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single cell methylation

Zi-Yue Wang, Li-Juan Wang, Qianyi Zhang, Bo Tang, Chun-Yang Zhang
DNA methylation is an important epigenetic modification in human genomes. Herein, we develop a single quantum dot (QD)-based nanosensor for sensitive detection of DNA methylation at both CpG and non-CpG sites using tricyclic ligation chain reaction (LCR)-mediated QD-based fluorescence resonance energy transfer (FRET). We design two sets of DNA probes (X and Y, X' and Y') for methylated DNA assay. In the presence of thermostable DNA ligase, probes X and Y may adjacently hybridize with the methylated DNA to obtain the ligated XY products which may function as the templates for probes X' and Y' to generate the X'Y' products...
February 7, 2018: Chemical Science
Ivana Jovčevska
The most aggressive brain malignancy, glioblastoma, accounts for 60-70% of all gliomas and is uniformly fatal. According to the molecular signature, glioblastoma is divided into four subtypes (proneural, neural, classical, and mesenchymal), each with its own genetic background. The Cancer Genome Atlas project provides information about the most common genetic changes in glioblastoma. They involve mutations in TP53, TERT, and PTEN, and amplifications in EFGR, PDGFRA, CDK4, CDK6, MDM2, and MDM4. Recently, epigenetics was used to demonstrate the oncogenic roles of miR-124, miR-137, and miR-128...
April 18, 2018: Critical Reviews in Clinical Laboratory Sciences
Andrew R Mendelsohn, James W Larrick
DNA methylation (DNAm) clocks such as the Horvath DNAm clock provide the most accurate biological determination of biological age relative to chronological age available today. However, there is little correlation between DNAm clocks, telomere-based aging clocks, and transcriptomic-based aging clocks. Recently, a genome-wide association study identified single-nucleotide polymorphism variants of TERT, the gene that encodes telomerase, as accelerating intrinsic aging in the Horvath DNAm clock. These same variants have been previously associated with long telomeres in leukocytes, suggesting that TERT acts paradoxically on telomere-associated aging and DNAm-associated aging...
April 2018: Rejuvenation Research
Stefanie Klein, Melek Kızaloğlu, Luis Portilla, Hyoungwon Park, Tobias Rejek, Julian Hümmer, Karsten Meyer, Rainer Hock, Luitpold V R Distel, Marcus Halik, Carola Kryschi
Efficient magnetic reactive oxygen species (ROS) formation enhancing agents after X-ray treatment are realized by functionalizing superparamagnetic magnetite (Fe3 O4 ) and Co-ferrite (CoFe2 O4 ) nanoparticles with self-assembled monolayers (SAMs). The Fe3 O4 and CoFe2 O4 nanoparticles are synthesized using Massart's coprecipitation technique. Successful surface modification with the SAM forming compounds 1-methyl-3-(dodecylphosphonic acid) imidazolium bromide, or (2-{2-[2-hydroxy-ethoxy]-ethoxy}-ethyl phosphonic acid provides biocompatibility and long-term stability of the Fe3 O4 and CoFe2 O4 nanoparticles in cell media...
April 18, 2018: Small
Mahalakshmi Shankaran, Gregg Czerwieniec, Chancy Fessler, Po-Yin Anne Wong, Salena Killion, Scott M Turner, Marc K Hellerstein, William J Evans
BACKGROUND: Muscle mass can be measured directly in vivo by isotope dilution, using Creatine-(methyl-d3 ) monohydrate (D3 -Cr) by mouth followed by measurement of the steady-state enrichment of D3 -creatinine (D3 -Crn) in urine. Isotope dilution methods require knowledge of the amount of tracer delivered to the pool of interest. In a subset of human subjects, a small amount of orally administered D3 -Cr 'spills' into urine after absorption and prior to transport into skeletal muscle cells...
April 16, 2018: Journal of Cachexia, Sarcopenia and Muscle
Julia Böck, Silke Appenzeller, Larissa Haertle, Tamara Schneider, Andrea Gehrig, Jörg Schröder, Simone Rost, Beat Wolf, Claus R Bartram, Christian Sutter, Thomas Haaf
To evaluate the role of constitutive epigenetic changes in normal body cells of BRCA1/BRCA2-mutation negative patients, we have developed a deep bisulfite sequencing assay targeting the promoter regions of 8 tumor suppressor (TS) genes (BRCA1, BRCA2, RAD51C, ATM, PTEN, TP53, MLH1, RB1) and the estrogene receptor gene (ESR1), which plays a role in tumor progression. We analyzed blood samples of two breast cancer (BC) cohorts with early onset (EO) and high risk (HR) for a heterozygous mutation, respectively, along with age-matched controls...
April 16, 2018: International Journal of Cancer. Journal International du Cancer
Weiguo Xiang, Shruti Choudhary, Ernest Hamel, Susan L Mooberry, Aleem Gangjee
We report a series of tubulin targeting agents, some of which demonstrate potent antiproliferative activities. These analogs were designed to optimize the antiproliferative activity of 1 by varying the heteroatom substituent at the 4'-position, the basicity of the 4-position amino moiety, and conformational restriction. The potential metabolites of the active compounds were also synthesized. Some compounds demonstrated single digit nanomolar IC50 values for antiproliferative effects in MDA-MB-435 melanoma cells...
