Concepts of Synthetic Virology

Synthetic virusWe define synthetic virology here as the self assembly of prefabricated components, which when combined mimic the physiology of natural viruses.  The most important components of viral physiology are their ability to package genetic information and their ability to place this information in a cell.  In this blog article I discuss the theoretical origins, ethics, goals and designs of synthetic viruses.

Now the idea of a completely synthetic virus could sound scary to the average person.  Essentially, what makes viruses frightening is their ability to create a disease.  However, some viruses have beneficial properties without which we could not exist.  For example, the human endogenous retrovirus (HERV) is a natural human virus that is produced and activated during the implantation of the human embryo into the uterine wall.  The HERV is essential to formation of a placenta without which we would not be able to bare young.  Our genomes are littered with retrotransposable DNA elements such as LINE-1 which copy themselves similar to viruses and often create genetic redundancy.  Little is known about the biological function of these retrotransposable DNA elements.  I hypothesize that the genetic redundancy created by things like LINE-1 are important in creating new adaptive genes in higher organisms, which help us to evolve and adapt to our environment.

So now that we know that a virus can be good, let’s focus on why they can be bad.  At its simplest level, a virus is a package of information which copies itself and re-coats this information for the next cell.  In the example of HERV, the viruses self replicates sufficiently to form a placenta and then turns its life cycle off until the next generation requires it.  In the case of the human immunodeficiency virus (HIV), the virus moves throughout the population and infects individuals who have insufficient immunity.  HIV first establishes infection in the genital mucosal membrane cells.  From their the virus moves to the immune system white blood cells that it prefers to infect.  Both HERV and HIV are human viruses in the same virus family.  One helps to create life and one, if left unchecked, causes AIDS.  So what makes HIV bad and HERV good?  Control and tailored physiology.  In HERV, the human species has harnessed the power of viral physiology for a beneficial goal, making the placenta.  Humans have no known control over HIV physiology, the virus does what it wants.  The biggest problem with HIV is not that it infects our cells but that it infects the wrong types of cells.  HIV kills the white blood cells of our immune system and supports its own growth at the expense of its host.  If HIV did not infect our white blood cells we wouldn’t care much about it since the infection would be self limiting, similar to other viruses.  In conclusion, live viruses are only “bad” when they infect in an uncontrolled fashion the cells we need to survive.

So let’s briefly discuss genetic diseases and why we want to use viruses.  The most common genetic disease you will hear about is Cystic Fibrosis (CF).  In the mid 1980’s we discovered that CF is caused by a one gene mutation to the gene we called the “cystic fibrosis transreceptor or “CFTR” for short.  This gene produces a protein in epithelial cells that line organs.  In these surface cells this CFTR protein allows chlorine ions to pass through the membrane of the cell.  When this protein is not in place, chlorine ions move around unnaturally which disrupts the movement of water in and around the cells.  It is thought that the thick mucous produced in CF lungs is a response to the water movement issues in the lung epithelial cells.  Since the 1980s we have tried to find a way to get the CFTR gene into the lungs of people with CF with mostly poor results.  For one thing, the entire body is covered with cells that use the CFTR gene, so by focusing in on the lungs we are only getting to the most critical of diseased organs.

In order to put the CFTR gene into the CF lungs the original idea was to take a natural virus that replicates in lung cells and re-engineer it to make the CFTR gene.  I could write a book about why this continues to not work.  Basically, the body has learned to figure out which viruses it can trust and which ones it can’t.  Nothing that grows in the lungs is considered good to the body, so even replication deficient cold viruses which have been engineered to make the CFTR are attacked.  What is more, the cells that the virus infect are also attacked before they can make much benefit from the CFTR gene.  As an aside, today we use engineered viruses to produce vaccines against Ebola proteins.  In these engineered vaccines, the immune response against the Ebola protein is driven by the tissue damage that the engineered virus does.  In the same way, a cold virus producing the CFTR gene in the lungs can create immunity against the “foreign” CFTR protein as a result of the response against the cold virus itself.  This is the worst case scenario.  In conclusion, the immune system’s response against the engineered virus itself negates the beneficial effects of the gene therapy.

You may have guessed by now that what controls the immune system is at the core of what is allowed to happen in the body.  The famous immunologist Polly Matzinger, theorized that the immune system is designed to respond to danger signals.  These danger signals can be anything out of the ordinary for the body.  In many cases, the danger signals that the body is designed to detect are molecules or chemicals that escape dead or dying cells, or common dangerous bacterial or virus components.  When these common danger signals are detected the immune system springs into action.  First it brings in white blood cells.  These cells often kill or clean up dead or dying cells and release killer components to the surrounding cells to kill and clean up any bacteria or viruses that may have slipped through the cracks.  The immune system is often messy and nonspecific, it will kill a lot of surrounding cells to make sure that in infection has been stamped out.  During this process the immune cells will take up bits of dead cell, bacteria or virus and create lasting specific immunity against anything considered foreign.  This lasting specific immunity comes in the two common forms: antibodies (which we will talk about) and cellular immunity (which we won’t talk about).  Antibodies are proteins that recognize that specific foreign part in a previous infection.  Vaccines are mostly designed to create antibodies to disease causing particles.  

