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T cell RNaseq

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https://www.readbyqxmd.com/read/29129226/measuring-bovine-%C3%AE-%C3%AE-t-cell-function-at-the-site-of-mycobacterium-bovis-infection
#1
Rachel A Rusk, Mitchell V Palmer, W Ray Waters, Jodi L McGill
Bovine γδ T cells are amongst the first cells to accumulate at the site of Mycobacterium bovis infection; however, their role in the developing lesion remains unclear. We utilized transcriptomics analysis, in situ hybridization, and a macrophage/γδ T cell co-culture system to elucidate the role of γδ T cells in local immunity to M. bovis infection. Transcriptomics analysis revealed that γδ T cells upregulated expression of several novel, immune-associated genes in response to stimulation with M. bovis antigen...
December 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/29065523/the-transcriptomes-of-xiphinema-index-and-longidorus-elongatus-suggest-independent-acquisition-of-some-plant-parasitism-genes-by-horizontal-gene-transfer-in-early-branching-nematodes
#2
Etienne G J Danchin, Laetitia Perfus-Barbeoch, Corinne Rancurel, Peter Thorpe, Martine Da Rocha, Simon Bajew, Roy Neilson, Elena Sokolova Guzeeva, Corinne Da Silva, Julie Guy, Karine Labadie, Daniel Esmenjaud, Johannes Helder, John T Jones, Sebastian Eves-van den Akker
Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus, representative of two genera within the early-branching Clade 2 of the phylum Nematoda...
October 23, 2017: Genes
https://www.readbyqxmd.com/read/29054368/an-intermediate-level-of-cd161-expression-defines-a-novel-activated-inflammatory-and-pathogenic-subset-of-cd8-t-cells-involved-in-multiple-sclerosis
#3
Bryan Nicol, Marion Salou, Isabel Vogel, Alexandra Garcia, Emilie Dugast, Jeremy Morille, Stéphanie Kilens, Eric Charpentier, Audrey Donnart, Steven Nedellec, Marylène Jacq-Foucher, Fabienne Le Frère, Sandrine Wiertlewski, Arnaud Bourreille, Sophie Brouard, Laure Michel, Laurent David, Pierre-Antoine Gourraud, Nicolas Degauque, Arnaud B Nicot, Laureline Berthelot, David-Axel Laplaud
Several lines of evidence support a key role for CD8(+) T cells in central nervous system tissue damage of patients with multiple sclerosis. However, the precise phenotype of the circulating CD8(+) T cells that may be recruited from the peripheral blood to invade the CNS remains largely undefined to date. It has been suggested that IL-17 secreting CD8 (Tc17) T cells may be involved, and in humans these cells are characterized by the expression of CD161. We focused our study on a unique and recently described subset of CD8 T cells characterized by an intermediate expression of CD161 as its role in neuroinflammation has not been investigated to date...
October 17, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/29021401/rnaseq-analysis-of-differentiated-keratinocytes-reveals-a-massive-response-to-late-events-during-human-papillomavirus-type-16-infection-including-loss-of-epithelial-barrier-function
#4
T Klymenko, Q Gu, I Herbert, A Stevenson, V Iliev, G Watkins, C Pollock, R Bhatia, K Cuschieri, P Herzyk, D Gatherer, S V Graham
The human papillomavirus (HPV) replication cycle is tightly linked to epithelial cell differentiation. To examine HPV-associated changes in the keratinocyte transcriptome, RNAs isolated from undifferentiated and differentiated cell populations of normal, spontaneously immortalised, keratinocytes (NIKS), and NIKS stably transfected with HPV16 episomal genomes (NIKS16), were compared using RNASeq. HPV16 infection altered expression of 2862 cellular genes. Next, to elucidate the role of keratinocyte gene expression in late events during the viral life cycle, RNASeq was carried out on triplicate differentiated populations of NIKS (uninfected) and NIKS16 (infected)...
