Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.


BACKGROUND:Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new information on the diagnosis and pathogenesis of sporadic PD. METHODS:Changes in gene expression in the blood of 40 sporadic PD patients and 20 healthy controls ("Discovery set") were analyzed by taking advantage of the Affymetrix platform. Patients were at the onset of motor symptoms and before initiating any pharmacological treatment. Data analysis was performed by applying Ranking-Principal Component Analysis, PUMA and Significance Analysis of Microarrays. Functional annotations were assigned using GO, DAVID, GSEA to unveil significant enriched biological processes in the differentially expressed genes. The expressions of selected genes were validated using RT-qPCR and samples from an independent cohort of 12 patients and controls ("Validation set"). RESULTS:Gene expression profiling of blood samples discriminates PD patients from healthy controls and identifies differentially expressed genes in blood. The majority of these are also present in dopaminergic neurons of the Substantia Nigra, the key site of neurodegeneration. Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation. Candidate transcripts as CBX5, TCF3, MAN1C1 and DOCK10 were validated by RT-qPCR. CONCLUSIONS:Our data support the use of blood transcriptomics to study neurodegenerative diseases. It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.


BMC Genomics


BMC genomics


Calligaris R,Banica M,Roncaglia P,Robotti E,Finaurini S,Vlachouli C,Antonutti L,Iorio F,Carissimo A,Cattaruzza T,Ceiner A,Lazarevic D,Cucca A,Pangher N,Marengo E,di Bernardo D,Pizzolato G,Gustincich S




Has Abstract


2015-10-28 00:00:00










  • The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions.

    abstract:BACKGROUND:A composite biological structure, such as an insect head or abdomen, contains many internal structures with distinct functions. Composite structures are often used in RNA-seq studies, though it is unclear how expression of the same gene in different tissues and structures within the same structure affects th...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Johnson BR,Atallah J,Plachetzki DC

    更新日期:2013-08-28 00:00:00

  • Mitochondrial dysregulation and oxidative stress in patients with chronic kidney disease.

    abstract:BACKGROUND:Chronic renal disease (CKD) is characterized by complex changes in cell metabolism leading to an increased production of oxygen radicals, that, in turn has been suggested to play a key role in numerous clinical complications of this pathological condition. Several reports have focused on the identification o...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Granata S,Zaza G,Simone S,Villani G,Latorre D,Pontrelli P,Carella M,Schena FP,Grandaliano G,Pertosa G

    更新日期:2009-08-21 00:00:00

  • Differential gene expression and alternative splicing in insect immune specificity.

    abstract:BACKGROUND:Ecological studies routinely show genotype-genotype interactions between insects and their parasites. The mechanisms behind these interactions are not clearly understood. Using the bumblebee Bombus terrestris/trypanosome Crithidia bombi model system (two bumblebee colonies by two Crithidia strains), we have ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Riddell CE,Lobaton Garces JD,Adams S,Barribeau SM,Twell D,Mallon EB

    更新日期:2014-11-27 00:00:00

  • Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing.

    abstract:BACKGROUND:Glandular trichomes produce a wide variety of commercially important secondary metabolites in many plant species. The most prominent anti-malarial drug artemisinin, a sesquiterpene lactone, is produced in glandular trichomes of Artemisia annua. However, only limited genomic information is currently available...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang W,Wang Y,Zhang Q,Qi Y,Guo D

    更新日期:2009-10-09 00:00:00

  • Effect of paleopolyploidy and allopolyploidy on gene expression in banana.

    abstract:BACKGROUND:Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, followed by inter- and intra-specific crosses between Musa acuminata and M. balbisiana (A and B ge...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cenci A,Hueber Y,Zorrilla-Fontanesi Y,van Wesemael J,Kissel E,Gislard M,Sardos J,Swennen R,Roux N,Carpentier SC,Rouard M

    更新日期:2019-03-27 00:00:00

  • Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring.

    abstract:BACKGROUND:Chloroplasts have their own genomes, independent from nuclear genomes, that play vital roles in growth, which is a major targeted trait for genetic improvement in Populus. Angiosperm chloroplast genomes are maternally inherited, but the chloroplast' variation pattern of poplar at the single-base level during...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhu S,Xu M,Wang H,Pan H,Wang G,Huang M

    更新日期:2018-05-29 00:00:00

  • Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

    abstract:BACKGROUND:New and improved antimicrobial countermeasures are urgently needed to counteract increased resistance to existing antimicrobial treatments and to combat currently untreatable or new emerging infectious diseases. We demonstrate that computational comparative genomics, together with experimental screening, can...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Stubben CJ,Duffield ML,Cooper IA,Ford DC,Gans JD,Karlyshev AV,Lingard B,Oyston PC,de Rochefort A,Song J,Wren BW,Titball RW,Wolinsky M

    更新日期:2009-10-29 00:00:00

  • Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias.