April 4, 2018: Bioorganic & Medicinal Chemistry
Antoine Italiano, Jean-Charles Soria, Maud Toulmonde, Jean-Marie Michot, Carlo Lucchesi, Andrea Varga, Jean-Michel Coindre, Stephen J Blakemore, Alicia Clawson, Benjamin Suttle, Alice A McDonald, Mark Woodruff, Scott Ribich, Eric Hedrick, Heike Keilhack, Blythe Thomson, Takashi Owa, Robert A Copeland, Peter T C Ho, Vincent Ribrag
BACKGROUND: Activating enhancer of zeste homolog 2 (EZH2) mutations or aberrations of the switch/sucrose non-fermentable (SWI/SNF) complex (eg, mutations or deletions of the subunits INI1 or SMARCA4) can lead to aberrant histone methylation, oncogenic transformation, and a proliferative dependency on EZH2 activity. In this first-in-human study, we aimed to investigate the safety, clinical activity, pharmacokinetics, and pharmacodynamics of tazemetostat, a first-in-class selective inhibitor of EZH2...
April 9, 2018: Lancet Oncology
Samara M A Alexandre, Maria L Corradi da Silva, Ana F D Vasconcelos, Diego T D Exposti, Cesar A Tischer, Alicia Prieto, Dolores Diaz, Ramon Kaneno
A fucomannogalactan from Rhizoctonia solani biomass was obtained after hot aqueous extraction and purified by freeze-thaw cycles and gel filtration chromatography on Sepharose CL-6B. The polysaccharide was homogeneous after HPSEC/RID analysis (Mw /Mn  ~ 1.1), displaying an average molecular weight of 15.4 × 103  Da. Its chemical structure was determined by methylation analysis (GC/MS) and spectroscopy (FTIR, 1D and 2D NMR). The polysaccharide had a branched α-1,6-linked Galp backbone with 66% linear residues, a number of which were at O-3 methylated...
April 9, 2018: International Journal of Biological Macromolecules
Jiuyang Liu, Shuya Zhang, Mingqing Liu, Yaqian Liu, Gilbert Nshogoza, Jia Gao, Rongsheng Ma, Yang Yang, Jihui Wu, Jiahai Zhang, Fudong Li, Ke Ruan
As a reader of di-methylated arginine on various proteins, such as histone, RNA polymerase II, PIWI and Fragile X mental retardation protein, the Tudor domain of Tudor domain-containing protein 3 (TDRD3) mediates transcriptional activation in nucleus and formation of stress granules in the cytoplasm. Despite the TDRD3 implication in cancer cell proliferation and invasion, warheads to block the di-methylated arginine recognition pocket of the TDRD3 Tudor domain have not yet been uncovered. Here we identified 14 small molecule hits against the TDRD3 Tudor domain through NMR fragment-based screening...
April 12, 2018: FEBS Journal
Ryan M Mulqueen, Dmitry Pokholok, Steven J Norberg, Kristof A Torkenczy, Andrew J Fields, Duanchen Sun, John R Sinnamon, Jay Shendure, Cole Trapnell, Brian J O'Roak, Zheng Xia, Frank J Steemers, Andrew C Adey
We present a highly scalable assay for whole-genome methylation profiling of single cells. We use our approach, single-cell combinatorial indexing for methylation analysis (sci-MET), to produce 3,282 single-cell bisulfite sequencing libraries and achieve read alignment rates of 68 ± 8%. We apply sci-MET to discriminate the cellular identity of a mixture of three human cell lines and to identify excitatory and inhibitory neuronal populations from mouse cortical tissue.
April 9, 2018: Nature Biotechnology
Kamila Kochan, Huadong Peng, Bayden R Wood, Victoria S Haritos
Background: Biodiesel is a valuable renewable fuel made from derivatized fatty acids produced in plants, animals, and oleaginous microbes. Of the latter, yeasts are of special interest due to their wide use in biotechnology, ability to synthesize fatty acids and store large amounts of triacylglycerols while utilizing non-food carbon sources. While yeast efficiently produce lipids, genetic modification and indeed, lipid pathway metabolic engineering, is usually required for cost-effective production...
2018: Biotechnology for Biofuels
Sophie F Roerink, Nobuo Sasaki, Henry Lee-Six, Matthew D Young, Ludmil B Alexandrov, Sam Behjati, Thomas J Mitchell, Sebastian Grossmann, Howard Lightfoot, David A Egan, Apollo Pronk, Niels Smakman, Joost van Gorp, Elizabeth Anderson, Stephen J Gamble, Chris Alder, Marc van de Wetering, Peter J Campbell, Michael R Stratton, Hans Clevers
Every cancer originates from a single cell. During expansion of the neoplastic cell population, individual cells acquire genetic and phenotypic differences from each other. Here, to investigate the nature and extent of intra-tumour diversification, we characterized organoids derived from multiple single cells from three colorectal cancers as well as from adjacent normal intestinal crypts. Colorectal cancer cells showed extensive mutational diversification and carried several times more somatic mutations than normal colorectal cells...
