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https://www.readbyqxmd.com/read/29350783/malignant-mesothelioma-in-situ
#1
Andrew Churg, Harry Hwang, Lawrence Tan, Gefei Qing, Altaf Taher, Amy Tong, AnaMaria Bilawich, Sanja Dacic
The existence of malignant mesothelioma in situ (MIS) is often postulated, but there are no accepted morphologic criteria for making such a diagnosis. Here we report two cases that appear to be true MIS on the basis of in situ genomic analysis. In one case the patient had repeated unexplained pleural unilateral effusions. Two thoracoscopies 9 months apart revealed only visually normal pleura. Biopsies from both thoracoscopies showed only a single layer of mildly reactive mesothelial cells. However, these cells had lost BAP1 and showed loss of CDKN2A ("p16″) by FISH...
January 19, 2018: Histopathology
https://www.readbyqxmd.com/read/29348912/genomic-and-molecular-control-of-cell-type-and-cell-type-conversions
#2
REVIEW
Xiuling Fu, Fangfang He, Yuhao Li, Allahverdi Shahveranov, Andrew Paul Hutchins
Organisms are made of a limited number of cell types that combine to form higher order tissues and organs. Cell types have traditionally been defined by their morphologies or biological activity, yet the underlying molecular controls of cell type remain unclear. The onset of single cell technologies, and more recently genomics (particularly single cell genomics), has substantially increased the understanding of the concept of cell type, but has also increased the complexity of this understanding. These new technologies have added a new genome wide molecular dimension to the description of cell type, with genome-wide expression and epigenetic data acting as a cell type 'fingerprint' to describe the cell state...
December 2017: Cell Regeneration
https://www.readbyqxmd.com/read/29348692/genome-wide-search-for-higher-order-epistasis-as-modifiers-of-treatment-effects-on-bone-mineral-density-in-childhood-cancer-survivors
#3
Cindy Im, Kirsten K Ness, Sue C Kaste, Wassim Chemaitilly, Wonjong Moon, Yadav Sapkota, Russell J Brooke, Melissa M Hudson, Leslie L Robison, Yutaka Yasui, Carmen L Wilson
Single-nucleotide polymorphisms (SNPs) contributing to interactions between regulatory elements that modulate gene transcription may explain some of the uncharacterized variation for complex traits. We explored this hypothesis among 856 adult survivors of pediatric cancer exposed to curative treatments that adversely affect bone mineral density (BMD). To restrict our search to interactions among SNPs in regulatory elements, our analysis considered 75523 SNPs mapped to putative promoter or enhancer regions. In anticipation that power to detect higher order epistasis would be low using an exhaustive search and a Bonferroni-corrected threshold for genome-wide significance (e...
January 18, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29348659/blm-helicase-suppresses-recombination-at-g-quadruplex-motifs-in-transcribed-genes
#4
Niek van Wietmarschen, Sarra Merzouk, Nancy Halsema, Diana C J Spierings, Victor Guryev, Peter M Lansdorp
Bloom syndrome is a cancer predisposition disorder caused by mutations in the BLM helicase gene. Cells from persons with Bloom syndrome exhibit striking genomic instability characterized by excessive sister chromatid exchange events (SCEs). We applied single-cell DNA template strand sequencing (Strand-seq) to map the genomic locations of SCEs. Our results show that in the absence of BLM, SCEs in human and murine cells do not occur randomly throughout the genome but are strikingly enriched at coding regions, specifically at sites of guanine quadruplex (G4) motifs in transcribed genes...
