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single cell RNA sequencing

Annacarmen Petrizzo, Maria Tagliamonte, Angela Mauriello, Valerio Costa, Marianna Aprile, Roberta Esposito, Andrea Caporale, Antonio Luciano, Claudio Arra, Maria Lina Tornesello, Franco M Buonaguro, Luigi Buonaguro
BACKGROUND: A novel prediction algorithm is needed for the identification of effective tumor associated mutated neoantigens. Only those with no homology to self wild type antigens are true predicted neoantigens (TPNAs) and can elicit an antitumor T cell response, not attenuated by central tolerance. To this aim, the mutational landscape was evaluated in HCV-associated hepatocellular carcinoma. METHODS: Liver tumor biopsies and adjacent non-tumor liver tissues were obtained from 9 HCV-chronically infected subjects and subjected to RNA-Seq analysis...
October 19, 2018: Journal of Translational Medicine
Li Zhou, Rongxue Peng, Rui Zhang, Jinming Li
The Streptococcus pyogenes CRISPR/Cas system has found widespread applications as a gene-editing and regulatory tool for the simultaneous delivery of the Cas9 protein and guide RNAs into the cell, thus making the recognition of specific DNA sequences possible. The recent study that shows that Cas9 can also bind to and cleave RNA in an RNA-programmable manner is suggestive of potential utility of this system as a universal nucleic-acid recognition tool. To increase the signal intensity of the CRISPR/Cas system, a signal amplification technique has to be exploited appropriately; this requirement is also a challenge for the detection of DNA or RNA...
October 19, 2018: Journal of Cellular and Molecular Medicine
Nobuhiko Kamoshita, Shin-Ichi Tominaga
The translation of capsid proteins of Plautia stali intestine virus (PSIV), encoded in its second open reading frame (ORF2), is directed by an internal ribosomal entry site (IRES) located in the intergenic region (IGR). Owing to the specific properties of PSIV IGR in terms of nucleotide length and frame organization, capsid proteins are also translated via stop codon readthrough in mammalian cultured cells as an extension of translation from the first ORF (ORF1) and IGR. To delineate stop codon readthrough in PSIV, we determined requirements of cis-acting elements, through a molecular genetic approach applied in both cell-free translation systems and cultured cells...
October 18, 2018: RNA
Songhee H Kim, Melissa Vieira, Jae Youn Shim, Hongyoung Choi, Hye Yoon Park
From biogenesis to degradation, mRNA goes through diverse types of regulation and interaction with other biomolecules. Uneven distribution of mRNA transcripts and the diverse isoforms and modifications of mRNA make us wonder how cells manage the complexity and keep the functional integrity for the normal development of cells and organisms. Single-molecule microscopy tools have expanded the scope of RNA research with unprecedented spatiotemporal resolution. In this review, we highlight the recent progress in the methods for labeling mRNA targets and analyzing the quantitative information from fluorescence images of single mRNA molecules...
October 19, 2018: RNA Biology
Sri H Kanuri, Joseph Ipe, Kameel Kassab, Hongyu Gao, Yunlong Liu, Todd C Skaar, Rolf P Kreutz
BACKGROUND AND AIMS: Variation in micro-RNA (miRNA) levels in blood has been associated with alterations of physiological functions of the cardiovascular system. Circulating miRNA have the potential to become reliable biomarkers for risk stratification and early detection of cardiovascular events. Recurrent thrombotic events in patients with established coronary artery disease (CAD) demonstrate the need for personalized approaches to secondary prevention, especially in light of recent novel treatment approaches...
October 3, 2018: Atherosclerosis
Shiv Prakash Verma, Parimal Das
The IGFN1 (Immunoglobulin-Like And Fibronectin Type III Domain Containing 1) gene has a role in skeletal muscle function and is also involved in metastatic breast cancer, and the isoforms with three N-terminal globular domains are sufficient for its function in skeletal muscle. Two novel splicing isoforms of IGFN1 have been identified in renal cell carcinoma (RCC), one with 5'exon extension and an isoform with a novel exon. The role of G-quadruplex, a non-B DNA, was explored for the splicing alteration of IGFN1 in RCC...
2018: PloS One
Teminioluwa Ajayi, Cynthia L Innes, Sara A Grimm, Prashant Rai, Ryan Finethy, Jörn Coers, Xuting Wang, Douglas A Bell, John A McGrath, Shepherd H Schurman, Michael B Fessler
Crohn's disease (CD) is a chronic inflammatory gastrointestinal disorder. Genetic association studies have implicated dysregulated autophagy in CD. Among risk loci identified are a promoter single nucleotide polymorphism (SNP)(rs13361189) and two intragenic SNPs (rs9637876, rs10065172) in immunity-related GTPase family M ( IRGM), a gene that encodes a protein of the autophagy initiation complex. All three SNPs have been proposed to modify IRGM expression, but reports have been divergent and largely derived from cell lines...
