Immunology & Inflammatory Diseases


Nir Hacohen, PhD

The Hacohen Laboratory investigates the initiation of immune responses, the sensing of pathogens, host-pathogen biology and the development of approaches to discover and model genetic and biochemical networks.



Principal Investigator, Center for Immunology and Inflammatory Diseases
Associate Immunologist, Department of Medicine, Massachusetts General Hospital
Associate Professor of Medicine, Harvard Medical School
Senior Associate Member, Broad Institute of Harvard and MIT

Innate Immunity and Systems Biology Laboratory

Pathogen-sensing by the innate immune system. The immune system can normally distinguish and respond appropriately to a broad diversity of pathogens and antigens that it encounters during a lifetime – including the products of bacteria, fungi, viruses and mammalian cells. Dendritic cells (DCs) play an important role in this process through their highly developed machinery to sense and engulf pathogens and to process and present digested peptides to T cells. We had previously shown that dendritic cells exhibit unique gene expression signatures, including specific cytokine, chemokine and costimulator expression, in response to distinct pathogens. Our current studies focus on revealing the genetic networks underlying innate immune responses and host-pathogen interactions. We are interested in addressing the following kinds of questions: (1) What are the mechanisms by which each innate sensor induces specific cellular responses? (2) What is the role of innate sensory pathways in the induction of protective immunity to infections and tumors? (3) How are these pathways dysregulated under some conditions, leading to inflammatory disorders or autoimmune disease? (4) How do pathogens manipulate the host response? To address these questions, we utilize genetic, biochemical and cell biological approaches to systematically dissect the genetic circuitry of pathogen-sensing pathways and their role in initiating and guiding immune responses.

Principal Investigator:

  • Nir Hacohen, PhD

Postdoctoral Fellows:

  • Arnon Arazi, PhD
  • Alice Lan, PhD
  • Moshe Sade, PhD
  • Alexandra-Chloe Villani, PhD

Graduate Students:

  • Karolina Maciag, HMS Immunology and MD/PhD Programs
  • Michael Rooney, MIT Bioinformatics PhD Program

Research Associates and Technicians:

  • Tom Eisenhaure
  • Weibo Li
  • Raktima Raychowdhury

The Hacohen lab uses systems-wide genetic and biochemical approaches to describe the mechanisms underlying specificity in pathogen-sensing pathways, the interactions of pathogens with their hosts and the initiation of autoimmunity. The major projects in the lab focus on how: (1) TLRs and other pathogen sensors achieve specificity in their induction of gene expression; (2) influenza virus modulates host responses; (3) to develop systematic methods to reconstruct signaling and transcriptional networks.

RNAi library for loss-of-function genetics in mammalian cells. Genetic screening in lower organisms has been the basis of critical discoveries across many fields. To develop a method for systematic genetic screens in mammals, we have (as part of a consortium with the Sabatini and Hahn labs, and under the direction of David Root at the Broad Institute): (a) generated genome-wide lentiviral shRNA libraries targeting human and mouse genes at the Broad Institute (Moffat et al., 2006; Luo et al., 2008); (b) developed high-throughput protocols to generate viral particles and infect cells in order to enable large-scale loss-of-function screens in mammalian cells; (c) demonstrated that these viruses can infect primary dendritic cells (and many other immune and non-immune cell types) and silence genes that control DC functions (Amit et al, 2009). As the Broad Institute RNAi Consortium and Platform continues to refine this technology and develop applications to many biological systems, we have begun to apply this powerful methodology to dissect the circuitry of the immune system (Oberdoerffer et al, 2008; Amit et al., 2009; Shapira et al., 2009).

What are the genes that control dendritic cell maturation and antigen presentation in response to microbes and their products? Dendritic cells exhibit an ordered cascade of processes during maturation including: pathogen recognition, engulfment and destruction; antigen processing and presentation; cytokine, chemokine and costimulator production; migration to draining lymph nodes; and finally, CD4 and CD8 T cell engagement. How are these processes regulated by TLR and other pathogen sensors upon exposure of DCs to microbes or their products? What are the pathway branchpoints that confer specificity of output? How are these pathways self-limiting? To enable the identification of genes and pathways required in these processes, we used the lentiviral RNAi library to infect primary mouse bone marrow-derived DCs, and then assayed the effects of gene perturbation on several cell biological outputs. Ongoing projects use this approach to identify and study critical genes of innate immunity. We have recently published an example of a systems biology strategy (in collaboration with Aviv Regev’s group) in which we discovered and characterized a set of transcription and chromatin factors that mediate TLR responses (Amit et al., 2009).

What are the host factors involved in detection and replication of RNA viruses? While most viral genomes encode for proteins that mediate viral entry, replication and assembly, viruses are still dependent on host factors for their life cycle within cells. The genome of RNA viruses, for example, is synthesized, processed, transported and packaged within a host cell. For many of these processes, the identity and function of the host factors are not known. In addition, RNA viruses are detected by a system of RNA sensors that trigger host defenses. Our focus is on the segmented negative-stranded influenza A virus and identifying host factors that confer susceptibility or resistance to influenza infection in primary human lung epithelial cells. In particular, we have developed another systems approach that combines transcriptional profiling, yeast-2-hybrid analysis and RNAi to comprehensively identify functional host gene products that play a role in: (1) innate immune sensing of viral RNA and influenza virus and (2) the life cycle of influenza (Shapira et al., 2009).

If you are interested in applying for a post-doctoral position, or are a Harvard Ph.D. student interested in a laboratory rotation, please email your interests, c.v. and reference letters or contacts to:



Hacohen Laboratory

CNY 149-8
149 13th Street
Charlestown, MA 02129

Phone: 617-724-3768
Fax: 617-726-5651
Hours: Mon-Fri 8:30am-5pm

Public Transportation Access: yes
Disabled Access: yes