October 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29020037/a-conserved-fungal-glycosyltransferase-facilitates-pathogenesis-of-plants-by-enabling-hyphal-growth-on-solid-surfaces
#5
Robert King, Martin Urban, Rebecca P Lauder, Nichola Hawkins, Matthew Evans, Amy Plummer, Kirstie Halsey, Alison Lovegrove, Kim Hammond-Kosack, Jason J Rudd
Pathogenic fungi must extend filamentous hyphae across solid surfaces to cause diseases of plants. However, the full inventory of genes which support this is incomplete and many may be currently concealed due to their essentiality for the hyphal growth form. During a random T-DNA mutagenesis screen performed on the pleomorphic wheat (Triticum aestivum) pathogen Zymoseptoria tritici, we acquired a mutant unable to extend hyphae specifically when on solid surfaces. In contrast "yeast-like" growth, and all other growth forms, were unaffected...
October 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28972046/inhibiting-pi3k%C3%AE-with-azd8186-regulates-key-metabolic-pathways-in-pten-null-tumours
#6
James Lynch, Urszula M Polanska, Oona Delpuech, Urs Hancox, Antonio Garcia-Trinidad, Filippos Michopoulos, Carol Lenaghan, Robert McEwen, James Bradford, Radoslaw Polanski, Rebecca Ellston, Alvaro Avivar-Valderas, James E Pilling, Anna D Staniszewska, Marie Cumberbatch, Susan E Critchlow, Francisco Cruzalegui, Simon T Barry
PURPOSE: PTEN null tumours become dependent on the PI3Kb isoform and can be targeted by molecules such as the selective PI3Kb inhibitor AZD8186. However beyond the modulation of the canonical PI3K pathway, the consequences of inhibiting PI3Kb are poorly defined. EXPERIMENTAL DESIGN: To determine the broader impact of AZD8186 in PTEN null tumours we performed a genome wide RNAseq analysis of PTEN null triple negative breast tumour xenografts treated with AZD8186...
October 2, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28965926/exposure-to-4100k-fluorescent-light-elicits-sex-specific-transcriptional-responses-in-xiphophorus-maculatus-skin
#7
William T Boswell, Mikki Boswell, Dylan J Walter, Kaela L Navarro, Jordan Chang, Yuan Lu, Markita G Savage, Jianjun Shen, Ronald B Walter
It has been reported that exposure to artificial light may affect oxygen intake, heart rate, absorption of vitamins and minerals, and behavioral responses in humans. We have reported specific gene expression responses in the skin of Xiphophorus fish after exposure to ultraviolet light (UV), as well as, both broad spectrum and narrow waveband visible light. In regard to fluorescent light (FL), we have shown that male X. maculatus exposed to 4100K FL (i.e. "cool white") rapidly suppress transcription of many genes involved with DNA replication and repair, chromosomal segregation, and cell cycle progression in skin...
September 29, 2017: Comparative Biochemistry and Physiology. Toxicology & Pharmacology: CBP
https://www.readbyqxmd.com/read/28928284/functional-and-evolutionary-insights-from-the-ciona-notochord-transcriptome
#8
Wendy M Reeves, Yuye Wu, Matthew J Harder, Michael T Veeman
The notochord of the ascidian Ciona consists of only 40 cells, and is a longstanding model for studying organogenesis in a small, simple embryo. Here, we perform RNAseq on flow-sorted notochord cells from multiple stages to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression and extensively validate the results by in situ hybridization. These genes are highly enriched for Gene Ontology terms related to the extracellular matrix, cell adhesion and cytoskeleton...
September 15, 2017: Development
https://www.readbyqxmd.com/read/28922848/aggressive-behavior-in-silent-subtype-iii-pituitary-adenomas-may-depend-on-suppression-of-local-immune-response-a-whole-transcriptome-analysis
#9
Timothy E Richardson, Zhong-Jian Shen, Mohammed Kanchwala, Chao Xing, Alexander Filatenkov, Ping Shang, Samuel Barnett, Zahidur Abedin, James S Malter, Jack M Raisanen, Dennis K Burns, Charles L White, Kimmo J Hatanpaa
Silent subtype III pituitary adenomas (SS-3) are clinically nonfunctional adenomas that are more aggressive in terms of invasion and risk of recurrence than their conventional null cell counterparts. We previously showed that these tumors can be distinguished by immunohistochemistry based on the identification of a markedly enlarged and fragmented Golgi apparatus. To understand the molecular correlates of differential aggressiveness, we performed whole transcriptome sequencing (RNAseq) on 4 SS-3 and 4 conventional null cell adenomas...
