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Computational strategies for dissecting the high-dimensional complexity
of adaptive immune repertoires [PDF]
, 2017 The adaptive immune system recognizes antigens via an immense array of
antigen-binding antibodies and T-cell receptors, the immune repertoire. The
interrogation of immune repertoires is of high relevance for understanding the
adaptive immune response in disease and infection (e.g., autoimmunity, cancer,
HIV).Afzal, Ahmed, Albert, Amanna, Andrews, Angermueller, Apeltsin, Arden, Atchley, Avnir, Barabási, Barak, Bashford-Rogers, Bastian, Baum, Becattini, Ben-Hamo, Berger, Betz, Boc, Bolen, Bolkhovskaya, Bolotin, Bouckaert, Boyd, Boyd, Breden, Brown, Burnet, Bürckert, Calis, Castro, Chang, Chao, Chen, Ching, Cobey, Collins, Corcoran, Covacu, Csardi, Cui, Dash, de Bourcy, DeKosky, DeKosky, DeWitt, Dziubianau, Elhanati, Elhanati, Elhanati, Ellebedy, Emerson, Felsenstein, Friedensohn, Gadala-Maria, Galson, Galson, Geering, Georgiou, Ghraichy, Giribet, Giudicelli, Glanville, Glanville, Glanville, Good, Granato, Greiff, Greiff, Greiff, Greiff, Greiff, Grigaityte, Guindon, Gupta, Gupta, Hagberg, Halliley, Hammarlund, Heather, Hershberg, Hochreiter, Hoehn, Hoehn, Hoehn, Horns, Howie, Iversen, Jackson, Janeway, Jiang, Johnston, Jost, Jurtz, Kaplinsky, Kaplinsky, Kendall, Khavrutskii, Kidd, Kidd, Kidera, Kirik, Konishi, Kumar, Landsverk, Larkin, Lavinder, Laydon, Laydon, Lee, Lee, Lewitus, Li, Lindeman, Lindner, Liu, Love, Lozupone, Madi, Madi, Malissen, Mamoshina, Mangul, Manz, Martin, Meng, Miho, Mora, Morisita, Murugan, Nazarov, Nouri, Oakes, Ostmeyer, Paradis, Parameswaran, Parola, Pinheiro, Pollok, Ralph, Ravn, Reddy, Rempala, Rempala, Revell, Rizzetto, Robinson, Ronquist, Roybal, Rubelt, Rubelt, Safonova, Schliep, Schramm, Schwab, Shannon, Sheng, Sheng, Shlemov, Shugay, Shugay, Shugay, Snir, Snir, Stamatakis, Stern, Strauli, Stubbington, Stubbington, Sun, Sun Cinelli, Swofford, Thomas, Tickotsky, Tonegawa, Torkamani, Trepel, VanDuijn, Venturi, Venturi, Vieira, Vita, Wang, Wardemann, Warren, Watson, Watson, Watson, Weinstein, Wine, Wine, Wu, Yaari, Yaari, Yang, Yeap, Yermanos, Yokota, Yu, Zhu +200 morearxiv +3 more sourcesRegulatory T cells suppress the formation of potent KLRK1 and IL-7R expressing effector CD8 T cells by limiting IL-2
eLife, 2023 Regulatory T cells (Tregs) are indispensable for maintaining self-tolerance by suppressing conventional T cells. On the other hand, Tregs promote tumor growth by inhibiting anticancer immunity.Oksana Tsyklauri, Tereza Chadimova, Veronika Niederlova, Jirina Kovarova, Juraj Michalik, Iva Malatova, Sarka Janusova, Olha Ivashchenko, Helene Rossez, Ales Drobek, Hana Vecerova, Virginie Galati, Marek Kovar, Ondrej Stepanek +13 moredoaj +1 more sourceSelf-reactivity of CD8 T-cell clones determines their differentiation status rather than their responsiveness in infections
Frontiers in Immunology, 2022 Mature T cells are selected for recognizing self-antigens with low to intermediate affinity in the thymus. Recently, the relative differences in self-reactivity among individual T-cell clones were appreciated as important factors regulating their fate ...Darina Paprckova, Veronika Niederlova, Veronika Niederlova, Alena Moudra, Ales Drobek, Michaela Pribikova, Michaela Pribikova, Sarka Janusova, Kilian Schober, Kilian Schober, Ales Neuwirth, Juraj Michalik, Martina Huranova, Veronika Horkova, Michaela Cesnekova, Michaela Cesnekova, Michaela Simova, Jan Prochazka, Jana Balounova, Dirk H. Busch, Radislav Sedlacek, Martin Schwarzer, Ondrej Stepanek +22 moredoaj +1 more sourcePinpointing the tumor-specific T cells via TCR clusters
