Germline DNA changes and bioethics

The BBC reports that Francis Collins, Director of the NIH, will not allow that agency to sponsor research on germline gene transfer.  Various new technologies seem promising in terms of being able to select a specific part of the genome that contains a clearly defective sequence, and replace that with a normal or healthy sequence.  Much of biotechnology is actually borrowed from what bacteria do naturally, as is the case for a recent approach, called CRISPR.

Genetic engineering has long been seen as the obvious thing to do when a clearly defective gene or genome segment is identified.  We are among the most skeptical when it comes to claims about high predictive power of genotypes relative to many human conditions, but there are clearly hundreds of known genetic variants that seem to have high 'penetrance', that is, are likely to cause disease or a disorder when present, and thus have high predictive power for serious, often pediatric diseases.  These disorders can devastate the person's entire life, so that prevention would be better than therapy once they've occurred. The idea of germline genetic engineering is to prevent the problem--and, indeed, do so permanently even in that individual's descendants.  It is the direct way to treat a defective gene by preventing its consequences in the first place, while other therapeutic approaches only work on the defect once it has been inherited.

Dr Collins notes that these current methods are by no means yet foolproof. Germline engineering also seems to cross an ethical or even religious line in terms of meddling with Mother Nature.  In the BBC story, he notes that embryo screening already can identify those embryos not carrying the harmful genetic material, those that are healthy to begin with (with respect to tested variants, at least), and can then be used without the risk of trying to engineer a change artificially, where mistakes can arise.  The problems with the CRISPR method at present include unwanted or undocumented changes elsewhere in the genome, and these could have serious consequences for the individual (and, again, his/her future offspring).

This seems to be a somewhat ironic, but sound, decision at least for the moment.  The idea of preventing harmful genetic conditions by removing them from our human patrimony is a noble one and has been seen as just around the corner ever since the modern era of molecular genetic technologies.  But genomes are complex, and one tinkers at one's peril, based on what is currently known.

Selective embryo choice has its own ethical issues, of course, as does abortion, cloning, or any tinkering with our nature.  Ethics are not always shared, however, and people vary in their ideas of right and wrong.  Indeed, ethical restraints don't always fare well in competition with selfish interests, which is why institutions and governments impose ethical considerations on research. Even if the NIH prevents germline genetic engineering, we probably cannot stop other countries and private companies from doing it.  Profits are to be made and, to be fair, parents' dreams of normal children will be catered to, hopefully in a positive way.  Generally, it is hard to believe that self-interests will not over-ride ethical interests, as they so often do when money is to be made.  Which is not to say that profit is the only motive--there is good to be done, and lives to improve as well.

Of course, germline engineering of various sorts is taking place in plants and animals for agricultural purposes.  The original level of controversy in terms of feasibility has seemingly waned and cloned animals and plants are routinely being made.  GMO plants are still controversial for many reasons both including potential health issues and, perhaps even more so, the economics of industrialized, highly profitable agriculture, especially as it impacts the developing world and distracts attention from more sustainable, soil-preserving practices.  At present it is hard to sort out the issues there, given the strength and diversity of feelings, and the hard-core economic and vested-interest issues involved. But it is always risky to bet against the power of technology to solve problems, and even to do that in an ethical way.

There are many who advocate genetic engineering for entirely good, moral reasons, related to human improvement.  But there are many also who are not willing to wait until things are shown to be safe.  In any case, at present, Dr Collins seems to be doing what he can to keep the Dr Frankensteins under control.  Whether it's a losing battle, and whether indeed far more good than evil will come from human germline manipulation, remain to be seen.  One can hope that the best will triumph.

Germline gene therapy: Frankenstein or Frankincense?

Science, like any other human enterprise, is largely reactionary.  People in established positions of influence like to have their own way but perhaps even more, like their ways to stay basically the same: change is threatening.  For that general reason, new ideas that promise to be transformative are often faced with reactionary opposition.

A few decades ago we had the recombinant DNA revolution.  Changing DNA in bacteria for experimental reasons was seen as a potential global threat: if recombinant bacteria escaped the lab, they could become a global pandemic disaster that would make malaria or the bubonic plague seem trivial by comparison.  Of course, those excited about the potential of the new method, for legitimate as well as venal reasons, pushed hard to be allowed to proceed.  After careful examination, various protections were imposed (like working with experimental strains of E. coli that could not really live outside of test tubes), but these were loosened or abandoned over time, as the threats never materialized.

