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Results: 15
Computational approaches for interpreting scRNA-seq data.
The recent developments in high-throughput single-cell RNA sequencing technology (scRNA-seq) have enabled the generation of vast amounts of transcriptomic data at cellular resolution. With these advances come new modes of data...
Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth.
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.
Gozde Kar, Jong Kyoung Kim, Aleksandra A Kolodziejczyk, Kedar Nath Natarajan, Elena Torlai Triglia, Borbala Mifsud, Sarah Elderkin, John C Marioni, Ana Pombo, Sarah A Teichmann
Sep 11, 2018
Polycomb repressive complexes (PRCs) are important histone modifiers, which silence gene expression; yet, there exists a subset of PRC-bound genes actively transcribed by RNA polymerase II (RNAPII). It is likely that the role of...
Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation.
Jhuma Pramanik, Xi Chen, Gozde Kar, Johan Henriksson, Tomás Gomes, Jong-Eun Park, Kedar Natarajan, Kerstin B Meyer, Zhichao Miao, Andrew NJ McKenzie, Bidesh Mahata, Sarah A Teichmann
May 14, 2019
BACKGROUND: The IRE1a-XBP1 pathway is a conserved adaptive mediator of the unfolded protein response. The pathway is indispensable for the development of secretory cells by facilitating protein folding and enhancing secretory...
Genome-wide XBP1 chromatin occupancy IRE1a IRE1a-XBP1 pathway RNA-seq T helper cell activation Th2 lymphocyte proliferation Th2 transcriptome xbp1 XBP1 ChIP-seq Animals Base Sequence Cell Cycle Cell Differentiation Cell Proliferation Cytokines Endoribonucleases Female Gene Expression Regulation Genome-Wide Association Study Lymphocyte Activation Mice Inbred C57BL Mice Transgenic Protein Serine-Threonine Kinases Signal Transduction Stress Physiological Th2 Cells Up-Regulation X-Box Binding Protein 1
Tumors induce de novo steroid biosynthesis in T cells to evade immunity
Bidesh Mahata, Jhuma Pramanik, Louise van der Weyden, Krzysztof Polanski, Gozde Kar, Angela Riedel, Xi Chen, Nuno A. Fonseca, Kousik Kundu, Lia S. Campos, Edward Ryder, Graham Duddy, Izabela Walczak, Klaus Okkenhaug, David J. Adams, Jacqueline D. Shields, Sarah A. Teichmann
Jul 17, 2020
Abstract: Tumors subvert immune cell function to evade immune responses, yet the complex mechanisms driving immune evasion remain poorly understood. Here we show that tumors induce de novo steroidogenesis in T lymphocytes to...
Tumors induce de novo steroid biosynthesis in T cells to evade immunity.
Bidesh Mahata, Jhuma Pramanik, Louise van der Weyden, Krzysztof Polanski, Gozde Kar, Angela Riedel, Xi Chen, Nuno A Fonseca, Kousik Kundu, Lia S Campos, Edward Ryder, Graham Duddy, Izabela Walczak, Klaus Okkenhaug, David J Adams, Jacqueline D Shields, Sarah A Teichmann
Jul 30, 2020
Tumors subvert immune cell function to evade immune responses, yet the complex mechanisms driving immune evasion remain poorly understood. Here we show that tumors induce de novo steroidogenesis in T lymphocytes to evade...
Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation.
Valentina Proserpio, Andrea Piccolo, Liora Haim-Vilmovsky, Gozde Kar, Tapio Lönnberg, Valentine Svensson, Jhuma Pramanik, Kedar Nath Natarajan, Weichao Zhai, Xiuwei Zhang, Giacomo Donati, Melis Kayikci, Jurij Kotar, Andrew NJ McKenzie, Ruddy Montandon, Oliver Billker, Steven Woodhouse, Pietro Cicuta, Mario Nicodemi, Sarah A Teichmann
May 16, 2019
BACKGROUND: Differentiation of lymphocytes is frequently accompanied by cell cycle changes, interplay that is of central importance for immunity but is still incompletely understood. Here, we interrogate and quantitatively model...
Adaptive Immunity CD4+ T cells Cell Cycle DIFFERENTIATION Live imaging Single-cell RNA-seq Animals CD4-Positive T-Lymphocytes Cell Differentiation Cell Proliferation Cells Cultured Cytokines Female Gene Expression Profiling Malaria Mice Mice Inbred C57BL Models Biological Sequence Analysis RNA Single-Cell Analysis Transcriptome
Tumors induce de novo steroid biosynthesis in T cells to evade immunity
Bidesh Mahata, Jhuma Pramanik, Louise van der Weyden, Krzysztof Polanski, Gozde Kar, Angela Riedel, Xi Chen, Nuno A. Fonseca, Kousik Kundu, Lia S. Campos, Edward Ryder, Graham Duddy, Izabela Walczak, Klaus Okkenhaug, David J. Adams, Jacqueline D. Shields, Sarah A. Teichmann
Jul 28, 2021
Abstract: Tumors subvert immune cell function to evade immune responses, yet the complex mechanisms driving immune evasion remain poorly understood. Here we show that tumors induce de novo steroidogenesis in T lymphocytes to...
