“In our society, we have an addiction to vertical genetic transmission. It’s called sec and having a child who looks like you”.
This was perhaps the most memorable quote from the event’s keynote speaker, Greg Simon, Director of the Biden Cancer Initiative. It also happens to highlight the most compelling reason to pursue this exciting technology.
CRISPRcon took place on August 16-17 at the UC Berkeley and was meant to encourage communication about the range of ethical and social implications surrounding the use of CRISPR in different fields, from agriculture to medicine.
Many people came to the event to share their thoughts, hopes and fears related to the use of gene editing.
Many people seemed to be unable to decide how they felt about it.
And I’m sure that many people found at least some of their views gradually changing throughout the course of the event.
Personally, I’ve been fascinated with the concept of gene editing ever since I first read about it. Although I was in middle school at the time and it was more in the realm of science fiction rather than a scientific prospect, I couldn’t stop thinking how much it could contribute towards happier, healthier lives.
But as this technology began to develop, while it was met with excitement from one group of people, there was also distrust and sometimes hostility from the other. Michael Specter, staff writer of The New Yorker and the author of Denialism: How Irrational Thinking Hinders Scientific Progress, Harms the Planet, and Threatens Our Lives, made an excellent point while participating in a discussion panel: “It’s easy to write stories that will scare the crap out of people”. Indeed, a scary story holds an undisputable allure, particularly in the case of CRISPR: if we perceive it as a genuine threat that will bring chaos, divide and discrimination then by not allowing it into our lives we get to be the heroes. And being a pendekar fighting for justice has never been so easy.
“Can polio vaccines give you polio? Yes, if they’re not made right”. Coming back to the keynote speech, this slide sums up how dangerous and deconstructive the “what-if” kind of thinking can get, and why we must not allow ourselves to get caught up in it.
Doubt is permanently connected to self-preservation, and it makes us cautious — which is a good thing. But it can also become a paralyzing, destructive force. Ask any person who desperately needed to make an important decision, but hesitated long enough and missed their shot — they’re likely to have at least one regret in life.
Sure enough, when we’re deciding the fate of CRISPR, we’re not deciding this for us but for our children — or possibly grandchildren — which means enormous responsibility. Which automatically means categorizing the issue under “proceed with caution”. However, moving slowly shouldn’t mean not moving at all. I believe there’s a real danger for this tech to be stuck in regulatory limbo, possibly to a point where there will no longer be an opportunity to use it — it is extremely difficult to make predictions in current climate. So let’s aim to give the next generation best possible start in life. They will have plenty of challenges ahead.
Anna is a freelance writer with a keen interest in biotechnology, follow her on twitter @annaeverette16 or email her at anna [at] endthread [dot] me.
The news that CRISPR-Cas9 gene editing in its current form may not work in a substantial fraction of people due to many of us having immunity to Cas9 came as a shock to many, but if you think about it, maybe it’s not so surprising. I don’t see it as the end of the world.
Motley Fool Headline on CRISPR stocks
A (preprint) from a group led by Matthew Porteus started this lively discussion a few days ago. The preprint is entitled, “Identification of Pre-Existing Adaptive Immunity to Cas9 Proteins in Humans.” Some people are freaking out about this finding for a variety of reasons including for some investors their financial concerns (see the headline snapshot from the investing site Motley Fool above, for instance).
Everyone needs to take a deep breath.
If you think back to the fact that CRISPR-Cas9 as a toolbox for “gene editing” was developed from a natural bacterial defense system against viral infections, it’s logical that the bacterial Cas9 protein (the most commonly used nuclease by which CRISPR gene editing works via DNA repair) might be sometimes viewed as foreign by our immune systems as we grow up.
The new preprint reports that the two main sources of Cas9 protein so far from the bacteria Staph aureus (S. aureus) and Strep pyogenes (S. pyogenes), are likely going to be recognized as a sign of infection in some people. In fact, probably in many people. A lot of us are likely to be immune sensitive to these bacterial Cas9 proteins (reportedly, 79% to S. aureus Cas9 and 65% to S. pyogenes Cas9 in the limited number of donors examined in the preprint) because we’ll have antibodies against these Cas9 proteins.