    abstract:BACKGROUND:Deep sequencing is a powerful tool for assessing viral genetic diversity. Such experiments harness the high coverage afforded by next generation sequencing protocols by treating sequencing reads as a population sample. Distinguishing true single nucleotide variants (SNVs) from sequencing errors remains chall...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: McElroy K,Zagordi O,Bull R,Luciani F,Beerenwinkel N

    更新日期:2013-07-24 00:00:00

  • Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes.

    abstract:BACKGROUND:Recent molecular studies have revealed considerably more diversity in the phylum Chlamydiae than was previously thought. Evidence is growing that many of these novel chlamydiae may be important pathogens in humans and animals. A significant barrier to characterising these novel chlamydiae is the requirement ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Taylor-Brown A,Bachmann NL,Borel N,Polkinghorne A

    更新日期:2016-09-05 00:00:00

  • A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes.

    abstract:BACKGROUND:Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Röske K,Foecking MF,Yooseph S,Glass JI,Calcutt MJ,Wise KS

    更新日期:2010-07-13 00:00:00

  • Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations.

    abstract:BACKGROUND:Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy langu...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kusuma P,Cox MP,Pierron D,Razafindrazaka H,Brucato N,Tonasso L,Suryadi HL,Letellier T,Sudoyo H,Ricaut FX

    更新日期:2015-03-17 00:00:00

  • The cytochrome P450 (CYP) gene superfamily in Daphnia pulex.

    abstract:BACKGROUND:Cytochrome P450s (CYPs) in animals fall into two categories: those that synthesize or metabolize endogenous molecules and those that interact with exogenous chemicals from the diet or the environment. The latter form a critical component of detoxification systems. RESULTS:Data mining and manual curation of ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Baldwin WS,Marko PB,Nelson DR

    更新日期:2009-04-21 00:00:00

  • Evaluation of variant identification methods for whole genome sequencing data in dairy cattle.

    abstract:BACKGROUND:Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less we...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Baes CF,Dolezal MA,Koltes JE,Bapst B,Fritz-Waters E,Jansen S,Flury C,Signer-Hasler H,Stricker C,Fernando R,Fries R,Moll J,Garrick DJ,Reecy JM,Gredler B

    更新日期:2014-11-01 00:00:00

  • Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats.

    abstract:BACKGROUND:Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on trans...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zeng H,Yu BF,Liu N,Yang YY,Xing HY,Liu XX,Zhou MW

    更新日期:2019-11-14 00:00:00

  • New data on robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures.

    abstract:BACKGROUND:Microarray gene expression (MAGE) signatures allow insights into the transcriptional processes of leukemias and may evolve as a molecular diagnostic test. Introduction of MAGE into clinical practice of leukemia diagnosis will require comprehensive assessment of variation due to the methodologies. Here we sys...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Campo Dell'Orto M,Zangrando A,Trentin L,Li R,Liu WM,te Kronnie G,Basso G,Kohlmann A

    更新日期:2007-06-22 00:00:00

  • Molecular dynamics study of the archaeal aquaporin AqpM.

    abstract:BACKGROUND:Aquaporins are a large family of transmembrane channel proteins that are present throughout all domains of life and are implicated in human disorders. These channels, allow the passive but selective movement of water and other small neutral solutes across cell membranes. Aquaporins have been classified into ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Araya-Secchi R,Garate JA,Holmes DS,Perez-Acle T

    更新日期:2011-12-22 00:00:00

  • Gene2vec: distributed representation of genes based on co-expression.

    abstract:BACKGROUND:Existing functional description of genes are categorical, discrete, and mostly through manual process. In this work, we explore the idea of gene embedding, distributed representation of genes, in the spirit of word embedding. RESULTS:From a pure data-driven fashion, we trained a 200-dimension vector represe...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Du J,Jia P,Dai Y,Tao C,Zhao Z,Zhi D

    更新日期:2019-02-04 00:00:00

  • Structure and evolution of barley powdery mildew effector candidates.

    abstract:BACKGROUND:Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal crops. B. graminis is an obligate biotrophic pathogen and as such has an absolute requirement to...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Pedersen C,Ver Loren van Themaat E,McGuffin LJ,Abbott JC,Burgis TA,Barton G,Bindschedler LV,Lu X,Maekawa T,Wessling R,Cramer R,Thordal-Christensen H,Panstruga R,Spanu PD

    更新日期:2012-12-11 00:00:00

  • A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production.

    abstract:BACKGROUND:Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: McKinlay JB,Laivenieks M,Schindler BD,McKinlay AA,Siddaramappa S,Challacombe JF,Lowry SR,Clum A,Lapidus AL,Burkhart KB,Harkins V,Vieille C

    更新日期:2010-11-30 00:00:00

  • Temporal transcriptome changes induced by MDV in Marek's disease-resistant and -susceptible inbred chickens.