January 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29348472/viral-highway-to-nucleus-exposed-by-image-correlation-analyses
#5
Elina Mäntylä, Jenu V Chacko, Vesa Aho, Colin R Parrish, Victor Shahin, Michael Kann, Michelle A Digman, Enrico Gratton, Maija Vihinen-Ranta
Parvoviral genome translocation from the plasma membrane into the nucleus is a coordinated multistep process mediated by capsid proteins. We used fast confocal microscopy line scan imaging combined with image correlation methods including auto-, pair- and cross-correlation, and number and brightness analysis, to study the parvovirus entry pathway at the single-particle level in living cells. Our results show that the endosome-associated movement of virus particles fluctuates from fast to slow. Fast transit of single cytoplasmic capsids to the nuclear envelope is followed by slow movement of capsids and fast diffusion of capsid fragments in the nucleoplasm...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348443/a-general-and-flexible-method-for-signal-extraction-from-single-cell-rna-seq-data
#6
Davide Risso, Fanny Perraudeau, Svetlana Gribkova, Sandrine Dudoit, Jean-Philippe Vert
Single-cell RNA-sequencing (scRNA-seq) is a powerful high-throughput technique that enables researchers to measure genome-wide transcription levels at the resolution of single cells. Because of the low amount of RNA present in a single cell, some genes may fail to be detected even though they are expressed; these genes are usually referred to as dropouts. Here, we present a general and flexible zero-inflated negative binomial model (ZINB-WaVE), which leads to low-dimensional representations of the data that account for zero inflation (dropouts), over-dispersion, and the count nature of the data...
January 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29348435/macrophage-sensing-of-single-walled-carbon-nanotubes-via-toll-like-receptors
#7
Sourav P Mukherjee, Olesja Bondarenko, Pekka Kohonen, Fernando T Andón, Táňa Brzicová, Isabel Gessner, Sanjay Mathur, Massimo Bottini, Paolo Calligari, Lorenzo Stella, Elena Kisin, Anna Shvedova, Reija Autio, Heli Salminen-Mankonen, Riitta Lahesmaa, Bengt Fadeel
Carbon-based nanomaterials including carbon nanotubes (CNTs) have been shown to trigger inflammation. However, how these materials are 'sensed' by immune cells is not known. Here we compared the effects of two carbon-based nanomaterials, single-walled CNTs (SWCNTs) and graphene oxide (GO), on primary human monocyte-derived macrophages. Genome-wide transcriptomics assessment was performed at sub-cytotoxic doses. Pathway analysis of the microarray data revealed pronounced effects on chemokine-encoding genes in macrophages exposed to SWCNTs, but not in response to GO, and these results were validated by multiplex array-based cytokine and chemokine profiling...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348307/non-mammalian-models-of-multiple-endocrine-neoplasia-type-2
#8
REVIEW
Tirtha K Das, Ross L Cagan
Twenty-five years ago, RET was identified as the primary driver of multiple endocrine neoplasia type 2 (MEN2) syndrome. MEN2 is characterized by several transformation events including pheochromocytoma, parathyroid adenoma and, especially penetrant, medullary thyroid carcinoma (MTC). Overall, MTC is a rare but aggressive type of thyroid cancer for which no effective treatment currently exists. Surgery, radiation, radioisotope treatment and chemotherapeutics have all shown limited success, and none of these approaches have proven durable in advanced disease...
February 2018: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29346494/novel-myopia-genes-and-pathways-identified-from-syndromic-forms-of-myopia
#9
D Ian Flitcroft, James Loughman, Christine F Wildsoet, Cathy Williams, Jeremy A Guggenheim
Purpose: To test the hypothesis that genes known to cause clinical syndromes featuring myopia also harbor polymorphisms contributing to nonsyndromic refractive errors. Methods: Clinical phenotypes and syndromes that have refractive errors as a recognized feature were identified using the Online Mendelian Inheritance in Man (OMIM) database. One hundred fifty-four unique causative genes were identified, of which 119 were specifically linked with myopia and 114 represented syndromic myopia (i...
