RNA editing alterations in a multi-ethnic Alzheimer disease cohort converge on immune and endocytic molecular pathways.

Abstract:

:Little is known about the post-transcriptional mechanisms that modulate the genetic effects in the molecular pathways underlying Alzheimer disease (AD), and even less is known about how these changes might differ across diverse populations. RNA editing, the process that alters individual bases of RNA, may contribute to AD pathogenesis due to its roles in neuronal development and immune regulation. Here, we pursued one of the first transcriptome-wide RNA editing studies in AD by examining RNA sequencing data from individuals of both African-American (AA) and non-Hispanic White (NHW) ethnicities. Whole transcriptome RNA sequencing and RNA editing analysis were performed on peripheral blood specimens from 216 AD cases (105 AA, 111 NHW) and 212 gender matched controls (105 AA, 107 NHW). 449 positions in 254 genes and 723 positions in 371 genes were differentially edited in AA and NHW, respectively. While most differentially edited sites localized to different genes in AA and NHW populations, these events converged on the same pathways across both ethnicities, especially endocytic and inflammatory response pathways. Furthermore, these differentially edited sites were preferentially predicted to disrupt miRNA binding and induce nonsynonymous coding changes in genes previously associated with AD in molecular studies, including PAFAH1B2 and HNRNPA1. These findings suggest RNA editing is an important post-transcriptional regulatory program in AD pathogenesis.

journal_name

Hum Mol Genet

journal_title

Human molecular genetics

authors

Gardner OK,Wang L,Van Booven D,Whitehead PL,Hamilton-Nelson KL,Adams LD,Starks TD,Hofmann NK,Vance JM,Cuccaro ML,Martin ER,Byrd GS,Haines JL,Bush WS,Beecham GW,Pericak-Vance MA,Griswold AJ

doi

10.1093/hmg/ddz110

subject

Has Abstract

pub_date

2019-09-15 00:00:00

pages

3053-3061

issue

18

eissn

0964-6906

issn

1460-2083

pii

5510615

journal_volume

28

pub_type

杂志文章
  • AAV9 delivered bispecific nanobody attenuates amyloid burden in the gelsolin amyloidosis mouse model.

    abstract::Gelsolin amyloidosis is a dominantly inherited, incurable type of amyloidosis. A single point mutation in the gelsolin gene (G654A is most common) results in the loss of a Ca2+  binding site in the second gelsolin domain. Consequently, this domain partly unfolds and exposes an otherwise buried furin cleavage site at t...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddx056

    authors: Verhelle A,Nair N,Everaert I,Van Overbeke W,Supply L,Zwaenepoel O,Peleman C,Van Dorpe J,Lahoutte T,Devoogdt N,Derave W,Chuah MK,VandenDriessche T,Gettemans J

    更新日期:2017-04-01 00:00:00

  • SPEG binds with desmin and its deficiency causes defects in triad and focal adhesion proteins.

    abstract::SPEG, a member of the myosin light chain kinase family, is localized at the level of triad surrounding myofibrils in skeletal muscles. In humans, SPEG mutations are associated with centronuclear myopathy and cardiomyopathy. Using a striated muscle specific Speg-knockout (KO) mouse model, we have previously shown that ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddaa276

    authors: Luo S,Li Q,Lin J,Murphy Q,Marty I,Zhang Y,Kazerounian S,Agrawal PB

    更新日期:2020-12-23 00:00:00

  • Microbiomic subprofiles and MDR1 promoter methylation in head and neck squamous cell carcinoma.

    abstract::Clinical observations and epidemiologic studies suggest that the incidence of head and neck squamous cell carcinoma (HNSCC) correlates with dental hygiene, implying a role for bacteria-induced inflammation in its pathogenesis. Here we begin to explore the pilot hypothesis that specific microbial populations may contri...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddr593

    authors: Bebek G,Bennett KL,Funchain P,Campbell R,Seth R,Scharpf J,Burkey B,Eng C

    更新日期:2012-04-01 00:00:00

  • Combining P301L and S320F tau variants produces a novel accelerated model of tauopathy.

    abstract::Understanding the biological functions of tau variants can illuminate differential etiologies of Alzheimer's disease (AD) and primary tauopathies. Though the end-stage neuropathological attributes of AD and primary tauopathies are similar, the etiology and behavioral outcomes of these diseases follow unique and diverg...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddz151

    authors: Koller EJ,Gonzalez De La Cruz E,Machula T,Ibanez KR,Lin WL,Williams T,Riffe CJ,Ryu D,Strang KH,Liu X,Janus C,Golde TE,Dickson D,Giasson BI,Chakrabarty P

