keyword
MENU ▼
Read by QxMD icon Read
search

T cell RNaseq

keyword
https://www.readbyqxmd.com/read/29767749/association-of-brca2-k3326-with-small-cell-lung-cancer-and-squamous-cell-cancer-of-the-skin
#1
Thorunn Rafnar, Gudbjorg R Sigurjonsdottir, Simon N Stacey, Gisli Halldorsson, Patrick Sulem, Luba M Pardo, Hannes Helgason, Stefan T Sigurdsson, Thorkell Gudjonsson, Laufey Tryggvadottir, Gudridur H Olafsdottir, Jon G Jonasson, Kristin Alexiusdottir, Asgeir Sigurdsson, Julius Gudmundsson, Jona Saemundsdottir, Jon K Sigurdsson, Hrefna Johannsdottir, Andre Uitterlinden, Sita H Vermeulen, Tessel E Galesloot, Dawn C Allain, Martin Lacko, Bardur Sigurgeirsson, Kristin Thorisdottir, Oskar T Johannsson, Fridbjorn Sigurdsson, Gunnar B Ragnarsson, Helgi Isaksson, Hronn Hardardottir, Tomas Gudbjartsson, Daniel F Gudbjartsson, Gisli Masson, Lambertus A M L Kiemeney, Amanda Ewart Toland, Tamar Nijsten, Wilbert H M Peters, Jon H Olafsson, Steinn Jonsson, Unnur Thorsteinsdottir, Gudmar Thorleifsson, Kari Stefansson
Background: Most pathogenic mutations in the BRCA2 gene carry a high risk of hereditary breast and ovarian cancer (HBOC). However, a stop-gain mutation, K3326* (rs11571833), confers risk of lung cancer and cancers of the upper-aero-digestive tract but only a modest risk of breast or ovarian cancer. The Icelandic population provides an opportunity for comprehensive characterization of the cancer risk profiles of K3326* and HBOC mutations because a single mutation, BRCA2 999del5, is responsible for almost all BRCA2-related HBOC in the population...
May 14, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29759078/transcriptome-analysis-of-alcohol-treated-microglia-reveals-downregulation-of-beta-amyloid-phagocytosis
#2
Sergey Kalinin, Marta González-Prieto, Hannah Scheiblich, Lucia Lisi, Handojo Kusumo, Michael T Heneka, Jose L M Madrigal, Subhash C Pandey, Douglas L Feinstein
BACKGROUND: Microglial activation contributes to the neuropathology associated with chronic alcohol exposure and withdrawal, including the expression of inflammatory and anti-inflammatory genes. In the current study, we examined the transcriptome of primary rat microglial cells following incubation with alcohol alone, or alcohol together with a robust inflammatory stimulus. METHODS: Primary microglia were prepared from mixed rat glial cultures. Cells were incubated with 75 mM ethanol alone or with proinflammatory cytokines ("TII": IL1β, IFNγ, and TNFα)...
May 14, 2018: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/29703133/cross-site-comparison-of-ribosomal-depletion-kits-for-illumina-rnaseq-library-construction
#3
Zachary T Herbert, Jamie P Kershner, Vincent L Butty, Jyothi Thimmapuram, Sulbha Choudhari, Yuriy O Alekseyev, Jun Fan, Jessica W Podnar, Edward Wilcox, Jenny Gipson, Allison Gillaspy, Kristen Jepsen, Sandra Splinter BonDurant, Krystalynne Morris, Maura Berkeley, Ashley LeClerc, Stephen D Simpson, Gary Sommerville, Leslie Grimmett, Marie Adams, Stuart S Levine
BACKGROUND: Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs...
March 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29695691/-identification-of-fusion-transcripts-in-leuk%C3%B0%C2%B5mic-cells-by-whole-transcriptome-sequencing
#4
A Yu Ikonnikova, Yu I Ammour, A V Snezhkina, G S Krasnov, A V Kudryavtseva, T V Nasedkina
Genetic aberrations in leukemia often lead to the formation of expressed chimeric genes, which should be assessed for proper diagnosis and therapy. Modern methods of molecular diagnostic mainly allow to identify already known fusion genes. RNAseq is an efficient tool for identification of rare and novel chimeric transcripts. Here we present the results of the whole transcriptome analysis of bone marrow samples from five patients with acute myeloblastic leukemia and one, with myelodysplastic syndrome. The whole-transcriptome analysis was performed using Illumina/Solexa approach...
