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JOURNAL ARTICLE
Hakhyun Kim, Jang Hee Han, Hyosil Kim, Minjee Kim, Seung-Il Jo, NaKyoung Lee, Seungbin Cha, Myung Joon Oh, GaWon Choi, Hyun Seok Kim
CRISPR/Cas9 technology has effectively targeted cancer-specific oncogenic hotspot mutations or insertion-deletions. However, their limited prevalence in tumors restricts their application. We propose a novel approach targeting passenger single nucleotide variants (SNVs) in haploinsufficient or essential genes to broaden therapeutic options. By disrupting haploinsufficient or essential genes through the cleavage of DNA in the SNV region using CRISPR/Cas9, we achieved the selective elimination of cancer cells without affecting normal cells...
March 28, 2024: Scientific Reports
#2
JOURNAL ARTICLE
Tzu-Wei Chuang, Chun-Hao Su, Pei-Yu Wu, Yao-Ming Chang, Woan-Yuh Tarn
The eukaryotic exon junction complex component Y14 participates in double-strand break (DSB) repair via its RNA-dependent interaction with the non-homologous end-joining (NHEJ) complex. Using immunoprecipitation-RNA-seq, we identified a set of Y14-associated long non-coding RNAs (lncRNAs). The lncRNA HOTAIRM1 serves as a strong candidate that mediates the interaction between Y14 and the NHEJ complex. HOTAIRM1 localized to near ultraviolet laser-induced DNA damage sites. Depletion of HOTAIRM1 delayed the recruitment of DNA damage response and repair factors to DNA lesions and compromised the efficiency of NHEJ-mediated DSB repair...
March 7, 2023: Nucleic Acids Research
#3
JOURNAL ARTICLE
Georgia Katsioudi, René Dreos, Enes S Arpa, Sevasti Gaspari, Angelica Liechti, Miho Sato, Christian H Gabriel, Achim Kramer, Steven A Brown, David Gatfield
Nonsense-mediated messenger RNA (mRNA) decay (NMD) has been intensively studied as a surveillance pathway that degrades erroneous transcripts arising from mutations or RNA processing errors. While additional roles in physiological control of mRNA stability have emerged, possible functions in mammalian physiology in vivo remain unclear. Here, we created a conditional mouse allele that allows converting the NMD effector nuclease SMG6 from wild-type to nuclease domain-mutant protein. We find that NMD down-regulation affects the function of the circadian clock, a system known to require rapid mRNA turnover...
January 13, 2023: Science Advances
#4
JOURNAL ARTICLE
Xiaoqing Xu, Yuxi Zhang, Zhaobing Pan, Xiaojing Zhang, Xiaonan Liu, Lili Tang, Xiaoguang Zhang, Fusheng Zhou, Hui Cheng
INTRODUCTION: Munro's microabscess is a typical pathological feature in the early psoriatic lesion, mainly characterized by the accumulation of neutrophils in the epidermis. DNA methylation microenvironment of Munro's microabscess and the crosstalk with transcription and its effect on neutrophils have not yet been revealed. METHODS: Performed genome-wide DNA methylation analysis and further differential methylation analysis of psoriatic skin lesions with and without Munro's microabscess from two batch samples consisting of 114 former samples in the discovery stage and 21 newly-collected samples in the validation stage...
2022: Frontiers in Immunology
#5
JOURNAL ARTICLE
Koya Suzuki, Masaki Tange, Ryota Yamagishi, Hiroyuki Hanada, Satomi Mukai, Tatsuhiro Sato, Takeshi Tanaka, Tomohiro Akashi, Kenji Kadomatsu, Tohru Maeda, Takashi Miida, Ichiro Takeuchi, Hiroshi Murakami, Yoshitaka Sekido, Yuko Murakami-Tonami
Many genes responsible for Malignant mesothelioma (MM) have been identified as tumor suppressor genes and it is difficult to target these genes directly at a molecular level. We searched for the gene which showed synthetic lethal phenotype with LATS2, one of the MM causative genes and one of the kinases in the Hippo pathway. Here we showed that knockdown of SMG6 results in synthetic lethality in LATS2-inactivated cells. We found that this synthetic lethality required the nuclear translocation of YAP1 and TAZ...
November 5, 2022: Cell Death Discovery
#6
JOURNAL ARTICLE
Tiina Lehtiniemi, Matthieu Bourgery, Lin Ma, Ammar Ahmedani, Margareeta Mäkelä, Juho Asteljoki, Opeyemi Olotu, Samuli Laasanen, Fu-Ping Zhang, Kun Tan, Jennifer N Chousal, Dana Burow, Satu Koskinen, Asta Laiho, Laura L Elo, Frédéric Chalmel, Miles F Wilkinson, Noora Kotaja
Nonsense-mediated RNA decay (NMD) is a highly conserved and selective RNA turnover pathway that depends on the endonuclease SMG6. Here, we show that SMG6 is essential for male germ cell differentiation in mice. Germ-cell conditional knockout (cKO) of Smg6 induces extensive transcriptome misregulation, including a failure to eliminate meiotically expressed transcripts in early haploid cells, and accumulation of NMD target mRNAs with long 3' untranslated regions (UTRs). Loss of SMG6 in the male germline results in complete arrest of spermatogenesis at the early haploid cell stage...
