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JOURNAL ARTICLE
Yanhua Cheng, Jingying Liu, Huimin Fan, Kangcheng Liu, Hua Zou, Zhipeng You
We aimed to create a mitophagy-related risk model via data mining of gene expression profiles to predict prognosis in uveal melanoma (UM) and develop a novel method for improving the prediction of clinical outcomes. Together with clinical information, RNA-seq and microarray data were gathered from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. ConsensusClusterPlus was used to detect mitophagy-related subgroups. The genes involved with mitophagy, and the UM prognosis were discovered using univariate Cox regression analysis...
2022: Frontiers in Genetics
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JOURNAL ARTICLE
Yixi Li, Chiyu Ma, Shengyou Liao, Suwen Qi, Shuhui Meng, Wanxia Cai, Weier Dai, Rui Cao, Xiangnan Dong, Bernhard K Krämer, Chen Yun, Berthold Hocher, Xiaoping Hong, Dongzhou Liu, Donge Tang, Jingquan He, Lianghong Yin, Yong Dai
INTRODUCTION: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease for which there is no cure. Effective diagnosis and precise assessment of disease exacerbation remains a major challenge. METHODS: We performed peripheral blood mononuclear cell (PBMC) proteomics of a discovery cohort, including patients with active SLE and inactive SLE, patients with rheumatoid arthritis (RA), and healthy controls (HC). Then, we performed a machine learning pipeline to identify biomarker combinations...
2022: Frontiers in Immunology
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JOURNAL ARTICLE
Agalya Periasamy, Naomi Mitchell, Olga Zaytseva, Arjun S Chahal, Jiamin Zhao, Peter M Colman, Leonie M Quinn, Jacqueline M Gulbis
Intronic polymorphic TOMM40 variants increasing TOMM40 mRNA expression are strongly correlated to late onset Alzheimer's Disease. The gene product, hTomm40, encoded in the APOE gene cluster, is a core component of TOM, the translocase that imports nascent proteins across the mitochondrial outer membrane. We used Drosophila melanogaster eyes as an in vivo model to investigate the relationship between elevated Tom40 (the Drosophila homologue of hTomm40) expression and neurodegeneration. Here we provide evidence that an overabundance of Tom40 in mitochondria invokes caspase-dependent cell death in a dose-dependent manner, leading to degeneration of the primarily neuronal eye tissue...
December 14, 2022: Scientific Reports
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JOURNAL ARTICLE
Wenliang Tan, Yong Yang, Huogeng Bao, Xinjun Kang, Hong Zeng, Lang Hong, Liang Shao
microRNA (miR) -22-3p has been confirmed to be engaged in the phenotype transformation and proliferation of vascular smooth muscle cells (VSMCs), which is intimately correlated with restenosis. The current research set out to explore the detailed mechanism and function of miR-22-3p in VSMC proliferation, phenotype transformation, and migration via the translocase of outer mitochondrial membrane (TOMM40). Peripheral blood samples were acquired from patients with in-stent restenosis (ISR) after percutaneous coronary intervention (PCI), with subsequent quantitative reverse transcription (qRT) -polymerase chain reaction (PCR) and Western blot analyses of miR-22-3p and TOMM40 expression...
2022: International Heart Journal
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JOURNAL ARTICLE
Jing Chen, Bingjie Shi, Yihao Li, Yaru Feng, Jingnian Ni, Jing Shi, Chenyi Luo, Jianxun Wang, Jinzhou Tian
Alzheimer's disease (AD) is one of the most serious neurodegenerative diseases in the world and has a strong genetic predisposition. At present, there is still no effective method for the early diagnosis and prevention of AD. Accumulating evidence shows the association of several loci with AD risk, such as apolipoprotein E (APOE) and translocase of outer mitochondrial membrane 40 (TOMM40). However, for routine disease diagnosis in clinics, genotype detection methods based on gene sequencing technology are time-consuming and excessively costly...
November 27, 2022: Journal of Cellular Biochemistry
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JOURNAL ARTICLE
Jiajin Chen, Yunjie Song, Yi Li, Yongyue Wei, Sipeng Shen, Yang Zhao, Dongfang You, Li Su, Maria Moksnes Bjaanaes, Anna Karlsson, Maria Planck, Johan Staaf, Åslaug Helland, Manel Esteller, Hongbing Shen, David C Christiani, Ruyang Zhang, Feng Chen
Epigenome-wide gene-gene (G×G) interactions associated with non-small cell lung cancer (NSCLC) survival may provide insights into molecular mechanisms and therapeutic targets. Hence, we proposed a three-step analytic strategy to identify significant and robust G×G interactions that are relevant to NSCLC survival. In the first step, among 49 billion pairs of DNA methylation probes, we identified 175,775 G×G interactions with PBonferroni ≤0.05 in the discovery phase of epigenomic analysis; among them, 15,534 were confirmed with P≤0...