March 2018: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/29682616/human-ccl3l1-copy-number-variation-gene-expression-and-the-role-of-the-ccl3l1-ccr5-axis-in-lung-function
#5
Adeolu B Adewoye, Nick Shrine, Linda Odenthal-Hesse, Samantha Welsh, Anders Malarstig, Scott Jelinsky, Iain Kilty, Martin D Tobin, Edward J Hollox, Louise V Wain
Background: The CCL3L1-CCR5 signaling axis is important in a number of inflammatory responses, including macrophage function, and T-cell-dependent immune responses. Small molecule CCR5 antagonists exist, including the approved antiretroviral drug maraviroc, and therapeutic monoclonal antibodies are in development. Repositioning of drugs and targets into new disease areas can accelerate the availability of new therapies and substantially reduce costs. As it has been shown that drug targets with genetic evidence supporting their involvement in the disease are more likely to be successful in clinical development, using genetic association studies to identify new target repurposing opportunities could be fruitful...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29579191/glycosyltransferase-genes-that-cause-monogenic-congenital-disorders-of-glycosylation-are-distinct-from-glycosyltransferase-genes-associated-with-complex-diseases
#6
Hiren J Joshi, Lars Hansen, Yoshiki Narimatsu, Hudson H Freeze, Bernard Henrissat, Eric Bennett, Hans H Wandall, Henrik Clausen, Katrine T Schjoldager
Glycosylation of proteins, lipids and proteoglycans in human cells involves at least 167 identified glycosyltransferases (GTfs), and these orchestrate the biosynthesis of diverse types of glycoconjugates and glycan structures. Mutations in this part of the genome-the GTf-genome-cause more than 58 rare, monogenic congenital disorders of glycosylation (CDGs). They are also statistically associated with a large number of complex phenotypes, diseases or predispositions to complex diseases based on Genome-Wide Association Studies (GWAS)...
March 22, 2018: Glycobiology
https://www.readbyqxmd.com/read/29570727/mir-126-5p-by-direct-targeting-of-jnk-interacting-protein-2-jip-2-plays-a-key-role-in-theileria-infected-macrophage-virulence
#7
Malak Haidar, Zineb Rchiad, Hifzur Rahman Ansari, Fathia Ben-Rached, Shahin Tajeri, Perle Latre De Late, Gordon Langsley, Arnab Pain
Theileria annulata is an apicomplexan parasite that infects and transforms bovine macrophages that disseminate throughout the animal causing a leukaemia-like disease called tropical theileriosis. Using deep RNAseq of T. annulata-infected B cells and macrophages we identify a set of microRNAs induced by infection, whose expression diminishes upon loss of the hyper-disseminating phenotype of virulent transformed macrophages. We describe how infection-induced upregulation of miR-126-5p ablates JIP-2 expression to release cytosolic JNK to translocate to the nucleus and trans-activate AP-1-driven transcription of mmp9 to promote tumour dissemination...
March 23, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29558679/regulation-of-ceacam1-protein-expression-by-the-transcription-factor-ets-1-in-braf-mutant-human-metastatic-melanoma-cells
#8
Karin Kfir-Elirachman, Rona Ortenberg, Bella Vizel, Michal J Besser, Iris Barshack, Jacob Schachter, Yael Nemlich, Gal Markel
BRAF becomes constitutively activated in 50% to 70% of melanoma cases. CEACAM1 has a dual role in melanoma, including facilitation of cell proliferation and suppression of infiltrating lymphocytes, which are consistent with its value as a marker for poor prognosis in melanoma patients. Here we show that BRAFV600E melanoma cells treated with BRAF and MEK inhibitors (MAPKi) downregulate CEACAM1 mRNA and protein expression in a dose- and exposure time-dependent manners. Indeed, there is a significant correlation between the presence of BRAFV600E and CEACAM1 expression in melanoma specimens obtained from 45 patients...