November 11, 2022: Nucleic Acids Research
#7
JOURNAL ARTICLE
Anneleen Decock, David Creytens, Steve Lefever, Joni Van der Meulen, Jasper Anckaert, Ariane De Ganck, Jill Deleu, Bram De Wilde, Carolina Fierro, Scott Kuersten, Manuel Luypaert, Isabelle Rottiers, Gary P Schroth, Sandra Steyaert, Katrien Vanderheyden, Eveline Vanden Eynde, Kimberly Verniers, Joke Verreth, Jo Van Dorpe, Jo Vandesompele
We assess the performance of mRNA capture sequencing to identify fusion transcripts in FFPE tissue of different sarcoma types, followed by RT-qPCR confirmation. To validate our workflow, six positive control tumors with a specific chromosomal rearrangement were analyzed using the TruSight RNA Pan-Cancer Panel. Fusion transcript calling by FusionCatcher confirmed these aberrations and enabled the identification of both fusion gene partners and breakpoints. Next, whole-transcriptome TruSeq RNA Exome sequencing was applied to 17 fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated round cell sarcoma (URCS) tumors, for whom fluorescence in situ hybridization (FISH) did not identify the classical pathognomonic rearrangements...
September 20, 2022: International Journal of Molecular Sciences
#8
JOURNAL ARTICLE
Edward J Sanderlin, Melissa M Keenan, Martin Mense, Alexey S Revenko, Brett P Monia, Shuling Guo, Lulu Huang
Approximately 10% of cystic fibrosis patients harbor nonsense mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene which can generate nonsense codons in the CFTR mRNA and subsequently activate the nonsense-mediated decay (NMD) pathway resulting in rapid mRNA degradation. However, it is not known which NMD branches govern the decay of CFTR mRNAs containing nonsense codons. Here we utilize antisense oligonucleotides targeting NMD factors to evaluate the regulation of nonsense codon-containing CFTR mRNAs by the NMD pathway...
April 29, 2022: Nature Communications
#9
JOURNAL ARTICLE
Chen Huang, Yalun Qu, Fan Feng, Hualu Zhang, Liliang Shu, Xiaohua Zhu, Gongcheng Huang, Jing Xu
Increased neutrophil recruitment represents a hallmark event in myocardial ischemia/reperfusion (I/R) injury due to the ensuing inflammatory response. Circular RNAs (circRNAs) are important regulatory molecules involved in cell physiology and pathology. Herein, we analyzed the role of a novel circRNA circ_SMG6 in the regulation of neutrophil recruitment following I/R injury, which may associate with the miR-138-5p/EGR1/TLR4/TRIF axis. Myocardial I/R injury was modeled in vivo by ligation of the left anterior descending (LAD) artery followed by reperfusion in mice and in vitro by exposing a cardiomyocyte cell line (HL-1) to hypoxia/reoxygenation (H/R)...
2022: Oxidative Medicine and Cellular Longevity
#10
JOURNAL ARTICLE
Tao Si, Xuejian Ning, Haihui Chen, Zhengguo Hu, Linglu Dun, Na Zheng, Ping Huang, Liu Yang, Ping Yi
BACKGROUND: With high incidence and mortality rates, hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors worldwide. Chronic hepatitis B virus (HBV) infection is a leading cause of HCC, especially for Asians and blacks. However, the molecular mechanisms underlying HBV-related HCC are unclear. This study sought to identify novel prognostic biomarkers and explore the potential pathogenesis of HBV-related HCC. METHODS: The gene expression profiles and corresponding clinical information of HCC from The Cancer Genome Atlas Liver Hepatocellular Carcinoma data set were analyzed by a weighted gene co-expression network analysis...
December 2021: Journal of Gastrointestinal Oncology
#11
JOURNAL ARTICLE
Gabriela Maria Guerra, Doreen May, Torsten Kroll, Philipp Koch, Marco Groth, Zhao-Qi Wang, Tang-Liang Li, Paulius Grigaravičius
SMG6 is an endonuclease, which cleaves mRNAs during nonsense-mediated mRNA decay (NMD), thereby regulating gene expression and controling mRNA quality. SMG6 has been shown as a differentiation license factor of totipotent embryonic stem cells. To investigate whether it controls the differentiation of lineage-specific pluripotent progenitor cells, we inactivated Smg6 in murine embryonic neural stem cells. Nestin-Cre-mediated deletion of Smg6 in mouse neuroprogenitor cells (NPCs) caused perinatal lethality. Mutant mice brains showed normal structure at E14...
