A medical first: CRISPR gene-editing used to treat a genetic disorder—sickle cell anemia

This medical intervention, which may in the end prove unsuccessful, nevertheless represents a first, at least according to the NPR article below.  I’m not quite sure this is a first, though, so see the discussion below. But the “precedence” aspect isn’t that important. What’s important is that if this treatment works, it opens up a whole new panorama on curing genetic disease.

CRISPR, as I described in a 2017 book review in the Washington Post, is a method of precise gene editing that grew out of pure research: the observation of strange repeated sequences in bacterial DNA. Those repeated sequences turned out to be stored viral DNA that the bacterium used to precisely cut invading viruses whose DNA matched the stored sequences.

From that observation, a whole group of people, as described in my article, developed CRISPR as a system to edit DNA in many organisms, and now it’s being used in humans. CRISPR is a remarkable technology which, when it works properly—and that’s not always the case—can be used to snip a defective gene—or part of a defective gene—out of an organism’s DNA and replace it with a normally functioning gene. It can also be used to change the DNA any way you want: put wanted genes into crops or food animals, or change the DNA of your offspring in a frozen embryo, say giving it genes for brown eyes instead of blue.  Theoretically it’s possible to change both the DNA in the gametes (sperm and eggs), so that a change can be permanently inherited by one’s descendants, or just change the DNA in the body itself in a way that isn’t inherited.

The latter method is what’s being used in an attempt to cure a devastating disease, sickle cell anemia. The subject is an African-American woman, Victoria Gray (34) of Mississippi, who’s being treated in Nashville. Eventually 45 other patients from 18 to 35 will be treated. There aren’t any results yet, but if it works it will be the first step in using CRISPR to cure a variety of genetic diseases. (The diseases have to be based on changes in the DNA because CRISPR works by replacing one gene with another.)

In this case the disease is caused by a lesion in hemoglobin (see below): a replacement of one amino acid (glutamic acid in normal hemoglobin, Hb-A) with another (valine in sickle-cell hemoglobin Hb-S), and this is caused by a change in a single nucleotide in the DNA coding for the β chain of hemoglobin. (A single hemoglobin molecule has two α and two β chains.)  That change is a mutation from the triplet GAG, which codes for glutamic acid, to GTG, which codes for valine. The β-hemoglobin gene is on chromosome 11 (we have 46 chromosomes, present in 23 pairs).

This one nucleotide change out of the 3.2 billion in our genome produces the devastating disease, as the mutant hemoglobin causes the red blood cells containing it to assume a sickle shape, producing a whole syndrome of debilitating and painful traits: joint damage, strokes (the sickled cells clog the circulatory system), spleen damage, anemia, and infections.  Most of the afflicted die by their mid-forties.

Below is a picture of sickled red-blood cells from the New York Times story below:

The vast preponderance of African-American sufferers in the U.S. is important because sickle-cell anemia is found almost entirely in people of West African origin.

This is a famous evolutionary story: the sickle-cell gene, when present in one copy along with a “normal” gene, doesn’t cause the disease, as enough normal red blood cells are produced to prevent symptoms. It’s only when you inherit two copies of the “Hb-S” gene that you’re afflicted. In other words, the genes producing the disease act as “recessives”. Yet many in sub-Saharan Africa and India have the disease: it’s estimated that about 4 million people worldwide are afflicted, and 43 million people are “carriers,” asymptomatic people who have but a single copy of the mutant β-chain in their DNA.

Why does this debilitating gene persist? Why hasn’t natural selection reduced its frequency to almost zero? It’s because if you’re a carrier of one copy and asymptomatic, you have a lower chance of dying from malaria than people with two “normal” genes. It’s not clear why this is true, but it surely has something to do with an altered hemoglobin environment in the blood that reduces growth of the malaria-producing protozoan. (Mosquitoes, acting as flying syringes, carry the protozoan from person to person.)  So the reproductive fitness (judged by survival) of the three types is like this: HbS/HbA (heterozygote) is fittest because it doesn’t have the disease and is protected from malaria (which is often fatal), HbA/HbA (normal homozygotes) are of high but a bit lower fitness, as they can get malaria) and the HbS/HbS type is the genotype with sickle-cell anemia, and most don’t have children as they’re very sick.