March 17, 2018: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/29529099/gene-expression-profiling-in-a-mouse-model-of-retinal-vein-occlusion-induced-by-laser-treatment-reveals-a-predominant-inflammatory-and-tissue-damage-response
#9
Gottfried Martin, David Conrad, Bertan Cakir, Günther Schlunck, Hansjürgen T Agostini
PURPOSE: Retinal vein occlusion (RVO) has been investigated in several laser-induced animal models using pigs, rabbits and rats. However, laser-induced RVO has been rarely reported in mice, despite the impressive number of available mutants, ease of handling and cost effectiveness. The aim of this study was to further assess the feasibility of a RVO mouse model for gene expression analysis and its possible use to investigate effects of hypoxia. METHODS: C57Bl/6J mice were injected with eosin Y for photo-sensitization...
2018: PloS One
https://www.readbyqxmd.com/read/29491349/the-circadian-regulator-bmal1-programmes-responses-to-parasitic-worm-infection-via-a-dendritic-cell-clock
#10
Thomas W Hopwood, Sarah Hall, Nicola Begley, Ruth Forman, Sheila Brown, Ryan Vonslow, Ben Saer, Matthew C Little, Emma A Murphy, Rebecca J Hurst, David W Ray, Andrew S MacDonald, Andy Brass, David A Bechtold, Julie E Gibbs, Andrew S Loudon, Kathryn J Else
Resistance to the intestinal parasitic helminth Trichuris muris requires T-helper 2 (TH 2) cellular and associated IgG1 responses, with expulsion typically taking up to 4 weeks in mice. Here, we show that the time-of-day of the initial infection affects efficiency of worm expulsion, with strong TH 2 bias and early expulsion in morning-infected mice. Conversely, mice infected at the start of the night show delayed resistance to infection, and this is associated with feeding-driven metabolic cues, such that feeding restriction to the day-time in normally nocturnal-feeding mice disrupts parasitic expulsion kinetics...
February 28, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29483513/clonally-diverse-cd38-hla-dr-cd8-t-cells-persist-during-fatal-h7n9-disease
#11
Zhongfang Wang, Lingyan Zhu, Thi H O Nguyen, Yanmin Wan, Sneha Sant, Sergio M Quiñones-Parra, Jeremy Chase Crawford, Auda A Eltahla, Simone Rizzetto, Rowena A Bull, Chenli Qiu, Marios Koutsakos, E Bridie Clemens, Liyen Loh, Tianyue Chen, Lu Liu, Pengxing Cao, Yanqin Ren, Lukasz Kedzierski, Tom Kotsimbos, James M McCaw, Nicole L La Gruta, Stephen J Turner, Allen C Cheng, Fabio Luciani, Xiaoyan Zhang, Peter C Doherty, Paul G Thomas, Jianqing Xu, Katherine Kedzierska
Severe influenza A virus (IAV) infection is associated with immune dysfunction. Here, we show circulating CD8+ T-cell profiles from patients hospitalized with avian H7N9, seasonal IAV, and influenza vaccinees. Patient survival reflects an early, transient prevalence of highly activated CD38+ HLA-DR+ PD-1+ CD8+ T cells, whereas the prolonged persistence of this set is found in ultimately fatal cases. Single-cell T cell receptor (TCR)-αβ analyses of activated CD38+ HLA-DR+ CD8+ T cells show similar TCRαβ diversity but differential clonal expansion kinetics in surviving and fatal H7N9 patients...
February 26, 2018: Nature Communications
https://www.readbyqxmd.com/read/29444188/switching-and-loss-of-cellular-cytokine-producing-capacity-characterize-in-vivo-viral-infection-and-malignant-transformation-in-human-t-lymphotropic-virus-type-1-infection
#12
Huseini Kagdi, Maria Antonietta Demontis, Juan Carlos Ramos, Graham P Taylor
Adult T-cell leukaemia/lymphoma (ATL) arises from chronic non-malignant human T lymphotropic virus type-1 (HTLV-1) infection which is characterized by high plasma pro-inflammatory cytokines whereas ATL is characterized by high plasma anti-inflammatory (IL-10) concentrations. The poor prognosis of ATL is partly ascribed to disease-associated immune suppression. ATL cells have a CD4+CCR4+CD26-CD7- immunophenotype but infected cells with this immunophenotype ('ATL-like' cells) are also present in non-malignant HTLV-1 infection...
