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posted by martyb on Thursday July 27 2017, @03:35PM   Printer-friendly
from the baby-steps dept.

U.S. scientists have genetically modified human embyros using CRISPR and have apparently avoided the worst of the off-target effects that have plagued previous efforts. The results are unpublished and the team is not commenting yet:

The first known attempt at creating genetically modified human embryos in the United States has been carried out by a team of researchers in Portland, Oregon, Technology Review has learned.

The effort, led by Shoukhrat Mitalipov of Oregon Health and Science University, involved changing the DNA of a large number of one-cell embryos with the gene-editing technique CRISPR, according to people familiar with the scientific results.

Until now, American scientists have watched with a combination of awe, envy, and some alarm as scientists elsewhere were first to explore the controversial practice. To date, three previous reports of editing human embryos were all published by scientists in China.

Now Mitalipov is believed to have broken new ground both in the number of embryos experimented upon and by demonstrating that it is possible to safely and efficiently correct defective genes that cause inherited diseases.

Although none of the embryos were allowed to develop for more than a few days—and there was never any intention of implanting them into a womb—the experiments are a milestone on what may prove to be an inevitable journey toward the birth of the first genetically modified humans.

Also at STAT News.

Previously: Chinese Scientists Have Genetically Modified Human Embryos
NIH Won't Fund Human Germline Modification
Group of Scientists and Bioethicists Back Genetic Modification of Human Embryos
The International Summit on Human Gene Editing
UK Scientist Makes the Case for Editing Human Embryos
Second Chinese Team Reports Gene Editing in Human Embryos
Scientists Keep Human Embryos Alive Longer Outside of the Womb
Francis Collins Retains Position as Director of the National Institutes of Health


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  • (Score: 2) by jimtheowl on Thursday July 27 2017, @04:10PM (14 children)

    by jimtheowl (5929) on Thursday July 27 2017, @04:10PM (#545242)
    Very much like every AC first post on this site.
    Starting Score:    1  point
    Karma-Bonus Modifier   +1  

    Total Score:   2  
  • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @04:37PM (13 children)

    by Anonymous Coward on Thursday July 27 2017, @04:37PM (#545258)

    A person familiar with the research says “many tens” of human IVF embryos were created for the experiment using the donated sperm of men carrying inherited disease mutations. Embryos at this stage are tiny clumps of cells invisible to the naked eye.

    Based on this phrasing, they probably used between 50 and 100 embryos consisting of 4-16 cells each. This gives a range of 200-1600 total exposed cells. How many "successful modifications" were there? Knowing mutation rates, I'd naively expect 0-16 of these cells to spontaneously gain/have a mutation at the site they were considering in the case of NEHJ (when they only see any random mutation at a given site).

    Actually, is this about NEHJ or HDR (where they insert exogenous DNA)? Because that makes a huge difference. Why should we even think about this without having such basic information?

    • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @05:07PM (12 children)

      by Anonymous Coward on Thursday July 27 2017, @05:07PM (#545275)

      Knowing mutation rates, I'd naively expect 0-16 of these cells to spontaneously gain/have a mutation at the site they were considering in the case of NEHJ (when they only see any random mutation at a given site).

      I'd expect so close to 0 spontaneous mutations at a specific region, that I wouldn't even say 0-1. For NHEJ to occur, you need a DNA break.

      Multiply the likelihood of a break at the ROI by the probability of error at the specific site and the chance of that error being the "correct" one.

      • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @05:34PM (2 children)

        by Anonymous Coward on Thursday July 27 2017, @05:34PM (#545284)

        Table S2 (~0.15%):
        https://www.ncbi.nlm.nih.gov/pubmed/26121415 [nih.gov]

        Tables S5, S12 (~0.1%):
        http://www.nature.com/nchembio/journal/v10/n8/abs/nchembio.1550.html#supplementary-information [nature.com]

        Figure S1 (~1%):
        http://www.nature.com/nbt/journal/v33/n11/full/nbt.3389.html#supplementary-information [nature.com]

        Figure S5 (~1%):
        http://advances.sciencemag.org/content/suppl/2015/08/11/1.7.e1500454.DC1 [sciencemag.org]

        Similar values are found in every paper that reports on spontaneous mutation rates.

        • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @06:03PM (1 child)

          by Anonymous Coward on Thursday July 27 2017, @06:03PM (#545299)

          First link:

          K562 cells (a triploid leukemic cell line) were electroporated with Cas9 plasmids (mock) - doesn't sound spontaneous to me. Their results do show that guide RNA can greatly enhance indel frequency at a specific region.

          https://www.atcc.org/products/all/CCL-243.aspx [atcc.org]

      • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @05:59PM (8 children)

        by Anonymous Coward on Thursday July 27 2017, @05:59PM (#545294)

        Heres another:
        Fig 3(1-2%)
        "Although rare (~1–2%), edits were detected with Cas9-only control treatment, including
        at the predicted CXCR4 cut site, potentially indicating trace amounts of experimental contamination of the Cas9 RNPs.""
        http://www.pnas.org/content/early/2015/07/21/1512503112.abstract [pnas.org]

        There are more I've seen, just not finding them at the moment...

        • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @06:05PM (7 children)

          by Anonymous Coward on Thursday July 27 2017, @06:05PM (#545303)

          edits were detected with Cas9-only control treatment

          Alright, I guess we have different definitions of spontaneous.

          • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @06:42PM (6 children)

            by Anonymous Coward on Thursday July 27 2017, @06:42PM (#545335)

            I'm not sure what you are trying to insinuate. Of course mutation rates depend on cell line and conditions. By your definition of "spontaneous" there would be no interference at all (changing media, etc) and these cells would all just die.

            • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @07:06PM (5 children)

              by Anonymous Coward on Thursday July 27 2017, @07:06PM (#545347)

              I thought you meant spontaneous mutations arising from the normal error rate in mammalian cells (~10^-10 per cell division). Your definition seems to be what I'd call Cas9-induced, independent of guide RNA.

              https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761330/ [nih.gov]

              • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @09:24PM (4 children)

                by Anonymous Coward on Thursday July 27 2017, @09:24PM (#545448)

                That paper gives two estimates (5e-5 and 7e-9) in fig 2 but say 10^-10 in the intro. Then the drake paper estimates 2e-8 per generation and assumes 400(!) divisions between zygote and sperm, so end up with 5e-11. They cite Drost and Lee 1995 for that 400 generations number, but that paper estimate mutations per division to be 1e^-8 (fig 1). I have seen 1e-8 mutations/cell/division as the more generally cited number, but ok.

                Lets consider starting with a single cell is 400 divisions removed from its ancestor (the fertilized egg). You would have 2^400 = 2.6e120 cells produced during those 30 years (until the sperm fertilizes an egg). Apparently a sperm is ~1e-14 kg, while an average human cell is ~1e-12 kg.[1] Therefore 2.6e106 to 2.6e108 kg worth of human cells need to be produced over the course of 30 years for this scheme to work. The mass of the observable universe is estimated at 1e52 kg.[1] Why nature use such an insane scheme when it is totally unnecessary?[2]

                [1] https://en.wikipedia.org/wiki/Orders_of_magnitude_%28mass%29 [wikipedia.org]
                [2] https://www.ncbi.nlm.nih.gov/pubmed/25459141 [nih.gov]

                • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @10:13PM

                  by Anonymous Coward on Thursday July 27 2017, @10:13PM (#545483)

                  Sorry, that should be "1e-8 mutations/bp/division"

                • (Score: 0) by Anonymous Coward on Thursday July 27 2017, @10:52PM (2 children)

                  by Anonymous Coward on Thursday July 27 2017, @10:52PM (#545502)

                  unless the orderly progression of the hierarchy is disturbed by inflammation, ulceration or trauma

                  That is a very big "unless" when used in the context of cancer.

                  Figure 2 is looking at adult mouse tissue (some of which are heavily exposed to the external environment or have a very different internal environment), so it makes sense that the estimates exceed the ideal error rate of DNA polymerase and the error correction machinery of the cell.

                  The paper probably isn't the best for an estimate, but I came across it while I was looking for the maximum tolerated mutation rate for mammals. If you're interested: It seems that ~100x is tolerated (though the mice die around 3 months compared to 27), while 10000X is embryonically lethal (some random citation that I came across) for mice.

                  • (Score: 0) by Anonymous Coward on Friday July 28 2017, @03:46AM (1 child)

                    by Anonymous Coward on Friday July 28 2017, @03:46AM (#545590)

                    He goes into carcinogenesis later, and discusses how the "multi-stage" theory requires much higher mutation rates. If you get epidemiological data from seer and plot age specific incidence, there is a "turnover" for many cancers where they become less common. This also requires many more divisions and/or much higher mutation rates than usually assumed.

                    Anyway, the best would be if they take a sample of cells before doing any of this "gene modification", and see how many are "modified", then send the rest on to be treated, but that doesn't seem to be a thing. So all we have are their controls. Apparently when someone publishes a paper about this, its is usually 0.1% to 1% are mutated at the target site either before anything happens or due to environmental factors. I couldn't find it earlier, but there is a paper that reports for one situation it was as high as 10%, and low as .001% for another.

                    • (Score: 0) by Anonymous Coward on Friday July 28 2017, @11:55AM

                      by Anonymous Coward on Friday July 28 2017, @11:55AM (#545724)

                      take a sample of cells before doing any of this "gene modification", and see how many are "modified", then send the rest on to be treated, but that doesn't seem to be a thing

                      Yes, I've always found it frustrating that lots of studies skip controls or have few biological and technical replicates. This is more true for expensive techniques (whole genome/transcriptions, ChIP-seq, IP-MS, micro-array, animal models, etc.) as there is little incentive to produce good quality data at the expense of novel, positive data.

                      was as high as 10%, and low as .001% for another

                      Since most quantifications in biology are relative and the systems and techniques can be extremely noisy, most baseline numbers reflect the noise and error instead of being an accurate value (excepting studies that set out to specifically determine this).