November 21, 2022: Molecular Oncology
#47
JOURNAL ARTICLE
Alexander M Kulminski, Ethan Jain-Washburn, Elena Loiko, Yury Loika, Fan Feng, Irina Culminskaya
Capturing the genetic architecture of Alzheimer's disease (AD) is challenging because of the complex interplay of genetic and non-genetic factors in its etiology. It has been suggested that AD biomarkers may improve the characterization of AD pathology and its genetic architecture. Most studies have focused on connections of individual genetic variants with AD biomarkers, whereas the role of combinations of genetic variants is substantially underexplored. We examined the associations of the APOE ε2 and ε4 alleles and polygenic profiles comprising the ε4-encoding rs429358, TOMM40 rs2075650, and APOC1 rs12721046 polymorphisms with cerebrospinal fluid (CSF) and plasma amyloid β (Aβ40 and Aβ42) and tau biomarkers...
November 17, 2022: Aging
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JOURNAL ARTICLE
Alexander M Kulminski, Ethan Jain-Washburn, Ian Philipp, Liang He, Yury Loika, Elena Loiko, Olivia Bagley, Svetlana Ukraintseva, Anatoliy Yashin, Konstantin Arbeev, Eric Stallard, Mary F Feitosa, Nicole Schupf, Kaare Christensen, Irina Culminskaya
Age-related diseases characteristic of post-reproductive life, aging, and life span are the examples of polygenic non-Mendelian traits with intricate genetic architectures. Polygenicity of these traits implies that multiple variants can impact their risks independently or jointly as combinations of specific variants. Here, we examined chances to live to older ages, 85 years and older, for carriers of compound genotypes comprised of combinations of genotypes of rs429358 (APOE ɛ4 encoding polymorphism), rs2075650 (TOMM40), and rs12721046 (APOC1) polymorphisms using data from four human studies...
November 3, 2022: Aging Cell
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JOURNAL ARTICLE
Dong Hyeok Kim, Kyung Eun Lee
BACKGROUND: Research on the discovery of tumor biomarkers based on big data analysis is actively being conducted. This study aimed to secure foundational data for identifying new biomarkers of breast cancer via breast cancer datasets in The Cancer Genome Atlas (TCGA). METHODS: The mRNA profiles of 526 breast cancer and 60 adjacent non-cancerous breast tissues collected from TCGA datasets were analyzed via MultiExperiment Viewer and GraphPad Prism. Diagnostic performance was analyzed by identifying the pathological grades of the selected differentially expressed (DE) mRNAs and the expression patterns of molecular subtypes...
October 21, 2022: Journal of Personalized Medicine
#50
JOURNAL ARTICLE
Guillermo G Torres, Janina Dose, Tim P Hasenbein, Marianne Nygaard, Ben Krause-Kyora, Jonas Mengel-From, Kaare Christensen, Karen Andersen-Ranberg, Daniel Kolbe, Wolfgang Lieb, Matthias Laudes, Siegfried Görg, Stefan Schreiber, Andre Franke, Amke Caliebe, Gregor Kuhlenbäumer, Almut Nebel
Longevity is a complex phenotype influenced by both environmental and genetic factors. The genetic contribution is estimated at about 25%. Despite extensive research efforts, only a few longevity genes have been validated across populations. Long-lived individuals (LLI) reach extreme ages with a relative low prevalence of chronic disability and major age-related diseases (ARDs). We tested whether the protection from ARDs in LLI can partly be attributed to genetic factors by calculating polygenic risk scores (PRSs) for seven common late-life diseases (Alzheimer's disease (AD), atrial fibrillation (AF), coronary artery disease (CAD), colorectal cancer (CRC), ischemic stroke (ISS), Parkinson's disease (PD) and type 2 diabetes (T2D))...
September 19, 2022: International Journal of Molecular Sciences
#51
REVIEW
Nicola Mammarella, Matteo Gatti, Irene Ceccato, Adolfo Di Crosta, Alberto Di Domenico, Rocco Palumbo
Fighting stress-related effects during spaceflight is crucial for a successful mission. Emotional, motivational, and cognitive mechanisms have already been shown to be involved in the decrease of negative emotions. However, emerging evidence is pointing to a neurogenetic profile that may render some individuals more prone than others to focusing on positive information in memory and increasing affective health. The relevance for adaptation to the space environment and the interaction with other stressors such as ionizing radiations is discussed...
