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https://www.readbyqxmd.com/read/28902624/rna-seq-mouse-brain-regions-expression-data-analysis-focus-on-apoe-functional-network
#1
Vladimir N Babenko, Dmitry A Smagin, Natalia N Kudryavtseva
ApoE expression status was proved to be a highly specific marker of energy metabolism rate in the brain. Along with its neighbor, Translocase of Outer Mitochondrial Membrane 40 kDa (TOMM40) which is involved in mitochondrial metabolism, the corresponding genomic region constitutes the neuroenergetic hotspot. Using RNA-Seq data from a murine model of chronic stress a significant positive expression coordination of seven neighboring genes in ApoE locus in five brain regions was observed. ApoE maintains one of the highest absolute expression values genome-wide, implying that ApoE can be the driver of the neighboring gene expression alteration observed under stressful loads...
September 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28870582/linking-alzheimer-s-disease-and-type-2-diabetes-novel-shared-susceptibility-genes-detected-by-cfdr-approach
#2
Xia-Fang Wang, Xu Lin, Ding-You Li, Rou Zhou, Jonathan Greenbaum, Yuan-Cheng Chen, Chun-Ping Zeng, Lin-Ping Peng, Ke-Hao Wu, Zeng-Xin Ao, Jun-Min Lu, Yan-Fang Guo, Jie Shen, Hong-Wen Deng
BACKGROUND: Both type 2 diabetes (T2D) and Alzheimer's disease (AD) occur commonly in the aging populations and T2D has been considered as an important risk factor for AD. The heritability of both diseases is estimated to be over 50%. However, common pleiotropic single-nucleotide polymorphisms (SNPs)/loci have not been well-defined. The aim of this study is to analyze two large public accessible GWAS datasets to identify novel common genetic loci for T2D and/or AD. METHODS AND MATERIALS: The recently developed novel conditional false discovery rate (cFDR) approach was used to analyze the summary GWAS datasets from International Genomics of Alzheimer's Project (IGAP) and Diabetes Genetics Replication And Meta-analysis (DIAGRAM) to identify novel susceptibility genes for AD and T2D...
September 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28800603/genetic-variants-specific-to-aging-related-verbal-memory-insights-from-gwass-in-a-population-based-cohort
#3
Thalida E Arpawong, Neil Pendleton, Krisztina Mekli, John J McArdle, Margaret Gatz, Chris Armoskus, James A Knowles, Carol A Prescott
Verbal memory is typically studied using immediate recall (IR) and delayed recall (DR) scores, although DR is dependent on IR capability. Separating these components may be useful for deciphering the genetic variation in age-related memory abilities. This study was conducted to (a) construct individual trajectories in IR and independent aspects of delayed recall, or residualized-DR (rDR), across older adulthood; and (b) identify genetic markers that contribute to four estimated phenotypes: IR and rDR levels and changes after age 60...
2017: PloS One
https://www.readbyqxmd.com/read/28768149/the-biological-foundation-of-the-genetic-association-of-tomm40-with-late-onset-alzheimer-s-disease
#4
Kahli Zeitlow, Lefko Charlambous, Isaac Ng, Sonal Gagrani, Mirta Mihovilovic, Shuhong Luo, Daniel L Rock, Ann Saunders, Allen D Roses, W Kirby Gottschalk
A variable-length poly-T variant in intron 6 of the TOMM40 gene, rs10524523, is associated with risk and age-of-onset of sporadic (late-onset) Alzheimer's disease. In Caucasians, the three predominant alleles at this locus are Short (S), Long (L) or Very long (VL). On an APOE ε3/3 background, the S/VL and VL/VL genotypes are more protective than S/S. The '523 poly-T has regulatory properties, in that the VL poly-T results in higher expression than the S poly-T in luciferase expression systems. The aim of the current work was to identify effects on cellular bioenergetics of increased TOM40 protein expression...
July 30, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28686695/coronary-artery-disease-associated-genetic-variants-and-biomarkers-of-inflammation
#5
Morten Krogh Christiansen, Sanne Bøjet Larsen, Mette Nyegaard, Søs Neergaard-Petersen, Ramzi Ajjan, Morten Würtz, Erik Lerkevang Grove, Anne-Mette Hvas, Henrik Kjærulf Jensen, Steen Dalby Kristensen
INTRODUCTION: Genetic constitution and inflammation both contribute to development of coronary artery disease (CAD). Several CAD-associated single-nucleotide polymorphisms (SNPs) have recently been identified, but their functions are largely unknown. We investigated the associations between CAD-associated SNPs and five CAD-related inflammatory biomarkers. METHODS: We genotyped 45 CAD-associated SNPs in 701 stable CAD patients in whom levels of high-sensitivity C-reactive protein (hsRCP), interleukin-6, calprotectin, fibrinogen and complement component 3 levels had previously been measured...
