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Amit Golding, Samuel Darko, William H Wylie, Daniel C Douek, Ethan M Shevach
Maintenance of peripheral tolerance requires a balance between auto-reactive conventional T cells (Tconv) and thymically-derived Foxp3(+) regulatory T cells (tTregs). Considerable controversy exists regarding the similarities/differences in TCR repertoires expressed by Tconv and tTregs. We generated highly purified populations of human adult and cord blood Tconv and tTregs based on the differential expression of CD25 and CD127. The purity of the sorted populations was validated by intracellular staining for Foxp3 and Helios...
November 23, 2016: Clinical and Experimental Immunology
N V Kirbaeva, N E Sharanova, V M Zhminchenko, I Yu Toropygin, E V Koplik, S S Pertsov, A V Vasil'ev
Differences in the proteomic profiles of the brain amygdala in rats with different prognostic resistance to stress were found on the model of metabolic stress. Differential expression of tropomodulin-2, GTP-binding protein SAR1, peroxiredoxin-2, calcineurin B homologous protein 1, Ras-related protein Rab-14, glutathione S-transferase omega-1, Tcrb protein, and NADH dehydrogenase [ubiquinone] iron-sulfur protein 8 (mitochondrial) was shown to depend on the behavioral pattern of animals and stage of the study...
August 2016: Bulletin of Experimental Biology and Medicine
Yangbo Yue, Stanley G Leung, Yueyong Liu, Yurong Huang, Kirsten Grundt, Anne-Carine Østvold, Kuang-Yu Jen, David Schild, Jian-Hua Mao, Claudia Wiese
NUCKS1 is a 27 kD vertebrate-specific protein, with a role in the DNA damage response. Here, we show that after 4 Gy total-body X-irradiation, Trp53+/- Nucks1+/- mice more rapidly developed tumors, particularly thymic lymphoma (TL), than Trp53+/- mice. TLs in both cohorts showed loss of heterozygosity (LOH) of the Trp53+ allele in essentially all cases. In contrast, LOH of the Nucks1+ allele was rare. Nucks1 expression correlated well with Nucks1 gene dosage in normal thymi, but was increased in the majority of TLs from Trp53+/- Nucks1+/- mice, suggesting that elevated Nucks1 message may be associated with progression towards malignancy in vivo...
September 20, 2016: Oncotarget
B Rojo-Bezares, J M Azcona-Gutiérrez, C Martin, M S Jareño, C Torres, Y Sáenz
We investigated the antibiotic and heavy-metal resistance mechanisms, virulence genes and clonal relationships of macrolide- and/or lincosamide-resistant (M+/-LR) Streptococcus agalactiae (group B Streptococcus, GBS) isolates from pregnant women in La Rioja in Northern Spain, a region with a significant immigrant population. In total 375 GBS isolates were recovered during 2011. About three-quarters of isolates were from European nationals and the remainder distributed among 23 other nationalities. Seventy-five (20%) were classified as M+/-LR strains and 28 (37%) of these were resistant to ⩾3 classes of antibiotics...
November 2016: Epidemiology and Infection
Ruth A Ettinger, Pedro Paz, Eddie A James, Devi Gunasekera, Fred Aswad, Arthur R Thompson, Dana C Matthews, Kathleen P Pratt
Factor VIII (FVIII) neutralizing antibodies ("inhibitors") are a serious problem in hemophilia A (HA). The aim of this study was to characterize HLA-restricted T-cell responses from a severe HA subject with a persistent inhibitor and from two previously studied mild HA inhibitor subjects. MHCII tetramers corresponding to both of the severe HA subject's HLA-DRA-DRB1 alleles were loaded with peptides spanning FVIII-A2, C1 and C2 domains. Interestingly, only one epitope was identified, in peptide FVIII2194-2213, and it was identical to the HLA-DRA*01-DRB1*01:01-restricted epitope recognized by the mild HA subjects...