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29346449/within-host-selection-for-faster-replicating-bacterial-symbionts
#10
Ewa Chrostek, Luis Teixeira
Wolbachia is a widespread, intracellular symbiont of arthropods, able to induce reproductive distortions and antiviral protection in insects. Wolbachia can also be pathogenic, as is the case with wMelPop, a virulent variant of the endosymbiont of Drosophila melanogaster. An extensive genomic amplification of the 20kb region encompassing eight Wolbachia genes, called Octomom, is responsible for wMelPop virulence. The Octomom copy number in wMelPop can be highly variable between individual D. melanogaster flies, even when comparing siblings arising from a single female...
2018: PloS One
https://www.readbyqxmd.com/read/29346103/wavedec-a-wavelet-approach-to-identify-both-shared-and-individual-patterns-of-copy-number-variations
#11
Hongmin Cai, Peihua Chen, Jiazhou Chen, Jiulun Cai, Yan Song, Guoqiang Han
Copy-number variations (CNVs) are associated with complex diseases and particular tumor types. Array-based comparative genomic hybridization (aCGH) is a common approach for the detection of CNVs. Traditional CNV detection methods for multiple aCGH samples mainly use batch samples to find common variations, not accounting for the individual characteristics of each sample. Accurately differentiating both the commonly shared and the individual CNV patterns is pivotal to identify cell populations, or to distinguish cell growth (as in cancer) from invasion of new cells...
February 2018: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/29345572/breaking-the-dna-damage-response-via-serine-threonine-kinase-inhibitors-to-improve-cancer-treatment
#12
Wioletta Rozpedek, Dariusz Pytel, Alicja Nowak-Zdunczyk, Dawid Lewko, Radoslaw Wojtczak, John Alan Diehl, Ireneusz Majsterek
Multiple, both endogenous and exogenous, sources may induce DNA damage and DNA replication stress. Cells have developed DNA damage response (DDR) signaling pathways to maintain genomic stability and effectively detect and repair DNA lesions. Serine/threonine kinases such as Ataxia-telangiectasia mutated (ATM) and Ataxia-telangiectasia and Rad3-Related (ATR) are the major regulators of DDR, since after sensing stalled DNA replication forks, DNA double- or single-strand breaks, may directly phosphorylate and activate their downstream targets, that play a key role in DNA repair, cell cycle arrest and apoptotic cell death...
January 16, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29344885/microrna-networks-in-breast-cancer-cells
#13
Andliena Tahiri, Miriam R Aure, Vessela N Kristensen
A variety of molecular techniques can be used in order to unravel the molecular composition of cells. In particular, the microarray technology has been used to identify novel biomarkers that may be useful in the diagnosis, prognosis, or treatment of cancer. The microarray technology is ideal for biomarker discovery as it allows for the screening of a large number of molecules at once. In this review, we focus on microRNAs (miRNAs) which are key molecules in cells and regulate gene expression post-transcriptionally...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344184/therapeutic-effects-of-adenovirus-mediated-cd-and-nis-expression-combined-with-na131i-5-fc-on-human-thyroid-cancer
#14
Meng-Hui Yuan, Long-Xiao Wei, Run-Suo Zhou, Hai-Feng Xu, Jun-Yan Wang, Qian-Rong Bai
Thyroid cancer is the most common type of malignant endocrine tumor diagnosed. Previous studies have indicated that gene therapy is the most promising and effective therapeutic method for thyroid cancer. Therefore, in the present study, Na131I/5-fluorocytosine (5-FC) treatment was combined with cytosine deaminase (CD, encoded by the CDA gene) and sodium iodide symporter (NIS, encoded by the SLC5A5 gene) to act together as a therapeutic tool for thyroid cancer. The present study explored the combined cytotoxic effects of adenovirus-mediated CD and NIS under the control of the progression elevated gene-3 (PEG-3) promoter (Ad-PEG-3-CD-NIS) with Na131I/5-FC against the human thyroid cancer TT cell line in vitro...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343791/single-plasmid-systems-for-inducible-dual-protein-expression-and-for-crispr-cas9-crispri-gene-regulation-in-lactic-acid-bacterium-lactococcus-lactis
#15