2017: PloS One
https://www.readbyqxmd.com/read/28672022/apoe-%C3%AE%C2%B54-tomm40-523-haplotypes-and-the-risk-of-alzheimer-s-disease-in-older-caucasian-and-african-americans
#6
Lei Yu, Michael W Lutz, Robert S Wilson, Daniel K Burns, Allen D Roses, Ann M Saunders, Jingyun Yang, Chris Gaiteri, Philip L De Jager, Lisa L Barnes, David A Bennett
Patterns of linkage between the ε4 allele of Apolipoprotein E (APOE) and '523 poly-T alleles in the adjacent gene, TOMM40, differ between Caucasian and African Americans. The extent to which this difference affects the risk of Alzheimer's disease (AD) is unclear. We compared the APOE ε4-TOMM40 '523 haplotypes between older Caucasian and African Americans, and examined their relationship with AD dementia. Data came from three community based cohort studies of diverse participants. APOE genotypes were determined by polymorphisms of rs429358 and rs7412...
2017: PloS One
https://www.readbyqxmd.com/read/28650998/functional-annotation-of-alzheimer-s-disease-associated-loci-revealed-by-gwass
#7
Zengpeng Han, Han Huang, Yue Gao, Qingyang Huang
Genome-wide association studies (GWASs) discovered a number of SNPs and genes associated with Alzheimer's disease (AD). However, how these SNPs and genes influence the liability to AD is not fully understood. We deployed computational approaches to explore the function and action mechanisms of AD -related SNPs and genes identified by GWASs, including the effects of 195 GWAS lead SNPs and 338 proxy SNPs on miRNAs binding and protein phosphorylation, their RegulomeDB and 3DSNP scores, and gene ontology, pathway enrichment and protein-protein interaction network of 126 AD-associated genes...
2017: PloS One
https://www.readbyqxmd.com/read/28641921/genome-wide-association-and-interaction-studies-of-csf-t-tau-a%C3%AE-42-ratio-in-adni-cohort
#8
Jin Li, Qiushi Zhang, Feng Chen, Xianglian Meng, Wenjie Liu, Dandan Chen, Jingwen Yan, Sungeun Kim, Lei Wang, Weixing Feng, Andrew J Saykin, Hong Liang, Li Shen
The pathogenic relevance in Alzheimer's disease (AD) presents a decrease of cerebrospinal fluid amyloid-ß42 (Aß42) burden and an increase in cerebrospinal fluid total tau (T-tau) levels. In this work, we performed genome-wide association study (GWAS) and genome-wide interaction study of T-tau/Aß42 ratio as an AD imaging quantitative trait on 843 subjects and 563,980 single-nucleotide polymorphisms (SNPs) in ADNI cohort. We aim to identify not only SNPs with significant main effects but also SNPs with interaction effects to help explain "missing heritability"...
September 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28624335/neuropathologic-features-of-tomm40-523-variant-on-late-life-cognitive-decline
#9
Lei Yu, Michael W Lutz, Jose M Farfel, Robert S Wilson, Daniel K Burns, Ann M Saunders, Philip L De Jager, Lisa L Barnes, Julie A Schneider, David A Bennett
INTRODUCTION: The study investigated the role of neuropathologies in the relationship between TOMM40 '523 genotype and late-life cognitive decline. METHODS: Participants were community-dwelling older persons who had annual cognitive assessments and brain autopsies after death. Genotyping used DNA from peripheral blood or postmortem brain tissue. Linear mixed models assessed the extent to which the association of '523 genotype with cognitive decline is attributable to neuropathologies...