There are still some rumblings about this, as for example, the recent controversy over labs refusing to desist from engineering dangerous flu viruses to see what changes were needed to enable them to transfer from person to person more easily (they originate now in animals).  The rationale is to anticipate such occurrences and develop preventive measures or vaccines etc.  This work is on-again-off-again, in response to governmental and other dictates, and then pressure from investigators to do this no matter what, and then back again, as the issues are batted back and forth, unresolved.

A few years ago there was the reaction to cloning, when it was done to make Dolly, the sheep in a lab in Scotland.  There are many issues about this process, both the sci-fi horrors of cloning armies of humans who are genetically unable to experience fear, and the fact that cloning from an adult's cell would make newborns more vulnerable to age-related diseases.  Human cloning is not allowed as yet, though there are some rather similar things going on in the in vitro fertilization world to select embryos without known disease-related genetic variants.  As we understand it, various types of cloning are widespread in agricultural animals.

Another example is the reaction to genetically modified organisms (GMOs) and their potential to make proteins that would turn out to be allergenic or in other ways harmful, or to damage ecosystems by altering pests infestations as well as inadvertently destroying insect pollinators, the enabling of large-scale monocropping, and so on.  This debate is ongoing, and widely publicized.  It has stimulated 'natural' foods, non-GMO containing foods, local sustainable agriculture, etc.  Some of the resistance was, in essence, not about personal health but about the way GMOs threaten local farmers around the world, deplete natural variability, threaten bees and other pollinators, and more.

Much of the opposition to these sorts of change is emotional and sociopolitical--but that is not a criticism, because people are emotional and sociopolitical.  And that applies to people on both sides of the debates: nobody can claim that the proponents of the new technologies are dispassionate and without self-interest and limited perspectives.

Human genetic engineering: a blessing like Frankincense?
There is now the beginning, or perhaps continuation, of a debate about human genetic engineering.  Should it be done?  What is it, exactly.  One recent discussion outlines the issues.  New technologies are being developed, one of which is called CRISPR, to engineer changes in specific genes in situ in cells.  This is being done in cell culture and experimental animals and plants, to see what the specifically transgenic effects on them are.  But the potential for genetic engineering to produce human babies that do not carry deleterious genes that there parent(s) may be known to carry hasn't been ignored--and, even better, the dangerous genes are removed from the population because when the babies themselves reproduce they only have the normal version to transmit to their children.

This is different from genetic engineering that tries to deliver therapy based on genetic methods to persons who are affected by genetically based diseases (like cystic fibrosis) or to deliver genetic changes to diseased tissues to counter the pathology.  Those approaches are struggling to live up to their widespread promise, but there is little opposition that we know of to their implementation.

The resistance to germ line gene therapy seems to be that engineering of specific heritable genetic changes could backfire and generate new pathologies, monsters, or other unexpected side effects if the methods, still yet unproven and undergoing testing in lab species, don't work as precisely as their proponents claim.

An old way wise men tried to bless the human future: Frankincense therapy

But the idea of germ-line and hence permanent fixes is not at all new.  It's a scientific analog, one might say, of the religious doctrine of the blessing conferred on humankind by the wise men one Christmas eve.  An effort to save our patrimony from much suffering.

Selective abortion, prenatal counseling, and even IVF are now used to prevent the birth of babies that carry known dangerous variants that one or both parents may be known to carry.  This has greatly reduced the incidence of thalassemia (a blood disease related to anemia) in Sardinia, and of Tay Sachs disease in Ashkenazi Jews, and there are likely many examples we just haven't heard about.  There are now two- and even recently three-parent IVF conceptions being constructed.

So this time, the reactionary response to a new idea does seem to be reactionary.  It isn't that there's no risk of horrible misadventures occurring if the new techniques fail, and it's fair enough to say this should be stopped cold until the techniques are reliable (or early enough tests available to do instantaneous aborting of dysgenic conceptuses).  But that is not the same as reacting to the idea of germ-line therapy in the first place as if it were new in concept.

