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T cell RNaseq

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
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
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
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
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
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...
August 29, 2016: Oncotarget
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
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...
2016: Genome Medicine
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
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
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
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
Giampaolo Trivellin, Ivana Bjelobaba, Adrian F Daly, Darwin O Larco, Leonor Palmeira, Fabio R Faucz, Albert Thiry, Letícia F Leal, Liliya Rostomyan, Martha Quezado, Marie Helene Schernthaner-Reiter, Marija M Janjic, Chiara Villa, T John Wu, Stanko S Stojilkovic, Albert Beckers, Benjamin Feldman, Constantine A Stratakis
We recently showed that Xq26.3 microduplications cause X-linked acrogigantism (X-LAG). X-LAG patients mainly present with growth hormone and prolactin-secreting adenomas and share a minimal duplicated region containing at least four genes. GPR101 was the only gene highly expressed in their pituitary lesions, but little is known about its expression patterns. In this work, GPR101 transcripts were characterized in human tissues by 5'-Rapid Amplification of cDNA Ends (RACE) and RNAseq, while the putative promoter was bioinformatically predicted...
August 2016: Journal of Molecular Endocrinology
Hristina Nedelkovska, Alexander F Rosenberg, Shannon P Hilchey, Ollivier Hyrien, W Richard Burack, Sally A Quataert, Christina M Baker, Mitra Azadniv, Stephen L Welle, Stephen M Ansell, Minsoo Kim, Steven H Bernstein
We have previously shown that regulatory T cells (Tregs) infiltrating follicular lymphoma lymph nodes are quantitatively and qualitatively different than those infiltrating normal and reactive nodes. To gain insight into how such Treg populations differ, we performed RNA sequence (RNAseq) analyses on flow sorted Tregs from all three sources. We identify several molecules that could contribute to the observed increased suppressive capacity of follicular lymphoma nodal tregs, including upregulation of CTLA-4, IL-10, and GITR, all confirmed by protein expression...
2016: PloS One
Ellen Stelloo, Marco A Versluis, Hans W Nijman, Marco de Bruyn, Annechien Plat, Elisabeth M Osse, Reinhardt H van Dijk, Remi A Nout, Carien L Creutzberg, Geertruida H de Bock, Vincent T Smit, Tjalling Bosse, Harry Hollema
JAK1 frameshift mutations may promote cancer cell immune evasion by impeding upregulation of the antigen presentation pathway in microsatellite unstable endometrial cancers (ECs). This study investigated the JAK1 mutation frequency, its functional implication in immune evasion and its prognostic significance in microsatellite unstable EC. Microsatellite instability and three microsatellite repeats within JAK1 were analyzed in 181 ECs. Sixty-two (34%) ECs showed microsatellite instability, of which 22 (35%) had a JAK1 mutation...
May 17, 2016: Oncotarget
Martha Brown, Pascal Hablützel, Ida M Friberg, Anna G Thomason, Alexander Stewart, Justin A Pachebat, Joseph A Jackson
BACKGROUND: Fishes show seasonal patterns of immunity, but such phenomena are imperfectly understood in vertebrates generally, even in humans and mice. As these seasonal patterns may link to infectious disease risk and individual condition, the nature of their control has real practical implications. Here we characterize seasonal dynamics in the expression of conserved vertebrate immunity genes in a naturally-occurring piscine model, the three-spined stickleback. RESULTS: We made genome-wide measurements (RNAseq) of whole-fish mRNA pools (n = 36) at the end of summer and winter in contrasting habitats (riverine and lacustrine) and focussed on common trends to filter habitat-specific from overarching temporal responses...
2016: BMC Genomics
Valentina Gianfelici, Sabina Chiaretti, Sofie Demeyer, Filomena Di Giacomo, Monica Messina, Roberta La Starza, Nadia Peragine, Francesca Paoloni, Ellen Geerdens, Valentina Pierini, Loredana Elia, Marco Mancini, Maria Stefania De Propris, Valerio Apicella, Gianluca Gaidano, Anna Maria Testi, Antonella Vitale, Marco Vignetti, Cristina Mecucci, Anna Guarini, Jan Cools, Robin Foà
Despite therapeutic improvements, a sizable number of patients with T-cell acute lymphoblastic leukemia still have a poor outcome. To unravel the genomic background associated with refractoriness, we evaluated the transcriptome of 19 cases of refractory/early relapsed T-cell acute lymphoblastic leukemia (discovery cohort) by performing RNA-sequencing on diagnostic material. The incidence and prognostic impact of the most frequently mutated pathways were validated by Sanger sequencing on genomic DNA from diagnostic samples of an independent cohort of 49 cases (validation cohort), including refractory, relapsed and responsive cases...
August 2016: Haematologica
Kilian Schober, Dirk H Busch
No abstract text is available yet for this article.
July 2016: Immunology and Cell Biology
R Szabo, A L Samson, D A Lawrence, R L Medcalf, T H Bugge
UNLABELLED: Essentials C57BL/6J-tissue plasminogen activator (tPA)-deficient mice are widely used to study tPA function. Congenic C57BL/6J-tPA-deficient mice harbor large 129-derived chromosomal segments. The 129-derived chromosomal segments contain gene mutations that may confound data interpretation. Passenger mutation-free isogenic tPA-deficient mice were generated for study of tPA function. SUMMARY: Background The ability to generate defined null mutations in mice revolutionized the analysis of gene function in mammals...
August 2016: Journal of Thrombosis and Haemostasis: JTH
Thomas R Gill, Mohammad D Samy, Shanitra N Butler, James A Mauro, Wade J Sexton, George Blanck
Tumor immunoscoring is rapidly becoming a universal parameter of prognosis, and T-cells isolated from tumor masses are used for ex vivo amplification and readministration to patients to facilitate an antitumor immune response. We recently exploited the cancer genome atlas (TCGA) RNASeq data to assess T-cell receptor (TcR) expression and, in particular, discovered strong correlations between major histocompatibility class II (MHCII) and TcR-α constant region expression levels. In this article, we describe the results of searching TCGA exome files for TcR-α V-regions, followed by searching the V-region datasets for TcR-α-J regions...
2016: Cancer Informatics
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