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single cell RNAseq

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https://www.readbyqxmd.com/read/29101321/contribution-of-epigenetic-landscapes-and-transcription-factors-to-x-chromosome-reactivation-in-the-inner-cell-mass
#1
Maud Borensztein, Ikuhiro Okamoto, Laurène Syx, Guillaume Guilbaud, Christel Picard, Katia Ancelin, Rafael Galupa, Patricia Diabangouaya, Nicolas Servant, Emmanuel Barillot, Azim Surani, Mitinori Saitou, Chong-Jian Chen, Konstantinos Anastassiadis, Edith Heard
X-chromosome inactivation is established during early development. In mice, transcriptional repression of the paternal X-chromosome (Xp) and enrichment in epigenetic marks such as H3K27me3 is achieved by the early blastocyst stage. X-chromosome inactivation is then reversed in the inner cell mass. The mechanisms underlying Xp reactivation remain enigmatic. Using in vivo single-cell approaches (allele-specific RNAseq, nascent RNA-fluorescent in situ hybridization and immunofluorescence), we show here that different genes are reactivated at different stages, with more slowly reactivated genes tending to be enriched in H3meK27...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29080867/-multiomics-study-of-hepg2-cell-line-proteome
#2
E V Poverennaya, O I Kiseleva, E A Ponomarenko, S N Naryzhny, V G Zgoda, A V Lisitsa
Current proteomic studies are generally focused on the most abundant proteoforms encoded by canonical nucleic sequences. Transcriptomic and proteomic data, accumulated in a variety of postgenome sources and coupled with state-of-art analytical technologies, allow to start the identification of aberrant (non-canonical) proteoforms. The main sources of aberrant proteoforms are alternative splicing, single nucleotide polymorphism, and post-translational modifications. The aim of this work was to estimate the heterogeneity of HepG2 proteome...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29055423/going-single-but-not-solo-with-podocytes-potentials-limitations-and-pitfalls-of-single-cell-analysis
#3
Mario Schiffer
Single-cell RNA-sequence (RNA-seq) is a widely used tool to study biological questions in single cells. The discussed study identified 92 genes being predominantly expressed in podocytes based on a 5-fold higher expression compared with endothelial and mesangial cells. In addition to technical pitfalls, the question that is discussed in this commentary is whether results of a single-cell RNAseq study are able to deliver expression data that truly characterize a podocyte.
November 2017: Kidney International
https://www.readbyqxmd.com/read/28957348/-stealth-dissemination-of-macrophage-tumor-cell-fusions-cultured-from-blood-of-patients-with-pancreatic-ductal-adenocarcinoma
#4
Gary A Clawson, Gail L Matters, Ping Xin, Christopher McGovern, Eric Wafula, Claude dePamphilis, Morgan Meckley, Joyce Wong, Luke Stewart, Christopher D'Jamoos, Naomi Altman, Yuka Imamura Kawasawa, Zhen Du, Loren Honaas, Thomas Abraham
Here we describe isolation and characterization of macrophage-tumor cell fusions (MTFs) from the blood of pancreatic ductal adenocarcinoma (PDAC) patients. The MTFs were generally aneuploidy, and immunophenotypic characterizations showed that the MTFs express markers characteristic of PDAC and stem cells, as well as M2-polarized macrophages. Single cell RNASeq analyses showed that the MTFs express many transcripts implicated in cancer progression, LINE1 retrotransposons, and very high levels of several long non-coding transcripts involved in metastasis (such as MALAT1)...