To prevent Frankensteins?
There will, of course, be those who agree with all of this so far, but foresee the mis-use of the procedure by rogue elements or governments for example to create fearless soldiers, drones, slaves, and so on based on mass-scale genetic engineering of this type.  Or doing the same kind of thing to create super-plagues (e.g., to visit on enemies).  Rogue elements can be expected to arise here and there within governments (e.g., in intelligence services, military, or other agencies).

Blessing gone awry: Boris Karloff style

Dr Frankensteins would perhaps find willing employers in such places.  Some would be rogues. Some might offer their services to our enemies.  Some might engineer irresistible plague germs. Such elements always exist in society.  There is plenty of evidence to think that otherwise respectable scientists will be (or are) doing this covertly or will find ways, such as by leaving universities to set up companies, moving to more permissive countries, and so on, to do this and skirt regulations and restrictions.

It is also true that the same sorts of claims have been around for a long time. That the predicted disasters haven't occurred--yet--is no reason to relax vigilance.  After all, the Nazi 'scientists' and 'doctors' were among the leading professionals of their days.  And this sort of thing wasn't restricted to Germany in the 20th century: it was part of global eugenics thinking and actions taken against those deemed to be inherently (that is, genetically) inferior.  Only a newborn babe would be so naive as to think the same sort of mentality cannot be found among today's leading scientists.

But perhaps every blessing comes with a curse, and to gain the former we must guard against the latter.  While vigilance is never perfect, and risks always do exist, at least we should recognize the positive potential for removing dangerous genetic elements from human patrimony.

Gene therapy -- a technological challenge, but we're good at meeting technological challenges

A friend told me recently that gene therapy for diseases of the skin was making a lot of progress.  Given the fits-and-starts history of the field of gene therapy, the fact that the US Institute of Medicine has recommended that most research in gene therapy no longer require the special review it has long been subject to (discussed in Nature this week here), as well as recent announcements of progress and hope, I was interested in looking into it.

Gene therapy, or more generally genetic engineering, is the replacement of a disease-causing allele with a working one, or the silencing of a causal allele.  Gene therapy has a long history, and not always a successful one.  It first looked possible in the early 1970's when Friedmann and Roblin proposed in Science that "gene therapy may ameliorate some human genetic diseases in the future", before much at all about the association between genes and disease was understood. 

There has been much progress since the 70's in understanding the essentials of gene function, of course; the genetic underpinnings of many diseases, primarily rare, have been identified and, while gene therapy has seen some tragic failings, progress is being made.  In theory, while promises in the past were too grandiose, medicine is likely to see many more successes in treating single-gene diseases.  After all, when faced with a clear problem, humans are very good at engineering solutions.

The theory is straightforward: find the gene, figure out what's going wrong, and stop or replace it.  Once a faulty gene has been identified, though, the fundamental problem has been delivering the therapeutic DNA into the nucleus of cells in the affected organ, and then into the right site in the genome so that it can either halt coding for the defective protein or begin telling the cell how to make a working copy of the protein.

Gene therapy using an adenovirus vector: Wikipedia

One way to do the delivery is with a viral vector.  Viruses are naturals at delivering their own genes into host cells, so, in theory harnessing that ability for therapeutic purposes is ideal.  Target the right type of cell, and the introduced gene can be expressed directly or integrated into the host-cell's genome where it will be expressed.  However, most genetic diseases would require repeated delivery of the therapeutic DNA, which would mean repeated exposure to the virus.  Our immune systems are very good at identifying and targeting invading viruses; while this is usually a good thing, it's not so good for virus-based gene therapy that needs to be repeated.  And, if the patient was exposed to the virus before its use in therapy, it's less likely to be effective, again because of the immune response.

Gene therapy makes a comeback
Indeed, it was a severe inflammatory response to an adenovirus-delivered therapy that was responsible for the death of Jesse Gelsinger in 1999, a 19-year old subject in a clinical trial.  His death greatly reduced enthusiasm for gene therapy, and rightly so.  But it did eventually give researchers insight into safer and more effective DNA delivery systems, adeno-associated virus (AAV) being one, although the length of DNA that it can carry is limited, and thus so are the diseases it can eventually be used to treat.  Even so, as reported in a paper in ABBS last year ("Phoenix rising: gene therapy makes a comeback", ABBS (2012) 44 (8): 632-640, Lamberis), AAV-based therapy has been successful now for a genetic cause of blindness, LCA, and there were 80 on-going clinical trials testing the efficacy of AAV-based gene therapy in 2012. 