    更新日期:2019-10-01 00:00:00

  • RGS4 mRNA expression in postmortem human cortex is associated with COMT Val158Met genotype and COMT enzyme activity.

    abstract::Linkage, association and postmortem studies have implicated regulator of G-protein signaling 4 (RGS4), which negatively modulates signal transduction at G-protein-coupled receptors, as a candidate schizophrenia susceptibility gene. We compared RGS4 mRNA expression in the dorsolateral prefrontal cortex (DLPFC), between...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddl222

    authors: Lipska BK,Mitkus S,Caruso M,Hyde TM,Chen J,Vakkalanka R,Straub RE,Weinberger DR,Kleinman JE

    更新日期:2006-09-15 00:00:00

  • The phenotypic landscape of a Tbc1d24 mutant mouse includes convulsive seizures resembling human early infantile epileptic encephalopathy.

    abstract::Epilepsy, deafness, onychodystrophy, osteodystrophy and intellectual disability are associated with a spectrum of mutations of human TBC1D24. The mechanisms underlying TBC1D24-associated disorders and the functions of TBC1D24 are not well understood. Using CRISPR-Cas9 genome editing, we engineered a mouse with a prema...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddy445

    authors: Tona R,Chen W,Nakano Y,Reyes LD,Petralia RS,Wang YX,Starost MF,Wafa TT,Morell RJ,Cravedi KD,du Hoffmann J,Miyoshi T,Munasinghe JP,Fitzgerald TS,Chudasama Y,Omori K,Pierpaoli C,Banfi B,Dong L,Belyantseva IA,Friedma

    更新日期:2019-05-01 00:00:00

  • Enhanced excitation-coupled Ca(2+) entry induces nuclear translocation of NFAT and contributes to IL-6 release from myotubes from patients with central core disease.

    abstract::Prolonged depolarization of skeletal muscle cells induces entry of extracellular calcium into muscle cells, an event referred to as excitation-coupled calcium entry. Skeletal muscle excitation-coupled calcium entry relies on the interaction between the 1,4-dihydropyridine receptor on the sarcolemma and the ryanodine r...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddq506

    authors: Treves S,Vukcevic M,Jeannet PY,Levano S,Girard T,Urwyler A,Fischer D,Voit T,Jungbluth H,Lillis S,Muntoni F,Quinlivan R,Sarkozy A,Bushby K,Zorzato F

    更新日期:2011-02-01 00:00:00

  • Glucosylceramide synthase inhibition with lucerastat lowers globotriaosylceramide and lysosome staining in cultured fibroblasts from Fabry patients with different mutation types.

    abstract::Fabry disease is an X-linked lysosomal storage disorder caused by mutations in the GLA gene coding for α-galactosidase A (α-GalA). The deleterious mutations lead to accumulation of α-GalA substrates, including globotriaosylceramide (Gb3) and globotriaosylsphingosine. Progressive glycolipid storage results in cellular ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddy248

    authors: Welford RWD,Mühlemann A,Garzotti M,Rickert V,Groenen PMA,Morand O,Üçeyler N,Probst MR

    更新日期:2018-10-01 00:00:00

  • An extended genome-wide association study identifies novel susceptibility loci for nasopharyngeal carcinoma.

    abstract::To further identify novel susceptibility loci of nasopharyngeal carcinoma (NPC), we here extended our previous genome-wide association study (GWAS) by boosting statistical power with larger sample size and validating more SNPs in the ranking list based on the GWAS P-values. The discovery stage consisting of 463,250 SN...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw200

    authors: Cui Q,Feng QS,Mo HY,Sun J,Xia YF,Zhang H,Foo JN,Guo YM,Chen LZ,Li M,Liu WS,Xu M,Zhou G,He F,Yu X,Jia WH,Liu J,Zeng YX,Bei JX

    更新日期:2016-08-15 00:00:00

  • Site-specific Mtm1 mutagenesis by an AAV-Cre vector reveals that myotubularin is essential in adult muscle.