August 2, 2022: Life
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JOURNAL ARTICLE
Jari Lahti, Samuli Tuominen, Qiong Yang, Giulio Pergola, Shahzad Ahmad, Najaf Amin, Nicola J Armstrong, Alexa Beiser, Katharina Bey, Joshua C Bis, Eric Boerwinkle, Jan Bressler, Archie Campbell, Harry Campbell, Qiang Chen, Janie Corley, Simon R Cox, Gail Davies, Philip L De Jager, Eske M Derks, Jessica D Faul, Annette L Fitzpatrick, Alison E Fohner, Ian Ford, Myriam Fornage, Zachary Gerring, Hans J Grabe, Francine Grodstein, Vilmundur Gudnason, Eleanor Simonsick, Elizabeth G Holliday, Peter K Joshi, Eero Kajantie, Jaakko Kaprio, Pauliina Karell, Luca Kleineidam, Maria J Knol, Nicole A Kochan, John B Kwok, Markus Leber, Max Lam, Teresa Lee, Shuo Li, Anu Loukola, Tobias Luck, Riccardo E Marioni, Karen A Mather, Sarah Medland, Saira S Mirza, Mike A Nalls, Kwangsik Nho, Adrienne O'Donnell, Christopher Oldmeadow, Jodie Painter, Alison Pattie, Simone Reppermund, Shannon L Risacher, Richard J Rose, Vijay Sadashivaiah, Markus Scholz, Claudia L Satizabal, Peter W Schofield, Katharina E Schraut, Rodney J Scott, Jeannette Simino, Albert V Smith, Jennifer A Smith, David J Stott, Ida Surakka, Alexander Teumer, Anbupalam Thalamuthu, Stella Trompet, Stephen T Turner, Sven J van der Lee, Arno Villringer, Uwe Völker, Robert S Wilson, Katharina Wittfeld, Eero Vuoksimaa, Rui Xia, Kristine Yaffe, Lei Yu, Habil Zare, Wei Zhao, David Ames, John Attia, David A Bennett, Henry Brodaty, Daniel I Chasman, Aaron L Goldman, Caroline Hayward, M Arfan Ikram, J Wouter Jukema, Sharon L R Kardia, Todd Lencz, Markus Loeffler, Venkata S Mattay, Aarno Palotie, Bruce M Psaty, Alfredo Ramirez, Paul M Ridker, Steffi G Riedel-Heller, Perminder S Sachdev, Andrew J Saykin, Martin Scherer, Peter R Schofield, Stephen Sidney, John M Starr, Julian Trollor, William Ulrich, Michael Wagner, David R Weir, James F Wilson, Margaret J Wright, Daniel R Weinberger, Stephanie Debette, Johan G Eriksson, Thomas H Mosley, Lenore J Launer, Cornelia M van Duijn, Ian J Deary, Sudha Seshadri, Katri Räikkönen
Understanding the genomic basis of memory processes may help in combating neurodegenerative disorders. Hence, we examined the associations of common genetic variants with verbal short-term memory and verbal learning in adults without dementia or stroke (N = 53,637). We identified novel loci in the intronic region of CDH18, and at 13q21 and 3p21.1, as well as an expected signal in the APOE/APOC1/TOMM40 region. These results replicated in an independent sample. Functional and bioinformatic analyses supported many of these loci and further implicated POC1...
August 16, 2022: Molecular Psychiatry
#53
JOURNAL ARTICLE
Sunny Chen, Sara M Sarasua, Nicole J Davis, Jane M DeLuca, Luigi Boccuto, Stephen M Thielke, Chang-En Yu
INTRODUCTION: Healthy aging relies on mitochondrial functioning because this organelle provides energy and diminishes oxidative stress. Single nucleotide polymorphisms (SNPs) in TOMM40, a critical gene that produces the outer membrane protein TOM40 of mitochondria, have been associated with mitochondrial dysfunction and neurodegenerative processes. Yet it is not clear whether or how the mitochondria may impact human longevity. We conducted this review to ascertain which SNPs have been associated with markers of healthy aging...
August 13, 2022: BMC Geriatrics
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JOURNAL ARTICLE
Emmanuel O Adewuyi, Eleanor K O'Brien, Dale R Nyholt, Tenielle Porter, Simon M Laws
Consistent with the concept of the gut-brain phenomenon, observational studies suggest a relationship between Alzheimer's disease (AD) and gastrointestinal tract (GIT) disorders; however, their underlying mechanisms remain unclear. Here, we analyse several genome-wide association studies (GWAS) summary statistics (N = 34,652-456,327), to assess the relationship of AD with GIT disorders. Findings reveal a positive significant genetic overlap and correlation between AD and gastroesophageal reflux disease (GERD), peptic ulcer disease (PUD), gastritis-duodenitis, irritable bowel syndrome and diverticulosis, but not inflammatory bowel disease...