November 30, 2021: Cells
#12
JOURNAL ARTICLE
Shengyu Zhou, Jintao Zhang, Jiawei Xu, Fayan Zhang, Peng Li, Yujie He, Julong Wu, Chunting Wang, Ximing Wang, Wei Zhang, Kang Ning, Yun Pan, Tian Liu, Jiping Zhao, Lixia Yin, Rumin Zhang, Feng Gao, Jintong Zhao, Liang Dong
In the early 2000s, emerging SARS-CoV-2, which is highly pathogenic, posed a great threat to public health. During COVID-19, epigenetic regulation is deemed to be an important part of the pathophysiology and illness severity. Using the Illumina Infinium Methylation EPIC BeadChip (850 K), we investigated genome-wide differences in DNA methylation between healthy subjects and COVID-19 patients with different disease severities. We conducted a combined analysis and selected 35 "marker" genes that could indicate a SARS-CoV-2 infection, including 12 (ATHL1, CHN2, CHST15, CPLX2, CRHR2, DCAKD, GNAI2, HECW1, HYAL1, MIR510, PDE11A, and SMG6) situated in the promoter region...
November 2021: Annals of Human Genetics
#13
JOURNAL ARTICLE
Volker Boehm, Sabrina Kueckelmann, Jennifer V Gerbracht, Sebastian Kallabis, Thiago Britto-Borges, Janine Altmüller, Marcus Krüger, Christoph Dieterich, Niels H Gehring
Eukaryotic gene expression is constantly controlled by the translation-coupled nonsense-mediated mRNA decay (NMD) pathway. Aberrant translation termination leads to NMD activation, resulting in phosphorylation of the central NMD factor UPF1 and robust clearance of NMD targets via two seemingly independent and redundant mRNA degradation branches. Here, we uncover that the loss of the first SMG5-SMG7-dependent pathway also inactivates the second SMG6-dependent branch, indicating an unexpected functional connection between the final NMD steps...
June 25, 2021: Nature Communications
#14
JOURNAL ARTICLE
Sergiy Kyryachenko, Adrien Georges, Mengyao Yu, Takiy Berrandou, Lilong Guo, Patrick Bruneval, Tony Rubio, Judith Gronwald, Hassina Baraki, Ingo Kutschka, Kedar Aras, Igor R Efimov, Russell A Norris, Niels Voigt, Nabila Bouatia-Naji
Rationale: Mitral valve prolapse (MVP) is a common valvopathy that leads to mitral insufficiency, heart failure and sudden death. Functional genomic studies in mitral valves are needed to better characterize MVP associated variants and target genes. Objective: To establish the chromatin accessibility profiles and assess functionality of variants and narrow down target genes at MVP loci. Methods and Results: We mapped the open chromatin regions in nuclei from 11 human pathogenic and 7 non-pathogenic mitral valves by an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq)...
January 28, 2021: Circulation Research
#15
JOURNAL ARTICLE
Michelle S Yau, Allison L Kuipers, Ryan Price, Aude Nicolas, Salman M Tajuddin, Samuel K Handelman, Liubov Arbeeva, Alessandra Chesi, Yi-Hsiang Hsu, Ching-Ti Liu, David Karasik, Babette S Zemel, Struan Fa Grant, Joanne M Jordan, Rebecca D Jackson, Michele K Evans, Tamara B Harris, Joseph M Zmuda, Douglas P Kiel
Genetic studies of bone mineral density (BMD) largely have been conducted in European populations. We therefore conducted a meta-analysis of six independent African ancestry cohorts to determine whether previously reported BMD loci identified in European populations were transferable to African ancestry populations. We included nearly 5000 individuals with both genetic data and assessments of BMD. Genotype imputation was conducted using the 1000G reference panel. We assessed single-nucleotide polymorphism (SNP) associations with femoral neck and lumbar spine BMD in each cohort separately, then combined results in fixed effects (or random effects if study heterogeneity was high, I2 index >60) inverse variance weighted meta-analyses...
March 2021: Journal of Bone and Mineral Research
#16
JOURNAL ARTICLE
Giuditta Annibaldis, Michal Domanski, René Dreos, Lara Contu, Sarah Carl, Nina Kläy, Oliver Mühlemann
To gain insight into the mechanistic link between translation termination and nonsense-mediated mRNA decay (NMD), we depleted the ribosome recycling factor ABCE1 in human cells, resulting in an upregulation of NMD-sensitive mRNAs. Suppression of NMD on these mRNAs occurs prior to their SMG6-mediated endonucleolytic cleavage. ABCE1 depletion caused ribosome stalling at termination codons (TCs) and increased ribosome occupancy in 3' UTRs, implying enhanced TC readthrough. ABCE1 knockdown indeed increased the rate of readthrough and continuation of translation in different reading frames, providing a possible explanation for the observed NMD inhibition, since enhanced readthrough displaces NMD activating proteins from the 3' UTR...