April 11, 2018: Nature
Shanshan Zhang, Shuyi Han, Maoxiu Zhang, Yunshan Wang
Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future...
April 1, 2018: Legal Medicine
Deniz Öner, Manosij Ghosh, Matthieu Moisse, Radu Corneliu Duca, Robin Coorens, Jeroen A J Vanoirbeek, Diether Lambrechts, Lode Godderis, Peter H M Hoet
Inhalation exposure to asbestos is associated with lung and pleural diseases in humans and remains a major public health issue worldwide. Human bronchial epithelial cells (16HBE) were exposed to UICC amosite, crocidolite and chrysotile. Cytotoxicity, genotoxicity, global DNA methylation on cytosine residues (using LC-MS/MS) were investigated at different doses (2.5-100 μg/ml). Gene-specific DNA methylation alterations at the whole genome were investigated using a microarray that interrogates >450 thousand CpG sites...
April 4, 2018: Environment International
Rebeqa Gunnarsson, Sebastian Dilorenzo, Kristina B Lundin-Ström, Linda Olsson, Andrea Biloglav, Henrik Lilljebjörn, Marianne Rissler, Per Wahlberg, Anders Lundmark, Anders Castor, Mikael Behrendtz, Thoas Fioretos, Kajsa Paulsson, Anders Isaksson, Bertil Johansson
High-throughput sequencing was applied to investigate the mutation/methylation patterns on 1q and gene expression profiles in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL) with/without (w/wo) dup(1q). Sequencing of the breakpoint regions and all exons on 1q in seven dup(1q)-positive cases revealed non-synonymous somatic single nucleotide variants (SNVs) in BLZF1, FMN2, KCNT2, LCE1C, NES, and PARP1. Deep sequencing of these in a validation cohort w (n = 17)/wo (n = 94) dup(1q) revealed similar SNV frequencies in the two groups (47% vs...
March 12, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Blas Blázquez, Manuel Carmona, Eduardo Díaz
Alkylbenzenes, such as toluene and m -xylene, are an important class of contaminant hydrocarbons that are widespread and tend to accumulate in subsurface anoxic environments. The peripheral pathway for the anaerobic oxidation of toluene in bacteria consists of an initial activation catalyzed by a benzylsuccinate synthase (encoded by bss genes), and a subsequent modified β-oxidation of benzylsuccinate to benzoyl-CoA and succinyl-CoA (encoded by bbs genes). We have shown here that the bss and bbs genes, which are located within an integrative and conjugative element, are essential for anaerobic degradation of toluene but also for m -xylene oxidation in the denitrifying beta-proteobacterium Azoarcus sp...
2018: Frontiers in Microbiology
Yoichi Ohshima, Kazumi Iwata, Masakazu Ibi, Misaki Matsumoto, Masato Katsuyama, Chihiro Yabe-Nishimura
The increased ratio of longer amyloid-β (Aβ1-42)/shorter amyloid-β (Aβ1-40) peptides, generated from amyloid precursor protein (APP), is known to promote the development of Alzheimer's disease (AD). To investigate the role of smoking in Aβ production, we determined the production of Aβ species in the presence of nicotine or methyl vinyl ketone (MVK), major components of cigarette smoke extracts, in Flp-In™ T-REx™ -293 (T-REx293) cells harboring a single copy of human APP. While treatment with nicotine or MVK did not affect the amount of APP, the levels of Aβ1-40 in the culture media were significantly increased...
2018: Journal of Toxicological Sciences
Bhavana Sharma, Renu Deswal
A facile one-pot green synthesis of gold nanoparticles (AuNPs) with different geometries was achieved using an underutilized Himalayan bioresource Hippophae rhamnoides. Aqueous leaf (LE) and berry extracts (BE) showed rapid synthesis of monodispersed spherical LEAuNPs (27 ± 3.2 nm) and anisotropic BEAuNPs (55 ± 4.5 nm) within 2 and 15 min, respectively. The Fourier-transform infrared (FTIR) spectroscopy showed involvement of polyphenolics/flavonoids in AuNPs reduction. LE AuNPs (IC50 49 µg) exhibited higher antioxidant potential than BE AuNPs (IC50 57 µg)...
April 4, 2018: Artificial Cells, Nanomedicine, and Biotechnology
Tetsuya Suzuki, Yoshie Kuramoto, Hiroyuki Kamiya
O6-Methylguanine (O6-MeG) is a damaged base produced by methylating reagents. The Werner syndrome protein (WRN) is a cancer-related human DNA helicase. The effects of WRN reduction on O6-MeG-caused mutagenesis were assessed by an siRNA-mediated knockdown in human U2OS cells, using a shuttle plasmid with a single O6-MeG base in the supF gene. The plasmid DNA was replicated in the cells, isolated, and electroporated into an Escherichia coli indicator strain. The lowered amount of WRN increased the frequency of mutations induced by O6-MeG, mainly G:C-->A:T substitution...
April 4, 2018: Chemical Research in Toxicology
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