July 18, 2022: Communications Biology
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JOURNAL ARTICLE
Jong Y Park, Cecile A Lengacher, Richard R Reich, Hyun Y Park, Junmin Whiting, Anh Thy Nguyen, Carmen Rodríguez, Hongdao Meng, Sara Tinsley, Katterine Chauca, Liliana Gordillo-Casero, Trudy Wittenberg, Anisha Joshi, Katherine Lin, Roohi Ismail-Khan, John V Kiluk, Kevin E Kip
Introduction: Emerging evidence suggests that Chemotherapy (CT) treated breast cancer survivors (BCS) who have "risk variants" in genes may be more susceptible to cognitive impairment (CI) and/or poor cardiac phenotypes. The objective of this preliminary study was to examine whether there is a relationship between genetic variants and objective/subjective cognitive or cardiac phenotypes. Methods and Analysis: BCS were recruited from Moffitt Cancer Center, Morsani College of Medicine, AdventHealth Tampa and Sarasota Memorial Hospital...
May 2, 2022: Biological Research for Nursing
#56
JOURNAL ARTICLE
Pradeep Varathan, Priyanka Gorijala, Tanner Jacobson, Danai Chasioti, Kwangsik Nho, Shannon L Risacher, Andrew J Saykin, Jingwen Yan
BACKGROUND: Large-scale genome-wide association studies have successfully identified many genetic variants significantly associated with Alzheimer's disease (AD), such as rs429358, rs11038106, rs723804, rs13591776, and more. The next key step is to understand the function of these SNPs and the downstream biology through which they exert the effect on the development of AD. However, this remains a challenging task due to the tissue-specific nature of transcriptomic and proteomic data and the limited availability of brain tissue...
April 23, 2022: BMC Medical Genomics
#57
JOURNAL ARTICLE
Magdalena Arnal Segura, Giorgio Bini, Dietmar Fernandez Orth, Eleftherios Samaras, Maya Kassis, Fotis Aisopos, Jordi Rambla De Argila, George Paliouras, Peter Garrard, Claudia Giambartolomei, Gian Gaetano Tartaglia
Introduction: Genome-wide association studies (GWAS) in late onset Alzheimer's disease (LOAD) provide lists of individual genetic determinants. However, GWAS do not capture the synergistic effects among multiple genetic variants and lack good specificity. Methods: We applied tree-based machine learning algorithms (MLs) to discriminate LOAD (>700 individuals) and age-matched unaffected subjects in UK Biobank with single nucleotide variants (SNVs) from Alzheimer's disease (AD) studies, obtaining specific genomic profiles with the prioritized SNVs...
2022: Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring
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JOURNAL ARTICLE
Alexander M Kulminski, Ian Philipp, Leonardo Shu, Irina Kulminskaya
BACKGROUND: The APOE gene harboring the ε2 and ε4 alleles encoded by minor alleles of rs7412 and rs429358 single nucleotide polymorphisms (SNPs), respectively, is one of the most studied genes in humans. Despite that, the problem of whether the associations between these alleles and the late-onset Alzheimer's disease (referred to as AD) are due to these alleles themselves remains controversial. This problem is complicated by an inherent heterogeneity in genetic predisposition to AD, which is common for complex diseases in late life...
December 2021: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
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JOURNAL ARTICLE
Karen Nuytemans, Marina Lipkin Vasquez, Farid Rajabli, Katrina Celis, Oded Oron, Derek Van Booven, Natalia K Hofmann, Mariana Argenziano, Alessandra Chesi, Struan F A Grant, Christopher D Brown, Anthony J Griswold, Margaret A Pericak-Vance, Jeffery M Vance
BACKGROUND: The risk for late-onset Alzheimer disease (AD) in APOEε4 carriers differs between ancestral groups, where APOEε4's odds ratio for AD risk is lower in African (AFR) homozygous carriers than in non-Hispanic White (NHW) or Japanese (JPT) carriers (odds ratio ∼2-5 vs >15). Local ancestry (LA) analyses in APOEε4 carrier populations have shown the protective effect in AFR relative to EUR/JPT is due to noncoding factors lying in the LA surrounding APOEε4. Thus, regulatory differences between risk and protective LA haplotypes are most likely involved in the differential risk effect seen for APOEε4 on different backgrounds...
December 2021: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
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JOURNAL ARTICLE
Yinuo Zhang, Brian N Lee, Li Shen
BACKGROUND: The relationship between genetic variations such as single nucleotide polymorphisms (SNPs) and quantitative traits (QTs) is integral in the understanding of Alzheimer's Disease (AD). Given AD as a progressive disorder, QT-based rate of change (RoC) measures are important phenotypes to study in AD genetics. Further mediation analysis provides a promising method to help reveal causal relationship from genetic determinants to longitudinal changes in QTs and to clinical diagnosis...
December 2021: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
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