July 28, 2016: Blood
Katsumi Nakanishi, Yoji Kukita, Hidenobu Segawa, Norimitsu Inoue, Masayuki Ohue, Kikuya Kato
Tumor-infiltrating lymphocytes (TILs) are direct effectors of tumor immunity, and their characterization is important for further development of immunotherapy. Recent advances in high-throughput sequencing technologies have enabled a comprehensive analysis of T-cell receptor (TCR) complementarity-determining region 3 (CDR3) sequences, which may provide information of therapeutic importance. We developed a high-fidelity target sequencing method with the ability for absolute quantitation, and performed large-scale sequencing of TCR beta chain (TCRB) CDR3 regions in TILs and peripheral blood lymphocytes (PBLs)...
September 2016: Cancer Medicine
Eric Levy, Rachel Marty, Valentina Gárate Calderón, Brian Woo, Michelle Dow, Ricardo Armisen, Hannah Carter, Olivier Harismendy
Tumor infiltrating lymphocytes (TILs) have been associated with favorable prognosis in multiple tumor types. The Cancer Genome Atlas (TCGA) represents the largest collection of cancer molecular data, but lacks detailed information about the immune environment. Here, we show that exome reads mapping to the complementarity-determining-region 3 (CDR3) of mature T-cell receptor beta (TCRB) can be used as an immune DNA (iDNA) signature. Specifically, we propose a method to identify CDR3 reads in a breast tumor exome and validate it using deep TCRB sequencing...
2016: Scientific Reports
Tingting Jiang, Ramya Raviram, Valentina Snetkova, Pedro P Rocha, Charlotte Proudhon, Sana Badri, Richard Bonneau, Jane A Skok, Yuval Kluger
Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these...
October 14, 2016: Nucleic Acids Research
Yulema Valero, Elham Awad, Francesco Buonocore, Marta Arizcun, M Ángeles Esteban, José Meseguer, Elena Chaves-Pozo, Alberto Cuesta
Vaccines for fish need to be improved for the aquaculture sector, with DNA vaccines and the oral administration route providing the most promising improvements. In this study, we have created an oral chitosan-encapsulated DNA vaccine (CP-pNNV) for the nodavirus (NNV) in order to protect the very susceptible European sea bass (Dicentrarchus labrax). Our data show that the oral CP-pNNV vaccine failed to induce serum circulating or neutralizing specific antibodies (immunoglobulin M) or to up-regulate their gene expression in the posterior gut...
December 2016: Developmental and Comparative Immunology
Anna Pasetto, Alena Gros, Paul F Robbins, Drew C Deniger, Todd D Prickett, Rodrigo Matus-Nicodemos, Daniel C Douek, Bryan Howie, Harlan Robins, Maria R Parkhurst, Jared Gartner, Katarzyna Trebska-McGowan, Jessica S Crystal, Steven A Rosenberg
Adoptive transfer of T cells with engineered T-cell receptor (TCR) genes that target tumor-specific antigens can mediate cancer regression. Accumulating evidence suggests that the clinical success of many immunotherapies is mediated by T cells targeting mutated neoantigens unique to the patient. We hypothesized that the most frequent TCR clonotypes infiltrating the tumor were reactive against tumor antigens. To test this hypothesis, we developed a multistep strategy that involved TCRB deep sequencing of the CD8(+)PD-1(+) T-cell subset, matching of TCRA-TCRB pairs by pairSEQ and single-cell RT-PCR, followed by testing of the TCRs for tumor-antigen specificity...
September 2, 2016: Cancer Immunology Research
Charlotte Proudhon, Valentina Snetkova, Ramya Raviram, Camille Lobry, Sana Badri, Tingting Jiang, Bingtao Hao, Thomas Trimarchi, Yuval Kluger, Iannis Aifantis, Richard Bonneau, Jane A Skok
V(D)J recombination relies on the presence of proximal enhancers that activate the antigen receptor (AgR) loci in a lineage- and stage-specific manner. Unexpectedly, we find that both active and inactive AgR enhancers cooperate to disseminate their effects in a localized and long-range manner. Here, we demonstrate the importance of short-range contacts between active enhancers that constitute an Igk super-enhancer in B cells. Deletion of one element reduces the interaction frequency between other enhancers in the hub, which compromises the transcriptional output of each component...
