Now showing items 1-19 of 19

    • The ALS-Linked Gene TDP-43 Regulates \(IFN\beta\) Expression through a Novel Mechanism of 3' UTR-Mediated Promoter cis-Regulation 

      Deering, Raquel Payzant (2013-03-20)
      The TAR DNA-binding protein (TDP-43) is a heterogeneous nuclear ribonucleprotein that is involved in multiple stages of RNA processing. Mutations in the TDP-43 gene and mislocalization of TDP-43 protein have been implicated ...
    • Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli 

      Gat-Viks, Irit; Chevrier, Nicolas; Wilentzik, Roni; Eisenhaure, Thomas; Raychowdhury, Raktima; Steuerman, Yael; Shalek, Alex; Hacohen, Nir; Amit, Ido; Regev, Aviv (2013)
      Individual genetic variation affects gene expression in response to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational ...
    • Development and Application of a High-Throughput RNAi Screen to Reveal Novel Components of the DNA Sensing Pathway 

      Roy, Matthew Stephen (2013-09-27)
      The mammalian immune system has evolved a complex and diverse set of mechanisms to detect and respond to pathogens by recognizing conserved molecular structures and inducing protective immune responses. While many of these ...
    • Evolutionarily Conserved Recognition and Innate Immunity to Fungal Pathogens by the Scavenger Receptors SCARF1 and CD36 

      Tampakakis, Emmanouil; Puckett, Lindsay; Tai, Melissa F.; Stewart, Cameron R.; Hickman, Suzanne E.; Moore, Kathryn J.; El Khoury, Joseph; Means, Terry K.; Mylonakis, Eleftherios; Colvin, Richard Anthony; Seung, Edward N.; Pukkila-Worley, Read; Calderwood, Stephen Beaven; Hacohen, Nir; Luster, Andrew David (Rockefeller University Press, 2009)
      Receptors involved in innate immunity to fungal pathogens have not been fully elucidated. We show that the Caenorhabditis elegans receptors CED-1 and C03F11.3, and their mammalian orthologues, the scavenger receptors SCARF1 ...
    • Genomic Approaches to Dissect Innate Immune Pathways 

      Lee, Mark N (2013-03-14)
      The innate immune system is of central importance to the early containment of infection. When receptors of innate immunity recognize molecular patterns on pathogens, they initiate an immediate immune response by inducing ...
    • Impact of autoimmune risk alleles on the immune system 

      Ray, John P; Hacohen, Nir (BioMed Central, 2015)
      Genetic analyses of autoimmune diseases have revealed hundreds of disease-associated DNA variants, but the identity and function of the causal variants are understudied and warrant deeper mechanistic studies. Here, we ...
    • Musashi-2 controls cell fate, lineage bias, and TGF-β signaling in HSCs 

      Park, Sun-Mi; Deering, Raquel P.; Lu, Yuheng; Tivnan, Patrick; Lianoglou, Steve; Al-Shahrour, Fatima; Ebert, Benjamin L.; Hacohen, Nir; Leslie, Christina; Daley, George Q.; Lengner, Christopher J.; Kharas, Michael G. (The Rockefeller University Press, 2014)
      Hematopoietic stem cells (HSCs) are maintained through the regulation of symmetric and asymmetric cell division. We report that conditional ablation of the RNA-binding protein Msi2 results in a failure of HSC maintenance ...
    • Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia 

      Shalek, Alexander Kann; Gaublomme, Jellert Thomas; Wang, Lili; Yosef, Nir; Chevrier, Nicolas; Andersen, Mette S.; Robinson, Jacob T.; Pochet, Nathalie; Neuberg, Donna S.; Gertner, Rona S.; Amit, Ido; Brown, Jennifer Ruth; Hacohen, Nir; Regev, Aviv; Wu, Cathy Ju-Ying; Park, Hongkun (American ChemicalSociety, 2012)
      A circuit level understanding of immune cells and hematological cancers has been severely impeded by a lack of techniques that enable intracellular perturbation without significantly altering cell viability and function. ...
    • Novel HIV-1 Knockdown Targets Identified by an Enriched Kinases/Phosphatases shRNA Library Using a Long-Term Iterative Screen in Jurkat T-Cells 

      Moita, Luis Ferreira; Goncalves, Joao; Schwartz, Olivier; Rato, Sylvie; Maia, Sara; Brito, Paula M.; Resende, Leonor; Pereira, Carina F.; Moita, Catarina; Freitas, Rui P.; Moniz-Pereira, José; Hacohen, Nir (Public Library of Science, 2010)
      HIV-1 is a complex retrovirus that uses host machinery to promote its replication. Understanding cellular proteins involved in the multistep process of HIV-1 infection may result in the discovery of more adapted and effective ...
    • Personal neoantigen cancer vaccines: The momentum builds 

      Fritsch, Edward F; Hacohen, Nir; Wu, Catherine J (Landes Bioscience, 2014)
      Neoantigen-based cancer vaccines designed to target the unique immunogenic mutations arising in each patient’s tumor are breathing new life into a struggling approach. Data continue to demonstrate the importance of neoantigens ...
    • RNAi Screens in Primary Human Lung Cells Reveal Hermansky-Pudlak Syndrome Proteins as Influenza Suppressors 

