Cell‐Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes

Autor: Zachary Cutts, Sarah Patterson, Lenka Maliskova, Kimberly E. Taylor, Chun Jimmie Ye, Maria Dall'Era, Jinoos Yazdany, Lindsey A. Criswell, Gabriela K. Fragiadakis, Charles Langelier, John A. Capra, Marina Sirota, Cristina M. Lanata

Publikováno v: ACR Open Rheumatology, Vol 6, Iss 11, Pp 769-779 (2024)

Objective There is an established yet unexplained link between interferon (IFN) and systemic lupus erythematosus (SLE). The expression of sequences derived from transposable elements (TEs) may contribute to SLE phenotypes, specifically production of

Externí odkaz: https://doaj.org/article/fcd04e74aa0c45c4ad770819f2b9d24d

Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Autor: Drew Neavin, Anne Senabouth, Himanshi Arora, Jimmy Tsz Hang Lee, Aida Ripoll-Cladellas, sc-eQTLGen Consortium, Lude Franke, Shyam Prabhakar, Chun Jimmie Ye, Davis J. McCarthy, Marta Melé, Martin Hemberg, Joseph E. Powell

Publikováno v: Genome Biology, Vol 25, Iss 1, Pp 1-24 (2024)

Abstract Recent innovations in single-cell RNA-sequencing (scRNA-seq) provide the technology to investigate biological questions at cellular resolution. Pooling cells from multiple individuals has become a common strategy, and droplets can subsequent

Externí odkaz: https://doaj.org/article/7209fadf8e984cfb87325f01f83f0d88

SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models

Autor: Benjamin J. Strober, Karl Tayeb, Joshua Popp, Guanghao Qi, M. Grace Gordon, Richard Perez, Chun Jimmie Ye, Alexis Battle

Publikováno v: Genome Biology, Vol 25, Iss 1, Pp 1-23 (2024)

Abstract Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-speci

Externí odkaz: https://doaj.org/article/913a45bed23149fdbebfd53e9e332fab

Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy

Autor: Hanna M. Ollila, Eilon Sharon, Ling Lin, Nasa Sinnott-Armstrong, Aditya Ambati, Selina M. Yogeshwar, Ryan P. Hillary, Otto Jolanki, Juliette Faraco, Mali Einen, Guo Luo, Jing Zhang, Fang Han, Han Yan, Xiao Song Dong, Jing Li, Jun Zhang, Seung-Chul Hong, Tae Won Kim, Yves Dauvilliers, Lucie Barateau, Gert Jan Lammers, Rolf Fronczek, Geert Mayer, Joan Santamaria, Isabelle Arnulf, Stine Knudsen-Heier, May Kristin Lyamouri Bredahl, Per Medbøe Thorsby, Giuseppe Plazzi, Fabio Pizza, Monica Moresco, Catherine Crowe, Stephen K. Van den Eeden, Michel Lecendreux, Patrice Bourgin, Takashi Kanbayashi, Francisco J. Martínez-Orozco, Rosa Peraita-Adrados, Antonio Benetó, Jacques Montplaisir, Alex Desautels, Yu-Shu Huang, FinnGen, Poul Jennum, Sona Nevsimalova, David Kemlink, Alex Iranzo, Sebastiaan Overeem, Aleksandra Wierzbicka, Peter Geisler, Karel Sonka, Makoto Honda, Birgit Högl, Ambra Stefani, Fernando Morgadinho Coelho, Vilma Mantovani, Eva Feketeova, Mia Wadelius, Niclas Eriksson, Hans Smedje, Pär Hallberg, Per Egil Hesla, David Rye, Zerrin Pelin, Luigi Ferini-Strambi, Claudio L. Bassetti, Johannes Mathis, Ramin Khatami, Adi Aran, Sheela Nampoothiri, Tomas Olsson, Ingrid Kockum, Markku Partinen, Markus Perola, Birgitte R. Kornum, Sina Rueger, Juliane Winkelmann, Taku Miyagawa, Hiromi Toyoda, Seik-Soon Khor, Mihoko Shimada, Katsushi Tokunaga, Manuel Rivas, Jonathan K. Pritchard, Neil Risch, Zoltan Kutalik, Ruth O’Hara, Joachim Hallmayer, Chun Jimmie Ye, Emmanuel J. Mignot