It turns out that if the “heterozygote” has the highest fitness, as in this case, then both forms of the gene are maintained in the population (this is called “overdominance” or “heterosis”), regardless of the fact that every generation a number of HbS/HbS people are born, fated to suffer and die. This shows that genetics and biology doesn’t produce the optimum situation, which would be true if everyone was a heterozygote. But this is impossible, because the nature of genetics dictates that heterozygotes segregate the two alleles every generation. The evolutionary dynamics of heterozygous advantage maintains the bad gene in the population: many carriers are protected from malaria, but the mating of two such carriers produces sickle-cell disease in 25% of their offspring.

The Hb-S gene, then, is found largely where fatal malaria is endemic: west Africa and India (and parts of the Middle East).

The coincidence of the distribution of endemic malaria (first figure) with the distribution of the Hb-S allele (second figure) is striking, and is further evidence that the presence of malaria is responsible for the evolutionary maintenance of the deleterious Hb-S allele:

Frequency of the sickle cell allele (pink and purple):

Because American black people derive largely from West Africans brought over as slaves, the gene has persisted in this population, and that’s why African-Americans are almost the only people in the U.S. who get sickle-cell anemia. (The frequency of the gene here is decreasing, though, as malaria isn’t endemic in the U.S.—eliminating the evolutionary advantage of carriers of the gene—and intermarriage with whites has also reduced its frequency among blacks.)

Enough of that story, which is one that we all tell in evolution class, for it’s one of the very few cases we know of in which a heterozygote for a single gene is superior to either homozygote.

Sickle-cell anemia is almost incurable, though in some people a bone-marrow transplant can get rid of it. But that’s a painful and often unsuccessful process. What researchers are doing now is taking a sickle-cell patient’s stem cells, which can differentiate into the bone marrow that produces red blood cells, treating those cells’ DNA with CRISPR, and injecting them back into the patient, hoping that they’ll take up residence in the bones and produce normal red blood cells, eliminating the disease. The NPR story below (click on screenshot) describes the treatment received by Ms. Gray.

Now you might think that they’re editing the β-hemoglobin gene itself to turn that nasty GAG triplet to GTG, but there’s apparently another tactic they’re using. What they’re doing is first killing off the patient’s bone marrow with chemotherapy, getting rid of the cells that make sickle-cell blood cells, and then replacing them with genetically altered stem cells that allow fetal hemoglobin (the first hemoglobin we produce, which is usually turned off by four months of age) to persist. The hope is that this fetal hemoglobin will act like Hb-A and cure the disease. I’m not sure why they do this rather than inject stem cells with an edited GTG codon in the gene for β-hemoglobin, but it must be easier to use the modified fetal hemoglobin than to edit the sickle-cell gene.


If this works, and of course it may not (the bone-marrow killing can kill the patient, the injected, altered stem cells may not take hold, etc.), it will be a revolution, and the use of this promising new technology to relieve considerable suffering. I have my fingers crossed.

The article below, which appeared in January, explains why Victoria Gray’s treatment may not be a real first. It may be the first use of CRISPR-altered cells from a patient to cure their own sickle-cell anemia, but it’s not the first time that fetal hemoglobin-producing cells have been used to treat the disease. Also, CRISPR-altered cells have been used to treat human patients with a different genetic disease—one causing blindness,—apparently with some success.

So there’s some confusion about whether Victoria Gray is really a first, but never mind. It’s likely she’s the first sickle-cell patient to receive CRISPR-modified cells in an attempt to replace her defective hemoglobin with a form of hemoglobin (fetal) that may work. I fervently hope it does work, as she’ll be free of the disease that has debilitated her since her childhood. And then thousands of other patients could then receive the treatment, though of course it won’t work for all of them.

CRISPR, as I said in my book review, offers enormous promise for curing genetic diseases, and even eliminating “disease-genes” from the germline (sperm and eggs). It also has promise for genetic engineering of plants and animals, though it’s considered unethical to use the method to do eugenic manipulation in humans, like making kids taller or smarter. And even then it wouldn’t work well, since things like height and intelligence, insofar as they are genetic, are based on many genes, and you can’t edit all of them. Nor would the treatment be useful for “polygenic” diseases like familial hypertension, which is also based on several to many genes. But for single-gene diseases like sickle-cell anemia or Huntington’s chorea, CRISPR is the direction to go.

It’s certain that a Nobel Prize will be awarded for this new form of genetic manipulation. The question is who will get it, as many are in contention. My guesses are given the Washington Post article above.

One final lesson that I’ll drive home again: CRISPR, with all its benefits and promises, derived from pure research: seemingly mundane sequencing of bacterial DNA. The consequences of that work were completely unforeseeable.

