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https://www.readbyqxmd.com/read/28489605/genetic-rearrangements-result-in-altered-gene-expression-and-novel-fusion-transcripts-in-s%C3%A3-zary-syndrome
#1
Katarzyna Iżykowska, Grzegorz K Przybylski, Claudia Gand, Floriane C Braun, Piotr Grabarczyk, Andreas W Kuss, Karolina Olek-Hrab, Armando N Bastidas Torres, Maarten H Vermeer, Willem H Zoutman, Cornelis P Tensen, Christian A Schmidt
Sézary syndrome (SS) is an aggressive, leukemic cutaneous T-cell lymphoma variant. Molecular pathogenesis of SS is still unclear despite many studies on genetic alterations, gene expression and epigenetic regulations. Through whole genome and transcriptome next generation sequencing nine Sézary syndrome patients were analyzed in terms of copy number variations and rearrangements affecting gene expression. Recurrent copy number variations were detected within 8q (MYC, TOX), 17p (TP53, NCOR1), 10q (PTEN, FAS), 2p (DNMT3A), 11q (USP28), 9p (CAAP1), but no recurrent rearrangements were identified...
April 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28448599/simulation-of-the-dynamics-of-primary-immunodeficiencies-in-cd4-t-cells
#2
Gabriel N Teku, Mauno Vihinen
Primary immunodeficiencies (PIDs) form a large and heterogeneous group of mainly rare disorders that affect the immune system. T-cell deficiencies account for about one-tenth of PIDs, most of them being monogenic. Apart from genetic and clinical information, lots of other data are available for PID proteins and genes, including functions and interactions. Thus, it is possible to perform systems biology studies on the effects of PIDs on T-cell physiology and response. To achieve this, we reconstructed a T-cell network model based on literature mining and TPPIN, a previously published core T-cell network, and performed semi-quantitative dynamic network simulations on both normal and T-cell PID failure modes...
2017: PloS One
https://www.readbyqxmd.com/read/28405513/tumor-sqstm1-p62-expression-and-t-cells-in-colorectal-cancer
#3
Keisuke Kosumi, Yohei Masugi, Juhong Yang, Zhi Rong Qian, Sun A Kim, Wanwan Li, Yan Shi, Annacarolina da Silva, Tsuyoshi Hamada, Li Liu, Mancang Gu, Tyler S Twombly, Yin Cao, David A Barbie, Katsuhiko Nosho, Hideo Baba, Wendy S Garrett, Jeffery A Meyerhardt, Edward L Giovannucci, Andrew T Chan, Charles S Fuchs, Shuji Ogino, Reiko Nishihara
Evidence suggests that activation of autophagy in neoplastic cells potentiates antitumor immunity through cross-presentation of tumor-associated antigens to T cells and release of immune mediators. The SQSTM1 (sequestosome 1, p62) protein is degraded by activated autophagy, and might enhance immune response to tumor cells. We hypothesized that tumor SQSTM1 expression level might be inversely associated with T-cell densities in colorectal carcinoma tissue. We evaluated tumor SQSTM1 expression by immunohistochemistry in 601 rectal and colon cancer cases within the Nurses' Health Study and Health Professionals Follow-up Study...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28356067/probiotic-bacteria-prevent-salmonella-induced-suppression-of-lymphoproliferation-in-mice-by-an-immunomodulatory-mechanism
#4
R Doug Wagner, Shemedia J Johnson
BACKGROUND: Salmonella enterica infections often exhibit a form of immune evasion. We previously observed that probiotic bacteria could prevent inhibition of lymphoproliferation and apoptosis responses of T cells associated with S. enterica infections in orally challenged mice. RESULTS: In this study, changes in expression of genes related to lymphocyte activation in mucosa-associated lymphoid tissues (MALT) of mice orally infected with S. enterica with and without treatment with probiotic bacteria were evaluated...