    abstract::Manipulation of the mouse genome by site-specific mutagenesis has been extensively used to study gene function and model human disorders. Mouse models of myotubular myopathy (XLMTM), a severe congenital muscular disorder due to loss-of-function mutations in the MTM1 gene, have been generated by homologous recombinatio...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt038

    authors: Joubert R,Vignaud A,Le M,Moal C,Messaddeq N,Buj-Bello A

    更新日期:2013-05-01 00:00:00

  • The sarcoglycan complex in the six autosomal recessive limb-girdle muscular dystrophies.

    abstract::To enhance our understanding of the autosomal recessive limb-girdle muscular dystrophy (LGMD), patients from six genetically distinct forms (LGMD2A to LGMD2F) were studied with antibodies directed against four sarcoglycan subunits (alpha-, beta-, gamma-, delta-SG), dystrophin, beta-dystroglycan (beta-DG) and merosin. ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/5.12.1963

    authors: Vainzof M,Passos-Bueno MR,Canovas M,Moreira ES,Pavanello RC,Marie SK,Anderson LV,Bonnemann CG,McNally EM,Nigro V,Kunkel LM,Zatz M

    更新日期:1996-12-01 00:00:00

  • Reduced SMN protein impairs maturation of the neuromuscular junctions in mouse models of spinal muscular atrophy.

    abstract::Spinal muscular atrophy (SMA) is a common pediatric neuromuscular disorder caused by insufficient levels of the survival of motor neuron (SMN) protein. Studies involving SMA patients and animal models expressing the human SMN2 gene have yielded relatively little information about the earliest cellular consequences of ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddn156

    authors: Kariya S,Park GH,Maeno-Hikichi Y,Leykekhman O,Lutz C,Arkovitz MS,Landmesser LT,Monani UR

    更新日期:2008-08-15 00:00:00

  • Increased tumour risk for BWS patients correlates with aberrant H19 and not KCNQ1OT1 methylation: occurrence of KCNQ1OT1 hypomethylation in familial cases of BWS.

    abstract::Beckwith-Wiedemann syndrome (BWS) is an overgrowth malformation syndrome that maps to human chromosome 11p15.5, a region that harbours a number of imprinted genes. We studied the methylation status of H19 and KCNQ1OT1 (LIT1/KvDMR1) in a large series of BWS patients. Different patient groups were identified: group I pa...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/10.5.467

    authors: Bliek J,Maas SM,Ruijter JM,Hennekam RC,Alders M,Westerveld A,Mannens MM

    更新日期:2001-03-01 00:00:00

  • L-2-Hydroxyglutaric aciduria: identification of a mutant gene C14orf160, localized on chromosome 14q22.1.

    abstract::l-2-Hydroxyglutaric aciduria (l-2-HGA) is characterized by progressive deterioration of central nervous system function including epilepsy and macrocephaly in 50% of cases, and elevated levels of l-2-hydroxyglutaric acid in urine, blood and cerebrospinal fluid (CSF). Nuclear magnetic resonance imaging shows distinct a...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddh300

    authors: Topçu M,Jobard F,Halliez S,Coskun T,Yalçinkayal C,Gerceker FO,Wanders RJ,Prud'homme JF,Lathrop M,Ozguc M,Fischer J

    更新日期:2004-11-15 00:00:00

  • A whole-blood transcriptome meta-analysis identifies gene expression signatures of cigarette smoking.

    abstract::Cigarette smoking is a leading modifiable cause of death worldwide. We hypothesized that cigarette smoking induces extensive transcriptomic changes that lead to target-organ damage and smoking-related diseases. We performed a meta-analysis of transcriptome-wide gene expression using whole blood-derived RNA from 10,233...

    journal_title:Human molecular genetics

    pub_type: 杂志文章,meta分析

    doi:10.1093/hmg/ddw288

    authors: Huan T,Joehanes R,Schurmann C,Schramm K,Pilling LC,Peters MJ,Mägi R,DeMeo D,O'Connor GT,Ferrucci L,Teumer A,Homuth G,Biffar R,Völker U,Herder C,Waldenberger M,Peters A,Zeilinger S,Metspalu A,Hofman A,Uitterlinden

    更新日期:2016-11-01 00:00:00

  • Effects of dyskeratosis congenita mutations in dyskerin, NHP2 and NOP10 on assembly of H/ACA pre-RNPs.