One never knows what benefits to humanity can come from such pure research. That in itself is a reason to fund pure research not directly aimed at improving human welfare. But of course there are other reasons, too—the biggest being that pure knowledge about the universe is a benefit in itself, regardless of whether it makes our species taller, smarter, or healthier.

h/t: Matthew Cobb

 

38 Comments

  1. ThyroidPlanet
    Posted August 1, 2019 at 9:31 am | Permalink

    Sub

  2. Sue B
    Posted August 1, 2019 at 9:43 am | Permalink

    Fascinating!

  3. Jonathan Wallace
    Posted August 1, 2019 at 9:52 am | Permalink

    “That in itself is a reason to fund pure research not directly aimed at improving human welfare, but of course there are other reasons, too…”

    Well said. There is a worrying trend – certainly in the UK where I live – for universities to be seen increasingly as utilitarian tools of the economy: producing graduates trained with the specific skills ‘industry needs’ on the one hand and carrying out research that is aimed at applications with commercial potential. Of course within the universities there are still many people engaged in pure research and teaching academic subjects with no direct application to a particular career but the weight of the funding is definitely aimed at applied research and vocational teaching.

  4. Posted August 1, 2019 at 9:58 am | Permalink

    Excellent!

  5. GBJames
    Posted August 1, 2019 at 9:59 am | Permalink

    sub

  6. Posted August 1, 2019 at 10:17 am | Permalink

    Onward science! It is realistic to believe that eventually this technique, one similar, will work.

    Curious how religion will usurp this benefit as a brainchild of God?

    • EdwardM
      Posted August 1, 2019 at 10:23 am | Permalink

      One thing we can count on – future beneficiaries of this kind of therapy will be thanking g*d on their instagrams and facebooks.

      There will be no mention of the researchers who said to themselves; “hmmm, that’s odd” when they saw those strange repeated sequences in their bacterial lines. Nor even thanks to the people who figured out how to harness the biochemistry involved and the clinicians who implemented it. Thanks will be given instead to a giant invisible sky pixie.

      Bet on it.

    • gravelinspector-Aidan
      Posted August 2, 2019 at 12:44 pm | Permalink

      They already have. The effect of the sickle-cell mutation on susceptibility to malaria has been touted by the god-squaddies as an example of “god knows better than you stinking scientists” for … oh, certainly since the mid-90s, if not earlier.
      And EdwardM’s prediction that “beneficiaries of this kind of therapy will be thanking g*d on their instagrams and facebooks” is too late. They were thanking god for sickle-cell mutations (and thus disease) years before any of FaceGram, Twitbook or Instawer existed. That boat has left the harbour, long since.

  7. dd
    Posted August 1, 2019 at 10:20 am | Permalink

    Couple of basic questions:

    1. I understand that people have 46 chromosomes. So, when we say chromosome 11, Does that mean 11 out of the 46 or does it mean the 11th pair?

    2. A more complicated one: In sequencing genomes, How is it known that you have a full chromosome worth of bases…and a full genome with all the bases?

    3. What is a good basic book explaining these basic concepts regarding sequencing and chromosomes?

    • EdwardM
      Posted August 1, 2019 at 10:26 am | Permalink

      I can help on the first two…

      1) 11th pair.

      2) There is no one human genome. There are (roughly) 7 billion. All are different in sequence and length but the differences are small.

      • gravelinspector-Aidan
        Posted August 2, 2019 at 12:57 pm | Permalink

        2) There is no one human genome. There are (roughly) 7 billion. All are different in sequence and length but the differences are small.

        There was a disagreement in process between the for-profit process of Celera Genomics and the taxation-funded Human Genome Project. Celera used material from five reference genomes (including it’s CEO, Craig Venter), while the HGP used a pool of 40 anonymous donors, half male, half female. From those, they selected libraries of four donors on a gene-by-gene (or chromosome-by-chromosome, I’m not quite sure) basis, on quality grounds. That led to one of the genomes (“RP11”) being most used, but not exclusively.
        Since that reference set was analysed, the process of looking at individual variants has lead to thousands more genomes being analysed, looking at individual variations (“SNP”s) and family, country and population variations.

  8. Randall Schenck
    Posted August 1, 2019 at 10:21 am | Permalink

    I remember seeing this story on 60 minutes some time ago. It seemed to be the great cure if you lived through it.

