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https://www.readbyqxmd.com/read/28286708/transcriptomic-analysis-reveals-metabolic-switches-and-surface-remodeling-as-key-processes-for-stage-transition-in-trypanosoma-cruzi
#1
Luisa Berná, Maria Laura Chiribao, Gonzalo Greif, Matias Rodriguez, Fernando Alvarez-Valin, Carlos Robello
American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes...
2017: PeerJ
https://www.readbyqxmd.com/read/28192147/systemic-innate-immune-activation-in-food-protein-induced-enterocolitis-syndrome
#2
Ritobrata Goswami, Ana Belen Blazquez, Roman Kosoy, Adeeb Rahman, Anna Nowak-Węgrzyn, M Cecilia Berin
BACKGROUND: Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated food allergy of infancy whose pathophysiology is poorly understood. OBJECTIVES: We set out to identify and phenotype allergen-responsive cells in peripheral blood of a cohort of subjects undergoing supervised food challenge for FPIES. METHODS: We profiled antigen-responsive cells in PBMCs by flow cytometry, and examined cells in whole blood obtained before and after challenge by CyTOF mass cytometry and RNAseq...
February 10, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28138401/t-cadherin-in-prostate-cancer-relationship-with-cancer-progression-differentiation-and-drug-resistance
#3
Boris Dasen, Tatjana Vlajnic, Chantal Mengus, Christian Ruiz, Lukas Bubendorf, Giulio Spagnoli, Stephen Wyler, Paul Erne, Thérèse J Resink, Maria Philippova
Prostate cancer represents the second leading cause of cancer-related death in men. T-cadherin (CDH13) is an atypical GPI-anchored member of the cadherin family of adhesion molecules. Its gene was reported to be downregulated in a small series of prostate tumours. T-cadherin protein expression/localisation in prostate tissue has never been investigated. The purpose of our study was to analyse CDH13 gene and protein levels in large sets of healthy and cancer prostate tissue specimens and evaluate CDH13 effects on the sensitivity of prostate cancer cells to chemotherapy...
January 2017: Journal of Pathology. Clinical Research
https://www.readbyqxmd.com/read/28068412/a-comparison-of-gene-expression-profiles-between-glucocorticoid-responder-and-non-responder-bovine-trabecular-meshwork-cells-using-rna-sequencing
#4
Jaclyn Y Bermudez, Hannah C Webber, Bartley Brown, Terry A Braun, Abbot F Clark, Weiming Mao
The most common ocular side effect of glucocorticoid (GC) therapy is GC-induced ocular hypertension (OHT) and GC-induced glaucoma (GIG). GC-induced OHT occurs in about 40% of the general population, while the other 60% are resistant. This study aims to determine the genes and pathways involved in differential GC responsiveness in the trabecular meshwork (TM). Using paired bovine eyes, one eye was perfusion-cultured with 100nM dexamethasone (DEX), while the fellow eye was used to establish a bovine TM (BTM) cell strain...
2017: PloS One
https://www.readbyqxmd.com/read/28003262/defining-the-clonality-of-peripheral-t-cell-lymphomas-using-rna-seq
#5
Scott D Brown, Greg Hapgood, Christian Steidl, Andrew P Weng, Kerry J Savage, Robert A Holt
MOTIVATION: In T-cell lymphoma, malignant T cells arising from a founding clone share an identical T cell receptor (TCR) and can be identified by the over-representation of this TCR relative to TCRs from the patient's repertoire of normal T cells. Here, we demonstrate that TCR information extracted from RNA-seq data can provide a higher resolution view of peripheral T cell lymphomas (PTCLs) than that provided by conventional methods. RESULTS: For 60 subjects with PTCL, flow cytometry/FACS was used to identify and sort aberrant T cell populations from diagnostic lymph node cell suspensions...
December 21, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27999734/molecular-and-clinical-characterization-of-pd-l1-expression-at-transcriptional-level-via-976-samples-of-brain-glioma
#6
Zheng Wang, Chuanbao Zhang, Xing Liu, Zhiliang Wang, Lihua Sun, Guanzhang Li, Jingshan Liang, Huimin Hu, Yanwei Liu, Wei Zhang, Tao Jiang
Background: PD-L1 has been widely reported as immune check points in a range of malignancies as well as some immune-originated diseases. In glioma, the role of PD-L1 remains unclear. We aimed at investigating its role at transcriptome level and relationship with clinical practice. Method and patients: In total, 976 glioma samples with transcriptome data, including 301 microarray data from Chinese Glioma Genome Atlas (CGGA project) and 675 RNAseq data from TCGA project, were enrolled into our study. Clinical and IDH mutation data were also available...
