Tell Me Why - Obscura

Discussion in 'Education & Personal Growth' started by Cimorene, Oct 6, 2016.

  1. Cimorene

    Cimorene Platinum IL'ite

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    Questions that always pinballed in your head but you don't known the answers because

    (1) You were too embarrassed to ask
    (2) You were too confused about the subject
    (3) You didn't think it mattered much
    (4) You didn't want to glow like the only "idiot" in the room
     
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  2. Cimorene

    Cimorene Platinum IL'ite

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    Question:

    When I read articles on gene alteration on adults, I can never grasp how is a cell identified for genome modification.
    There is an organ, tissue, then cells.

    How can modification of a single cell alter the behaviour of the organ in adults. In stem and gamete cells it is different but how does gene modification work in treating diseases in adults. How many cells are rectified? More than one cell? All the cells in a tissue are rectified (impossible!)

    What if the cell that was tampered dies? Can really such splicing in a single cell propagate in a way to fix the genetic defect across an organ?
     
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  3. sokanasanah

    sokanasanah IL Hall of Fame

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    Hmmm, no takers for this? OK, here goes:

    A comprehensive answer would be an essay, but in short, most often, therapy is still directed at stem cells, especially hematopoietic (blood) stem cells. They are relatively easily harvested (from bone marrow), engineered ex vivo (outside the body), expanded to tens of millions in culture in the laboratory and then re-injected.
    One doesn't try to rectify every cell. Although there are many variations, the easiest way to think about it conceptually is to consider it as "enzyme replacement therapy" i.e. just provide enough of an enzyme that is missing to overcome the debilitating effects of a lack.

    The greatest unqualified success so far, after 30 years of research, the only gene-therapy approved (earlier this year, in the EU) for clinical (non-research) use, at a cost of ~$1 million per patient, is for ADA-SCID; it works exactly in this way. In principle, this is no different than injecting insulin for diabetics.

    Things get more complicated for cells that do not divide, where there may not be a stem cell option - Parkinson's disease for example, which is thought be a result of a lack of dopamine due to the death of dopamine-producing neurons. Brain cells do not divide. They cannot be removed and put back as easily as blood cells and made to reconstitute functional tissue. Then one attempts the next best thing. Engineer a virus with a gene(s), for dopamine in this case, inject millions of copies of it driectly into the brain and coax cells that don't normally make dopamine to now do so. This can relieve symptoms. Less effective, but progress nonetheless, not approved clinically, still only for research use.

    You just have to find a way to correct the deficiency in the right tissue or get whatever is required, there. No point delivering dopamine to the kidney.

    Many, many variations exist, specific to disease, target tissue, mode of delivery etc. but these two examples cover the broad categories of options. The rest is detail.
     
    Last edited: Oct 6, 2016
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  4. sokanasanah

    sokanasanah IL Hall of Fame

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  5. magician

    magician Silver IL'ite

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    What's on the other side of a black hole?

    If I pretend to be pretentious, am I still pretentious?

    Is it easier to be unhinged than uh... hinged?

    Where do babies come from?

    Why do people have babies?

    ...oh wait, I'm pretty sure I've asked that one before.
     
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  6. vaidehi71

    vaidehi71 IL Hall of Fame

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    Oh yes, and I remember replying as well!:)
     
  7. Cimorene

    Cimorene Platinum IL'ite

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    sokanasanah, thanks for being the taker.

    I found your link: Gene-therapy treatment for “bubble boy” syndrome finally moves from concept to cure
    very informative esp. the below part which you also mentioned in your post.

    Strimvelis uses a “repair and replace” strategy, so called because doctors first remove stem cells from a patient’s bone marrow then soak them with viruses to transfer a correct copy of the ADA gene.

    To provide you the backdrop of my original post, I came across a popular science (not academic) article on viruses used as vectors to fix genes last week. How cystic fibrosis (CF) can be treated with gene therapy by compensating the faulty cystic fibrosis transmembrane conductance regulator (CFTR) protein with DNA from lentivirus or adeno-associated virus as vectors. Link: Cystic fibrosis and Gene therapy

    Lentivirus to fix CFTR

    In the new studies two teams tested two different gene therapy strategies to get functional CFTR into the airway cells of CF pigs. One group led by McCray and Patrick Sinn, UI research associate professor of pediatrics and director of the UI Viral Vector Core, focused on a lentivirus. This type of virus has been successfully and safely used as a gene therapy vector for patients with rare immune diseases. A major advantage of lentiviruses is the delivered gene is directly incorporated (integrated) in to the cell's genome, meaning the fix is permanent. However, it is challenging to produce large quantities of lentivirus, and this virus has not yet been tested for safety in human lungs.

