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posted by martyb on Saturday September 02 2017, @07:16PM   Printer-friendly
from the crispr...-where's-the-bacon? dept.

Tech Review warns of a possible investment scam?

https://www.technologyreview.com/s/608749/in-a-sign-of-gene-editing-frenzy-startup-pitches-editing-without-crispr/

Having something better than CRISPR would be high-impact. But Homology's scientific results aren't yet widely accepted. In fact, several scientists told MIT Technology Review that they believe the claims are probably wrong.

"What's surprising is this company raised so much money on something thought to be untrue in the scientific community," says David Russell, a researcher at the University of Washington, in Seattle. "I think there is just a gene-editing frenzy."

Something about specially designed viruses that don't have to "slash open" human genes to change them. Sounds like something the herd (Wall St speculators) would be happy to get behind.

The paper has not yet been published, but here are some additional links to further information:

From Dr. Lowe's "In the Pipeline" blog - http://blogs.sciencemag.org/pipeline/archives/2017/08/31/good-craziness-and-bad-craziness
Conference abstract on the research - http://www.abstractsonline.com/pp8/#!/4399/presentation/1352
AAV vectors -- use in gene therapy - https://en.wikipedia.org/wiki/Adeno-associated_virus#Use_in_gene_therapy


Original Submission #1Original Submission #2

 
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  • (Score: 0) by Anonymous Coward on Sunday September 03 2017, @03:12PM (6 children)

    by Anonymous Coward on Sunday September 03 2017, @03:12PM (#563148)

    It is a functional assay.

    Functional assays are important as a proof of concept and demonstrate that there isn't any obvious or non-obvious problems. In this particular example, it could be possible that there was successful recombination (detected by sequencing) but subsequent methylation or histone re-shuffling could render the region transcriptionally silent. Green fluorescence and luciferase activity demonstrate that this is not the case and provide additional information not given by the sequencing results.

    Another functional assay that would be useful is to demonstrate that the HSCs maintain their full differentiation capacity after AAV-induced recombination.

  • (Score: 0) by Anonymous Coward on Sunday September 03 2017, @03:49PM (5 children)

    by Anonymous Coward on Sunday September 03 2017, @03:49PM (#563153)

    It doesn't show anything beyond that GFP is in the cell and being expressed (or not)... I bet this happens in some percent of the control cells too. Actually on rereading that description it sounds like they used lack of fluorescence to indicate "editing".

    • (Score: 0) by Anonymous Coward on Sunday September 03 2017, @04:40PM (4 children)

      by Anonymous Coward on Sunday September 03 2017, @04:40PM (#563170)

      I bet this happens in some percent of the control cells too.

      Please clarify this for me because I'm having trouble figuring out your position:
      1. You assume that some percentage of primary human cells are intrinsically green fluorescent.
      2. You accept that the gene encoding GFP was delivered into the cells at a specific position, as determined by sequencing.
      3. You believe that the green fluorescence observed after the treatment with the AAV vectors is only a result of #1 and not #2.

      it sounds like they used lack of fluorescence to indicate "editing"

      No, read the conference abstract.

      • (Score: 0) by Anonymous Coward on Sunday September 03 2017, @05:04PM (3 children)

        by Anonymous Coward on Sunday September 03 2017, @05:04PM (#563182)

        No, the human cells should not contain GFP, but you don't need CRISPR/cas8 to get GFP incorporated into human cells. If you mix the cells with vector containing GFP some of it will get spliced into the genome of some cells (how much depends on the conditions).

        Also, I do not "accept #2" automatically, but those results render the GFP results irrelevant for their purposes. Just skip the GFP (fine, use it as a quick screen internally... but don't report it as some kind of main result) and do more in depth sequencing analysis (single cell, percentage of various variants, primers at various distances from the target site, etc).

        • (Score: 0) by Anonymous Coward on Sunday September 03 2017, @05:35PM (2 children)

          by Anonymous Coward on Sunday September 03 2017, @05:35PM (#563188)

          CRISPR was not involved at all - it's right in the title.

          some of it will get spliced into the genome of some cells (how much depends on the conditions)

          The whole point of the study was to find AAV vectors that were more efficient at mediating recombination in HSCs.

          DNA sequencing does not demonstrate transcriptional activity. Sustained GFP expression is also a form of independent confirmation that the sequencing data isn't a result of sequence contamination.

          • (Score: 0) by Anonymous Coward on Sunday September 03 2017, @05:43PM (1 child)

            by Anonymous Coward on Sunday September 03 2017, @05:43PM (#563191)

            Yea, sorry. I just grouped it in as "editing" and forgot we aren't talking about CRISPR here.

            Let's see what their purpose was in measuring fluorescence: "Editing was measured by GFP expression".

            They are trying to measure editing, not transcriptional activity.

            • (Score: 0) by Anonymous Coward on Sunday September 03 2017, @07:11PM

              by Anonymous Coward on Sunday September 03 2017, @07:11PM (#563205)

              Editing was measured by GFP expression at the cellular level and confirmed by multiple molecular assays including Sanger and Next Generation sequencing

              The full quote is relevant.

              The GFP phenotype implies a functional gene and can be used as a quantifiable measure of efficiency, depending on how you perform the assay. Flow cytometric analysis, likely what was used, could provide quantification of the number of cells that became GFP positive as a result of the treatment.

              GFP signal alone would not be sufficient as a measure of recombination efficiency, but it acts as a good proxy. Sequencing data can provide a quantification of efficiency as well if the experiments are designed with that in mind.