October 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28851949/hypertension-susceptibility-loci-are-associated-with-anthracycline-related-cardiotoxicity-in-long-term-childhood-cancer-survivors
#10
Michelle A T Hildebrandt, Monica Reyes, Xifeng Wu, Xia Pu, Kara A Thompson, Jianzhong Ma, Andrew P Landstrom, Alanna C Morrison, Joann L Ater
Anthracycline-based chemotherapy is associated with dose-dependent, irreversible damage to the heart. Childhood cancer survivors with hypertension after anthracycline exposure are at increased risk of cardiotoxicity, leading to the hypothesis that genetic susceptibility loci for hypertension may serve as predictors for development of late cardiotoxicity. Therefore, we determined the association between 12 GWAS-identified hypertension-susceptibility loci and cardiotoxicity in a cohort of long-term childhood cancer survivors (N = 108) who received anthracyclines and were screened for cardiac function via echocardiograms...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28805806/lung-tumor-exome-files-with-t-cell-receptor-recombinations-a-mouse-model-of-t-cell-infiltrates-reflecting-mutation-burdens
#11
Yaping N Tu, Wei Lue Tong, Timothy J Fawcett, George Blanck
Tumor exomes and RNASeq data were originally intended for obtaining tumor mutations and gene expression profiles, respectively. However, recent work has determined that tumor exome and RNAseq read files contain reads representing T-cell and B-cell receptor (TcR and BcR) recombinations, presumably due to infiltrating lymphocytes. Furthermore, the recovery of immune receptor recombination reads has demonstrated correlations with specific, previously appreciated aspects of tumor immunology. To further understand the usefulness of recovering TcR and BcR recombinations from tumor exome files, we developed a scripted algorithm for recovery of reads representing these recombinations from a previously described mouse model of lung tumorigenesis...
August 14, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28775251/niche-specific-gene-expression-in-a-parasitic-nematode-increased-expression-of-immunomodulators-in-teladorsagia-circumcincta-larvae-derived-from-host-mucosa
#12
Tom N McNeilly, David Frew, Stewart T G Burgess, Harry Wright, David J Bartley, Yvonne Bartley, Alasdair J Nisbet
Metazoan parasites have to survive in many different niches in order to complete their life-cycles. In the absence of reliable methods to manipulate parasite genomes and/or proteomes, identification of the molecules critical for parasite survival within these niches has largely depended on comparative transcriptomic and proteomic analyses of different developmental stages of the parasite; however, changes may reflect differences associated with transition between developmental stages rather than specific adaptations to a particular niche...
August 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28727807/digoxin-reveals-a-functional-connection-between-hiv-1-integration-preference-and-t-cell-activation
#13
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/28711779/hyperactive-foxo1-results-in-lack-of-tip-stalk-identity-and-deficient-microvascular-regeneration-during-kidney-injury
#14
Lan T H Dang, Takahide Aburatani, Graham A Marsh, Bryce G Johnson, Stella Alimperti, Christine J Yoon, Angela Huang, Suzanne Szak, Naoki Nakagawa, Ivan Gomez, Shuyu Ren, Sarah K Read, Chris Sparages, Alfred C Aplin, Roberto F Nicosia, Chris Chen, Giovanni Ligresti, Jeremy S Duffield
Loss of the microvascular (MV) network results in tissue ischemia, loss of tissue function, and is a hallmark of chronic diseases. The incorporation of a functional vascular network with that of the host remains a challenge to utilizing engineered tissues in clinically relevant therapies. We showed that vascular-bed-specific endothelial cells (ECs) exhibit differing angiogenic capacities, with kidney microvascular endothelial cells (MVECs) being the most deficient, and sought to explore the underlying mechanism...