Aleš Berlec, Katja Škrlec, Janja Kocjan, Maria Olenic, Borut Štrukelj
Lactococcus lactis is a food-grade lactic acid bacterium that is used in the dairy industry as a cell factory and as a host for recombinant protein expression. The nisin-controlled inducible expression (NICE) system is frequently applied in L. lactis; however new tools for its genetic modification are highly desirable. In this work NICE was adapted for dual protein expression. Plasmid pNZDual, that contains two nisin promoters and multiple cloning sites (MCSs), and pNZPolycist, that contains a single nisin promoter and two MCSs separated by the ribosome binding site, were constructed...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#16
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342113/mitochondria-oxidative-stress-and-the-kynurenine-system-with-a-focus-on-ageing-and-neuroprotection
#17
REVIEW
Katalin Sas, Elza Szabó, László Vécsei
In this review, the potential causes of ageing are discussed. We seek to gain insight into the main physiological functions of mitochondria and discuss alterations in their function and the genome, which are supposed to be the central mechanisms in senescence. We conclude by presenting the potential modulating role of the kynurenine pathway in the ageing processes. Mitochondrial dynamics are supposed to have important physiological roles in maintaining cell homeostasis. During ageing, a decrease in mitochondrial dynamics was reported, potentially compromising the function of mitochondria...
January 17, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29341473/somatic-mosaic-deletions-involving-scn1a-cause-dravet-syndrome
#18
Tojo Nakayama, Atsushi Ishii, Takeshi Yoshida, Hirosato Nasu, Keiko Shimojima, Toshiyuki Yamamoto, Shigeo Kure, Shinichi Hirose
Somatic mosaicism in single nucleotide variants of SCN1A is known to occur in a subset of parents of children with Dravet syndrome (DS). Here, we report recurrent somatic mosaic microdeletions involving SCN1A in children diagnosed with DS. Through the evaluation of 237 affected individuals with DS who did not show SCN1A or PCHD19 mutations in prior sequencing analyzes, we identified two children with mosaic microdeletions covering the entire SCN1A region. The allele frequency of the mosaic deletions estimated by multiplex ligation-dependent probe amplification and array comparative genomic hybridization was 25-40%, which was comparable to the mosaic ratio in lymphocytes and buccal mucosa cells observed by fluorescence in situ hybridization analysis...
January 17, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29339801/cardiac-glycoside-aglycones-inhibit-hiv-1-gene-expression-by-a-mechanism-requiring-mek1-2-erk1-2-signaling
#19
Raymond W Wong, Clifford A Lingwood, Mario A Ostrowski, Tyler Cabral, Alan Cochrane
The capacity of HIV-1 to develop resistance to current drugs calls for innovative strategies to control this infection. We aimed at developing novel inhibitors of HIV-1 replication by targeting viral RNA processing-a stage dependent on conserved host processes. We previously reported that digoxin is a potent inhibitor of this stage. Herein, we identify 12 other cardiac glycoside/aglycones or cardiotonic steroids (CSs) that impede HIV growth in HIV-infected T cells from clinical patients at IC50s (1.1-1.3 nM) that are 2-26 times below concentrations used in patients with heart conditions...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29337376/crispr-cas9-mediated-genome-editing-in-epstein-barr-virus-transformed-lymphoblastoid-b-cell-lines
#20
Sizun Jiang, Liang Wei Wang, Michael J Walsh, Stephen J Trudeau, Catherine Gerdt, Bo Zhao, Benjamin E Gewurz
Epstein-Barr virus (EBV) efficiently transforms primary human B cells into immortalized lymphoblastoid cell lines (LCLs), which are extensively used in human genetic, immunological and virological studies. LCLs provide unlimited sources of DNA for genetic investigation, but can be difficult to manipulate, for instance because low retroviral or lentiviral transduction frequencies hinder experiments that require co-expression of multiple components. This unit details Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 engineering for robust LCL genome editing...
January 16, 2018: Current Protocols in Molecular Biology
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