Adaptive Immunity to Cas9, challenge for CRISPR gene editing, Figure 1, Charlesworth, et al.
You can see in a pic from Figure 1 from the preprint that Western blots demonstrate endogenous human antibodies against Cas9 proteins often recognize clear protein bands. These human antibodies that make Western blot bands show up for Cas9 are in all likelihood present at a pretty decent concentration because so many of us have had and responded to S. aureus and S. pyogenes infections during our lifetimes and those bacteria express Cas9. Every time we are infected with a pathogen we stand a good chance of developing antibodies against unique proteins expressed by the pathogen and apparently Cas9 is fairly immunogenic.
Since many of us likely have Cas9 antibodies in our bloodstreams, if we were to receive CRISPR-Cas9 gene therapy our bodies may effectively inactive the CRISPR-Cas9 system via those antibodies. In addition, Porteus’ report (Charlesworth, et al.) found reactive T-cells as well in humans. Thus, not only might our antibodies inactivate CRISPR-Cas9, but also the resulting immune response could pose risks to patients getting CRISPR-Cas9 gene therapy. These data are so new though that it’s hard to know what will actually happen in patients who have Cas9 antibodies after getting CRISPR-Cas9 introduced into their systems. So, we know these antibodies are present in some people, but we don’t know the functional significance in a gene editing therapeutic setting. Another caveat for this paper is that the group of human donors was relatively small so in a wider, more genetically diverse population it is possible not such a high percentage of people are reactive to Cas9…or it could unfortunately go the other way and even more people may have antibodies. Functionally significant levels of Cas9 antibodies could be present yet undetectable so that’s another potential headache.
So what happens next?
A number of discussions are ongoing now about workarounds to this immunity hurdle, including some discuss in the piece from Antonio Regalado:
“New CRISPR systems are out there, just waiting to be discovered in bacteria that the human body has never seen—like those living in hydrothermal vents, say. Extracting cells from our bodies, treating them with CRISPR, and then putting them back might also work.”
These are good ideas.
Those of us with antibodies to S. aureus and/or S. pyogenes Cas9 may react with Cas proteins from other bacterial species. Still, it seems reasonably likely that other nucleases can be found that work well for gene editing but against which humans generally do not have antibodies. Importantly, transient use of Cas9 in patients’ cells in vitro followed by read ministration in vivo back into the patient could prove effective in getting good gene editing and at the same time avoiding immune responses. However, such an approach may not always be practical for gene editing of cell types other than those of the immune system. For example, you can’t easily remove brain precursor cells to gene edit in vitro without damaging the brain.
Other longer-standing issues are still out there too as some have pointed out such as human immune reactions to the viruses such as AAV sometimes used to deliver CRISPR-Cas9 systems. I don’t see any of these things as insurmountable though across the board. I believe some CRISPR-Cas9-based gene therapy will be proven safe and effective down the road.
Even more challenges and uncertainty await those who would use CRISPR in human embryos for proposed heritable prevention of genetic diseases as we can see exemplified by the complications and limbo status of the Mitalipov lab human embryo CRISPR paper from last year, the main conclusions of which were challenged by the Egli, et al. preprint (this is not even including societal and bioethical issues with heritable human gene editing). Note that I don’t see such ethical issues with CRISPR use for gene therapy.
The bottom line from this past week’s new finding on Cas9 antibodies and reactive T cells is that using CRISPR-Cas9 for applications such as gene therapy in humans is still almost certainly going to be workable, but in many cases it’ll be more complicated than hoped and other enzymes besides Cas9 might often be needed. The road ahead, as has been found to be true for so many transformative biomedical translational pipelines including for stem cells, is going to be tougher than imagined at first with more steps involved to maximize chances of success and lower risks for patients and the field. As a technology like CRISPR matures, the field needs to mature in our expectations and realize there will be big challenges along the way without panicking. Challenges are just the norm for science. In fact, usually the more exciting something is, the more hurdles we’ll run into along the way.