Mapping Rora expression in resting and activated CD4+ T cells.
Liora Haim-Vilmovsky, Johan Henriksson, Jennifer A Walker, Zhichao Miao, Eviatar Natan, Gozde Kar, Simon Clare, Jillian L Barlow, Evelina Charidemou, Lira Mamanova, Xi Chen, Valentina Proserpio, Jhuma Pramanik, Steven Woodhouse, Anna V Protasio, Mirjana Efremova, Julian L Griffin, Matt Berriman, Gordon Dougan, Jasmin Fisher, John C Marioni, Andrew N J McKenzie, Sarah A Teichmann
Jun 19, 2021
The transcription factor Rora has been shown to be important for the development of ILC2 and the regulation of ILC3, macrophages and Treg cells. Here we investigate the role of Rora across CD4+ T cells in general, but with an...
Published by: PLOS ONE
Erratum to
Valentina Proserpio, Andrea Piccolo, Liora Haim-Vilmovsky, Gozde Kar, Tapio Lönnberg, Valentine Svensson, Jhuma Pramanik, Kedar Nath Natarajan, Weichao Zhai, Xiuwei Zhang, Giacomo Donati, Melis Kayikci, Jurij Kotar, Andrew NJ McKenzie, Ruddy Montandon, Kylie R James, Daniel Fernandez-Ruiz, William R Heath, Ashraful Haque, Oliver Billker, Steven Woodhouse, Pietro Cicuta, Mario Nicodemi, Sarah A Teichmann
May 16, 2019
Mapping Rora expression in resting and activated CD4+ T cells
Liora Haim-Vilmovsky, Johan Henriksson, Jennifer A. Walker, Zhichao Miao, Eviatar Natan, Gozde Kar, Simon Clare, Jillian L. Barlow, Evelina Charidemou, Lira Mamanova, Xi Chen, Valentina Proserpio, Jhuma Pramanik, Steven Woodhouse, Anna V. Protasio, Mirjana Efremova, Julian L. Griffin, Matt Berriman, Gordon Dougan, Jasmin Fisher, John C. Marioni, Andrew N. J. McKenzie, Sarah A. Teichmann
May 20, 2021
Mapping Rora expression in resting and activated CD4+ T cells.
Liora Haim-Vilmovsky, Johan Henriksson, Jennifer A Walker, Zhichao Miao, Eviatar Natan, Gozde Kar, Simon Clare, Jillian L Barlow, Evelina Charidemou, Lira Mamanova, Xi Chen, Valentina Proserpio, Jhuma Pramanik, Steven Woodhouse, Anna V Protasio, Mirjana Efremova, Julian L Griffin, Matt Berriman, Gordon Dougan, Jasmin Fisher, John C Marioni, Andrew NJ McKenzie, Sarah A Teichmann
Jul 20, 2021
The transcription factor Rora has been shown to be important for the development of ILC2 and the regulation of ILC3, macrophages and Treg cells. Here we investigate the role of Rora across CD4+ T cells in general, but with an...
Animals Antigens Helminth CD4-Positive T-Lymphocytes Cells Cultured Cytokines Disease Models Animal Female Gene Expression Regulation Lymphocyte Activation MACROPHAGES Mice Mice Inbred C57BL Mice Knockout Mice Transgenic Nippostrongylus Nuclear Receptor Subfamily 1 Group F Member 1 Pneumonia Strongylida Infections Th2 Cells
A cellular census of human lungs identifies novel cell states in health and in asthma.
Felipe A Vieira Braga, Gozde Kar, Marijn Berg, Orestes A Carpaij, Krzysztof Polanski, Lukas M Simon, Sharon Brouwer, Tomás Gomes, Laura Hesse, Jian Jiang, Eirini S Fasouli, Mirjana Efremova, Roser Vento-Tormo, Carlos Talavera-López, Marnix R Jonker, Karen Affleck, Subarna Palit, Paulina M Strzelecka, Helen V Firth, Krishnaa T Mahbubani, Ana Cvejic, Kerstin B Meyer, Kourosh Saeb-Parsy, Marjan Luinge, Corry-Anke Brandsma, Wim Timens, Ilias Angelidis, Maximilian Strunz, Gerard H Koppelman, Antoon J van Oosterhout, Herbert B Schiller, Fabian J Theis, Maarten van den Berge, Martijn C Nawijn, Sarah A Teichmann
May 03, 2019
Identification of susceptibility loci for Takayasu arteritis through a large multi-ancestral genome-wide association study.