2016: Oncoimmunology
https://www.readbyqxmd.com/read/27995306/t-cell-receptor-gene-recombinations-in-human-tumor-specimen-exome-files-detection-of-t-cell-receptor-%C3%AE-vdj-recombinations-associates-with-a-favorable-oncologic-outcome-for-bladder-cancer
#7
Mohammad D Samy, Wei Lue Tong, John M Yavorski, Wade J Sexton, George Blanck
Understanding tumor-resident T cells is important for cancer prognosis and treatment options. Conventional, solid tumor specimen exome files can be searched directly for recombined T cell receptor (TcR)-α segments; RNASeq files can include TcR-β VDJ recombinations. To learn whether there are medically relevant uses of exome-based detection of TcR V(D)J recombinations in the tumor microenvironment, we searched cancer genome atlas and Moffitt Cancer Center, tumor specimen exome files for TcR-β, TcR-γ, and TcR-δ recombinations, for bladder and stomach cancer...
March 2017: Cancer Immunology, Immunotherapy: CII
https://www.readbyqxmd.com/read/27994070/characterization-of-meningeal-type-2-innate-lymphocytes-and-their-response-to-cns-injury
#8
Sachin P Gadani, Igor Smirnov, Ashtyn T Smith, Christopher C Overall, Jonathan Kipnis
The meningeal space is occupied by a diverse repertoire of immune cells. Central nervous system (CNS) injury elicits a rapid immune response that affects neuronal survival and recovery, but the role of meningeal inflammation remains poorly understood. Here, we describe type 2 innate lymphocytes (ILC2s) as a novel cell type resident in the healthy meninges that are activated after CNS injury. ILC2s are present throughout the naive mouse meninges, though are concentrated around the dural sinuses, and have a unique transcriptional profile...
February 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/27836953/correlates-of-tuberculosis-risk-predictive-biomarkers-for-progression-to-active-tuberculosis
#9
REVIEW
Elisa Petruccioli, Thomas J Scriba, Linda Petrone, Mark Hatherill, Daniela M Cirillo, Simone A Joosten, Tom H Ottenhoff, Claudia M Denkinger, Delia Goletti
New approaches to control the spread of tuberculosis (TB) are needed, including tools to predict development of active TB from latent TB infection (LTBI). Recent studies have described potential correlates of risk, in order to inform the development of prognostic tests for TB disease progression. These efforts have included unbiased approaches employing "omics" technologies, as well as more directed, hypothesis-driven approaches assessing a small set or even individual selected markers as candidate correlates of TB risk...
December 2016: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/27789416/compound-heterozygous-variants-in-nbas-as-a-cause-of-atypical-osteogenesis-imperfecta
#10
M Balasubramanian, J Hurst, S Brown, N J Bishop, P Arundel, C DeVile, R C Pollitt, L Crooks, D Longman, J F Caceres, F Shackley, S Connolly, J H Payne, A C Offiah, D Hughes, M J Parker, W Hide, T M Skerry
BACKGROUND: Osteogenesis imperfecta (OI), the commonest inherited bone fragility disorder, affects 1 in 15,000 live births resulting in frequent fractures and reduced mobility, with significant impact on quality of life. Early diagnosis is important, as therapeutic advances can lead to improved clinical outcome and patient benefit. REPORT: Whole exome sequencing in patients with OI identified, in two patients with a multi-system phenotype, compound heterozygous variants in NBAS (neuroblastoma amplified sequence)...
January 2017: Bone
https://www.readbyqxmd.com/read/27713134/a-three-ion-channel-genes-based-signature-predicts-prognosis-of-primary-glioblastoma-patients-and-reveals-a-chemotherapy-sensitive-subtype
#11
Hao-Yuan Wang, Ji-Ye Li, Xiu Liu, Xiao-Yan Yan, Wen Wang, Fan Wu, Ting-Yu Liang, Fan Yang, Hui-Min Hu, Heng-Xu Mao, Yan-Wei Liu, Shi-Zhong Zhang
Increasing evidence suggests that ion channels not only regulate electric signaling in excitable cells but also play important roles in the development of brain tumor. However, the roles of ion channels in glioma remain controversial. In the present study, we systematically analyzed the expression patterns of ion channel genes in a cohort of Chinese patients with glioma using RNAseq expression profiling. First, a molecular signature comprising three ion channel genes (KCNN4, KCNB1 and KCNJ10) was identified using Univariate Cox regression and two-tailed student's t test conducted in overall survival (OS) and gene expression...