2017: PloS One
https://www.readbyqxmd.com/read/28931675/comparative-transcriptomics-highlights-the-role-of-the-ap1-transcription-factor-in-the-host-response-to-ebolavirus
#5
James W Wynne, Shawn Todd, Victoria Boyd, Mary Tachedjian, Reuben Klein, Brian Shiell, Megan Dearnley, Alexander J McAuley, Amanda P Woon, Anthony W Purcell, Glenn A Marsh, Michelle L Baker
Ebolavirus and Marburgvirus comprise two genera of negative-sense single-stranded RNA viruses that cause severe hemorrhagic fevers in humans. Despite considerable research efforts, the molecular events following Ebola virus (EBOV) infection are poorly understood. With the view of identifying host factors that underpin EBOV pathogenesis, we compared the transcriptomes of EBOV-infected human, pig and bat kidney cells using an RNAseq approach. Despite a significant difference in viral transcription/replication between the cell lines, all cells responded to EBOV infection through a robust induction of extracellular growth factors...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28900252/profiling-of-the-metabolic-transcriptome-via-single-molecule-molecular-inversion-probes
#6
Tessa de Bitter, Carlijn van de Water, Corina van den Heuvel, Carolien Zeelen, Astrid Eijkelenboom, Bastiaan Tops, Egbert Oosterwijk, Dimitar Kolev, Peter Mulders, Mark Ter Laan, Sanne van Lith, William Leenders
Cancer-specific metabolic alterations are of high interest as therapeutic targets. These alterations vary between tumor types, and to employ metabolic targeting to its fullest potential there is a need for robust methods that identify candidate targetable metabolic pathways in individual cancers. Currently, such methods include (13)C-tracing studies and mass spectrometry/ magnetic resonance spectroscopic imaging. Due to high cost and complexity, such studies are restricted to a research setting. We here present the validation of a novel technique of metabolic profiling, based on multiplex targeted next generation sequencing of RNA with single molecule molecular inversion probes (smMIPs), designed to measure activity of and mutations in genes that encode metabolic enzymes...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28727807/digoxin-reveals-a-functional-connection-between-hiv-1-integration-preference-and-t-cell-activation
#7
Alexander Zhyvoloup, Anat Melamed, Ian Anderson, Delphine Planas, Chen-Hsuin Lee, Janos Kriston-Vizi, Robin Ketteler, Andy Merritt, Jean-Pierre Routy, Petronela Ancuta, Charles R M Bangham, Ariberto Fassati
HIV-1 integrates more frequently into transcribed genes, however the biological significance of HIV-1 integration targeting has remained elusive. Using a selective high-throughput chemical screen, we discovered that the cardiac glycoside digoxin inhibits wild-type HIV-1 infection more potently than HIV-1 bearing a single point mutation (N74D) in the capsid protein. We confirmed that digoxin repressed viral gene expression by targeting the cellular Na+/K+ ATPase, but this did not explain its selectivity. Parallel RNAseq and integration mapping in infected cells demonstrated that digoxin inhibited expression of genes involved in T-cell activation and cell metabolism...
July 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28722025/nanopore-long-read-rnaseq-reveals-widespread-transcriptional-variation-among-the-surface-receptors-of-individual-b-cells
#8
Ashley Byrne, Anna E Beaudin, Hugh E Olsen, Miten Jain, Charles Cole, Theron Palmer, Rebecca M DuBois, E Camilla Forsberg, Mark Akeson, Christopher Vollmers
Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level. Short-read RNAseq is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencer is able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification...
July 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28712804/identifying-cell-populations-with-scrnaseq
#9
REVIEW
Tallulah S Andrews, Martin Hemberg
Single-cell RNASeq (scRNASeq) has emerged as a powerful method for quantifying the transcriptome of individual cells. However, the data from scRNASeq experiments is often both noisy and high dimensional, making the computational analysis non-trivial. Here we provide an overview of different experimental protocols and the most popular methods for facilitating the computational analysis. We focus on approaches for identifying biologically important genes, projecting data into lower dimensions and clustering data into putative cell-populations...
July 13, 2017: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/28694034/insertion-and-deletion-derived-tumour-specific-neoantigens-and-the-immunogenic-phenotype-a-pan-cancer-analysis
#10
Samra Turajlic, Kevin Litchfield, Hang Xu, Rachel Rosenthal, Nicholas McGranahan, James L Reading, Yien Ning S Wong, Andrew Rowan, Nnennaya Kanu, Maise Al Bakir, Tim Chambers, Roberto Salgado, Peter Savas, Sherene Loi, Nicolai J Birkbak, Laurent Sansregret, Martin Gore, James Larkin, Sergio A Quezada, Charles Swanton
BACKGROUND: The focus of tumour-specific antigen analyses has been on single nucleotide variants (SNVs), with the contribution of small insertions and deletions (indels) less well characterised. We investigated whether the frameshift nature of indel mutations, which create novel open reading frames and a large quantity of mutagenic peptides highly distinct from self, might contribute to the immunogenic phenotype. METHODS: We analysed whole-exome sequencing data from 5777 solid tumours, spanning 19 cancer types from The Cancer Genome Atlas...