eLife, 2022 Adoptive cell transfer (ACT) is a promising approach to cancer immunotherapy, but its efficiency fundamentally depends on the extent of tumor-specific T cell enrichment within the graft. This can be estimated via activation with identifiable neoantigens, Mikhail M Goncharov, Ekaterina A Bryushkova, Nikita I Sharaev, Valeria D Skatova, Anastasiya M Baryshnikova, George V Sharonov, Vadim Karnaukhov, Maria T Vakhitova, Igor V Samoylenko, Lev V Demidov, Sergey Lukyanov, Dmitriy M Chudakov, Ekaterina O Serebrovskaya +12 moredoaj +1 more sourceHuman rhinovirus promotes STING trafficking to replication organelles to promote viral replication
Nature Communications, 2022 Evidence exists that the typically antiviral signaling mediator STING is, counterintuitively, needed for optimal human rhinovirus infection. Here the authors confirm this finding and show how human rhinovirus can reduce stored Ca2+ levels to drive this ...Martha Triantafilou, Joshi Ramanjulu, Lee M. Booty, Gisela Jimenez-Duran, Hakan Keles, Ken Saunders, Neysa Nevins, Emma Koppe, Louise K. Modis, G. Scott Pesiridis, John Bertin, Kathy Triantafilou +11 moredoaj +1 more sourceMeasuring Intratumoral Heterogeneity of Immune Repertoires
Frontiers in Oncology, 2020 There is considerable clinical and fundamental value in measuring the clonal heterogeneity of T and B cell expansions in tumors and tumor-associated lymphoid structures—along with the associated heterogeneity of the tumor neoantigen landscape—but such ...Diana Vladimirovna Yuzhakova, Lilia N. Volchkova, Mikhail Valerievich Pogorelyy, Mikhail Valerievich Pogorelyy, Ekaterina O. Serebrovskaya, Ekaterina O. Serebrovskaya, Irina A. Shagina, Irina A. Shagina, Ekaterina A. Bryushkova, Ekaterina A. Bryushkova, Tatiana O. Nakonechnaya, Tatiana O. Nakonechnaya, Tatiana O. Nakonechnaya, Anna V. Izosimova, Daria S. Zavyalova, Maria M. Karabut, Mark Izraelson, Mark Izraelson, Mark Izraelson, Igor V. Samoylenko, Vladimir E. Zagainov, Vladimir E. Zagainov, Dmitriy M. Chudakov, Dmitriy M. Chudakov, Dmitriy M. Chudakov, Dmitriy M. Chudakov, Dmitriy M. Chudakov, Elena V. Zagaynova, George Vladimirovich Sharonov, George Vladimirovich Sharonov, George Vladimirovich Sharonov +30 moredoaj +1 more sourceRNA-Seq-Based TCR Profiling Reveals Persistently Increased Intratumoral Clonality in Responders to Anti-PD-1 Therapy
Frontiers in Oncology, 2020 Substantial effort is being invested in the search for peripheral or intratumoral T cell receptor (TCR) repertoire features that could predict the response to immunotherapy.Ekaterina A. Zhigalova, Anna I. Izosimova, Diana V. Yuzhakova, Lilia N. Volchkova, Irina A. Shagina, Irina A. Shagina, Maria A. Turchaninova, Maria A. Turchaninova, Maria A. Turchaninova, Ekaterina O. Serebrovskaya, Ekaterina O. Serebrovskaya, Ekaterina O. Serebrovskaya, Elena V. Zagaynova, Dmitriy M. Chudakov, Dmitriy M. Chudakov, Dmitriy M. Chudakov, Dmitriy M. Chudakov, George V. Sharonov, George V. Sharonov, George V. Sharonov +19 moredoaj +1 more sourceNovel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity
Frontiers in Immunology, 2023 T-cell receptor (TR) diversity of the variable domains is generated by recombination of both the alpha (TRA) and beta (TRB) chains. The textbook process of TRB chain production starts with TRBD and TRBJ gene rearrangement, followed by the rearrangement ...Anastasia O. Smirnova, Anastasia O. Smirnova, Anna M. Miroshnichenkova, Laima D. Belyaeva, Ilya V. Kelmanson, Yuri B. Lebedev, Yuri B. Lebedev, Ilgar Z. Mamedov, Dmitriy M. Chudakov, Dmitriy M. Chudakov, Dmitriy M. Chudakov, Dmitriy M. Chudakov, Alexander Y. Komkov, Alexander Y. Komkov, Alexander Y. Komkov +14 moredoaj +1 more source