March 29, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28334849/icf-specific-dnmt3b-dysfunction-interferes-with-intragenic-regulation-of-mrna-transcription-and-alternative-splicing
#5
Sole Gatto, Miriam Gagliardi, Monica Franzese, Sylwia Leppert, Mariarosaria Papa, Marco Cammisa, Giacomo Grillo, Guillame Velasco, Claire Francastel, Shir Toubiana, Maurizio D'Esposito, Claudia Angelini, Maria R Matarazzo
Hypomorphic mutations in DNA-methyltransferase DNMT3B cause majority of the rare disorder Immunodeficiency, Centromere instability and Facial anomalies syndrome cases (ICF1). By unspecified mechanisms, mutant-DNMT3B interferes with lymphoid-specific pathways resulting in immune response defects. Interestingly, recent findings report that DNMT3B shapes intragenic CpG-methylation of highly-transcribed genes. However, how the DNMT3B-dependent epigenetic network modulates transcription and whether ICF1-specific mutations impair this process remains unknown...
March 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28129010/single-cell-rna-sequencing-highlights-transcription-activity-of-autophagy-related-genes-during-hematopoietic-stem-cell-formation-in-mouse-embryos
#6
Yongfei Hu, Yan Huang, Ying Yi, Hongwei Wang, Bing Liu, Jia Yu, Dong Wang
Accumulating evidence has demonstrated that macroautophagy/autophagy plays an essential role in self-renewal and differentiation in embryonic hematopoiesis. Here, according to the RNA sequencing data sets of 5 population cells related to hematopoietic stem cell (HSC) formation during mouse embryogenesis (endothelial cells, PTPRC/CD45(-) and PTPRC/CD45(+) pre-HSCs in the E11 aorta-gonad-mesonephros (AGM) region, mature HSCs in E12 and E14 fetal liver), we explored the dynamic expression of mouse autophagy-related genes in this course at the single-cell level...
April 3, 2017: Autophagy
https://www.readbyqxmd.com/read/28068922/functional-changes-in-mrna-expression-and-alternative-pre-mrna-splicing-associated-with-the-effects-of-nutrition-on-apoptosis-and-spermatogenesis-in-the-adult-testis
#7
Yongjuan Guan, Guanxiang Liang, Graeme B Martin, Le Luo Guan
BACKGROUND: The effects of nutrition on testis mass in the sexually mature male have long been known, however, the cellular and molecular processes of the testis response to nutrition was not fully understood. METHODS: We tested whether the defects in spermatogenesis and increases in germ cell apoptosis in the testis that are induced by under-nutrition are associated with changes in mRNA expression and pre-mRNA alternative splicing using groups of 8 male sheep fed for a 10% increase or 10% decrease in body mass over 65 days...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/27829444/potential-molecular-characteristics-in-situ-in-response-to-repetitive-uvb-irradiation
#8
Wenqi Chen, Jinhai Zhang
BACKGROUND: To identify molecular characteristics in situ in response to repetitive UVB (ultraviolet-B) irradiation. METHODS: Microarray data from the Gene Expression Omnibus were re-analyzed to identify DEGs (differentially expressed genes) between UVB-irradiated and non-irradiated skin biopsies. Enrichment and annotation analyses were performed respectively using DAVID, and TSGene and TAG databases. PPIs (protein-protein interactions) were analyzed using STRING, and miRNAs (microRNAs) and TFs (transcription factors) were predicted separately by miRNA-related databases and ENCODE...
November 10, 2016: Diagnostic Pathology
https://www.readbyqxmd.com/read/27761697/differential-expression-analysis-of-the-broiler-tracheal-proteins-responsible-for-the-immune-response-and-muscle-contraction-induced-by-high-concentration-of-ammonia-using-itraq-coupled-2d-lc-ms-ms
#9
Yan Xiong, Xiangfang Tang, Qingshi Meng, Hongfu Zhang
Ammonia has been considered the contaminant primarily responsible for respiratory disease in poultry. Even though it can cause tracheal lesions, its adverse effects on the trachea have not been sufficiently studied. The present study investigated tracheal changes in Arbor Acres broilers (Gallus gallus) induced by high concentration of ammonia using isobaric tag for relative and absolute quantification (iTRAQ)-based proteome analysis. In total, 3,706 proteins within false discovery rate of 1% were identified, including 119 significantly differentially expressed proteins...