February 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29428306/cumulus-cell-transcriptome-profiling-is-not-predictive-of-live-birth-after-in-vitro-fertilization-a-paired-analysis-of-euploid-sibling-blastocysts
#13
Katherine A Green, Jason M Franasiak, Marie D Werner, Xin Tao, Jessica N Landis, Richard T Scott, Nathan R Treff
OBJECTIVE: To compare the transcriptome of cumulus cells associated with a euploid embryo that resulted in live birth with that of a sibling euploid embryo without sustained implantation. DESIGN: Paired analysis. SETTING: Academic institution. PATIENT(S): Couples undergoing in vitro fertilization (IVF)/intracytoplasmic sperm injection with preimplantation genetic screening with female age ≤42 years and normal ovarian reserve...
March 2018: Fertility and Sterility
https://www.readbyqxmd.com/read/29408715/single-cell-profiling-of-peanut-responsive-t-cells-in-patients-with-peanut-allergy-reveals-heterogeneous-effector-t-h-2-subsets
#14
David Chiang, Xintong Chen, Stacie M Jones, Robert A Wood, Scott H Sicherer, A Wesley Burks, Donald Y M Leung, Charuta Agashe, Alexander Grishin, Peter Dawson, Wendy F Davidson, Leah Newman, Robert Sebra, Miriam Merad, Hugh A Sampson, Bojan Losic, M Cecilia Berin
BACKGROUND: The contribution of phenotypic variation of peanut-specific T cells to clinical allergy or tolerance to peanut is not well understood. OBJECTIVES: Our objective was to comprehensively phenotype peanut-specific T cells in the peripheral blood of subjects with and without peanut allergy (PA). METHODS: We obtained samples from patients with PA, including a cohort undergoing baseline peanut challenges for an immunotherapy trial (Consortium of Food Allergy Research [CoFAR] 6)...
January 31, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29399967/exosomes-derived-from-b16f0-melanoma-cells-alter-the-transcriptome-of-cytotoxic-t-cells-that-impacts-mitochondrial-respiration
#15
EDITORIAL
Cassidy L Bland, Christina N Byrne-Hoffman, Audry Fernandez, Stephanie L Rellick, Wentao Deng, David J Klinke
While recent clinical studies demonstrate the promise of cancer immunotherapy, a barrier for broadening the clinical benefit is identifying how tumors locally suppress cytotoxic immunity. As an emerging mode of intercellular communication, exosomes secreted by malignant cells can deliver a complex payload of coding and noncoding RNA to cells within the tumor microenvironment. Here, we quantified the RNA payload within tumor-derived exosomes and the resulting dynamic transcriptomic response to cytotoxic T cells upon exosome delivery to better understand how tumor-derived exosomes can alter immune cell function...
March 2018: FEBS Journal
https://www.readbyqxmd.com/read/29361059/tcr-%C3%AE-recombinations-in-renal-cell-carcinoma-exome-files-correlate-with-an-intermediate-level-of-t-cell-exhaustion-biomarkers
#16
Anne T Mai, Wei Lue Tong, Yaping N Tu, George Blanck
Renal cell carcinoma exome-derived, V(D)J recombination reads had an elevated presence and variability, for both TcR-α and -β, when compared to marginal tissue, reflecting an opportunity to assess tumor immunogenicity by comparison with marginal tissue T cells. PD-1, PD-L2, CTLA4 and FOXP3, all of which are implicated in the evasion of an anti-tumor immune response, had a significantly higher expression for samples representing co-detection of productive TcR-α and -β recombination reads. Samples representing tumors with productive TcR-α recombination reads but no detectable, productive TcR-β recombination reads, reflected a 20% survival advantage, and RNASeq data indicated an intermediate level of immune checkpoint gene expression for those samples...