Lourdes Ortiz-Fernández, Güher Saruhan-Direskeneli, Fatma Alibaz-Oner, Sema Kaymaz-Tahra, Patrick Coit, Xiufang Kong, Allan P Kiprianos, Robert T Maughan, Sibel Z Aydin, Kenan Aksu, Gokhan Keser, Sevil Kamali, Murat Inanc, Jason Springer, Servet Akar, Fatos Onen, Nurullah Akkoc, Nader A Khalidi, Curry Koening, Omer Karadag, Sedat Kiraz, Lindsy Forbess, Carol A Langford, Carol A McAlear, Zeynep Ozbalkan, Sule Yavuz, Gozde Yildirim Çetin, Nilufer Alpay-Kanitez, Sharon Chung, Askin Ates, Yasar Karaaslan, Kathleen McKinnon-Maksimowicz, Paul A Monach, Hüseyin TE Ozer, Emire Seyahi, Izzet Fresko, Ayse Cefle, Philip Seo, Kenneth J Warrington, Mehmet A Ozturk, Steven R Ytterberg, Veli Cobankara, Ahmet Mesut Onat, Nurşen Duzgun, Muge Bıcakcıgil, Sibel P Yentür, Lindsay Lally, Angelo A Manfredi, Elena Baldissera, Eren Erken, Ayten Yazici, Bünyamin Kısacık, Timuçin Kaşifoğlu, Ediz Dalkilic, David Cuthbertson, Christian Pagnoux, Antoine Sreih, Guillermo Reales, Chris Wallace, Jonathan D Wren, Deborah S Cunninghame-Graham, Timothy J Vyse, Ying Sun, Huiyong Chen, Peter C Grayson, Enrico Tombetti, Lindi Jiang, Justin C Mason, Peter A Merkel, Haner Direskeneli, Amr H Sawalha
Nov 26, 2020
Takayasu arteritis is a rare inflammatory disease of large arteries. We performed a genetic study in Takayasu arteritis comprising 6,670 individuals (1,226 affected individuals) from five different populations. We discovered HLA...
COVIDiSTRESS Global Survey dataset on psychological and behavioural consequences of the COVID-19 outbreak
Yuki Yamada, Dominik-Borna Ćepulić, Tao Coll-Martín, Stéphane Debove, Guillaume Gautreau, Hyemin Han, Jesper Rasmussen, Thao P. Tran, Giovanni A. Travaglino, Andreas Lieberoth, Angélique M. Blackburn, Loïs Boullu, Mila Bujić, Grace Byrne, Marjolein C. J. Caniëls, Ivan Flis, Marta Kowal, Nikolay R. Rachev, Vicenta Reynoso-Alcántara, Oulmann Zerhouni, Oli Ahmed, Rizwana Amin, Sibele Aquino, João Carlos Areias, John Jamir Benzon R. Aruta, Dastan Bamwesigye, Jozef Bavolar, Andrew R. Bender, Pratik Bhandari, Tuba Bircan, Huseyin Cakal, Tereza Capelos, Jiří Čeněk, Brendan Ch’ng, Fang-Yu Chen, Stavroula Chrona, Carlos C. Contreras-Ibáñez, Pablo Sebastián Correa, Irene Cristofori, Wilson Cyrus-Lai, Guillermo Delgado-Garcia, Eliane Deschrijver, Carlos Díaz, İlknur Dilekler, Vilius Dranseika, Dmitrii Dubrov, Kristina Eichel, Eda Ermagan-Caglar, Rebekah Gelpí, Rubén Flores González, Amanda Griffin, Moh Abdul Hakim, Krzysztof Hanusz, Yuen Wan Ho, Dayana Hristova, Barbora Hubena, Keiko Ihaya, Gozde Ikizer, Md. Nurul Islam, Alma Jeftic, Shruti Jha, Fernanda Pérez-Gay Juárez, Pavol Kacmar, Kalina Kalinova, Phillip S. Kavanagh, Mehmet Kosa, Karolina Koszałkowska, Raisa Kumaga, David Lacko, Yookyung Lee, Antonio G. Lentoor, Gabriel A. De Leon, Shiang-Yi Lin, Samuel Lins, Claudio Rafael Castro López, Agnieszka E. Lys, Samkelisiwe Mahlungulu, Tsvetelina Makaveeva, Salomé Mamede, Silvia Mari, Tiago A. Marot, Liz Martinez, Dar Meshi, Débora Jeanette Mola, Sara Morales-Izquierdo, Arian Musliu, Priyanka A. Naidu, Arooj Najmussaqib, Jean C. Natividade, Steve Nebel, Jana Nezkusilova, Irina Nikolova, Manuel Ninaus, Valdas Noreika, María Victoria Ortiz, Daphna Hausman Ozery, Daniel Pankowski, Tiziana Pennato, Martin Pírko, Lotte Pummerer, Cecilia Reyna, Eugenia Romano, Hafize Sahin, Aybegum Memisoglu Sanli, Gülden Sayılan, Alessia Scarpaci, Cristina Sechi, Maor Shani, Aya Shata, Pilleriin Sikka, Nidhi Sinha, Sabrina Stöckli, Anna Studzinska, Emilija Sungailaite, Zea Szebeni, Benjamin Tag, Mihaela Taranu, Franco Tisocco, Jarno Tuominen, Fidan Turk, Muhammad Kamal Uddin, Ena Uzelac, Sara Vestergren, Roosevelt Vilar, Austin Horng-En Wang, J. Noël West, Charles K. S. Wu, Teodora Yaneva, Yao-Yuan Yeh
Jan 04, 2021