October 9, 2020: Nucleic Acids Research
#17
JOURNAL ARTICLE
Yanjun Guo, Pamela M Rist, Iyas Daghlas, Franco Giulianini, Tobias Kurth, Daniel I Chasman
Blood pressure (BP) was inconsistently associated with migraine and the mechanisms of BP-lowering medications in migraine prophylaxis are unknown. Leveraging large-scale summary statistics for migraine (Ncases /Ncontrols = 59,674/316,078) and BP (N = 757,601), we find positive genetic correlations of migraine with diastolic BP (DBP, rg = 0.11, P = 3.56 × 10-06 ) and systolic BP (SBP, rg = 0.06, P = 0.01), but not pulse pressure (PP, rg = -0.01, P = 0.75). Cross-trait meta-analysis reveals 14 shared loci (P ≤ 5 × 10-08 ), nine of which replicate (P < 0...
July 6, 2020: Nature Communications
#18
JOURNAL ARTICLE
Z Wang, X Zhang, E Jiang, H Yan, H Zhu, H Chen, J Liu, L Qu, C Pan, X Lan
Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) is involved in the Hedgehog pathway and has been shown to regulate the RNA stability of several growth-related target genes. It is located in a quantitative trait locus showing a strong association with traits related to body size in ducks. Fibroblast growth factor receptor 1 (FGFR1) also participates in Hedgehog signaling pathways and has been reported to be associated with organic growth and development. FGFR1-knockout mice have been shown to have severe postnatal growth defects, including an approximately 50% reduction in body weight and bone mass...
February 2020: Animal Genetics
#19
LETTER
Xingchen Wang, Xingbo Mo, Huan Zhang, Yonghong Zhang, Yueping Shen
PURPOSE: Phosphorylation-related SNP (phosSNP) is a non-synonymous SNP that might influence protein phosphorylation status. The aim of this study was to assess the effect of phosSNPs on blood pressure (BP), coronary artery disease (CAD) and ischemic stroke (IS). METHODS: We examined the association of phosSNPs with BP, CAD and IS in shared data from genome-wide association studies (GWAS) and tested if the disease loci were enriched with phosSNPs. Furthermore, we performed quantitative trait locus analysis to find out if the identified phosSNPs have impacts on gene expression, protein and metabolite levels...
2019: Current Molecular Medicine
#20
JOURNAL ARTICLE
Sara Lindström, Lu Wang, Erin N Smith, William Gordon, Astrid van Hylckama Vlieg, Mariza de Andrade, Jennifer A Brody, Jack W Pattee, Jeffrey Haessler, Ben M Brumpton, Daniel I Chasman, Pierre Suchon, Ming-Huei Chen, Constance Turman, Marine Germain, Kerri L Wiggins, James MacDonald, Sigrid K Braekkan, Sebastian M Armasu, Nathan Pankratz, Rebecca D Jackson, Jonas B Nielsen, Franco Giulianini, Marja K Puurunen, Manal Ibrahim, Susan R Heckbert, Scott M Damrauer, Pradeep Natarajan, Derek Klarin, Paul S de Vries, Maria Sabater-Lleal, Jennifer E Huffman, Theo K Bammler, Kelly A Frazer, Bryan M McCauley, Kent Taylor, James S Pankow, Alexander P Reiner, Maiken E Gabrielsen, Jean-François Deleuze, Chris J O'Donnell, Jihye Kim, Barbara McKnight, Peter Kraft, John-Bjarne Hansen, Frits R Rosendaal, John A Heit, Bruce M Psaty, Weihong Tang, Charles Kooperberg, Kristian Hveem, Paul M Ridker, Pierre-Emmanuel Morange, Andrew D Johnson, Christopher Kabrhel, David-Alexandre Trégouët, Nicholas L Smith
Venous thromboembolism (VTE) is a significant contributor to morbidity and mortality. To advance our understanding of the biology contributing to VTE, we conducted a genome-wide association study (GWAS) of VTE and a transcriptome-wide association study (TWAS) based on imputed gene expression from whole blood and liver. We meta-analyzed GWAS data from 18 studies for 30 234 VTE cases and 172 122 controls and assessed the association between 12 923 718 genetic variants and VTE. We generated variant prediction scores of gene expression from whole blood and liver tissue and assessed them for association with VTE...
November 7, 2019: Blood
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