    AAV2 to fix CFTR

    The other research team, led by Zabner and David Schaffer at University of California, Berkeley, focused on an adeno-associated virus AAV2. AAVs are safe for use in humans, including human lungs, and relatively easy to produce in large quantities. Genes delivered by AAV vectors are not permanently incorporated into the cell's genome, but expression of the gene is often long-lived.


    The confusion in my question is the below challenging aspect of gene therapy. Is this bleeding technology ten or twenty years from now, or we are almost there. How is this challenging aspect jerry-rigged today - "safely delivering genes to the correct cells"?

    Despite the simplicity of the gene therapy concept -- replace a disease-causing gene with a normal version -- safely delivering genes to the correct cells so that they produce sufficient amounts of the replacement protein to treat a disease has proved difficult to achieve.

    Your post has given me enough pointers. I still have that rattle in my brain around this whole as-good-as-magic medical breakthroughs, and that is because I have only superficial understanding of the process and not in-depth disciplinary finesse.

    While we are with the genes and stem cells, a quick query on the Berlin patient (the second one) here

    Today, researchers point to three different factors that could independently or in combination have rid Brown’s body of HIV. The first is the process of conditioning, in which doctors destroyed Brown’s own immune system with chemotherapy and whole body irradiation to prepare him for his bone marrow transplant. His oncologist, Gero Hütter, who was then with the Free University of Berlin, also took an extra step that he thought might not only cure the leukemia but also help rid Brown’s body of HIV. He found a bone marrow donor who had a rare mutation in a gene that cripples a key receptor on white blood cells the virus uses to establish an infection. (For years, researchers referred to Brown as “the Berlin patient.”) The third possibility is his new immune system attacked remnants of his old one that held HIV-infected cells, a process known as graft versus host disease.

    Let's assume that from the above factors: conditioning, mutation in gene and graft versus host disease factors , "mutation in gene" did contribute. In both Case A: corrupted CF protein and Case B: HIV infected cells, if the DNA is delivered and the gene is implanted in faulty cells either using the non-viral or viral vector methods, my schoolgirl doubt would be

    (1) How is that DNA synthesised?

    1.a) Extract DNA from a healthy cell of a donor (this is viable)

    2.b) Are we technologically advanced to manipulate nucleotide bases and re-programme the genes of host cells ( in situ or ex vivo ) instead of implanting healthy donor cells so as not to enrage the immune system from foreign insertion. May be my understanding is wrong, perhaps, at a microscopic level the rejection level is imperceptible and only more macroscopic level we run into organ transplants failures.
     
    Last edited: Oct 7, 2016
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  8. sokanasanah

    sokanasanah IL Hall of Fame

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    No need to do this. Technology exists to "copy" any gene you want from any organism you want. Putting it into any organism you want is slightly harder, but putting it where you want in the genome just became ridiculously, garage-lab easy. It is trivial to do this in human cells these days. A high-school student could do it.
    You can do this in a machine, imaginatively called a "DNA Synthesizer". You can pretty much chemically synthesize any gene you want, on demand. Type in a gene sequence into the computer (an instrument controller), screw in bottles of reagents and it will spit out whatever you want. Then you do some QC and get on with your plans for annihilating human civilization, world domination, contaminating planets and asteroids or whatever you have on your calendar. You can make Ebola or plague DNA if you want to. It is dirt cheap, with a little up-front investment for equipment. It is so easy that this is a serious biosecurity issue. You can have any DNA you want made by mail-order. They will first check whether you are making something dangerous (by law in the US and EU). So if you want to make something pestilential, you have to buy your own machine (not that hard to do, although controlled) and do it in your volcano or undersea hideout.
    Genes, yes, we have the technology, entire bacterial or viral genomes yes, has already been done many times over, whole chromosomes, not yet (can't do anything about Down's Syndrome trisomy yet, for example), but moving very fast.
    It's all pretty microscopic isn't it? The hierarchy you are probably looking for is: molecular -> cellular -> tissue -> organ.
    The "immune system" is not an impediment to DNA manipulation. It begins to become a factor when that DNA makes foreign proteins once inside a cell, gets more serious with cells (that's why you have to match BM donors, kill off the old immune system etc.) and becomes even more of a factor when it's entire organs (kidney transplants, liver transplants etc.).
     
    Last edited: Oct 7, 2016
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  9. Cimorene

    Cimorene Platinum IL'ite

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    This is truly astounding! I feel like I'm trapped in some jurassic amber while the world has whizzed by.
    Thank you for taking your time out to write here. Your writing is very coherent like a tutorial series.

    Do you teach Optics and Particle Physics also by any chance :rolleyes:
     
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