Retrovirus-based vectors are another approach.  An advantage over AAV is that these can incorporate much larger transgenes, but they have been associated with leukemia-like T lymphoproliferative disorder due to insertional mutagenesis, or random insertion of the virus and its engineered load into the target DNA.  Lentivirus-based vectors are another possibility, but they, too, have their downsides. 

Non-viral vectors consisting of "lipids, peptides, carbohydrates or nanoparticles that fuse with the cell membrane and release the therapeutic DNA in the cell cytoplasm" (Lamberis) depend on natural mechanisms of the target cell to take them in and transport them within the cell.  They aren't as efficient as viral systems, but are safer and less likely to trigger immune responses than virus-based vectors.  

A prime candidate for successful genetic engineering is skin disease.  The skin is an eminently accessible organ, so that if the problem of getting the therapeutic agent through the epidermal barrier is soluable, topical treatment of many skin diseases could be envisioned.  Amy Paller and colleagues reported success with this last year in PNAS.  They introduced "spherical nucleic acid nanoparticles conjugates" into the keratinocytes of mice, and in human skin grafted onto a mouse, with the ultimate goal of delivering RNA silencing systems that can inhibit the expression of faulty genes for a variety of keratin-associated skin diseases.

FIRST, the Foundation for Ichthyosis and Related Skin Types, awarded Paller with funding to continue with this work.  The foundation's announcement describes Paller's work this way: 

The blistering and thickening of skin seen in EI [epidermolytic ichthyosis] usually results from a change in a single letter of the DNA code (a mutation) in one copy of the gene that provides the codes for manufacture of a keratin protein in the upper layers of skin. Small interfering RNAs (siRNAs) are small pieces of genetic material that can identify DNA pieces and bind to them, preventing the gene from being translated into protein. siRNAs are able to distinguish the mutated DNA from the normal DNA, and thus are able to prevent only the abnormal keratin protein from being formed. The problem with siRNA has been getting it through the skin barrier to where it needs to go. Dr. Paller and her team have found a way to get the siRNAs through the skin, through nanotechnology. By putting about 30 copies of the siRNA all around a central gold nanoparticle (leading to what her group calls “spherical nucleic acids”), the siRNAs are able to be rubbed into skin in a simple moisturizer.

This indeed sounds as though it has potential.

CRISPR -- the next big thing
We can't end this post without mentioning another technological advance getting a lot of attention these days.  It exploits a portion of some prokaryotic immune systems, CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats.  Found in bacterial and archaeal genomes, these short repeat DNA sequence loci, from invading structures called phage or plasmids, get incorporated into the prokaryote's genome between CRISPR repeats, as a 'search' sequence.  The CRISPR resulting structure is then the basis for recognition of exogenous invading genomes. The structure moves along an incomer's DNA till it detects a match to the incorporated 'search' sequence.  Then, aided by genes called CAS genes, it cuts the detected DNA.  Normally that destroys it, but other enzymes can be targeted to this cut, and repair it.  Here's where genetic engineering comes in -- the repair process can insert a user-designed sequence into the targeted break.

As Elizabeth Pennisi described in her piece, "The CRISPR Craze", (Science 23 August 2013 341(6148), 833-836), CRISPR are also showing potential for use in gene therapy if they can be used to "delete, add, activate or suppress targeted genes in human cells". The idea in general is that a harmful sequence could be detected, the DNA cut at this point, and a 'good' sequence inserted to replace the harmful part. Here's a video that shows the idea.  Mark Wanner at Jackson Labs also nicely describes the potential uses of CRISPR on his blog. 

There is much excitement about CRISPR's potential.  A story in The Independent quoted several scientists the other day, among them George Church, a geneticist at Harvard, who was one of the first to use CRISPR to actually edit nucleotides in human sequence. "“The efficiency and ease of use is completely unprecedented. I’m jumping out of my skin with excitement,” said Church."  Ok.  But there is still a lot of work to be done.  Getting the edited gene to the right place in the target genome without undesirable effects elsewhere will be a challenge, as with conventional gene therapy.

But, if humans are good at anything, it's technology, and gene therapy and genetic engineering are primarily technological challenges.  We often criticize the science of genetics as it portrays itself and its successes, but if these technologies live up to their potential, they can change a lot of lives for the better.