October 4, 2016: Oncotarget
https://www.readbyqxmd.com/read/27638840/clinical-response-of-a-patient-to-anti-pd-1-immunotherapy-and-the-immune-landscape-of-testicular-germ-cell-tumors
#12
Shalin Shah, James E Ward, Riyue Bao, Curtis R Hall, Bruce E Brockstein, Jason J Luke
Anti-Programed Death 1 (PD-1) is standard immunotherapy for multiple cancers, and the expression of one of its ligands, PD-L1, has been described in germ cell tumors (GCT). Neither the clinical activity of anti-PD-1 nor the incidence of an immunoresponsive tumor microenvironment has been described for GCTs. A patient initially diagnosed with melanoma via fine needle aspiration was treated with one dose of antibody to PD-1. A core needle biopsy was subsequently performed to acquire sufficient tissue for molecular analysis, which led to a change in diagnosis to metastatic embryonal carcinoma...
November 2016: Cancer Immunology Research
https://www.readbyqxmd.com/read/27617643/zeb1-induces-epb41l5-in-the-cancer-mesenchymal-program-that-drives-arf6-based-invasion-metastasis-and-drug-resistance
#13
A Hashimoto, S Hashimoto, H Sugino, A Yoshikawa, Y Onodera, H Handa, T Oikawa, H Sabe
Onset of the cancer mesenchymal program is closely associated with cancer malignancy and drug resistance. Among the different epithelial-mesenchymal transition (EMT)-associated transcriptional factors, ZEB1 has a key role in inducing the mesenchymal phenotypes and stem cell-like properties of different breast cancer cells. ARF6 and its effector AMAP1 are frequently overexpressed in breast cancer cells, and promote invasion, metastasis and drug resistance. EPB41L5 is induced during EMT, and mediates the disruption of E-cadherin-based cell-cell adhesion and the promotion of focal adhesion dynamics...
2016: Oncogenesis
https://www.readbyqxmd.com/read/27589570/prognostic-value-of-pdl1-expression-in-pancreatic-cancer
#14
David J Birnbaum, Pascal Finetti, Alexia Lopresti, Marine Gilabert, Flora Poizat, Olivier Turrini, Jean-Luc Raoul, Jean-Robert Delpero, Vincent Moutardier, Daniel Birnbaum, Emilie Mamessier, François Bertucci
Pancreatic cancer is one of the most aggressive human cancers. PD1/PDL1-inhibitors recently showed promising results in different cancers with correlation between PDL1 tumor expression and responses. Expression of programmed cell death receptor ligand 1 (PDL1) has been scarcely studied in pancreatic cancer. In this retrospective study, we analyzed PDL1 mRNA expression in 453 clinical pancreatic cancer samples profiled using DNA microarrays and RNASeq. Compared to normal pancreatic samples, PDL1 expression was upregulated in 19% of cancer samples...
November 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27526110/systemic-chromosome-instability-in-shugoshin-1-mice-resulted-in-compromised-glutathione-pathway-activation-of-wnt-signaling-and-defects-in-immune-system-in-the-lung
#15
H Y Yamada, G Kumar, Y Zhang, E Rubin, S Lightfoot, W Dai, C V Rao
Mitotic error-mediated chromosome instability (CIN) can lead to aneuploidy, chromothripsis, DNA damage and/or whole chromosome gain/loss. CIN may prompt rapid accumulation of mutations and genomic alterations. Thus, CIN can promote carcinogenesis. This CIN process results from a mutation in certain genes or environmental challenge such as smoking, and is highly prevalent in various cancers, including lung cancer. A better understanding of the effects of CIN on carcinogenesis will lead to novel methods for cancer prevention and treatment...