    abstract::Dyskeratosis congenita (DC) is a rare genetic syndrome that gives rise to a variety of disorders in affected individuals. Remarkably, all causative gene mutations identified to date share a link to telomere/telomerase biology. We found that the most prevalent dyskerin mutation in DC (A353V) did not affect formation of...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddp551

    authors: Trahan C,Martel C,Dragon F

    更新日期:2010-03-01 00:00:00

  • Defective nephrin trafficking caused by missense mutations in the NPHS1 gene: insight into the mechanisms of congenital nephrotic syndrome.

    abstract::Congenital nephrotic syndrome of the Finnish type (CNF or NPHS1) is an autosomal recessive kidney disorder resulting in severe proteinurea and renal dysfunction. Although the disease occurs predominantly in the Finnish population, many cases in other populations have also been reported. The disease gene (NPHS1) encode...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/10.23.2637

    authors: Liu L,Doné SC,Khoshnoodi J,Bertorello A,Wartiovaara J,Berggren PO,Tryggvason K

    更新日期:2001-11-01 00:00:00

  • Gclc deficiency in mouse CNS causes mitochondrial damage and neurodegeneration.

    abstract::Gamma glutamyl cysteine ligase (GCL) is the rate-limiting enzyme for intracellular glutathione (GSH) synthesis. The GSH concentration and GCL activity are declining with age in the central nervous system (CNS), and is accompanied by elevated reactive oxygen species (ROS). To study the biological effects of low GSH lev...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddx040

    authors: Feng W,Rosca M,Fan Y,Hu Y,Feng P,Lee HG,Monnier VM,Fan X

    更新日期:2017-04-01 00:00:00

  • Pax2 gene dosage influences cystogenesis in autosomal dominant polycystic kidney disease.

    abstract::Mutations in PKD1 cause dominant polycystic kidney disease (PKD), characterized by large fluid-filled kidney cysts in adult life, but the molecular mechanism of cystogenesis remains obscure. Ostrom et al. [Dev. Biol., 219, 250-258 (2000)] showed that reduced dosage of Pax2 caused increased apoptosis, and ameliorated c...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddl428

    authors: Stayner C,Iglesias DM,Goodyer PR,Ellis L,Germino G,Zhou J,Eccles MR

    更新日期:2006-12-15 00:00:00

  • Unequal interchromosomal rearrangements may result in elastin gene deletions causing the Williams-Beuren syndrome.

    abstract::Williams-Beuren syndrome (WBS) is generally the consequence of an interstitial microdeletion at 7q11.23, which includes the elastin gene, thus causing hemizygosity at the elastin gene locus. The origin of the deletion has been reported by many authors to be maternal in approximately 60% and paternal in 40% of cases. S...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/5.12.1893

    authors: Dutly F,Schinzel A

    更新日期:1996-12-01 00:00:00

  • Evidence for inter-generational instability in the CAG repeat in the MJD1 gene and for conserved haplotypes at flanking markers amongst Japanese and Caucasian subjects with Machado-Joseph disease.

    abstract::The size of the (CAG)n repeat array in the 3' end of the MJD1 gene and the haplotype at a series of microsatellite markers surrounding the MJD1 gene were examined in a large cohort of Japanese and Caucasian subjects affected with Machado-Joseph disease (MJD). Our data provide five novel observations. First, MJD is ass...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/4.7.1137

    authors: Takiyama Y,Igarashi S,Rogaeva EA,Endo K,Rogaev EI,Tanaka H,Sherrington R,Sanpei K,Liang Y,Saito M

    更新日期:1995-07-01 00:00:00

  • A novel mouse model for genetic variation in 10-formyltetrahydrofolate synthetase exhibits disturbed purine synthesis with impacts on pregnancy and embryonic development.

    abstract::Genetic variants in one-carbon folate metabolism have been identified as risk factors for disease because they may impair the production or use of one-carbon folates required for nucleotide synthesis and methylation. p.R653Q (1958G>A) is a single-nucleotide polymorphism (SNP) in the 10-formyltetrahydrofolate (formylTH...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt223

    authors: Christensen KE,Deng L,Leung KY,Arning E,Bottiglieri T,Malysheva OV,Caudill MA,Krupenko NI,Greene ND,Jerome-Majewska L,MacKenzie RE,Rozen R

    更新日期:2013-09-15 00:00:00

  • Selective vulnerability of motor neurons and dissociation of pre- and post-synaptic pathology at the neuromuscular junction in mouse models of spinal muscular atrophy.

