016) Angiographic Stenosis in a Genetically Diverse Population Abstract of a dissertation at the University of Miami. Dissertation supervised by Professor Gary W.
    [Show full text]
  • API5 Confers Tumoral Immune Escape Through FGF2- Dependent Cell Survival Pathway
    Published OnlineFirst April 25, 2014; DOI: 10.1158/0008-5472.CAN-13-3225 Cancer Therapeutics, Targets, and Chemical Biology Research API5 Confers Tumoral Immune Escape through FGF2- Dependent Cell Survival Pathway Kyung Hee Noh1, Seok-Ho Kim1,3, Jin Hee Kim1, Kwon-Ho Song1, Young-Ho Lee1, Tae Heung Kang4, Hee Dong Han4,6, Anil K. Sood5,6, Joanne Ng2, Kwanghee Kim2,7,9, Chung Hee Sonn2, Vinay Kumar8, Cassian Yee7,9, Kyung-Mi Lee2, and Tae Woo Kim1,2 Abstract Identifying immune escape mechanisms used by tumors may define strategies to sensitize them to immu- notherapies to which they are otherwise resistant. In this study, we show that the antiapoptotic gene API5 acts as an immune escape gene in tumors by rendering them resistant to apoptosis triggered by tumor antigen-specificT cells. Its RNAi-mediated silencing in tumor cells expressing high levels of API5 restored antigen-specific immune sensitivity. Conversely, introducing API5 into API5low cells conferred immune resistance. Mechanistic investiga- tions revealed that API5 mediated resistance by upregulating FGF2 signaling through a FGFR1/PKCd/ERK effector pathway that triggered degradation of the proapoptotic molecule BIM. Blockade of FGF2, PKCd, or ERK phenocopied the effect of API5 silencing in tumor cells expressing high levels of API5 to either murine or human antigen-specific T cells. Our results identify a novel mechanism of immune escape that can be inhibited to potentiate the efficacy of targeted active immunotherapies. Cancer Res; 74(13); 3556–66. Ó2014 AACR. Introduction of immunosuppressive cytokines such as TGFb and IL10 and – Despite the presence of a competent immune system, tumor the accumulation of regulatory cells (1 4) can exacerbate the cells may elude detection from host immune surveillance immune inhibitory milieu, whereas intrinsic genetic instability through a process of cancer immune editing.
    [Show full text]
  • Population-Haplotype Models for Mapping and Tagging Structural Variation Using Whole Genome Sequencing
    Population-haplotype models for mapping and tagging structural variation using whole genome sequencing Eleni Loizidou Submitted in part fulfilment of the requirements for the degree of Doctor of Philosophy Section of Genomics of Common Disease Department of Medicine Imperial College London, 2018 1 Declaration of originality I hereby declare that the thesis submitted for a Doctor of Philosophy degree is based on my own work. Proper referencing is given to the organisations/cohorts I collaborated with during the project. 2 Copyright Declaration The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work 3 Abstract The scientific interest in copy number variation (CNV) is rapidly increasing, mainly due to the evidence of phenotypic effects and its contribution to disease susceptibility. Single nucleotide polymorphisms (SNPs) which are abundant in the human genome have been widely investigated in genome-wide association studies (GWAS). Despite the notable genomic effects both CNVs and SNPs have, the correlation between them has been relatively understudied. In the past decade, next generation sequencing (NGS) has been the leading high-throughput technology for investigating CNVs and offers mapping at a high-quality resolution. We created a map of NGS-defined CNVs tagged by SNPs using the 1000 Genomes Project phase 3 (1000G) sequencing data to examine patterns between the two types of variation in protein-coding genes.
    [Show full text]
  • Ejhg2009157.Pdf
    European Journal of Human Genetics (2010) 18, 342–347 & 2010 Macmillan Publishers Limited All rights reserved 1018-4813/10 $32.00 www.nature.com/ejhg ARTICLE Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects Zari Dastani1,2,Pa¨ivi Pajukanta3, Michel Marcil1, Nicholas Rudzicz4, Isabelle Ruel1, Swneke D Bailey2, Jenny C Lee3, Mathieu Lemire5,9, Janet Faith5, Jill Platko6,10, John Rioux6,11, Thomas J Hudson2,5,7,9, Daniel Gaudet8, James C Engert*,2,7, Jacques Genest1,2,7 Low levels of high-density lipoprotein cholesterol (HDL-C) are an independent risk factor for cardiovascular disease. To identify novel genetic variants that contribute to HDL-C, we performed genome-wide scans and quantitative association studies in two study samples: a Quebec-wide study consisting of 11 multigenerational families and a study of 61 families from the Saguenay– Lac St-Jean (SLSJ) region of Quebec. The heritability of HDL-C in these study samples was 0.73 and 0.49, respectively. Variance components linkage methods identified a LOD score of 2.61 at 98 cM near the marker D16S515 in Quebec-wide families and an LOD score of 2.96 at 86 cM near the marker D16S2624 in SLSJ families. In the Quebec-wide sample, four families showed segregation over a 25.5-cM (18 Mb) region, which was further reduced to 6.6 Mb with additional markers. The coding regions of all genes within this region were sequenced. A missense variant in CHST6 segregated in four families and, with additional families, we observed a P value of 0.015 for this variant.