      DeGrace, Marciela (2013-02-21)
      Influenza is an important human pathogen that causes fatal disease in 250,000-500,000 people worldwide each year. Because of high levels of variation between influenza strains, vaccines are not always effective and must ...
    • The scavenger receptor SCARF1 mediates apoptotic cell clearance and prevents autoimmunity 

      Ramirez-Ortiz, Zaida G.; Pendergraft, William F.; Prasad, Amit; Byrne, Michael H.; Iram, Tal; Blanchette, Christopher J.; Luster, Andrew D.; Hacohen, Nir; Khoury, Joseph El; Means, Terry K. (2013)
      Clearance of apoptotic cells is critical for control of tissue homeostasis however the full range of receptor(s) on phagocytes responsible for recognition of apoptotic cells remains to be identified. Here we show that ...
    • Semiconductor-based DNA sequencing of histone modification states 

      Cheng, Christine S.; Rai, Kunal; Garber, Manuel; Hollinger, Andrew; Robbins, Dana; Anderson, Scott; Macbeth, Alyssa; Tzou, Austin; Carneiro, Mauricio O.; Raychowdhury, Raktima; Russ, Carsten; Hacohen, Nir; Gershenwald, Jeffrey E.; Lennon, Niall; Nusbaum, Chad; Chin, Lynda; Regev, Aviv; Amit, Ido (2013)
      The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing ...
    • An shRNA-Based Screen of Splicing Regulators Identifies SFRS3 as a Negative Regulator of IL-1β Secretion 

      Moura-Alves, Pedro; Neves-Costa, Ana; Raquel, Helena; Pacheco, Teresa Raquel; Rodrigues, Raquel; Cadima-Couto, Iris; Oliveira, Mariana; Gama-Carvalho, Margarida; Moita, Luis F.; D'Almeida, Bruno; Hacohen, Nir; Chora, Angelo (Public Library of Science, 2011)
      The generation of diversity and plasticity of transcriptional programs are key components of effective vertebrate immune responses. The role of Alternative Splicing has been recognized, but it is underappreciated and poorly ...
    • Single cell RNA Seq reveals dynamic paracrine control of cellular variation 

      Shalek, Alex K.; Satija, Rahul; Shuga, Joe; Trombetta, John J.; Gennert, Dave; Lu, Diana; Chen, Peilin; Gertner, Rona S.; Gaublomme, Jellert T.; Yosef, Nir; Schwartz, Schraga; Fowler, Brian; Weaver, Suzanne; Wang, Jing; Wang, Xiaohui; Ding, Ruihua; Raychowdhury, Raktima; Friedman, Nir; Hacohen, Nir; Park, Hongkun; May, Andrew P.; Regev, Aviv (2014)
      High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis, and function of gene expression variation between seemingly identical cells. Here, we sequence single-cell RNA-Seq ...
    • Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells 

      Shalek, Alex K.; Satija, Rahul; Adiconis, Xian; Gertner, Rona S.; Gaublomme, Jellert T.; Raychowdhury, Raktima; Schwartz, Schragi; Yosef, Nir; Malboeuf, Christine; Lu, Diana; Trombetta, John T.; Gennert, Dave; Gnirke, Andreas; Goren, Alon; Hacohen, Nir; Levin, Joshua Z.; Park, Hongkun; Regev, Aviv (2013)
      Recent molecular studies have revealed that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels, and phenotypic output1–5, with ...
    • Systems-Level Analysis of the Toll-like Receptor Network of Dendritic Cells 

      Chevrier, Nicolas (2012-09-13)
      Cells detect and respond to environmental changes using intracellular networks, and defects in the wiring of these networks contribute to diseases. For example, Toll-like receptors (TLRs) sense microbial molecules and ...
    • TGF-β Suppresses β-Catenin-Dependent Tolerogenic Activation Program in Dendritic Cells 

      Vander Lugt, Bryan; Beck, Zachary T.; Fuhlbrigge, Robert Conrad; Hacohen, Nir; Campbell, James J.; Boes, Marianne (Public Library of Science, 2011)
      The mechanisms that underlie the critical dendritic cell (DC) function in maintainance of peripheral immune tolerance are incompletely understood, although the β-catenin signaling pathway is critical for this role. The ...
    • TREML4 amplifies TLR7-mediated signaling during antiviral responses and autoimmunity 

      Ramirez-Ortiz, Zaida G.; Prasad, Amit; Griffith, Jason W.; Pendergraft, William F.; Cowley, Glenn S.; Root, David E.; Tai, Melissa; Luster, Andrew D.; Khoury, Joseph El; Hacohen, Nir; Means, Terry K. (2015)
      The genes and pathways that fine-tune TLR7-mediated innate inflammatory responses remain to be fully elucidated. Using an unbiased genome-scale shRNA screen, we identified the receptor TREML4 as an essential positive ...