SCARF1: A Novel Receptor for Apoptotic Clearance

            Autoimmunity is one of the most difficult to treat and unfathomable types of disease, because we are not fighting a virus, bacterium, or parasite: we are fighting our own body. Usually, doctors can count on the immune system to help them out when their patients are sick; it is the job of this system to ensure that any foreign threat to the body is eliminated. But the nature of autoimmunity is such that the biggest ally we have in the quest to keep ourselves healthy turns against us and begins attacking that which it has evolved to protect.

There are many classes of autoimmune disease, each with a very different cause. The immune system is so diverse and complicated that a mutation in one of its parts can affect the entire system and ultimately manifest in disease. There are myriad ways in which this can happen, but the result is what is called “breaking tolerance”. When tolerance is broken, the immune system recognizes some small component of the body as a foreign object and mounts an immune response against it. This can cause differing amounts of damage, depending on how prevalent the component is, and if its recognition and destruction leads to the labeling of more self proteins as targets. There is the danger of a phenomenon called epitope spreading, which happens when a cell is targeted and destroyed, releasing its contents into the body. The immune system has not been desensitized, or “tolerized” to the proteins inside a cell, as it should have no need to recognize them in a healthy body. When this happens in the context of an already active self-targeted immune response, immune cells may further target the otherwise normal contents of the dying cells, leading to a more serious attack throughout the body.

            One important safeguard against autoimmunity is the safe breakdown clearance of apoptotic cells. An apoptotic cell is one that is infected, compromised, or simply too old and losing effective function. These cells are marked for uptake by phagocytes, which are a class of cell types that uptake and destroy their targets, breaking down anything in the cell that could be toxic if released into the body. It is known how and when phagocytes such as macrophages and dendritic cells destroy their targets, but the specifics of their identification are little investigated. In their paper “The scavenger receptor SCARF1 mediates the clearance of apoptotic cells and prevents autoimmunity”, Zaida G. Ramirez-Ortiz et al identify and characterize the receptor SCARF1 which, allows phagocytes to recognize their targets for destruction. SCARF1 is a transmembrane protein which has homologs even in the simple research model C. elegans, and acts by binding to a C1q and phosphatidylserine complex. Phosphatidylserine is a part of the inside of the cell membrane, and becomes exposed on the exterior portion of the membrane only when the cell needs to be phagocytosed. SCARF1, the researchers found, cannot recognize and destroy cells without this component bound to C1q, a peptide which also plays a role in the complement system. High concentrations of this peptide near a cell marked with phosphatidylserine cause a complex to form, which binds to SCARF1 and results in successful phagocytosis. 

   

1. Macrophage Engulfing Apoptotic Cells

A New Mechanism of Cell Death by HIV

            It’s a disease that is well known all over the world: human immunodeficiency virus, better known as HIV.  It is often talked about in tandem with acquired immunodeficiency syndrome, or AIDS, which develops in HIV patients over time and is the end stage of the disease.  HIV originated in chimpanzees as simian immunodeficiency virus (SIV) and transferred over into humans in the 1800s.  The first cases in the United States were reported in 1981.  Throughout the 1980s, cases increased dramatically, peaking in the early 1990s.  However, a breakthrough in drug treatment for people living with HIV and HIV prevention campaigns helped to bring the number of cases back down.  The drug therapy known as antiretroviral therapy (ART) is still used today as the main way to help people with HIV live normal lives, hopefully preventing/delaying the progression to AIDS.  They target different points in the HIV virus replication cycle to try and slow down its progression through the body.

Figure 1: HIV replication in a cell.  It is able to dump its
contents into the cell, reverse transcribe its RNA,
integrate it into host DNA, and use the host to create new viral copies.

HIV is a retrovirus, a form of RNA virus that can be inserted into the host DNA, and then uses host cells to replicate.  The virus comes with all sorts of proteins that let it do this.  For example, reverse transcriptase allows the viral RNA to be turned into viral DNA.  Integrase allows it to be inserted into the host DNA to then use the host’s own protein making mechanisms to make new viruses and viral proteins.  Figure 1 shows an outline of HIV replication.  It is possible to trace the viral RNA to viral DNA to host DNA and then back out to spread to other cells. 

HIV also specifically infects a certain class of immune cells known as CD4+ T cells.  CD4+ T cells are called this due to the presence of a cell surface receptor called CD4.  These cells can differentiate into all different subtypes of CD4+ T cells called T helper cells, or Th cells, whose name describes their function: they “help” other immune cells mount responses to pathogens.  CD4+ T cells and all of their progeny are crucial for providing immunity to all sorts of infections, pathogens, and the like.  HIV comes into play and infects the CD4+ T cells.  It creates a chain reaction, infecting, spreading, and slowly killing all the CD4+ T cells in the body.  In simple terms: HIV is slowly knocking out an entire branch of the immune system.  Any further immune function that would need a CD4+ cell to work won’t be able to work once the CD4+ T cells are gone.  Figure 2 lays this out in a graph showing CD4+ T cells in blue, viral RNA copies in read, and time in weeks on the x-axis.  It is possible to see that as the RNA copies go up, the CD4+ T cells go way down.  Many of the ART drugs target these proteins that prevent the HIV from infecting cells as easily or spreading once it has infected a cell.  However, it is still unknown how HIV actually kills CD4+ T cells.

Figure 2: Timeline of HIV infection.  As viral RNA increases,
CD4+ cells decrease.  A latent period exists where the
person may not know they are infected
until their cell count reaches a certain point.