August 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28671900/phenotyping-the-immune-response-to-trauma-a-multiparametric-systems-immunology-approach
#11
Anupamaa Seshadri, Gabriel A Brat, Brian K Yorkgitis, Joshua Keegan, James Dolan, Ali Salim, Reza Askari, James A Lederer
OBJECTIVE: Trauma induces a complex immune response that requires a systems biology research approach. Here, we used a novel technology, mass cytometry by time-of-flight, to comprehensively characterize the multicellular response to trauma. DESIGN: Peripheral blood mononuclear cells samples were stained with a 38-marker immunophenotyping cytometry by time-of-flight panel. Separately, matched peripheral blood mononuclear cells were stimulated in vitro with heat-killed Streptococcus pneumoniae or CD3/CD28 antibodies and stained with a 38-marker cytokine panel...
September 2017: Critical Care Medicine
https://www.readbyqxmd.com/read/28662063/rna-seq-and-cytof-immuno-profiling-of-regenerating-lacrimal-glands-identifies-a-novel-subset-of-cells-expressing-muscle-related-proteins
#12
Dillon Hawley, Jian Ding, Suharika Thotakura, Scott Haskett, Hema Aluri, Claire Kublin, Audrey Michel, Lisa Clapisson, Michael Mingueneau, Driss Zoukhri
The purpose of the present studies was to use CyTOF and RNA-Seq technologies to identify cells and genes involved in lacrimal gland repair that could be targeted to treat diseases of lacrimal gland dysfunction. Lacrimal glands of female BALB/c mice were experimentally injured by intra-glandular injection of interleukin 1 alpha (IL-1α). The lacrimal glands were harvested at various time points following injury (1 to 14 days) and used to either prepare single cell suspensions for CyTOF immuno-phenotyping analyses or to extract RNA for gene expression studies using RNA-Seq...
2017: PloS One
https://www.readbyqxmd.com/read/28652613/flipping-between-polycomb-repressed-and-active-transcriptional-states-introduces-noise-in-gene-expression
#13
Gozde Kar, Jong Kyoung Kim, Aleksandra A Kolodziejczyk, Kedar Nath Natarajan, Elena Torlai Triglia, Borbala Mifsud, Sarah Elderkin, John C Marioni, Ana Pombo, Sarah A Teichmann
Polycomb repressive complexes (PRCs) are important histone modifiers, which silence gene expression; yet, there exists a subset of PRC-bound genes actively transcribed by RNA polymerase II (RNAPII). It is likely that the role of Polycomb repressive complex is to dampen expression of these PRC-active genes. However, it is unclear how this flipping between chromatin states alters the kinetics of transcription. Here, we integrate histone modifications and RNAPII states derived from bulk ChIP-seq data with single-cell RNA-sequencing data...
June 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28582519/x-chromosome-inactivation-in-human-pluripotent-stem-cells-as-a-model-for-human-development-back-to-the-drawing-board
#14
Mieke Geens, Susana M Chuva De Sousa Lopes
BACKGROUND: Human pluripotent stem cells (hPSC), both embryonic and induced (hESC and hiPSC), are regarded as a valuable in vitro model for early human development. In order to fulfil this promise, it is important that these cells mimic as closely as possible the in vivo molecular events, both at the genetic and epigenetic level. One of the most important epigenetic events during early human development is X chromosome inactivation (XCI), the transcriptional silencing of one of the two X chromosomes in female cells...