October 18, 2018: American Journal of Physiology. Gastrointestinal and Liver Physiology
Leonard Y M Cheung, Akima S George, Stacey R McGee, Alexandre Z Daly, Michelle L Brinkmeier, Buffy S Ellsworth, Sally A Camper
Transcription factors and signaling pathways that regulate stem cells and specialized hormone-producing cells in the pituitary gland have been the subject of intense study and have yielded a mechanistic understanding of pituitary organogenesis and disease. Yet, the regulation of stem cell proliferation and differentiation, the heterogeneity among specialized hormone-producing cells, and the role of non-endocrine cells in the gland remain important, unanswered questions. Recent advances in single-cell RNA sequencing (scRNAseq) technologies provide new avenues to address these questions...
October 17, 2018: Endocrinology
Laura S M Müller, Raúl O Cosentino, Konrad U Förstner, Julien Guizetti, Carolin Wedel, Noam Kaplan, Christian J Janzen, Panagiota Arampatzi, Jörg Vogel, Sascha Steinbiss, Thomas D Otto, Antoine-Emmanuel Saliba, Robert P Sebra, T Nicolai Siegel
Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host1 . Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms to ensure the expression of one or very few antigens at any given time...
October 17, 2018: Nature
Yukihiko Sugita, Hideyuki Matsunami, Yoshihiro Kawaoka, Takeshi Noda, Matthias Wolf
Ebola virus causes haemorrhagic fever with a high fatality rate in humans and non-human primates. It belongs to the family Filoviridae in the order Mononegavirales, which are viruses that contain linear, non-segmented, negative-sense, single-stranded genomic RNA1,2 . The enveloped, filamentous virion contains the nucleocapsid, consisting of the helical nucleoprotein-RNA complex, VP24, VP30, VP35 and viral polymerase1,3 . The nucleoprotein-RNA complex acts as a scaffold for nucleocapsid formation and as a template for RNA replication and transcription by condensing RNA into the virion4,5 ...
October 17, 2018: Nature
Gary Wong, Shihua He, Anders Leung, Wenguang Cao, Yuhai Bi, Zirui Zhang, Wenjun Zhu, Liang Wang, Yuhui Zhao, Keding Cheng, Di Liu, Wenjun Liu, Darwyn Kobasa, George F Gao, Xiangguo Qiu
Sequencing of Ebola virus (EBOV) genomes during the 2014-16 epidemic identified several naturally-occurring, dominant mutations potentially impacting virulence or tropism. Here, we characterized EBOV variants carrying one of the following substitutions: A82V in the glycoprotein (GP), R111C in the nucleoprotein (NP), or D759G in the RNA-dependent RNA-polymerase (L). Compared with wild-type EBOV/C07 (WT), NP and L mutants conferred a replication advantage in monkey VeroE6, human A549 and insectivorous bat Tb1...
October 17, 2018: Journal of Virology
Zhengyun Xiao, Guo Cheng, Yang Jiao, Chen Pan, Ran Li, Danmei Jia, Jing Zhu, Chao Wu, Min Zheng, Junling Jia
Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a single-cell holo-transcriptome sequencing (Holo-Seq) that overcomes all three hurdles. Holo-Seq has the same quantitative accuracy and uniform coverage with a complete strand of origin information as bulk RNA-seq. Most importantly, Holo-Seq can simultaneously observe small RNAs and mRNAs in a single cell...
October 17, 2018: Genome Biology
Sokratis A Apostolidis, Giuseppina Stifano, Tracy Tabib, Lisa M Rice, Christina M Morse, Bashar Kahaleh, Robert Lafyatis
Objective: The mechanisms that lead to endothelial cell (EC) injury and propagate the vasculopathy in Systemic Sclerosis (SSc) are not well understood. Using single cell RNA sequencing (scRNA-seq), our goal was to identify EC markers and signature pathways associated with vascular injury in SSc skin. Methods: We implemented single cell sorting and subsequent RNA sequencing of cells isolated from SSc and healthy control skin. We used t-distributed stochastic neighbor embedding (t-SNE) to identify the various cell types...
2018: Frontiers in Immunology
Ye Zhu, Xiang Gu, Chao Xu
BACKGROUND: Nuclear genes or family-based mitochondrial screening have been the focus of genetic studies into essential hypertension. Studies into the role of mitochondria in sporadic Chinese hypertensives are lacking. The objective of the study was to explore the relationship between mitochondrial DNA (mtDNA) variations and the development of maternally inherited essential hypertension (MIEH) in China. METHODS: Yangzhou residents who were outpatients or in-patients at the Department of Cardiology in Northern Jiangsu People's Hospital (Jiangsu, China) from June 2009 to June 2015 were recruited in a 1:1 case control study of 600 gender-matched Chinese MIEH subjects and controls...