  9. DrBrydon
    Posted August 1, 2019 at 10:36 am | Permalink

    Thanks, Jerry. This is facinating. I had no idea of the relation of malaria to sickle cell anemia. As for pure research, how is acquiring new knowledge ever not worthwhile? As I say, there’s no such thing as trivia, only information not relevant to the current discussion.

    • W.T. Effingham
      Posted August 1, 2019 at 11:14 am | Permalink

      +1👍!

    • Steve Gerrard
      Posted August 1, 2019 at 12:01 pm | Permalink

      This is especially important to remember when research such as “the sex life of ducks” comes up for scorn from the pundits. In the duck case we are not obsessed with the duck sex per se, but stand to learn a lot about the evolution of sexual behavior in general, including human sexuality.

    • sted24
      Posted August 1, 2019 at 3:32 pm | Permalink

      “As for pure research, how is acquiring new knowledge ever not worthwhile?”
      I fully agree, with the proviso that it may not always be welcomed. The great fundamental physics adventures of the 20s and 30s, for example, led the way to the technologies of the A and H bombs. Who saw that coming?
      I have great respect for the complexity of biology over purely physical processes. But sometimes, it seems, astonishing simplicity is possible: ‘one nucleotide change out of the 3.2 billion in our genome produces the devastating disease.’
      Mostly, our host assures us, it will not. I don’t doubt him when he tells us that most genetic traits (of all kinds) are multifactorial. Very complicated. What I do wonder is whether this is an insurmountable barrier or more a problem of data collection and computing power.
      As Exhibit A I present the way the costs of whole genome analysis have tumbled in the past 20 years–from $100 million to $1000 today.
      Who saw that coming?

  10. Pliny the in Between
    Posted August 1, 2019 at 10:46 am | Permalink

    Similar work is underway to treat Huntington’s Disease. In that case they are using a modified virus to ‘infect’ targeted cells in the CNS with a sequence that leads to the production of a peptide that binds to the mRNA for the pathological protein preventing its synthesis.

  11. BJ
    Posted August 1, 2019 at 10:50 am | Permalink

    CRISPR and future versions of this kind of technology excite me to no end. It will allow for so many things, some acceptable and some unacceptable to talk about.

    I never wanted to have kids (I’d rather spend my money and time with the woman I love travelling the world and doing other cool shit), but, even if I did, I’ve always doubted that I ever would because I wouldn’t want to pass on the (what is likely) genes that have caused me severe depression and other mental health issues. Among many other things, technology like this can make that problem moot.

    • Liz
      Posted August 1, 2019 at 12:36 pm | Permalink

      +1

    • EdwardM
      Posted August 1, 2019 at 1:01 pm | Permalink

      Among many other things, technology like this can make that problem moot.

      For limited values of the word “can”, unfortunately BJ, this technology will not be able to make diseases like depression and mental illness moot because those are (SFAWK) under the control of more than one gene, probably many. As the good Dr. said, this kind of therapy will really only be useful for diseases (or traits) that are under the control of a single locus.

      • BJ
        Posted August 1, 2019 at 4:06 pm | Permalink

        Oh yeah, I understand. That’s why I said “technology like this.” I imagine that, down the road, it will develop to a point where it can eliminate multiple genes linked with mental health issues. But it’s entirely possible that I have no idea what I’m talking about, as I am not well-versed in these things…

  12. JZ
    Posted August 1, 2019 at 11:07 am | Permalink

    For many single gene disorders, such as Huntington’s, the real clinical breakthrough is actually anti-sense oligonucleotides, which have already made an enormous impact in the form of nusinersen, the FDA approved drug for SMA.

  13. Ken Kukec
    Posted August 1, 2019 at 11:08 am | Permalink

    Like a stream of bat’s piss, as the Pythons put it — a shaft of gold when all around is dark.

  14. merilee
    Posted August 1, 2019 at 11:16 am | Permalink

    Sub

  15. Mark Reaume
    Posted August 1, 2019 at 12:19 pm | Permalink

    This is excellent news (that treatments already exists, hopefully it is successful).

    I’m holding out hope that something like this will be available for CF patients. My nephew is on a 4 organ transplant list, it really is a difficult disease to live with.

  16. Jim Swetnam
    Posted August 1, 2019 at 12:22 pm | Permalink

    Ah! What a wonderful result, if it works. Thank you Professor Coyne for posting this, it is such a welcome respite from debates and political news.