November 2016: Science China. Life Sciences
https://www.readbyqxmd.com/read/27737877/microrna-let-7-t-cells-and-patient-survival-in-colorectal-cancer
#10
Ruoxu Dou, Reiko Nishihara, Yin Cao, Tsuyoshi Hamada, Kosuke Mima, Atsuhiro Masuda, Yohei Masugi, Yan Shi, Mancang Gu, Wanwan Li, Annacarolina da Silva, Katsuhiko Nosho, Xuehong Zhang, Jeffrey A Meyerhardt, Edward L Giovannucci, Andrew T Chan, Charles S Fuchs, Zhi Rong Qian, Shuji Ogino
Experimental evidence suggests that the let-7 family of noncoding RNAs suppresses adaptive immune responses, contributing to immune evasion by the tumor. We hypothesized that the amount of let-7a and let-7b expression in colorectal carcinoma might be associated with limited T-lymphocyte infiltrates in the tumor microenvironment and worse clinical outcome. Utilizing the molecular pathological epidemiology resources of 795 rectal and colon cancers in two U.S.-nationwide prospective cohort studies, we measured tumor-associated let-7a and let-7b expression levels by quantitative reverse-transcription PCR, and CD3(+), CD8(+), CD45RO (PTPRC)(+), and FOXP3(+) cell densities by tumor tissue microarray immunohistochemistry and computer-assisted image analysis...
November 2016: Cancer Immunology Research
https://www.readbyqxmd.com/read/27630154/accession-of-tumor-heterogeneity-by-multiplex-transcriptome-profiling-of-single-circulating-tumor-cells
#11
Tobias M Gorges, Andra Kuske, Katharina Röck, Oliver Mauermann, Volkmar Müller, Sven Peine, Karl Verpoort, Vendula Novosadova, Mikael Kubista, Sabine Riethdorf, Klaus Pantel
BACKGROUND: Transcriptome analysis of circulating tumor cells (CTCs) holds great promise to unravel the biology of cancer cell dissemination and identify expressed genes and signaling pathways relevant to therapeutic interventions. METHODS: CTCs were enriched based on their EpCAM expression (CellSearch(®)) or by size and deformability (Parsortix(TM)), identified by EpCAM and/or pan-keratin-specific antibodies, and isolated for single cell multiplex RNA profiling...
November 2016: Clinical Chemistry
https://www.readbyqxmd.com/read/27622043/il12-mediated-sensitizing-of-t-cell-receptor-dependent-and-independent-tumor-cell-killing
#12
Matthias Braun, Marie L Ress, Young-Eun Yoo, Claus J Scholz, Matthias Eyrich, Paul G Schlegel, Matthias Wölfl
Interleukin 12 (IL12) is a key inflammatory cytokine critically influencing Th1/Tc1-T-cell responses at the time of initial antigen encounter. Therefore, it may be exploited for cancer immunotherapy. Here, we investigated how IL12, and other inflammatory cytokines, shape effector functions of human T-cells. Using a defined culture system, we followed the gradual differentiation and function of antigen-specific CD8(+) T cells from their initial activation as naïve T cells through their expansion phase as early memory cells to full differentiation as clonally expanded effector T cells...