October 16, 2018: BMC Medical Genomics
Chang Liu, Cornelius Tlotliso Sello, Yongfeng Sun, Yuxuan Zhou, Hongtao Lu, Yujian Sui, Jingtao Hu, Chenguang Xu, Yue Sun, Jing Liu, Shengyi Li, Yiming Zhang, Kaiyan Zhang
The objective of this study was to evaluate the changes in the goose embryo transcriptome during feather development. RNA-Sequencing (RNA-Seq) was used to find the transcriptome profiles of feather follicles from three stages of embryonic dorsal skin at embryonic day 13, 18, and 28 (E13, E18, E28). The results showed that 3001, 6634, and 13,780 genes were differently expressed in three stages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially expressed genes (DEGs) in E13 vs...
October 15, 2018: International Journal of Molecular Sciences
Richard Peter Owen, Michael Joseph White, David Tyler Severson, Barbara Braden, Adam Bailey, Robert Goldin, Lai Mun Wang, Carlos Ruiz-Puig, Nicholas David Maynard, Angie Green, Paolo Piazza, David Buck, Mark Ross Middleton, Chris Paul Ponting, Benjamin Schuster-Böckler, Xin Lu
Barrett's oesophagus is a precursor of oesophageal adenocarcinoma. In this common condition, squamous epithelium in the oesophagus is replaced by columnar epithelium in response to acid reflux. Barrett's oesophagus is highly heterogeneous and its relationships to normal tissues are unclear. Here we investigate the cellular complexity of Barrett's oesophagus and the upper gastrointestinal tract using RNA-sequencing of single cells from multiple biopsies from six patients with Barrett's oesophagus and two patients without oesophageal pathology...
October 15, 2018: Nature Communications
Ishaan Gupta, Paul G Collier, Bettina Haase, Ahmed Mahfouz, Anoushka Joglekar, Taylor Floyd, Frank Koopmans, Ben Barres, August B Smit, Steven A Sloan, Wenjie Luo, Olivier Fedrigo, M Elizabeth Ross, Hagen U Tilgner
Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and sorted cells to characterize transcriptomes, but applying this technology to single cells has proven to be difficult, with less than ten single-cell transcriptomes having been analyzed thus far. Although single splicing events have been described for ≤200 single cells with statistical confidence, full-length mRNA analyses for hundreds of cells have not been reported. Single-cell short-read 3' sequencing enables the identification of cellular subtypes, but full-length mRNA isoforms for these cell types cannot be profiled...
October 15, 2018: Nature Biotechnology
Lin-Chen Li, Xin-Xin Yu, Yu-Wei Zhang, Ye Feng, Wei-Lin Qiu, Cheng-Ran Xu
Pancreatic endocrine cells, which are clustered in islets, regulate blood glucose stability and energy metabolism. The distinct cell types in islets, including insulin-secreting β cells, are differentiated from common endocrine progenitors during the embryonic stage. Immature endocrine cells expand via cell proliferation and mature during a long postnatal developmental period. However, the mechanisms underlying these processes are not clearly defined. Single-cell RNA-sequencing is a promising approach for the characterization of distinct cell populations and tracing cell lineage differentiation pathways...
September 30, 2018: Journal of Visualized Experiments: JoVE
Merav Cohen, Amir Giladi, Anna-Dorothea Gorki, Dikla Gelbard Solodkin, Mor Zada, Anastasiya Hladik, Andras Miklosi, Tomer-Meir Salame, Keren Bahar Halpern, Eyal David, Shalev Itzkovitz, Tibor Harkany, Sylvia Knapp, Ido Amit
Lung development and function arises from the interactions between diverse cell types and lineages. Using single-cell RNA sequencing (RNA-seq), we characterize the cellular composition of the lung during development and identify vast dynamics in cell composition and their molecular characteristics. Analyzing 818 ligand-receptor interaction pairs within and between cell lineages, we identify broadly interacting cells, including AT2, innate lymphocytes (ILCs), and basophils. Using interleukin (IL)-33 receptor knockout mice and in vitro experiments, we show that basophils establish a lung-specific function imprinted by IL-33 and granulocyte-macrophage colony-stimulating factor (GM-CSF), characterized by unique signaling of cytokines and growth factors important for stromal, epithelial, and myeloid cell fates...
September 28, 2018: Cell
Toomas Mets, Sergo Kasvandik, Merilin Saarma, Ülo Maiväli, Tanel Tenson, Niilo Kaldalu
MazEF and MqsRA are toxin-antitoxin systems, where the toxins MazF and MqsR sequence-specifically cleave single-stranded RNA, thereby shutting down protein synthesis and cell growth. However, it has been proposed that MazF functions in a highly specific pathway, where it truncates the 5' ends of a set of E. coli transcripts (the MazF regulon), which are then translated under stress conditions by specialized ribosomes. We mapped the cleavage sites of MazF and MqsR throughout the E. coli transcriptome. Our results show that both toxins cleave mRNA independently of the recognition site position and MazF freely cleaves transcripts of the proposed MazF regulon within coding sequences...
October 10, 2018: Biochimie
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