Publikováno v: Nature Communications, Vol 14, Iss 1, Pp 1-13 (2023)

Abstract Narcolepsy type 1 (NT1) is caused by a loss of hypocretin/orexin transmission. Risk factors include pandemic 2009 H1N1 influenza A infection and immunization with Pandemrix®. Here, we dissect disease mechanisms and interactions with environ

Externí odkaz: https://doaj.org/article/5ce5735744474cff8886bce42fe536b9

A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling

Autor: Jason A. Hackney, Haridha Shivram, Jason Vander Heiden, Chris Overall, Luz Orozco, Xia Gao, Eugene Kim, Nathan West, Aditi Qamra, Diana Chang, Arindam Chakrabarti, David F. Choy, Alexis J. Combes, Tristan Courau, Gabriela K. Fragiadakis, Arjun Arkal Rao, Arja Ray, Jessica Tsui, Kenneth Hu, Nicholas F. Kuhn, Matthew F. Krummel, David J. Erle, Kirsten Kangelaris, Aartik Sarma, Zoe Lyon, Carolyn S. Calfee, Prescott G. Woodruff, Rajani Ghale, Eran Mick, Ashley Byrne, Beth Shoshana Zha, Charles Langelier, Carolyn M. Hendrickson, Monique G.P. van der Wijst, George C. Hartoularos, Tianna Grant, Raymund Bueno, David S. Lee, John R. Greenland, Yang Sun, Richard Perez, Anton Ogorodnikov, Alyssa Ward, Chun Jimmie Ye, Thiru Ramalingam, Jacqueline M. McBride, Fang Cai, Anastasia Teterina, Min Bao, Larry Tsai, Ivan O. Rosas, Aviv Regev, Sharookh B. Kapadia, Rebecca N. Bauer, Carrie M. Rosenberger, Yumiko Abe-Jones, Michael Adkisson, K. Mark Ansel, Saurabh Asthana, Alexander Beagle, Sharvari Bhide, Cathy Cai, Saharai Caldera, Maria Calvo, Sidney A. Carrillo, Suzanna Chak, Stephanie Christenson, Zachary Collins, Spyros Darmanis, Angela Detweiler, Catherine DeVoe, Walter Eckalbar, Jeremy Giberson, Ana Gonzalez, Gracie Gordon, Paula Hayakawa Serpa, Alejandra Jauregui, Chayse Jones, Serena Ke, Divya Kushnoor, Tasha Lea, Deanna Lee, Aleksandra Leligdowicz, Yale Liu, Salman Mahboob, Lenka Maliskova, Michael Matthay, Elizabeth McCarthy, Priscila Muñoz-Sandoval, Norma Neff, Viet Nguyen, Nishita Nigam, Randy Parada, Maira Phelps, Logan Pierce, Priya Prasad, Sadeed Rashid, Gabriella Reeder, Nicklaus Rodriguez, Bushra Samad, Andrew Schroeder, Cole Shaw, Alan Shen, Austin Sigman, Pratik Sinha, Matthew Spitzer, Sara Sunshine, Kevin Tang, Luz Torres Altamirano, Alexandra Tsitsiklis, Erden Tumurbaatar, Vaibhav Upadhyay, Alexander Whatley, Andrew Willmore, Michael Wilson, Juliane Winkler, Kristine Wong, Kimberly Yee, Michelle Yu, Mingyue Zhou, Wandi S. Zhu

Publikováno v: iScience, Vol 26, Iss 10, Pp 107813- (2023)

Summary: Altered myeloid inflammation and lymphopenia are hallmarks of severe infections. We identified the upregulated EN-RAGE gene program in airway and blood myeloid cells from patients with acute lung injury from SARS-CoV-2 or other causes across

Externí odkaz: https://doaj.org/article/9fcf76e7c2d9439cbd17b0a0b7fa8d89