August 15, 2016: Oncogenesis
https://www.readbyqxmd.com/read/27460926/single-cell-tcrseq-paired-recovery-of-entire-t-cell-alpha-and-beta-chain-transcripts-in-t-cell-receptors-from-single-cell-rnaseq
#16
David Redmond, Asaf Poran, Olivier Elemento
Accurate characterization of the repertoire of the T-cell receptor (TCR) alpha and beta chains is critical to understanding adaptive immunity. Such characterization has many applications across such fields as vaccine development and response, clone-tracking in cancer, and immunotherapy. Here we present a new methodology called single-cell TCRseq (scTCRseq) for the identification and assembly of full-length rearranged V(D)J T-cell receptor sequences from paired-end single-cell RNA sequencing reads. The method allows accurate identification of the V(D)J rearrangements for each individual T-cell and has the novel ability to recover paired alpha and beta segments...
July 27, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27438473/flow-based-sorting-of-neonatal-lymphocyte-populations-for-transcriptomics-analysis
#17
Ravi S Misra, Soumyaroop Bhattacharya, Heidie L Huyck, Jyh-Chiang E Wang, Christopher G Slaunwhite, Sharleen L Slaunwhite, Terry R Wightman, Shelley Secor-Socha, Sara K Misra, Timothy P Bushnell, Ann-Marie Reynolds, Rita M Ryan, Sally A Quataert, Gloria S Pryhuber, Thomas J Mariani
RATIONALE: Emerging data suggest an important role for T lymphocytes in the pathogenesis of chronic lung disease in preterm infants. Comprehensive assessment of the lymphocyte transcriptome may identify biomarkers and mechanisms of disease. METHODS: Small volume peripheral blood samples were collected from premature infants enrolled with consent in the Prematurity and Respiratory Outcomes Program (PROP), at the time of discharge from the hospital. Blood samples were collected at two sites and shipped to a central laboratory for processing...
October 2016: Journal of Immunological Methods
https://www.readbyqxmd.com/read/27428423/glycosylation-is-an-androgen-regulated-process-essential-for-prostate-cancer-cell-viability
#18
Jennifer Munkley, Daniel Vodak, Karen E Livermore, Katherine James, Brian T Wilson, Bridget Knight, Paul Mccullagh, John Mcgrath, Malcolm Crundwell, Lorna W Harries, Hing Y Leung, Craig N Robson, Ian G Mills, Prabhakar Rajan, David J Elliott
Steroid androgen hormones play a key role in the progression and treatment of prostate cancer, with androgen deprivation therapy being the first-line treatment used to control cancer growth. Here we apply a novel search strategy to identify androgen-regulated cellular pathways that may be clinically important in prostate cancer. Using RNASeq data, we searched for genes that showed reciprocal changes in expression in response to acute androgen stimulation in culture, and androgen deprivation in patients with prostate cancer...
June 2016: EBioMedicine
https://www.readbyqxmd.com/read/27424527/systematic-analysis-of-an-evolved-thermobifida-fusca-muc-producing-malic-acid-on-organic-and-inorganic-nitrogen-sources
#19
Yu Deng, Jia Lin, Yin Mao, Xiaojuan Zhang
Thermobifida fusca is a thermophilic actinobacterium. T. fusca muC obtained by adaptive evolution preferred yeast extract to ammonium sulfate for accumulating malic acid and ammonium sulfate for cell growth. We did transcriptome analysis of T. fusca muC on Avicel and cellobiose with addition of ammonium sulfate or yeast extract, respectively by RNAseq. The transcriptional results indicate that ammonium sulfate induced the transcriptions of the genes related to carbohydrate metabolisms significantly more than yeast extract...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27385777/lineage-specific-effector-signatures-of-invariant-nkt-cells-are-shared-amongst-%C3%AE-%C3%AE-t-innate-lymphoid-and-th-cells
#20
You Jeong Lee, Gabriel J Starrett, Seungeun Thera Lee, Rendong Yang, Christine M Henzler, Stephen C Jameson, Kristin A Hogquist
Invariant NKT cells differentiate into three predominant effector lineages in the steady state. To understand these lineages, we sorted undifferentiated invariant NK T progenitor cells and each effector population and analyzed their transcriptional profiles by RNAseq. Bioinformatic comparisons were made to effector subsets among other lymphocytes, specifically Th cells, innate lymphoid cells (ILC), and γδ T cells. Myc-associated signature genes were enriched in NKT progenitors, like in other hematopoietic progenitors...
August 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
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