Cooper et al demonstrate one potential way HIV could kill CD4+ T cells.  They first infected cells with HIV and stained for a particular viral protein called p24.  They noticed that the CD4+ T cells that were killed didn’t express this viral protein, while cells that weren’t killed did.  Next, they looked at whether these cells that were lacking expression of this viral protein had been infected with the virus before they died.  More T cells were infected with HIV that also encoded for green fluorescent protein (GFP), which fluoresces green.  GFP is often used as an indicator for protein production. The gene for GFP is placed within the HIV genome, so if HIV proteins are being produced, GFP will also be produced.  If the cells are dead, no GFP will be detectable.  This is a commonly used method to visualize and also quantify protein production.  They analyzed the cells for GFP expression and cell viability, as well as viral cDNA.  Non-viable GFP- cells were found to have copies of viral cDNA.  When viable GFP+ cells were watched over time, the researchers saw that many of these cells eventually died (therefore losing their GFP expression) but retained viral cDNA.  These data together suggest that the cells that were killed died after successful HIV gene expression.

CD4+ T cells in HIV

Human immunodeficiency virus (HIV) is a member of the retrovirus family and progresses into AIDs after a period of time. AIDs is defined by a significant deficiency in T-cell count which causes a progressive failure of the immune system and allows life-threatening opportunistic infections and cancers to thrive. Infection with HIV occurs by the transfer of blood, semen, vaginal fluid, or breast milk. In order to slow the progression to AIDs, many people with HIV take antiretroviral therapy which combines a number of drugs that are designed to stop HIV from infecting cells: includes nonnucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors, and triple-nucleoside (or nucleotide) reverse transcriptase inhibitors (NRTIs) (1). HIV initially depletes the body’s CD4 T-cells and the point of this therapy is to boost the immune system back to normal to continue to fight the infection. However, 30% of patients with HIV who receive antiretroviral therapy fail to achieve a normal CD4⁺ T-cell count (2). This failure to achieve normal T-cell levels results in a steady decrease in T-cells to where, in less than 10 years, the count is below 500 (signifying AIDs) leaving the patient open to opportunistic infections and eventually death. Therefore it is necessary to study the reasons for this initial failure to reach normal T-cell counts with antiretroviral therapy in order to enhance its function.

HIV first infects CD4 T-cells, depleting the amount in the body. However, there is normally a period of time in which the T-cells regenerate in order to fight the infection. The balance of T-cells in the body is negatively regulated by interferon α (IFN-α) and evidence suggests that HIV increase the production of this interferon (3). This regulating interferon may promote apoptosis of uninfected CD4⁺ T cells by up-regulating expression of a death signal (TRAIL) and its death receptor (TRAIL receptor) (4). Therefore, the role of IFN-α may have important effects on CD4 T-cell populations in HIV patients.

A study by Sonia Fernandez at the School of Pathology and Laboratory Medicine in Australia looks at the effects of IFN-α on CD4 T-cell populations in HIV patients. They recruited HIV patients who have been receiving effective doses of antiretroviral therapy and measured the levels of CD 4 T-cells in the blood as well as levels of IFN-α. The patients were divided into low or high CD4 T-cell groups. Expression of markers of T-cell activation (HLA-DR), apoptotic potential (Fas), or aging (CD57) were assessed and it was found that the proportions of CD4⁺ T cells expressing HLA-DR or Fas were higher in patients with low CD4⁺ T-cell counts than in those with high counts such that the higher the levels of Fas and HLA-DR that are expressed, the lower the population of CD4+ T-cell count. The proportion of CD4⁺ T cells expressing CD57 did not differ between patients with low or high CD4⁺ T-cell counts. They left the cells in a culture for 72 hours and found that the proportions of CD4⁺ and CD8⁺ T cells that were apoptotic or preapoptotic was similar in patients with low and high CD4⁺ T-cell counts.

Dodging Natural Killing: HIV Innate Immune Evasion

Image via Wikipedia Commons

HIV, the virus that causes AIDS, is the cause of one of the most far-reaching and destructive epidemics in modern times. Responsible for approximately 1.8 million deaths and more than 2.5 million new infections annually, HIV is a major public health concern, particularly in the developing world. HIV-1, the most common and virulent strain of the virus, has been studied extensively by researchers hoping to better understand the virus’s life cycle and develop treatments that disrupt its ability to infect and reproduce. One of the greatest barriers to effective treatment and clearance of HIV-1 is the virus’s astonishing capacity for immune evasion. From constant mutation to active subversion of the body's immune system, HIV is a particularly difficult pathogen to eliminate. In a paper published in PLoS: Pathogens in March of 2010, researchers from the Institut Pasteur examined one method by which HIV-1 is able to evade the natural killer (NK) cells of the innate immune system and establish a persistent infection, providing both a better understanding of HIV-1 immune evasion and a possible target for future HIV treatments.

Under normal conditions, viruses and virus particles are taken up by a subset of the host’s white blood cells known as dendritic cells (DCs). The DCs act as the immune system’s sentries, scouting the body’s tissues for foreign particles or pathogens and presenting them to other immune cells to stimulate a response. DC function is closely regulated by the interactions that take place with NK cells following infection. When inflammation occurs at the site of an infection or injuries, chemical signals known as chemokines cause NK cells to migrate to the infection site. Upon arrival, NK cells interact with DCs, sending signals that may cause the DCs to mature, and receive activating signals from the DCs. If an NK cell encounters a DC that has been infected by a virus or other intracellular pathogen, the NK cell will kill the infected cell by inducing a process known as apoptosis. When the infected DCs undergo apoptosis – also known as programmed cell death – the virus inside them can no longer replicate. This process is essential to the immune system’s ability to clear a virus from the body, particularly during the early stages of infection. However, previous research has suggested that HIV positive people are deficient in killing DCs that are infected with HIV-1, causing the infected DCs to act as a reservoir in which the virus can replicate without interference. In this paper, the researcher set out to determine the methods by which HIV-1 is able to prevent NK cells from killing infected DCs.