June 15, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28549947/family-history-and-tomm40-523-interactive-associations-with-memory-in-middle-aged-and-alzheimer-s-disease-cohorts
#10
Auriel A Willette, Joseph L Webb, Michael W Lutz, Barbara B Bendlin, Alexandra M Wennberg, Jennifer M Oh, Allen Roses, Rebecca L Koscik, Bruce P Hermann, N Maritza Dowling, Sanjay Asthana, Sterling C Johnson
INTRODUCTION: Family history (FH) of Alzheimer's disease (AD) affects mitochondrial function and may modulate effects of translocase of the outer mitochondrial membrane 40 kDa (TOMM40) rs10524523 ('523) poly-T length on memory decline. METHODS: For 912 nonapolipoprotein ε4 middle-aged adults and 365 aged adults across the AD spectrum, linear mixed models gauged FH and TOMM40 '523 interactions on memory and global cognition between baseline and up to 10 years later...
May 10, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28539666/replication-and-fine-mapping-of-genetic-predictors-of-lipid-traits-in-african-americans
#11
QiPing Feng, Wei-Qi Wei, Rebecca T Levinson, Jonathan D Mosley, C Michael Stein
Circulating lipid concentrations are among the strongest modifiable risk factors for coronary artery disease (CAD). Most genetic studies have focused on Caucasian populations with little information available for populations of African ancestry. Using a cohort of ~2800 African-Americans (AAs) from a biobank at Vanderbilt University (BioVU), we sought to trans-ethnically replicate genetic variants reported by the Global Lipids Genetics Consortium to be associated with lipid traits in Caucasians, followed by fine-mapping those loci using all available variants on the MetaboChip...
May 25, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28387812/gene-based-association-studies-report-genetic-links-for-clinical-subtypes-of-frontotemporal-dementia
#12
Aniket Mishra, Raffaele Ferrari, Peter Heutink, John Hardy, Yolande Pijnenburg, Danielle Posthuma
Genome-wide association studies in frontotemporal dementia showed limited success in identifying associated loci. This is possibly due to small sample size, allelic heterogeneity, small effect sizes of single genetic variants, and the necessity to statistically correct for testing millions of genetic variants. To overcome these issues, we performed gene-based association studies on 3348 clinically identified frontotemporal dementia cases and 9390 controls (discovery, replication and joint-cohort analyses). We report association of APOE and TOMM40 with behavioural variant frontotemporal dementia, and ARHGAP35 and SERPINA1 with progressive non-fluent aphasia...
April 5, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334117/a-generalized-association-test-based-on-u-statistics
#13
Changshuai Wei, Qing Lu
Motivation: Second generation sequencing technologies are being increasingly used for genetic association studies, where the main research interest is to identify sets of genetic variants that contribute to various phenotypes. The phenotype can be univariate disease status, multivariate responses and even high-dimensional outcomes. Considering the genotype and phenotype as two complex objects, this also poses a general statistical problem of testing association between complex objects...
July 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28242298/the-alu-neurodegeneration-hypothesis-a-primate-specific-mechanism-for-neuronal-transcription-noise-mitochondrial-dysfunction-and%C3%A2-manifestation-of-neurodegenerative-disease
#14
Peter A Larsen, Michael W Lutz, Kelsie E Hunnicutt, Mirta Mihovilovic, Ann M Saunders, Anne D Yoder, Allen D Roses
It is hypothesized that retrotransposons have played a fundamental role in primate evolution and that enhanced neurologic retrotransposon activity in humans may underlie the origin of higher cognitive function. As a potential consequence of this enhanced activity, it is likely that neurons are susceptible to deleterious retrotransposon pathways that can disrupt mitochondrial function. An example is observed in the TOMM40 gene, encoding a β-barrel protein critical for mitochondrial preprotein transport. Primate-specific Alu retrotransposons have repeatedly inserted into TOMM40 introns, and at least one variant associated with late-onset Alzheimer's disease originated from an Alu insertion event...
February 24, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28183529/hippocampal-thinning-linked-to-longer-tomm40-poly-t-variant-lengths-in-the-absence-of-the-apoe-%C3%AE%C2%B54-variant
#15
Alison C Burggren, Zanjbeel Mahmood, Theresa M Harrison, Prabha Siddarth, Karen J Miller, Gary W Small, David A Merrill, Susan Y Bookheimer
INTRODUCTION: The translocase of outer mitochondrial membrane 40 (TOMM40), which lies in linkage disequilibrium with apolipoprotein E (APOE), has received attention more recently as a promising gene in Alzheimer's disease (AD) risk. TOMM40 influences AD pathology through mitochondrial neurotoxicity, and the medial temporal lobe (MTL) is the most likely brain region for identifying early manifestations of AD-related morphology changes. METHODS: In this study, we examined the effects of TOMM40 using high-resolution magnetic resonance imaging in 65 healthy, older subjects with and without the APOE ε4 AD-risk variant...