    abstract::Proximal spinal muscular atrophy (SMA) is a common autosomal recessive childhood form of motor neuron disease. Previous studies have highlighted nerve- and muscle-specific events in SMA, including atrophy of muscle fibres and post-synaptic motor endplates, loss of lower motor neuron cell bodies and denervation of neur...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddm367

    authors: Murray LM,Comley LH,Thomson D,Parkinson N,Talbot K,Gillingwater TH

    更新日期:2008-04-01 00:00:00

  • Consortin, a trans-Golgi network cargo receptor for the plasma membrane targeting and recycling of connexins.

    abstract::Targeting of numerous transmembrane proteins to the cell surface is thought to depend on their recognition by cargo receptors that interact with the adaptor machinery for anterograde traffic at the distal end of the Golgi complex. We report here on consortin, a novel integral membrane protein that is predicted to be i...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddp490

    authors: del Castillo FJ,Cohen-Salmon M,Charollais A,Caille D,Lampe PD,Chavrier P,Meda P,Petit C

    更新日期:2010-01-15 00:00:00

  • Aggresomes protect cells by enhancing the degradation of toxic polyglutamine-containing protein.

    abstract::Expression of misfolded protein in cultured cells frequently leads to the formation of juxtanuclear inclusions that have been termed 'aggresomes'. Aggresome formation is an active cellular response that involves trafficking of the offending protein along microtubules, reorganization of intermediate filaments and recru...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddg074

    authors: Taylor JP,Tanaka F,Robitschek J,Sandoval CM,Taye A,Markovic-Plese S,Fischbeck KH

    更新日期:2003-04-01 00:00:00

  • Cloning and expression of the murine homologue of a putative human X-linked nuclear protein gene closely linked to PGK1 in Xq13.3.

    abstract::Several human inherited diseases have been localized to the Xq13.3 region of the human X chromosome (X-linked dystonia with Parkinsonism, sideroblastic anemia, SCID, Menkes disease and X-linked mental retardation loci). Genes involved in the phenotypes have been isolated for only two of them (Menkes and SCIDX). It was...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/3.1.39

    authors: Gecz J,Pollard H,Consalez G,Villard L,Stayton C,Millasseau P,Khrestchatisky M,Fontes M

    更新日期:1994-01-01 00:00:00

  • A Drosophila model system to assess the function of human monogenic podocyte mutations that cause nephrotic syndrome.

    abstract::Many genetic mutations have been identified as monogenic causes of nephrotic syndrome (NS), but important knowledge gaps exist in the roles of these genes in kidney cell biology and renal diseases. More animal models are needed to assess the functions of these genes in vivo, and to determine how they cause NS in a tim...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw428

    authors: Fu Y,Zhu JY,Richman A,Zhao Z,Zhang F,Ray PE,Han Z

    更新日期:2017-02-15 00:00:00

  • Delivery of recombinant follistatin lessens disease severity in a mouse model of spinal muscular atrophy.

    abstract::Spinal muscular atrophy (SMA) is the most common genetic cause of infant mortality. SMA is caused by loss of functional survival motor neuron 1 (SMN1), resulting in death of spinal motor neurons. Current therapeutic research focuses on modulating the expression of a partially functioning copy gene, SMN2, which is reta...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddn426

    authors: Rose FF Jr,Mattis VB,Rindt H,Lorson CL

    更新日期:2009-03-15 00:00:00

  • Identification and analysis of large intergenic non-coding RNAs regulated by p53 family members through a genome-wide analysis of p53-binding sites.

    abstract::p53 is one of the most important known tumor suppressor genes, and it is inactivated in approximately half of human cancers. p53 family members execute various functions, such as apoptosis induction and cell cycle arrest, by modulating transcriptional regulation. Therefore, the direct transcriptional targets of the p5...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt673

    authors: Idogawa M,Ohashi T,Sasaki Y,Maruyama R,Kashima L,Suzuki H,Tokino T

    更新日期:2014-06-01 00:00:00

  • Rapid identification of gene sequences for transcriptional map assembly by direct cDNA screening of genomic reference libraries.

    abstract::We have used the direct cDNA screening protocol to identify sequences transcribed in cerebral cortex from a reference library of human Xq28. To derive coding sequences from these genomic clones, we first identified fragments containing transcribed sequences and subjected these to exon trapping or to partial sequencing...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/3.11.2019

    authors: Lawrence BJ,Schwabe W,Kioschis P,Coy JF,Poustka A,Brennan MB,Hochgeschwender U

    更新日期:1994-11-01 00:00:00