  17. Nicolaas Stempels
    Posted August 1, 2019 at 1:52 pm | Permalink

    Yes, sickle cell anaemia was the schoolbook example of a deleterious gene continuing in the gene pool by improved fitness of heterozygotes.
    Note that it is not the only deleterious mutation that protects against Malaria, there are the α and β Thalassemias too, with very different mutations, mainly found in South East Asia and the Mediterranean.
    Fascinating. I hope the CRISPR experiment turns out to be successful. Would be another shining victory for science.

  18. Posted August 1, 2019 at 3:43 pm | Permalink

    I sure hope it works but if not, something has been learnt. The human test tubes are to be commended as well, it cant be easy.

  19. Posted August 1, 2019 at 4:09 pm | Permalink

    I owe my extended life to medical science. End-stage lung cancer beaten by immunotherapy drugs. CRISPR certainly has its place in medical applications.

  20. Dragon
    Posted August 1, 2019 at 4:47 pm | Permalink

    Great description. Pure research sometimes gets derided in Congress, but it really has demonstrated its power multiple times.

    • gravelinspector-Aidan
      Posted August 2, 2019 at 1:02 pm | Permalink

      Pure research sometimes gets derided in Congress, but it really has demonstrated its power multiple times.

      That demonstrated power is why politicians fear it. They can’t control – or understand, generally – what is coming towards them, so they try to stop it.

  21. Ken Pidcock
    Posted August 1, 2019 at 9:44 pm | Permalink

    Another basic lesson from consideration of β-thalassemias concerns the impact of primary amino acid sequence on tertiary polypeptide structure. The “R group” of glutamic acid is hydrophilic, that of valine hydrophobic. Those two groups “want to be” very different places, the first interacting with water on the surface of the polypeptide, the second buried in the interior. Changing from one to the other, via mutation of CAG to CTG, means you get polypeptides of quite different three-dimensional shapes, the latter of which doesn’t function properly as the hemoglobin β chain.

  22. rickflick
    Posted August 1, 2019 at 11:06 pm | Permalink

    My first thought is that I’m horribly upset that I won’t live long enough to see the full flourishing of this new technology. I can imagine a time when before a child is born the genome is scanned for defects and immediately corrected. The susceptibility to disease will be practically eliminated. All the fancy ideas of enhancements to create a superhuman are a noisy side issue. I like the fact that susceptibility to illness can be intercepted shortly after conception. The race of humans will be enhanced and many more lives can be lives to their fullest.

    • Liz
      Posted August 2, 2019 at 12:34 am | Permalink

      For the younger people there might be some ethical dilemmas, but for the older people maybe not so much. We can keep y’all alive forever if you let us. We need you still. Please stay.

      • rickflick
        Posted August 2, 2019 at 1:11 am | Permalink

        That’s a nice thought. 😊

    • gravelinspector-Aidan
      Posted August 2, 2019 at 1:08 pm | Permalink

      I can imagine a time when before a child is born the genome is scanned for defects and immediately corrected.

      That’s the golden-edged glow of theory.
      The hard edged reality is that it will almost always be quicker and cheaper to make multiple embryos and discard the ones with defects. For some hopeful parents, selling the rejected embryos for research may already be a way of discounting the initial cost of the IVF programme.
      I know it’s illegal in some countries. Which just means that people who have to pay the costs of treatment up-front will go to other countries.

  23. Hempenstein
    Posted August 2, 2019 at 4:17 pm | Permalink

    If the CRISPR works on sickle-cell, there’d be a nice symmetry in that sickle cell anemia was the first heritable disorder to be unraveled at the molecular level – Vernon Ingram et al, 1956. Ingram was lucky in the sense that the amino acid substitution involved a charge difference, otherwise the change would have been invisible to the paper electrophoretic techniques used at the time to identify the site of the difference.

    Also of note, which I hadn’t known until just now on looking up his Wikipedia bio, I had always assumed that Ingram was British but it turns out his family fled the Nazis in 1936. Why he et al never won a Nobel Prize for this, I have no idea.

  24. Andrea Kenner
    Posted August 4, 2019 at 7:56 am | Permalink

    Thank you for this understandable science article! I am grateful to the scientists who keep working tirelessly to find cures for diseases that plague humans and animals. Because I am a cat person, I was also excited to see this article about researchers who are working on an antiviral drug for FIP in cats. https://www.k-state.edu/media/newsreleases/2018-09/fipantiviral92018.html?fbclid=IwAR202UYUouOQfyt8Jm970tyNh71r90vNalLzm6XeMtFckaTQGORTgPOHBh4#.XUCau3STyzh.facebook


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