Now, HERV isn’t known to generate an immune response but HIV most certainly is.  HIV will cause antibodies to be made against it right away, which is how the virus is initially identified.  When someone is “HIV positive” this means that a test has been done showing that this person has antibodies in their blood that are specific for the HIV virus coat proteins.  So why does the body treat HIV and HERV so differently?  Well according to Polly Matzinger’s theory, HERV does not cause cell death or and danger signals that would tell the body that something is wrong and therefore the body does not respond to HERV.  On the other side HIV kills the cells that it infects during its replication cycle.  Dead cells create the perfect immune stimulus to generate specific immunity like antibodies.  By extrapolation, if you take a cold virus and add the CFTR gene to it, one would expect that danger signals produced by the cold virus would help to generate a specific antibody response against the CFTR gene.

The moral of the story is that viruses can have common traits which cue the immune system to engage.  Some of these cues happen inside and others outside of the cell, but all cues wind up causing the same immune system problem.  To further the field of gene delivery we would need a vehicle which can deliver genetic material to a cell without creating danger signals along the way for the immune system to respond to.  But! If you begin taking away the danger signals of an engineered live virus, it becomes gradually less able to deliver a beneficial gene.  

If one is trying to treat a genetic disease with an engineered virus it would stand to reason that multiple treatments may be required.  Since the immune system creates neutralizing anti-viral antibodies within two weeks, the same live virus will never work more than once.  To get around this scientists have tried to find subtypes of the same virus with different coat proteins (serotypes) which allow for multiple treatments.  However, changing the viral coat protein also changes which cells that virus will prefer to infect.  One unexplored option would be to take all the components of a virus and create immune tolerance against them.  Therefore a virus would go undetected by the immune system during the treatment.  This option is not being explored because it is unethical to make someone tolerant to a disease causing agent.  If that person were to be exposed to the same wild virus, they would be unable to defend against it.  This means that virus components that are far removed from humans would be a better candidate for adoption.


Synthetic Viruses Mimic Natural Virus Physiology

To sum up all of the above, viruses are both the best and the worst way to deliver genes into a cell.  They function well to physically deliver the information but fail to circumvent the immune system along the way, mostly to the detriment of the treatment.  In response to these issues I theorize that a minimalistic synthetic virus which only mimics elements of a natural live virus life cycle would be able to circumvent the immune system while retaining the ability to deliver genetic material.  The main concepts of the natural virus we need are those that help to move through the barriers of the cell.  For example, membrane fusion proteins of enveloped viruses bind to the surface of the cell and fuse the virus coat membrane to the cell membrane.  This catalysis of membrane fusion dumps the viral capsule into the cell.  When the virus capsule makes it into the cell it must next navigate the complex cytoplasm innards to get its genes to the nucleus for production.  Virus capsules like herpes simplex virus-1 bind to a motor protein called dynein which pulls the virus toward the nucleus.  However, the subunits of the dynein motor that the virus uses are known and could also be used to shuttle a synthetic virus.  Viruses are designed to take genetic material and actively package them into a capsule.  The viruses’ genetic packaging becomes the scaffold upon which the rest of the live virus is fabricated.  This type of structural organization can be mimicked by creating a self assembling DNA pattern to create the outline of a virus particle.  When the scaffold of the synthetic virus is constructed it is then mixed with the therapeutic (gene, protein, siRNA, etc.) before the coat components are applied.


Immune Adoption of Synthetic Virus Antigens

Having studied immunology, I feel a great respect for the layered complexity of defensive pathways inherent to mammals.  The perfect human gene delivery system must look as naturally human to the immune system as possible.  This is something that live viruses do with limited success.  The unavoidable aspect of natural virus physiology is that they use the body to reproduce themselves and in doing so trigger many different danger signals.  We have both non-specific innate immunity that works ultra-fast and specific adaptive immunity that works much slower but protects us rapidly if we encounter the same disease twice.  

One ultimate goal of synthetic viruses is to be able to circumvent as many danger signals as possible so that the immune system creates what is called “antigen specific tolerance”.  Antigens are molecular patterns that the immune system can detect and can be anything from protein fragments, lipids, nucleic acids, or a combination of the above.  Specific tolerance means that the immune system actively resists making an immune response to the antigens; for example on a synthetic virus.  Immune tolerance is how the body tells the difference between a protein on a pathogenic bacteria and another protein on liver cell and is defined by white blood cells that mature in the thymus and bone marrow.  Since synthetic viruses are minimalistic, only a few different antigens are displayed to the immune system.  This also means that these few antigens can be displayed to the immune system in a tolerance generating treatment.  In this tolerance treatment, the antigens of the synthetic virus are delivered to the thymus and bone marrow.  The synthetic virus antigens are produced in a benign manner among maturing white blood cells, training them to see the synthetic virus components as “normal”.  This process is called “central immune tolerance generation” and has never been attempted with any gene delivery vehicle to my knowledge.  Now when the body sees a synthetic virus in the bloodstream or in the brain, it will turn off the immune response to it, allowing as many treatments for as long as needed.  This would be unethical to do with a natural engineered virus derived from a pathogen since the individual will never be able to defend itself against the wild virus.  But! The prefabricated components of the synthetic virus never interact with humans, making them suitable for immune adoption.  Once we have immune adoption of a synthetic virus, we can use that virus to treat many different types of disease repeatedly in the same person without worrying about losing the potency of the treatment over time.

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