    [Show full text]
  • Transcriptome Analysis of Signaling Pathways of Human Peritoneal
    Liu et al. BMC Nephrology (2019) 20:181 https://doi.org/10.1186/s12882-019-1376-0 RESEARCH ARTICLE Open Access Transcriptome analysis of signaling pathways of human peritoneal mesothelial cells in response to different osmotic agents in a peritoneal dialysis solution Bin Liu1,2†, Shijian Feng1,3†, Ghida Dairi1,4, Qiunong Guan1, Irina Chafeeva5, Hao Wang2, Richard Liggins6, Gerald da Roza7, Jayachandran N. Kizhakkedathu5,8 and Caigan Du1,9* Abstract Background: Glucose is a primary osmotic agent in peritoneal dialysis (PD) solutions, but its long-term use causes structural alteration of the peritoneal membrane (PM). Hyperbranched polyglycerol (HPG) is a promising alternative to glucose. This study was designed to compare the cellular responses of human peritoneal mesothelial cells (HPMCs) to these two different osmotic agents in a hypertonic solution using transcriptome analysis. Methods: Cultured HPMCs were repeatedly exposed to HPG-based or Physioneal 40 (PYS, glucose 2.27%) hypertonic solutions. Transcriptome datasets were produced using Agilent SurePrint G3 Human GE 8 × 60 microarray. Cellular signaling pathways were examined by Ingenuity Pathway Analysis (IPA). Protein expression was examined by flow cytometry analysis and Western blotting. Results: The HPG-containing solution was better tolerated compared with PYS, with less cell death and disruption of cell transcriptome. The levels of cell death in HPG- or PYS- exposed cells were positively correlated with the number of affected transcripts (HPG: 128 at day 3, 0 at day 7; PYS: 1799 at day 3, 212 at day 7). In addition to more affected “biosynthesis” and “cellular stress and death” pathways by PYS, both HPG and PYS commonly affected “sulfate biosynthesis”, “unfolded protein response”, “apoptosis signaling” and “NRF2-mediated oxidative stress response” pathways at day 3.
    [Show full text]
  • The Human Cranio Facial Development Protein 1 (Cfdp1)
    www.nature.com/scientificreports OPEN The human Cranio Facial Development Protein 1 (Cfdp1) gene encodes a protein required for Received: 30 September 2016 Accepted: 20 February 2017 the maintenance of higher-order Published: 03 April 2017 chromatin organization Giovanni Messina1,2, Maria Teresa Atterrato1,2, Yuri Prozzillo1,2, Lucia Piacentini2, Ana Losada3 & Patrizio Dimitri1,2 The human Cranio Facial Development Protein 1 (Cfdp1) gene maps to chromosome 16q22.2-q22.3 and encodes the CFDP1 protein, which belongs to the evolutionarily conserved Bucentaur (BCNT) family. Craniofacial malformations are developmental disorders of particular biomedical and clinical interest, because they represent the main cause of infant mortality and disability in humans, thus it is important to understand the cellular functions and mechanism of action of the CFDP1 protein. We have carried out a multi-disciplinary study, combining cell biology, reverse genetics and biochemistry, to provide the firstin vivo characterization of CFDP1 protein functions in human cells. We show that CFDP1 binds to chromatin and interacts with subunits of the SRCAP chromatin remodeling complex. An RNAi-mediated depletion of CFDP1 in HeLa cells affects chromosome organization, SMC2 condensin recruitment and cell cycle progression. Our findings provide new insight into the chromatin functions and mechanisms of the CFDP1 protein and contribute to our understanding of the link between epigenetic regulation and the onset of human complex developmental disorders. Chromatin organization is highly dynamic and subject to many epigenetic changes, mediated by histone modify- ing enzymes and ATP-dependent chromatin remodeling complexes1. These complexes are multi-protein molec- ular devices able to slide or displace nucleosomes, thus making DNA more accessible to specific binding proteins that control essential cellular processes, such as transcription, replication and DNA repair.
    [Show full text]