February 3, 2018: International Immunology
https://www.readbyqxmd.com/read/29282718/multispectral-imaging-for-quantitative-and-compartment-specific-immune-infiltrates-reveals-distinct-immune-profiles-that-classify-lung-cancer-patients
#17
Artur Mezheyeuski, Christian Holst Bergsland, Max Backman, Dijana Djureinovic, Tobias Sjöblom, Jarle Bruun, Patrick Micke
Semiquantitative assessment of immune markers by immunohistochemistry (IHC) has significant limitations for describing the diversity of the immune response in cancer. Therefore, we evaluated a fluorescence-based multiplexed immunohistochemical method in combination with a multispectral imaging system to quantify immune infiltrates in situ in the environment of non-small-cell lung cancer (NSCLC). A tissue microarray including 57 NSCLC cases was stained with antibodies against CD8, CD20, CD4, FOXP3, CD45RO, and pan-cytokeratin, and immune cells were quantified in epithelial and stromal compartments...
April 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29282299/an-anti-gdnf-family-receptor-alpha-1-gfra1-antibody-drug-conjugate-for-the-treatment-of-hormone-receptor-positive-breast-cancer
#18
Sunil Bhakta, Lisa M Crocker, Yvonne Chen, Meredith Hazen, Melissa M Schutten, Dongwei Li, Coenraad Kuijl, Rachana Ohri, Fiona Zhong, Kirsten A Poon, Mary Ann T Go, Eric Cheng, Robert Piskol, Ron Firestein, Aimee Fourie-O'Donohue, Katherine R Kozak, Helga Raab, Jo-Anne Hongo, Deepak Sampath, Mark S Dennis, Richard H Scheller, Paul Polakis, Jagath R Junutula
Luminal A (hormone receptor-positive) breast cancer constitutes 70% of total breast cancer patients. In an attempt to develop a targeted therapeutic for this cancer indication, we have identified and characterized Glial cell line-Derived Neurotrophic Factor (GDNF) Family Receptor Alpha 1 (GFRA1) antibody-drug conjugates (ADC) using a cleavable valine-citrulline-MMAE (vcMMAE) linker-payload. RNAseq and IHC analysis confirmed the abundant expression of GFRA1 in luminal A breast cancer tissues, whereas minimal or no expression was observed in most normal tissues...
December 27, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/29282132/design-and-validation-of-a-disease-network-of-inflammatory-processes-in-the-nsg-uc-mouse-model
#19
Henrika Jodeleit, Pia Palamides, Florian Beigel, Thomas Mueller, Eckhard Wolf, Matthias Siebeck, Roswitha Gropp
BACKGROUND: Ulcerative colitis (UC) is a highly progressive inflammatory disease that requires the interaction of epithelial, immune, endothelial and muscle cells and fibroblasts. Previous studies suggested two inflammatory conditions in UC-patients: 'acute' and 'remodeling' and that the design of a disease network might improve the understanding of the inflammatory processes. The objective of the study was to design and validate a disease network in the NOD-SCID IL2rγnull (NSG)-UC mouse model to get a better understanding of the inflammatory processes...
December 28, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29228356/dietary-intervention-rescues-myopathy-associated-with-neurofibromatosis-type-1
#20
Matthew A Summers, Thusitha Rupasinghe, Emily R Vasiljevski, Frances J Evesson, Kathy Mikulec, Lauren Peacock, Kate G R Quinlan, Sandra T Cooper, Ute Roessner, David A Stevenson, David G Little, Aaron Schindeler
Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disorder with complex symptomology. In addition to a predisposition to tumors, children with NF1 can present with reduced muscle mass, global muscle weakness, and impaired motor skills, which can have a significant impact on quality of life. Genetic mouse models have shown a lipid storage disease phenotype may underlie muscle weakness in NF1. Herein we confirm that biopsy specimens from six individuals with NF1 similarly manifest features of a lipid storage myopathy, with marked accumulation of intramyocellular lipid, fibrosis, and mononuclear cell infiltrates...
February 15, 2018: Human Molecular Genetics
keyword
keyword
63177
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"