Browsing by Author "Xavier, Ramnik Joseph"
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Clinical Activity and Quality of Life Indices Are Valid Across Ulcerative Colitis But Not Crohn’s Disease Phenotypes
Taleban, Sasha; Singh, Prashant; Yajnik, Vijay; Khalili, Hamed; Stewart, Kathleen O.; e.a. (Springer US, 2016-05)Background Clinical activity and quality of life (QOL) indices assess disease activity in Crohn’s disease (CD) and ulcerative colitis (UC). However, a paucity of data exists on the validity of these indices according ... -
The Csk-Associated Adaptor PAG Inhibits Effector T Cell Activation in Cooperation with Phosphatase PTPN22 and Dok Adaptors
Davidson, Dominique; Zhong, Ming-Chao; Pandolfi, Pier Paolo; Bolland, Silvia; Seed, Brian; e.a. (Elsevier, 2016-12)Summary - The transmembrane adaptor PAG (Cbp) has been proposed to mediate membrane recruitment of Csk, a cytoplasmic protein tyrosine kinase playing a critical inhibitory role during T cell activation, by inactivating ... -
Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits
Aguirre-Gamboa, Raul; Joosten, Irma; Urbano, Paulo C.M.; van der Molen, Renate G.; van Rijssen, Esther; e.a. (Elsevier, 2016-11)Effective immunity requires a complex network of cellular and humoral components that interact with each other and are influenced by different environmental and host factors. We used a systems biology approach to comprehensively ... -
Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1
Khor, Bernard; Conway, Kara L.; Omar, Abdifatah S.; Biton, Moshe; Haber, Adam L.; e.a. (American Association of Immunologists, 2019-08)The clear role of autophagy in human inflammatory diseases such as Crohn disease was first identified by genome-wide association studies and subsequently dissected in multiple mechanistic studies. ATG16L1 has been particularly ... -
Elevated rates of horizontal gene transfer in the industrialized human microbiome
Groussin, Mathieu; Poyet, Mathilde; Sistiaga Guiterrez, Maria Ainara; Kearney, Sean Michael; Moniz, Katya H; e.a. (Elsevier BV, 2021)Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely ... -
Host genetic variation and its microbiome interactions within the Human Microbiome Project
Kolde, Raivo; Rahnavard, Gholamali; Vlamakis, Hera; Stevens, Christine; Huttenhower, Curtis; e.a. (BioMed Central, 2018-01)Background: Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the ... -
Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis
Ordovas-Montanes, Jose Manuel; Graham, Daniel B.; Shalek, Alexander K; Xavier, Ramnik Joseph; Regev, Aviv (Elsevier BV, 2019-07)Genome-wide association studies (GWAS) have revealed risk alleles for ulcerative colitis (UC). To understand their cell type specificities and pathways of action, we generate an atlas of 366,650 cells from the colon mucosa ... -
Mobile genes in the human microbiome are structured from global to individual scales
Yilmaz, S.; Huang, K.; Xu, L.; Jupiter, S. D.; Jenkins, A. P.; e.a. (Nature Publishing Group, 2016-07)Recent work has underscored the importance of the microbiome in human health, and has largely attributed differences in phenotype to differences in the species present among individuals. However, mobile genes can confer ... -
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability
Yassour, Moran; Vatanen, Tommi; Siljander, Heli; Hämäläinen, Anu-Maaria; Härkönen, Taina; e.a. (American Association for the Advancement of Science (AAAS), 2015-06)The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. ... -
Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease
Walker, Rebecca L.; Vlamakis, Hera; Lee, Jonathan W. J.; Besse, Luke A.; Xanthakis, Vanessa; e.a. (BioMed Central, 2021-12-17)Abstract Background The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by ... -
RNF166 Determines Recruitment of Adaptor Proteins during Antibacterial Autophagy
Heath, Robert J.; Goel, Gautam; Baxt, Leigh A.; Rush, Jason S.; Mohanan, Vishnu; e.a. (Elsevier, 2016-11)Xenophagy is a form of selective autophagy that involves the targeting and elimination of intracellular pathogens through several recognition, recruitment, and ubiquitination events. E3 ubiquitin ligases control substrate ... -
SIKs control osteocyte responses to parathyroid hormone
Wein, Marc N.; Liang, Yanke; Goransson, Olga; Sundberg, Thomas B.; Wang, Jinhua; e.a. (Nature Publishing Group, 2016-10)Parathyroid hormone (PTH) activates receptors on osteocytes to orchestrate bone formation and resorption. Here we show that PTH inhibition of SOST (sclerostin), a WNT antagonist, requires HDAC4 and HDAC5, whereas PTH ... -
T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation
Biton, Moshe; Haber, Adam L.; Rogel, Noga; Burgin, Grace; Beyaz, Semir; e.a. (Elsevier Science Ltd., 2018-11-15)In the small intestine, a niche of accessory cell types supports the generation of mature epithelial cell types from intestinal stem cells (ISCs). It is unclear, however, if and how immune cells in the niche affect ISC ... -
TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation
Graham, Daniel B.; Lefkovith, Ariel; Deelen, Patrick; de Klein, Niek; Boroughs, Angela; e.a. (Elsevier, 2016-12)Summary - Significant insights into disease pathogenesis have been gleaned from population-level genetic studies; however, many loci associated with complex genetic disease contain numerous genes, and phenotypic associations ... -
Transcription factor TFEB cell-autonomously modulates susceptibility to intestinal epithelial cell injury in vivo
Murano, Tatsuro; Najibi, Mehran; Paulus, Geraldine L. C.; Adiliaghdam, Fatemeh; Valencia-Guerrero, Aida; e.a. (Nature Publishing Group, 2017-07)Understanding the transcription factors that modulate epithelial resistance to injury is necessary for understanding intestinal homeostasis and injury repair processes. Recently, transcription factor EB (TFEB) was implicated ... -
Translating the human microbiome: a path to improving health
Xavier, Ramnik Joseph (BioMed Central, 2021-05)