The people and the talks combine for a one-of-a-kind experience. The venue doesn’t hurt either at the Scripps Seaside Forum. The evening before the meeting I walked from the hotel to the venue and took a picture from below at sunset. If you look up by the palm trees you can see hang gliders puttering award in the sky, likely from the hang glider port just north up near the Salk.
This is now my 2nd year attending FOGM and each time I’ve greatly enjoyed the talks both inside the auditorium and outside just chatting with people. You can see my top 10 takeaways from last year’s FOGM here. I want to thank organizer Ali Torkamani, who took the lead this year, and Eric Topol for inviting me to come speak again.
FOGM venue Scripps Seaside Forum
Yesterday was Day 1 of FOGM18 and it was fantastic. There was a major emphasis on data (both in big and not so big forms), but also humanizing genomics.
Although it is outside my area of expertise, the talks on the Genetics of Human Origins were one highlight for me so I’ll start there as I think it is a fascinating, unusual area of research.
Grad student Viviane Slon of the Max Planck Institute for Evolutionary Anthropology gave an exciting talk on obtaining useable mammalian including hominin DNA from sediments (a.k.a layers of “dirt”). It turns out, you don’t need to necessarily find actual bones or fragments to get useful ancient DNA. Slon used some clever technical approaches to successfully fish out hominin and other mammalian DNA from the sea of heterogeneous DNA in sediment that can be dominated by microbial DNA. This approach opens the door to getting new knowledge of evolution and genetics of human origins. One of the questions I didn’t get a chance to ask was “What is the half-life of DNA ‘out in the wild’ and what influences that?” She also went over a nice approach that allows researchers to distinguish between the ancient DNA and modern human DNA contaminants. Great talk!
Her talk was followed by one given by Eske Willerslev of Cambridge. He gave a wonderful, sweeping overview of how genomics has taught us about human origins and migrations. He started on the Americas and addressed different hypotheses about where the first peoples originated and how they came to this last area that was settled by hominids. Lots of different ideas here and probably strong feelings. It’s interesting how there are also conflicts and tensions between physical and genomic anthropology. He went through global human migrations with key genomic insights. It was a scholarly, but very approachable talk.
One of the lessons from both these human origins talks is how much we can learn from DNA obtained out in the field and also about how complex human migrations likely were with many streams one way and then back, divergent streams, etc.
Most other FOGM speakers talked about “modern DNA and genomics” if you will, what we can do with it, how we can (and should carefully) interpret huge data sets, and how genomics and our world are changing in tandem.
Eric Topol slide, food blood sugar score chart
Eric Topol got things started with a wonderful overview of where we are and how fast genomics is changing medicine, both for physicians and patients. Genomic data when utilized properly can inform health and medical decisions in impactful ways.
Eric also talked about personal health in the context of both genomics and data collected from monitoring. It was striking to hear about how he had his own blood glucose monitored for 2 weeks, kept a food diary, and was able to map out a literal personalized score sheet for himself of which foods impact his blood glucose in different ways.
As for dairy foods, skim milk and especially non-fat yogurt scored poorly for Eric. Dang, I eat those. Being protein-rich is not enough! You need some fat in there. Amongst grains, granola was surprisingly far better than some other things including ciabatta with avocado, oatmeal, rice cakes, etc. I thought granola would be a problematic food for blood sugar. You can see a screenshot of one of his slides above (included with Eric’s permission). Notably, each of us will respond somewhat different to the foods we eat. Also, it seems that human genetics only plays a partial role in blood sugar (and likely other) responses to certain foods and it is thought that each of our own distinct microbiomes may play a relatively bigger role.
Right before I spoke, we all got to enjoy the talk “Genetic and Epigenetics Approaches to Treat Disease and Aging”
by Juan Carlos Izpisua Belmonte, He went over a whole host of cool projects ongoing in his lab, including quite a few involving reprogramming and epigenetic use of CRISPR, much of it to fight aging. Juan Carlos is a fearless scientist who does some game-changing, risky research. The idea of fighting aging via reprogramming related to IPS cell formation is intriguing, but I do worry about the risk of tumorigenesis.
