Alper Lab: Current Projects



The Innate Immune Response & Human Disease

Figure 1

The human immune response has both a rapid (innate) component and a slower but more specific (adaptive) component. The adaptive immune system involves cells and immune mediators such as T cells, B cells, and antibodies. The innate immune response involves the action of phagocytic and cytotoxic cells, which migrate to the site of infection and produce antimicrobial compounds. The innate response also plays a key role in the activation of adaptive immunity and is therefore critical to host defense. The innate immune response is still poorly understood, but we are beginning to unravel its mysteries. Over the past decade, it has become clear that the innate immune system also plays a critical role in the pathogenesis of many human diseases, ranging from sepsis to asthma to cancer to atherosclerosis and many others, as depicted in Figure 1. Thus, the identification of genes that regulate the body's innate immune system can have profound consequences for the diagnosis and treatment of many common diseases. These diseases affect millions of people worldwide, and the incidence of many of these diseases is rising. For example, sepsis affects approximately 800,000 people in the U.S. annually, with a mortality rate over 20 percent. Similarly, asthma affects more than 17 million people in the U.S., leading to significant suffering and several thousand deaths annually. We are interested in understanding the regulation of the innate immune response, particularly as it relates to the basis for such immunological diseases.


Innate Immunity Gene Discovery

Figure 2

We are using a comparative genomics approach in several "simple" and accessible model systems to identify novel regulators of the innate immune response. We have developed assays to monitor the response to pathogens in two different model systems: an in vivo system using the nematode C. elegans and an in vitro system using mouse macrophage cell culture. Thus far, we have used these assays to identify genes that control the response to Gram negative bacteria, and we are now testing the role of these genes in several mouse disease models. We are also examining these genes in human patient cohorts to determine whether DNA polymorphisms in these genes affect the incidence of diseases such as sepsis. Our overall approach is illustrated schematically below:

Figure 4
We have identified several novel candidate innate immune regulators. Many of these genes fall into two broad classes: genes that affect protein and vesicle transport within the cell and genes that regulate NF-kB activity. We have obtained mutations in several of these genes in both C. elegans and mice, and we are using these mutants to ask some key questions about how these genes regulate immunity and disease.


Membrane Trafficking and the Innate Immune Response

When we consider the regulation of the immune response, we tend to think about signal transduction pathways and circuit diagrams that culminate in transcriptional activation. However, the location and movement of these signaling molecules within the cell also plays a key role in regulating the immune response. We have identified several genes that regulate trafficking of cellular proteins in our screens for innate immune regulators. This has led us to ask several questions:

Figure 3

How do genes that control membrane traffic at the cellular level lead to a defect in innate immunity at the organismal level?  

For example, one of the genes that we have identified is a putative RAB-GAP, which regulates RAB-mediated membrane traffic. A knockout of this gene leads to a hyper-inflammatory phenotype in a mouse cell culture model (left panel in figure); conversely, overexpression of this gene completely abolishes the immune response (right panel in figure). 

What is the molecular function of this key regulatory gene? 

What specific aspect of membrane trafficking is regulated by this gene?

How does this trafficking defect cause a defect in the organismal immune response? 

We are investigating this gene and several other candidate protein trafficking genes to determine how they regulate cellular and organismal immunity.


Novel Regulators of NF-kB Activation

We have also identified several genes that are either direct or indirect regulators of a key transcription factor in immunity, NF-kB. Are these novel genes direct or indirect regulators of this transcription factor, and how do they regulate NF-kB activity? We are now addressing these questions using genetic techniques in C. elegans and biochemical techniques in mouse cells.

Together, these avenues of investigation are allowing us to unravel the mysteries of innate immunity on a genetic and molecular level.