July 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28108637/tomm40-523-variant-and-cognitive-decline-in-older-persons-with-apoe-%C3%AE%C2%B53-3-genotype
#16
Lei Yu, Michael W Lutz, Robert S Wilson, Daniel K Burns, Allen D Roses, Ann M Saunders, Chris Gaiteri, Philip L De Jager, Lisa L Barnes, David A Bennett
OBJECTIVE: To interrogate a poly-T variant (rs10524523, '523) in TOMM40, a gene adjacent to the APOE gene on chromosome 19, in older persons with APOE ε3/3 homozygosity for association with cognitive decline, the clinical hallmark of Alzheimer disease (AD). METHODS: Data came from participants in 2 cohort studies of aging and dementia who underwent annual clinical evaluations for up to 21 years. APOE and TOMM40'523 genotypes were determined from DNA from blood or brain samples...
February 14, 2017: Neurology
https://www.readbyqxmd.com/read/28065845/the-effects-of-ppar%C3%AE-on-the-regulation-of-the-tomm40-apoe-c1-genes-cluster
#17
Shobana Subramanian, William K Gottschalk, So Young Kim, Allen D Roses, Ornit Chiba-Falek
Chromosome 19q13.32 is a gene rich region, and has been implicated in multiple human phenotypes in adulthood including lipids traits, Alzheimer's disease, and longevity. Peroxisome Proliferator Activated Receptor Gamma (PPARγ) is a ligand-activated nuclear transcription factor that plays a role in human complex traits that are also genetically associated with the chromosome 19q13.32 region. Here, we study the effects of PPARγ on the regional expression regulation of the genes clustered within chromosome 19q13...
March 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28026009/transcriptomic-profiling-of-platelet-senescence-and-platelet-extracellular-vesicles
#18
Annika Pienimaeki-Roemer, Tatiana Konovalova, Melina M Musri, Alexander Sigruener, Alfred Boettcher, Gunter Meister, Gerd Schmitz
BACKGROUND: Platelets (PLTs) are derived from megakaryocytes during PLT shedding. Senescent or activated PLTs are expanded in vascular and neurological diseases and release PLT extracellular vesicles (PL-EVs). A systematic analysis of regular messenger RNA (mRNA) and small RNA composition in PLTs and PL-EVs during in vitro PLT senescence has not yet been published. STUDY DESIGN AND METHODS: We isolated PLTs, total PL-EVs, and PL-EV subsets on Days 0 and 5 from human stored donor platelet concentrates...
January 2017: Transfusion
https://www.readbyqxmd.com/read/27707806/replication-of-genome-wide-association-study-findings-of-longevity-in-white-african-american-and-hispanic-women-the-women-s-health-initiative
#19
Aladdin H Shadyab, Charles Kooperberg, Alexander P Reiner, Sonia Jain, JoAnn E Manson, Chancellor Hohensee, Caroline A Macera, Richard A Shaffer, Linda C Gallo, Andrea Z LaCroix
Background: No study has evaluated whether genetic factors are associated with longevity in African Americans or Hispanics, and it is unclear whether genetic factors are associated with healthy aging. Methods: In this prospective study, we determined whether 14 genetic variants previously associated with longevity in genome-wide association studies were associated with survival to ages 85 and 90 in 11,053 postmenopausal white, African American, and Hispanic women from the Women's Health Initiative...
October 1, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/27616904/proteomic-analysis-reveals-that-the-protective-effects-of-ginsenoside-rb1-are-associated-with-the-actin-cytoskeleton-in-%C3%AE-amyloid-treated-neuronal-cells
#20
Ji Yeon Hwang, Ji Seon Shim, Min-Young Song, Sung-Vin Yim, Seung Eun Lee, Kang-Sik Park
BACKGROUND: The ginsenoside Rb1 (Rb1) is the most abundant compound in the root of Panax ginseng. Recent studies have shown that Rb1 has a neuroprotective effect. However, the mechanisms underlying this effect are still unknown. METHODS: We used stable isotope labeling with amino acids in cell culture, combined with quantitative mass spectrometry, to explore a potential protective mechanism of Rb1 in β-amyloid-treated neuronal cells. RESULTS: A total of 1,231 proteins were commonly identified from three replicate experiments...
July 2016: Journal of Ginseng Research
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