Our session also included interesting updates on the use of gene editing for making next generation CAR-T cells for cancer therapies. For instance, Yvonne Chen of UCLA talked about cool technology evolving to make CAR-T kinds of cells that essentially have a “two-step authentication”-like process for activation that makes them more specific. After our session wrapped up with a panel discussion, Juan Carlos received the 11th Annual Scripps Translational Science Institute Award from Ali Torkamani. Well-deserved.
Other FOGM speakers emphasized the big (does the word “big” even do the magnitude justice?) extent of the data out there and the continuing explosion of data within which are currently existing. Jill Mesirov, Associate Vice Chancellor for Computational Health Sciences here at UCSD, and Jeffrey Hammerbacher at Icahn School of Medicine Mount Sinai, who also used to be Facebook’s head data guy, gave interesting talks. Mesirov updated us on her work on an area that has been a subject that I also work on: childhood brain tumors. She talked about how genomic data has helped classify medulloblastomas into different subgroups with important implications for treatment options for the kids. Her work on the role of the MYC family in medulloblastoma struck a chord for me as that’s something I have also worked on in the past.
We wrapped up with a big picture talk about genetics and genomics from Bonnie Rochman. I’m going to start reading her new book The Gene Machine on the plane back tonight. She is an exceptional science story-teller and does such an effective job personalizing dilemmas. I enjoyed both the science and the patient stories.
Overall, Day 1 was both fascinating and fun for me as a scientist. I learned a lot.
Images from artist Daisuke Takakura, human cloning imagined.
“If I’m going to the trouble of cloning myself, I want the clone to be a copy of me!”
I’m imagining what someone might say if they were told that their expensive and ethically dubious personal cloning efforts produced a clone that was somebody else instead of them. Even if the clone was very similar to the clonee, perhaps like a sibling who was nearly but not quite an identical twin, the clonee might be totally PO’d.
When I think about human “cloning” I too imagine generating a replica person, although I know enough to realize that a clone would start out as a baby even if it were cloned from a 100-year old person. However, I envision the clone as being identical to the clonee in terms of their shared genome and I think that the clone would be identical in many ways to the original person. I also know that epigenetics plays a huge role in human development so clones sometimes may be less similar than we imagine to the starter person (clonee). But until the last few years, I didn’t anticipate perhaps the largest potential monkey wrench in the reproductive cloning system.
What’s the potential problem?
Daisuke Takakura art work on human cloning
It turns out that we humans are chimeras or more accurately microchimeras. This reality means that contrary to decades of dogma, not all of our cells have the same genomes. In fact, within our one body we can have many subtly different genomes. The variance may functionally be at a single gene or a combination. These genomic variances in one person mean that our cells have a certain degree of randomness and such variability may alter how our bodies function such as how our brains operate. I highly recommend an excerpt from Carl Zimmer’s new book, She Has Her Mother’s Laugh, which was recently published in the NYT and beautifully captures the potential meanings of human chimerism. The book itself is on my summer reading list.
What this all also means is that if someone were to take the plunge, reproductive human cloning may often fail to work the way we generally think about it.
Since we are chimeras, if we pick the “wrong” somatic cell to use as the basis for us to be cloned in the sense that the cell in question is substantially genetically different than the rest of the cells in us, then the clone could be very different than the starting person in some ways even if very similar overall. Most cells in the body are probably not chimeric so perhaps this issue wouldn’t arise with every cloning attempt and surely some of the time the cloning attempt would fail entirely if a variant cell was highly gila providing a self-selection kind of filter, but sometimes it would work and the clone would just be very different than the original person.
Keep in mind that cloning will produce variable outcomes anyway because of environmental and epigenetic differences too. Also, the cloning process itself may change the cells including potentially via introducing mutations.
Of course, the ethics of human reproductive cloning are not trivial as well, but keep in mind all you DIY cloners that you may not get what you wanted anyway due to chimerism. You can read more about human cloning in my most recent book, GMO Sapiens, which also covers use of CRISPR in humans.
