[HN Gopher] HIV in cell culture can be completely eliminated usi...
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HIV in cell culture can be completely eliminated using CRISPR-Cas
gene editing [pdf]
Author : geox
Score : 290 points
Date : 2024-03-19 23:12 UTC (23 hours ago)
(HTM) web link (www.escmid.org)
(TXT) w3m dump (www.escmid.org)
| eganist wrote:
| Way out of my depth here, but I'm guessing the main hurdles to
| turning this into a drug are encapsulation in a way that survives
| injection (or better yet, ingestion) as well as either targeting
| of infected cells or at least ensuring that even if it touches
| every cell, it only affects HIV DNA?
|
| Basically, what's needed to commercialize this?
| colechristensen wrote:
| crispr also makes mistakes. The kind that lead to cancer,
| disability and death. It's not a magic wand. Being able to do
| something in cell culture is interesting but very far away from
| a therapy.
| smt88 wrote:
| How do Casgevy and Lyfgenia[1] avoid these dangerous
| mistakes? Is it something that can be generalized to other
| therapies, or does it need to be recreated for each "edit"
| that we want to turn into a therapy?
|
| 1. https://www.fda.gov/news-events/press-announcements/fda-
| appr...
| ghkbrew wrote:
| According to your link, both of those are applied to
| extracted stem cells which are then reintroduced. The
| ability to perform clonal expansion and DNA sequencing
| makes it possible that screening for off-target edits could
| be performed. Though I have no idea if it's actually done.
| jryb wrote:
| Your point is broadly correct (not sure about disability
| though), but I think it overstates the danger of what will
| happen in practice. Yes, if you picked a random target and
| blasted away, you probably wouldn't have a good time. But
| anything that even approaches clinical trials is going to get
| substantial engineering put into it to minimize (and
| characterize) all of the off-target loci. If there's
| meaningful editing near an oncogene then that's going to be a
| deal breaker for a particular guide. When the FDA was
| discussing the Casgevy application, they went into remarkable
| detail of how Vertex had measured the off-targets - the
| regulators really, really don't want to approve anything
| risky.
|
| Frankly just getting it to work at all is the real hurdle in
| this case.
| _heimdall wrote:
| > If there's meaningful editing near an oncogene then
| that's going to be a deal breaker for a particular guide.
|
| At this point do we know every gene that had the potential
| to cause cancer?
| a_bonobo wrote:
| We roughly know the space of possible mutations in the
| human genomes because we have so many sequenced genomes
| now: if we don't spot a mutation it's probably not good
| when it happens, survivorship bias.
|
| The problem with CRISPR is that we cannot control _where_
| the off-target effects happen, we can currently only
| optimise the guiding RNA and the Cas enzyme to have as
| little off-target effects as possible (but not 0, yet).
| It would be cool to engineer guiding RNAs that bind in
| those high mutation-rate areas when they have off-target
| effects, stuff can mutate there and nothing will happen
| (probably).
| colechristensen wrote:
| > Frankly just getting it to work at all is the real hurdle
| in this case
|
| This being the point. Many diseases have been cured dozens
| of times over in a tissue sample in a lab that never make
| it to actual therapies because the hurdle is elsewhere. The
| risks with crispr are as stated, especially flooding your
| entire body with it to target a virus.
| AllegedAlec wrote:
| > Your point is broadly correct (not sure about disability
| though), but I think it overstates the danger of what will
| happen in practice
|
| https://www.nature.com/articles/nrc1122
| amluto wrote:
| One thing I was confused by: why did Vertex choose to
| reactivate HbF instead of attempting to correct the
| mutation that causes sickle cell disease in the first
| place?
| bglazer wrote:
| CRISPR, in the form used by Vertex, is not capable of
| directly repairing an existing gene. In the case of
| sickle cell this means directly changing the mutated
| nucleotide in the HbA gene. CRISPR is very capable of
| _cutting_ the genome at precise locations. These cuts
| lead to lossy repair pathways that introduce mutations or
| deletions that disable the gene at the spot that CRISPR
| cut. So, the best you can hope for is that the CRISPR cut
| leads to a loss of function. It 's possible to use CRISPR
| to introduce new sequences into the DNA, by introducing a
| new DNA sequence alongside the CRISPR proteins, then
| hoping that DNA repair "accidentally" uses the genetic
| sequence you put in to repair the break in the DNA. This
| is even less efficient than just cutting the DNA, and it
| would not fix the mutated HbA, so it's not really
| therapeutically relevant for sickle cell.
|
| There are more recent techniques, notably prime editing,
| that use a modified version of the CRISPR system that can
| introduce changes to single bases (nucleotides) in the
| genome. These have some promise of directly fixing
| diseases caused by single mutations, but there are
| hurdles in terms of efficiently delivering the prime
| editor to the right tissues as well as efficiency of the
| actual repair.
| amluto wrote:
| So how is Vertex activating HbF? Did they find some bases
| to remove that cause the gene to be expressed more than
| usual?