July 2016: Oncoimmunology
https://www.readbyqxmd.com/read/27527602/aid-apobec-network-reconstruction-identifies-pathways-associated-with-survival-in-ovarian-cancer
#13
Martin Svoboda, Anastasia Meshcheryakova, Georg Heinze, Markus Jaritz, Dietmar Pils, Dan Cacsire Castillo-Tong, Gudrun Hager, Theresia Thalhammer, Erika Jensen-Jarolim, Peter Birner, Ioana Braicu, Jalid Sehouli, Sandrina Lambrechts, Ignace Vergote, Sven Mahner, Philip Zimmermann, Robert Zeillinger, Diana Mechtcheriakova
BACKGROUND: Building up of pathway-/disease-relevant signatures provides a persuasive tool for understanding the functional relevance of gene alterations and gene network associations in multifactorial human diseases. Ovarian cancer is a highly complex heterogeneous malignancy in respect of tumor anatomy, tumor microenvironment including pro-/antitumor immunity and inflammation; still, it is generally treated as single disease. Thus, further approaches to investigate novel aspects of ovarian cancer pathogenesis aiming to provide a personalized strategy to clinical decision making are of high priority...
August 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27475305/regular-aspirin-use-associates-with-lower-risk-of-colorectal%C3%A2-cancers-with-low-numbers-of-tumor-infiltrating-lymphocytes
#14
Yin Cao, Reiko Nishihara, Zhi Rong Qian, Mingyang Song, Kosuke Mima, Kentaro Inamura, Jonathan A Nowak, David A Drew, Paul Lochhead, Katsuhiko Nosho, Teppei Morikawa, Xuehong Zhang, Kana Wu, Molin Wang, Wendy S Garrett, Edward L Giovannucci, Charles S Fuchs, Andrew T Chan, Shuji Ogino
BACKGROUND & AIMS: Aspirin use reduces colorectal cancer risk. Aspirin, a nonsteroidal anti-inflammatory drug, inhibits prostaglandin-endoperoxide synthase 2 (PTGS2 or cyclooxygenase-2); PTGS2 promotes inflammation and suppresses T-cell-mediated adaptive immunity. We investigated whether the inverse association of aspirin use with colorectal carcinoma risk was stronger for tumors with lower degrees of lymphocytic infiltrates than for tumors with higher degrees of lymphocytic infiltrates...
November 2016: Gastroenterology
https://www.readbyqxmd.com/read/27386825/identification-of-a-reference-gene-for-the-quantification-of-mrna-and-mirna-expression-during-skin-wound-healing
#15
Julia Etich, Vera Bergmeier, Lena Pitzler, Bent Brachvogel
AIM: Wound healing is a coordinated process to restore tissue homeostasis and reestablish the protective barrier of the skin. miRNAs may modulate the expression of target genes to contribute to repair processes, but due to the complexity of the tissue it is challenging to quantify gene expression during the distinct phases of wound repair. Here, we aimed to identify a common reference gene to quantify changes in miRNA and mRNA expression during skin wound healing. METHODS: Quantitative real-time PCR and bioinformatic analysis tools were used to identify suitable reference genes during skin repair and their reliability was tested by studying the expression of mRNAs and miRNAs...
March 2017: Connective Tissue Research
https://www.readbyqxmd.com/read/27223437/establishment-of-a-multimarker-qpcr-panel-for-the-molecular-characterization-of-circulating-tumor-cells-in-blood-samples-of-metastatic-breast-cancer-patients-during-the-course-of-palliative-treatment
#16
Maren Bredemeier, Philippos Edimiris, Mitra Tewes, Pawel Mach, Bahriye Aktas, Doreen Schellbach, Jenny Wagner, Rainer Kimmig, Sabine Kasimir-Bauer
BACKGROUND: Circulating tumor cells (CTC) are discussed to be an ideal surrogate marker for individualized treatment in metastatic breast cancer (MBC) since metastatic tissue is often difficult to obtain for repeated analysis. We established a nine gene qPCR panel to characterize the heterogeneous CTC population in MBC patients including epithelial CTC, their receptors (EPCAM, ERBB2, ERBB3, EGFR) CTC in Epithelial-Mesenchymal-Transition [(EMT); PIK3CA, AKT2), stem cell-like CTC (ALDH1) as well as resistant CTC (ERCC1, AURKA] to identify individual therapeutic targets...