September 1, 2017: Human Reproduction Update
https://www.readbyqxmd.com/read/28577792/genome-wide-analysis-of-gene-expression-of-ems-induced-short-fiber-mutant-ligon-lintless-y-liy-in-cotton-gossypium-hirsutum-l
#15
Marina Naoumkina, Efrem Bechere, David D Fang, Gregory N Thyssen, Christopher B Florane
In this work we describe a chemically-induced short fiber mutant cotton line, Ligon-lintless-y (liy), which is controlled by a single recessive locus and affects multiple traits, including height of the plant, and length and maturity of fiber. An RNAseq analysis was used to evaluate global transcriptional changes during cotton fiber development at 3, 8 and 16days post anthesis. We found that 613, 2629 and 3397 genes were significantly down-regulated, while 2700, 477 and 3260 were significantly up-regulated in liy at 3, 8 and 16 DPA...
July 2017: Genomics
https://www.readbyqxmd.com/read/28475646/parallel-clickseq-and-nanopore-sequencing-elucidates-the-rapid-evolution-of-defective-interfering-rnas-in-flock-house-virus
#16
Elizabeth Jaworski, Andrew Routh
Defective-Interfering RNAs (DI-RNAs) have long been known to play an important role in virus replication and transmission. DI-RNAs emerge during virus passaging in both cell-culture and their hosts as a result of non-homologous RNA recombination. However, the principles of DI-RNA emergence and their subsequent evolution have remained elusive. Using a combination of long- and short-read Next-Generation Sequencing, we have characterized the formation of DI-RNAs during serial passaging of Flock House virus (FHV) in cell-culture over a period of 30 days in order to elucidate the pathways and potential mechanisms of DI-RNA emergence and evolution...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28438991/differentiation-of-v2a-interneurons-from-human-pluripotent-stem-cells
#17
Jessica C Butts, Dylan A McCreedy, Jorge Alexis Martinez-Vargas, Frederico N Mendoza-Camacho, Tracy A Hookway, Casey A Gifford, Praveen Taneja, Linda Noble-Haeusslein, Todd C McDevitt
The spinal cord consists of multiple neuronal cell types that are critical to motor control and arise from distinct progenitor domains in the developing neural tube. Excitatory V2a interneurons in particular are an integral component of central pattern generators that control respiration and locomotion; however, the lack of a robust source of human V2a interneurons limits the ability to molecularly profile these cells and examine their therapeutic potential to treat spinal cord injury (SCI). Here, we report the directed differentiation of CHX10(+) V2a interneurons from human pluripotent stem cells (hPSCs)...
May 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28430882/inhibition-of-the-cardiac-myocyte-mineralocorticoid-receptor-ameliorates-doxorubicin-induced-cardiotoxicity
#18
Achim Lother, Stella Bergemann, Jessica Kowalski, Michael Huck, Ralf Gilsbach, Christoph Bode, Lutz Hein
Aim: HASH(0x44c4dd0) Anthracyclines such as doxorubicin are widely used in cancer therapy but their use is limited by cardiotoxicity. Up to date there is no established strategy for the prevention of anthracyclin-induced heart failure. In this study, we evaluated the role of the cardiac myocyte mineralocorticoid receptor (MR) during doxorubicin-induced cardiotoxicity. Methods and results: HASH(0x44b44c8) A single high-dose or repetitive low-dose doxorubicin administration lead to markedly reduced left ventricular function in mice...
April 18, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/28400082/immune-dysregulation-in-immunodeficiency-disorders-the-role-of-t-cell-receptor-sequencing
#19
REVIEW
Gabriel K Wong, James M Heather, Sara Barmettler, Mark Cobbold
Immune dysregulation is a prominent feature of primary immunodeficiency disorders, which commonly manifested as autoimmunity, cytopenias and inflammatory bowel disease. In partial T-cell immunodeficiency disorders, it has been proposed that the imbalance between effector and regulatory T-cells drives the breakdown of peripheral tolerance. While there is no robust test for immune dysregulation, the T-cell receptor repertoire is used as a surrogate marker, and has been shown to be perturbed in a number of immunodeficiency disorders featuring immune dysregulation including Omenn's Syndrome, Wiskott-Aldrich Syndrome, and common variable immunodeficiency...
April 8, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28369191/the-rnaseq-er-api-a-gateway-to-systematically-updated-analysis-of-public-rna-seq-data
#20
Robert Petryszak, Nuno A Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y Amy Tang, Alvis Brazma
Motivation: The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer...
July 15, 2017: Bioinformatics
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