| aaauaucuggaa wrote:
| Generally speaking:
|
| - Delivery: getting the mRNA and guide RNA into the target
| cells
|
| - Expression: ensuring the target cell expresses the mRNA, thus
| making the protein
|
| - On Target Editing Efficiency: ensuring the intended edit
| happens at a high rate
|
| - Off Target Editing: ensuring other edits in other locations
| do not occur
| nextaccountic wrote:
| Does this means that in order to productionize this into a
| drug, one would need to basically engineer a biological virus?
| jjtheblunt wrote:
| https://en.wikipedia.org/wiki/Viral_vector
| lucioperca wrote:
| or mRNA
| XorNot wrote:
| CRISPR is pretty complicated - I'd say it's not clear
| whether mRNA of such length could stably produce enough
| enzyme in enough places. It's great when you need an
| antigen to be presented, but not so much when you need an
| entire restriction enzyme system.
| WheelsAtLarge wrote:
| There's a sickle cell therapy that uses CRISPR. I don't know
| the specifics but if one has been successful then a second can
| be too. I'm looking forward to getting more information in the
| future. Cell culture vs cure is a long road but at least
| there's hope. The big drawback is that these therapies are
| super expensive but time and experience in the past have proven
| that the costs can be lowered.
|
| "Sickle Cell Disease Approvals Include First CRISPR Gene
| Editing Therapy"
|
| https://jamanetwork.com/journals/jama/article-
| abstract/28137....
| crakenzak wrote:
| Yup Casgevy & Lyfgenia! These sickle cell (and now also
| approved for beta thalassemia) CRISPR therapies basically
| work in the following way:
|
| - Blood stem cells are removed from the patient and the
| CRISPR Cas9 protein outside of the body is injected to cut
| the gene responsible for suppressing fetal hemoglobin
| production (even people with sickle cell have healthy fetal
| hemoglobin, their adult hemoglobin gene is what causes the
| deformed red blood cells)
|
| - Chemotherapy is used to kill all living bone marrow and
| remove all previous unedited stem cells.
|
| - New edited stem cells are inserted, and patient recovers
| with new blood production being of healthy red blood cells.
|
| I'd say a huge step forward was FDA and EMA approval, but
| figuring out a way to remove previous unedited stem cells
| with chemotherapy would be a step change in the patient
| experience.
| Etheryte wrote:
| It's both extremely sci-fi and incredibly terrifying that
| one of the steps for a cure is to quote unquote kill all
| living bone marrow. Modern medicine is fascinating in how
| advanced it can be.
| l33tman wrote:
| Yeah it's a spectacular transplant procedure, though it's
| really not that modern medicine, it has been developed
| since the 50s! The step where you irradiate or apply
| chemo to kill off the existing bone marrow had to be done
| at first because the patients had leukemia so you had to
| do this anyway. An interesting thing is that if there are
| still cells left in you, they will be wiped clean by the
| new transplanted immune system in a so called graft-vs-
| host response that also sounds like a horror-movie
| concept :)
| renegade-otter wrote:
| And yet, measles are back.
| blkhawk wrote:
| not sure if you need to kill absolutely all living bone
| marrow. Unlike cancer having 5% sickle cell red blood
| cells is probably fine. That makes the chemo probably way
| less bad than what you would need for cancer.
| giantg2 wrote:
| "- Chemotherapy is used to kill all living bone marrow and
| remove all previous unedited stem cells.
|
| - New edited stem cells are inserted, and patient recovers
| with new blood production being of healthy red blood
| cells."
|
| It's very likely HIV could be cured similarly. I believe
| all the people who have been cured so far are bone marrow
| transplant recipients in which the marrow had a specific
| gene or genes.
| saati wrote:
| It's very different, you only have to fix some of the bone
| marrow to help someone with sickle-cell, but you have to
| eliminate all reservoirs of HIV to cure AIDS.
| WheelsAtLarge wrote:
| I was under the understanding that HIV attacks only immune
| cells, white blood cell, only. All the issues that
| eventually kill are due to the body not being able to
| defend itself. So it seems like a cure would be very much
| similar to a sickle cell cure. Is that not the case?
| dghughes wrote:
| A good video explanation of that too via Sci Show. It's quite
| complex; chemo, lab work and takes a long time and not always
| successful but the majority of the time it is successful.
|
| https://www.youtube.com/watch?v=uHWD8RSw4As
| notfish wrote:
| Relevant xkcd http://xkcd.com/1217
| stared wrote:
| Actually, a handgun is unlikely to kill bacteria.
| croemer wrote:
| It's a joke, also the xkcd talks about cancer cells, not
| bacteria
| ngcc_hk wrote:
| Is it the greatest day or the worst day (or both at the same
| time) of humanity when CRISPR is invented ?
| wigster wrote:
| probably great for humanity 2.0
|
| amazing and scary stuff
| passwordoops wrote:
| Like nuclear
| epgui wrote:
| Probably not "the greatest day", but definitely a very very
| good day.
|
| I think it's too easy to imagine Orwellian scenarios, but I
| think the real worries are much more subtle than people usually
| think, and they usually have more to do with how the world
| already works than with how it could change.