July 5, 2016: Oncotarget
https://www.readbyqxmd.com/read/27222482/screening-and-functional-analysis-of-differentially-expressed-genes-in-chronic-glomerulonephritis-by-whole-genome-microarray
#17
Jia-Rong Gao, Xiu-Juan Qin, Hui Jiang, Ting Wang, Jun-Mei Song, Shuang-Zhi Xu
BACKGROUND: Chronic glomerulonephritis (CGN) is the most common form of the glomerular disease with unclear molecular mechanisms, which related to immune-mediated inflammatory diseases. The aim of this study was to characterize differentially expressed genes in the normal and adriamycin-induced CGN rats by microarray analysis, and to determine the potential molecular mechanisms of CGN pathogenesis. METHODS: For the gene expression analysis, fresh glomerular tissues from both normal and adriamycin treated rats (n=4, respectively) were collected...
September 1, 2016: Gene
https://www.readbyqxmd.com/read/27196573/tumour-cd274-pd-l1-expression-and-t-cells-in-colorectal-cancer
#18
Yohei Masugi, Reiko Nishihara, Juhong Yang, Kosuke Mima, Annacarolina da Silva, Yan Shi, Kentaro Inamura, Yin Cao, Mingyang Song, Jonathan A Nowak, Xiaoyun Liao, Katsuhiko Nosho, Andrew T Chan, Marios Giannakis, Adam J Bass, F Stephen Hodi, Gordon J Freeman, Scott Rodig, Charles S Fuchs, Zhi Rong Qian, Shuji Ogino
OBJECTIVE: Evidence suggests that CD274 (programmed death-ligand 1, B7-H1) immune checkpoint ligand repress antitumour immunity through its interaction with the PDCD1 (programmed cell death 1, PD-1) receptor of T lymphocytes in various tumours. We hypothesised that tumour CD274 expression levels might be inversely associated with T-cell densities in colorectal carcinoma tissue. DESIGN: We evaluated tumour CD274 expression by immunohistochemistry in 823 rectal and colon cancer cases within the Nurses' Health Study and Health Professionals Follow-up Study...
May 5, 2016: Gut
https://www.readbyqxmd.com/read/27185283/single-targeted-exon-mutation-creates-a-true-congenic-mouse-for-competitive-hematopoietic-stem-cell-transplantation-the-c57bl-6-cd45-1-stem-mouse
#19
Francois E Mercier, David B Sykes, David T Scadden
Defining the molecular regulators of hematopoietic stem and progenitor cells (HSPCs) requires in vivo functional analyses. Competitive bone marrow transplants (BMTs) compare control and test HSPCs to demonstrate the functional role of a genetic change or chemical perturbation. Competitive BMT is enabled by antibodies that specifically recognize hematopoietic cells from congenic mouse strains due to variants of the cell surface protein CD45, designated CD45.1 and CD45.2. The current congenic competitor strain, B6...
June 14, 2016: Stem Cell Reports
https://www.readbyqxmd.com/read/27148825/marine-%C3%AF-3-polyunsaturated-fatty-acid-intake-and-risk-of-colorectal-cancer-characterized-by-tumor-infiltrating-t-cells
#20
Mingyang Song, Reiko Nishihara, Yin Cao, Eunyoung Chun, Zhi Rong Qian, Kosuke Mima, Kentaro Inamura, Yohei Masugi, Jonathan A Nowak, Katsuhiko Nosho, Kana Wu, Molin Wang, Edward Giovannucci, Wendy S Garrett, Charles S Fuchs, Shuji Ogino, Andrew T Chan
IMPORTANCE: Marine ω-3 polyunsaturated fatty acids (PUFAs), including eicosapentaenoic acid, docosahexaenoic acid, and docosapentaenoic acid, possess potent immunomodulatory activity and may protect against cancer development. However, evidence relating marine ω-3 PUFAs to colorectal cancer (CRC) risk remains inconclusive. OBJECTIVE: To test the hypothesis that marine ω-3 PUFA intake may be associated with lower risk of CRC subsets characterized by immune infiltrate...
September 1, 2016: JAMA Oncology
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