June 7, 2016: Cell Reports
Garima Singhal, Ffolliott Martin Fisher, Melissa J Chee, Tze Guan Tan, Abdelfattah El Ouaamari, Andrew C Adams, Robert Najarian, Rohit N Kulkarni, Christophe Benoist, Jeffrey S Flier, Eleftheria Maratos-Flier
Fibroblast growth factor 21 (FGF21) is an important endocrine metabolic regulator expressed in multiple tissues including liver and adipose tissue. Although highest levels of expression are in pancreas, little is known about the function of FGF21 in this tissue. In order to understand the physiology of FGF21 in the pancreas, we analyzed its expression and regulation in both acinar and islet tissues. We found that acinar tissue express 20-fold higher levels than that observed in islets. We also observed that pancreatic FGF21 is nutritionally regulated; a marked reduction in FGF21 expression was noted with fasting while obesity is associated with 3-4 fold higher expression...
2016: PloS One
S Ju Smirnova, Ju V Sidorova, N V Tsvetaeva, O F Nikulina, B V Biderman, E E Nikulina, S M Kulikov, A B Sudarikov
Autoimmune hemolytic anemia (AIHA) is a rare blood disease associated with the production of auto-antibodies and autoimmune hemolysis. A critical role of B-cells in the development of AIHA has been demonstrated before. Here, we present the analysis of the clonal T-cell populations in patients with AIHA. Thirty-three patients with AIHA were included in this study. Thirteen patients with other anemias, 14 patients with other autoimmune conditions (SLE - 6, RA - 8) and 20 healthy donors were included in the study as a control group...
2016: Autoimmunity
Lichen Jing, Kerry J Laing, Lichun Dong, Ronnie M Russell, Russell S Barlow, Juergen G Haas, Meena S Ramchandani, Christine Johnston, Soren Buus, Alec J Redwood, Katie D White, Simon A Mallal, Elizabeth J Phillips, Christine M Posavad, Anna Wald, David M Koelle
The Alphaherpesvirinae subfamily includes HSV types 1 and 2 and the sequence-divergent pathogen varicella zoster virus (VZV). T cells, controlled by TCR and HLA molecules that tolerate limited epitope amino acid variation, might cross-react between these microbes. We show that memory PBMC expansion with either HSV or VZV enriches for CD4 T cell lines that recognize the other agent at the whole-virus, protein, and peptide levels, consistent with bidirectional cross-reactivity. HSV-specific CD4 T cells recovered from HSV-seronegative persons can be explained, in part, by such VZV cross-reactivity...
March 1, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
Yu V Sidorova, N G Chernova, N V Ryzhikova, S Yu Smirnova, M N Sinicina, Yu E Vinogradova, H L Julhakyan, A M Kovrigina, E E Zvonkov, A B Sudarikov
AIM: To assess the feasibility and informative value of T-cell clonality testing in peripheral T-cell lymphoma (PTCL). PATIENTS AND METHODS: Biopsies of involved sites, blood, and bone marrow samples from 30 PTCL patients are included in the study. Rearranged TCRG and TCRB gene fragments were PCR-amplified according to the BIOMED-2 protocol and analyzed by capillary electrophoresis on ABI PRISM 3130 (Applied Biosystems). RESULTS: TCRG and TCRB gene clonality assay was valuable in confirming diagnosis in 97% of PTCL patients...