| kjkjadksj wrote:
| We had the ability to do what crispr did already, it just
| simplified the lab work. See TALEN and zinc finger nucleases.
| Khelavaster wrote:
| You'd hope so.. the treatment is already in phase 1/2 combined
| human trials!
|
| https://crisprmedicinenews.com/news/clinical-trial-update-po...
| Metacelsus wrote:
| The big problem is that the CRISPR would need to be delivered to
| 100% of infected cells. And as far as I know (I'm a biologist)
| nobody has a method that can achieve a delivery rate of 100% in
| vivo.
| cft wrote:
| That would be for a cure, but not for a recurrent therapy
| mlrtime wrote:
| Do we even need a cure or therapy if we can essentially use
| this as a vaccine?
|
| Doesn't help people now, but may eliminate it as a threat for
| future generations.
| huytersd wrote:
| Well you can't use it as a vaccine since there would be no
| hiv to preemptively excise.
| ac2u wrote:
| Could that risk evolutionary pressure on whatever is left
| behind so that mutations emerge that are more aggressive?
| SketchySeaBeast wrote:
| If we assume that the treatment needs to reach the HIV cell
| to effect it, and that the danger is not 100% of the cells
| are reached, would it produce evolutionary pressure? The
| survivors aren't interacting with whatever got its buddies,
| right?
| simcop2387 wrote:
| That itself is an evokutionary pressure. Whatever allowed
| them to get missed would get amplified by reproduction.
| Only if it's entirely utterly and only random chance and
| not something like the method doesn't target certain
| cells would it not be applying pressure
| yau8edq12i wrote:
| If you bomb a cow pasture with napalm, you aren't going
| to be left with napalm resistant cows. Just lucky ones.
| And luck isn't genetic.
| ac2u wrote:
| You're viewing the cows in isolation here. Replace the
| cows with cancer cells with different mutations and it
| doesn't work anymore.
|
| There's research going with certain types of cancer where
| the doses of cancer-killing drugs isn't intended to
| eradicate all cancer cells, but to keep it at a level
| that's manageable with future treatments.
|
| The theory being that if you go too far, cells that are
| left with a "lucky" mutation can grow without
| competition, leaving the patient in an even-less
| treatable state down the line.
| yau8edq12i wrote:
| ... Cancer cells? This is about HIV. What are you talking
| about?
| ac2u wrote:
| you're talking about cows in a HIV discussion, so I could
| have said "cows and napalm? we're talking about HIV!",
| but I'm charitably engaging with your analogy to show
| that evolutionary pressure is an active research area in
| disease treatment.
| throwawaymaths wrote:
| The selection pressure would have to be some form of
| resisting the crispr tools from entering the cell or
| functioning in the cell.
|
| The HIV genome is small and I would be surprised if it were
| so easy for such a thing to come about.
| ac2u wrote:
| I'm thinking more of a mutation already present that has
| less treatable traits but can't spread because
| neighbouring cells are already infected. But then when
| the treatment is delivered, it isn't cleared because of
| the difficulty of the delivery mechanism, but the
| treatment _does_ clear up the surrounding cells,
| providing fresh ground for the mutated strain to
| reinfect.
|
| (This is an active research area I've read about in
| cancer treatment, where it's been suggested that being
| too aggressive with clearing certain cancers encourages
| reservoirs of already mutated aggressive variants to be
| unleashed after treatment whereas before the avenues they
| had to spread were already infected with the less
| aggressive variant).
| tg180 wrote:
| ... and so?
|
| Evolutionary pressure is present in any situation and is
| unavoidable. It still has an effect even in cases where
| treatments are effective with a success rate of 100%: the
| selection of diseases for which there is no cure.
|
| Entertaining such a perspective can lead to an extreme
| and undesirable conclusion, that the only logical outcome
| is to do nothing and dismantle the entire modern medical
| practice.
|
| It's not very constructive.
| m3kw9 wrote:
| Does it need to be 100%? We have dormant viruses that are
| domant and would only activate when conditions are good, like
| colds, and we have ways to deal with it. It's an analogy, for
| aids we would deal with it with meds and press it back there by
| turning it into a sort of nuisance like colds. The issue is
| cost and stigma of passing it. I for one still wouldn't want
| aids to be as prevalent as the cold even if it's super easy to
| deal with.
| huytersd wrote:
| There are specific latent reservoirs the HIV hides in. It
| wouldn't need to get every cell in the body, just have a
| favorable probability distribution to hit the reservoirs.
| croemer wrote:
| Science by press release. The results aren't even preprinted yet.
| Only some methods in a 2022 preprint. Looks hyped up, I'd ignore.
|
| > This press release is based on abstracts P0004 P0006, P0013,
| P0026 and P0004 at the European Congress of Clinical Microbiology
| & Infectious Diseases (ECCMID). The material has been peer
| reviewed by the congress selection committee. Only material from
| P0004 has been published in a preprint article. The other three
| have not yet been submitted to a medical journal or as preprints.
| slackfan wrote:
| You can also eliminate most climate-change-causing pollution (and
| microplastics) via nuclear weapons.
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