October 2017: Biomaterials
https://www.readbyqxmd.com/read/28694034/insertion-and-deletion-derived-tumour-specific-neoantigens-and-the-immunogenic-phenotype-a-pan-cancer-analysis
#15
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/28686611/yorkie-is-required-to-restrict-the-injury-responses-in-planarians
#16
Alexander Y T Lin, Bret J Pearson
Regeneration requires the precise integration of cues that initiate proliferation, direct differentiation, and ultimately re-pattern tissues to the proper size and scale. Yet how these processes are integrated with wounding responses remains relatively unknown. The freshwater planarian, Schmidtea mediterranea, is an ideal model to study the stereotyped proliferative and transcriptional responses to injury due to its high capacity for regeneration. Here, we characterize the effector of the Hippo signalling cascade, yorkie, during planarian regeneration and its role in restricting early injury responses...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28671900/phenotyping-the-immune-response-to-trauma-a-multiparametric-systems-immunology-approach
#17
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/28593993/myc-activation-cooperates-with-vhl-and-ink4a-arf-loss-to-induce-clear-cell-renal-cell-carcinoma
#18
Sean T Bailey, Aleisha M Smith, Jordan Kardos, Sara E Wobker, Harper L Wilson, Bhavani Krishnan, Ryoichi Saito, Hyo Jin Lee, Jing Zhang, Samuel C Eaton, Lindsay A Williams, Ujjawal Manocha, Dorien J Peters, Xinchao Pan, Thomas J Carroll, Dean W Felsher, Vonn Walter, Qing Zhang, Joel S Parker, Jen Jen Yeh, Richard A Moffitt, Janet Y Leung, William Y Kim
Renal carcinoma is a common and aggressive malignancy whose histopathogenesis is incompletely understood and that is largely resistant to cytotoxic chemotherapy. We present two mouse models of kidney cancer that recapitulate the genomic alterations found in human papillary (pRCC) and clear cell RCC (ccRCC), the most common RCC subtypes. MYC activation results in highly penetrant pRCC tumours (MYC), while MYC activation, when combined with Vhl and Cdkn2a (Ink4a/Arf) deletion (VIM), produce kidney tumours that approximate human ccRCC...
June 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28520934/the-smap1-2-proteins-of-the-crenarchaeon-sulfolobus-solfataricus-interact-with-the-exosome-and-stimulate-a-rich-tailing-of-transcripts
#19
Birgit Märtens, Linlin Hou, Fabian Amman, Michael T Wolfinger, Elena Evguenieva-Hackenberg, Udo Bläsi
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated...
July 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28414090/rituximab-treatment-circumvents-the-prognostic-impact-of-tumor-infiltrating-t-cells-in-follicular-lymphoma-patients
#20
RANDOMIZED CONTROLLED TRIAL
Luc Xerri, Sarah Huet, Jeffrey M Venstrom, Edith Szafer-Glusman, Bettina Fabiani, Danielle Canioni, Catherine Chassagne-Clément, Peggy Dartigues-Cuilléres, Fréderic Charlotte, Camille Laurent, Benedicte Gelas-Dore, Christopher R Bolen, Elizabeth Punnoose, Reda Bouabdallah, Pauline Brice, Franck Morschhauser, Guillaume Cartron, Daniel Olive, Gilles Salles
Previous immunohistochemical (IHC) studies showed controversial data about the prognostic value of tumor-infiltrating lymphocytes (TILs) in follicular lymphoma (FL). To clarify this issue, a large series of FL samples from rituximab-treated patients enrolled in the randomized PRIMA trial was examined. IHC was quantified using automated image analysis in 417, 287, 418, 406, 379, and 369 patients for CD3, CD4, CD8, PD1, ICOS, and FOXP3, respectively. RNAseq analysis was used to quantify TIL-related mRNA transcripts from 148 patients...
June 2017: Human Pathology
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