July 2015: Acta Naturae
Mi Young Ahn, Min-Ji Kim, Ryun Hee Kwon, Jae Sam Hwang, Kun-Koo Park
BACKGROUND: Molecular genetic mechanisms underlying the anti-inflammatory effects of ethanol extract (GB) from G. bimaculatus, a type of cricket, are not fully elucidated. G. bimaculatus was reported to be rich in unsaturated fatty acid and to decrease the omega-6/omega-3 fatty acid ratio when fed to chickens. GB may reduce the amount of fat or increase the unsaturated fatty acid ratio. METHODS: Male Wistar rats fed a high-fat diet (HFD) were orally administered with 5 groups: phosphate buffered saline (PBS, control), GB (100 mg/kg or 200 mg/kg), Pravastatin or Isaria sinclairii (IS) extract, which is reported to have fat-reducing effects, for either 1 or 2 months...
2015: Lipids in Health and Disease
Manami Miyai, Shingo Eikawa, Akihiro Hosoi, Tamaki Iino, Hirokazu Matsushita, Midori Isobe, Akiko Uenaka, Heiichiro Udono, Jun Nakajima, Eiichi Nakayama, Kazuhiro Kakimi
Comprehensive immunological evaluation is crucial for monitoring patients undergoing antigen-specific cancer immunotherapy. The identification and quantification of T cell responses is most important for the further development of such therapies. Using well-characterized clinical samples from a high responder patient (TK-f01) in an NY-ESO-1f peptide vaccine study, we performed high-throughput T cell receptor β-chain (TCRB) gene next generation sequencing (NGS) to monitor the frequency of NY-ESO-1-specific CD8+ T cells...
2015: PloS One
Bryan Howie, Anna M Sherwood, Ashley D Berkebile, Jan Berka, Ryan O Emerson, David W Williamson, Ilan Kirsch, Marissa Vignali, Mark J Rieder, Christopher S Carlson, Harlan S Robins
The T cell receptor (TCR) protein is a heterodimer composed of an α chain and a β chain. TCR genes undergo somatic DNA rearrangements to generate the diversity of T cell binding specificities needed for effective immunity. Recently, high-throughput immunosequencing methods have been developed to profile the TCR α (TCRA) and TCR β (TCRB) repertoires. However, these methods cannot determine which TCRA and TCRB chains combine to form a specific TCR, which is essential for many functional and therapeutic applications...
August 19, 2015: Science Translational Medicine
Raghavendra G Amachawadi, H Morgan Scott, Javier Vinasco, Mike D Tokach, Steve S Dritz, Jim L Nelssen, Tiruvoor G Nagaraja
Heavy metals, such as copper, are increasingly supplemented in swine diets as an alternative to antibiotics to promote growth. Enterococci, a common gut commensal, acquire plasmid-borne, transferable copper resistance (tcrB) gene-mediated resistance to copper. The plasmid also carried resistance genes to tetracyclines and macrolides. The potential genetic link between copper and antibiotic resistance suggests that copper supplementation may exert a selection pressure for antimicrobial resistance. Therefore, a longitudinal study was conducted to investigate the effects of in-feed copper, chlortetracycline, and tylosin alone or in combination on the selection and co-selection of antimicrobial-resistant enterococci...
August 2015: Foodborne Pathogens and Disease
Kinjal Majumder, Levi J Rupp, Katherine S Yang-Iott, Olivia I Koues, Katherine E Kyle, Craig H Bassing, Eugene M Oltz
Considerable cross-talk exists between mechanisms controlling genome architecture and gene expression. AgR loci are excellent models for these processes because they are regulated at both conformational and transcriptional levels to facilitate their assembly by V(D)J recombination. Upon commitment to the double-negative stage of T cell development, Tcrb adopts a compact conformation that promotes long-range recombination between Vβ gene segments (Trbvs) and their DβJβ targets. Formation of a functional VβDβJβ join signals for robust proliferation of double-negative thymocytes and their differentiation into double-positive (DP) cells, where Trbv recombination is squelched (allelic exclusion)...
August 1, 2015: Journal of Immunology: Official Journal of the American Association of Immunologists
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