    abstract:BACKGROUND:Marek's disease (MD) is a lymphoproliferative disease in chickens caused by Marek's disease virus (MDV) and characterized by T cell lymphoma and infiltration of lymphoid cells into various organs such as liver, spleen, peripheral nerves and muscle. Resistance to MD and disease risk have long been thought to ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Yu Y,Luo J,Mitra A,Chang S,Tian F,Zhang H,Yuan P,Zhou H,Song J

    更新日期:2011-10-12 00:00:00

  • Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing.

    abstract:BACKGROUND:Exome sequencing has transformed human genetic analysis and may do the same for other vertebrate model systems. However, a major challenge is sifting through the large number of sequence variants to identify the causative mutation for a given phenotype. In models like Xenopus tropicalis, an incomplete and oc...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: del Viso F,Bhattacharya D,Kong Y,Gilchrist MJ,Khokha MK

    更新日期:2012-11-21 00:00:00

  • Genomic comparison of serogroups O159 and O170 with other Vibrio cholerae serogroups.

    abstract:BACKGROUND:Of the hundreds of Vibrio cholerae serogroups, O1 and O139 are the main epidemic-causing ones. Although non-O1/non-O139 serogroups rarely cause epidemics, the possibility exists for strains within them to have pathogenic potential. RESULTS:We selected 25 representative strains within 16 V. cholerae serogrou...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li Z,Lu X,Wang D,Liang WL,Zhang J,Li J,Xu J,Pang B,Kan B

    更新日期:2019-03-25 00:00:00

  • Identifying Mendelian disease genes with the variant effect scoring tool.

    abstract:BACKGROUND:Whole exome sequencing studies identify hundreds to thousands of rare protein coding variants of ambiguous significance for human health. Computational tools are needed to accelerate the identification of specific variants and genes that contribute to human disease. RESULTS:We have developed the Variant Eff...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Carter H,Douville C,Stenson PD,Cooper DN,Karchin R

    更新日期:2013-01-01 00:00:00

  • RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational Barred Plymouth Rock chicken line.

    abstract:BACKGROUND:Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive genetic selection for meat production. This study was designed to investigate the genetic alterations a...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kong BW,Hudson N,Seo D,Lee S,Khatri B,Lassiter K,Cook D,Piekarski A,Dridi S,Anthony N,Bottje W

    更新日期:2017-01-13 00:00:00

  • Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca).

    abstract:BACKGROUND:The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda w...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu W,Zhao Y,Liu Z,Zhang Y,Lian Z,Li N

    更新日期:2006-11-17 00:00:00

  • A UML profile for the OBO relation ontology.

    abstract:BACKGROUND:Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are develo...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Guardia GD,Vêncio RZ,de Farias CR

    更新日期:2012-01-01 00:00:00

  • A fast-linear mixed model for genome-wide haplotype association analysis: application to agronomic traits in maize.

    abstract:BACKGROUND:Haplotypes combine the effects of several single nucleotide polymorphisms (SNPs) with high linkage disequilibrium, which benefit the genome-wide association analysis (GWAS). In the haplotype association analysis, both haplotype alleles and blocks are tested. Haplotype alleles can be inferred with the same st...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Chen H,Hao Z,Zhao Y,Yang R

    更新日期:2020-02-11 00:00:00

  • A potential role for intragenic miRNAs on their hosts' interactome.

    abstract:BACKGROUND:miRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages. Due to their regulatory functions, they have lately been implicated in several diseases, including malignancies. Roughly half of known miRNA genes are located within previously annotated protein-coding ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Hinske LC,Galante PA,Kuo WP,Ohno-Machado L

    更新日期:2010-10-01 00:00:00

  • The receptor like kinase at Rhg1-a/Rfs2 caused pleiotropic resistance to sudden death syndrome and soybean cyst nematode as a transgene by altering signaling responses.

    abstract:BACKGROUND:Soybean (Glycine max (L. Merr.)) resistance to any population of Heterodera glycines (I.), or Fusarium virguliforme (Akoi, O'Donnell, Homma & Lattanzi) required a functional allele at Rhg1/Rfs2. H. glycines, the soybean cyst nematode (SCN) was an ancient, endemic, pest of soybean whereas F. virguliforme caus...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Srour A,Afzal AJ,Blahut-Beatty L,Hemmati N,Simmonds DH,Li W,Liu M,Town CD,Sharma H,Arelli P,Lightfoot DA

    更新日期:2012-08-02 00:00:00

  • ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins.

    abstract:BACKGROUND:Host genetics is one of several factors known to shape human gut microbiome composition, however, the physiological processes underlying the heritability are largely unknown. Inter-individual differences in host factors secreted into the gut lumen may lead to variation in microbiome composition. One such fac...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Davenport ER,Goodrich JK,Bell JT,Spector TD,Ley RE,Clark AG

    更新日期:2016-11-21 00:00:00