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spligak 2 hours ago

You're correct about CRISPR Cas9. The off-target affects are difficult to manage.

The paper describes Cas12a2. This is a different mechanism with discovery origins in - of all things - agriculture. It does not attempt in any way to reprogram cells. It uses a guide protein to locate a specific mutation with exacting precision and, when it activates, unleashes total destruction of the cell.

The implications of Cas12a2 on undruggable conditions that exhibit known driver mutation profiles is profound.

Source: I have personally funded novel research based on Cas12a2 for an undruggable condition I have. I have personally seen my condition "cured" in vitro using this technology and it left all of my WT cells unharmed. Some of the researchers I've funded are co-authors in the paper linked. I am a layperson in this field (I'm a SWE, not in biotech), but I am happy to answer questions.

Gethsemane an hour ago | parent | next [-]

Have you written about your experience anywhere? It would be interesting to see how you approached the research sector as a layperson. Are there any plans to move to in vivo? Best of luck with your research!

spligak a minute ago | parent | next [-]

I haven't written about it publicly, but I can elaborate here. I don't mind answering further questions about it even if you believe they'd make me uncomfortable - they won't.

I've come to terms with what's happening to my body and that I may not benefit from my efforts.

Background: ~3 years ago I was diagnosed with a very rare MPLW515L-driven blood cancer known as a myeloproliferative neoplasm. My hematopoietic stem cells (HSCs) acquired this mutation and they produce busted downstream products.

Most notably, one of those downstream products are hyper-lobulated megakaryocytes that spew inflammatory cytokines into my bone marrow and destroy the bone marrow niche over time. The destruction happens specifically because the inflammation mobilizes stromal cells and they erroneously produce scar tissue (fibrosis) all along the walls of the good, spongy marrow. There are other sources of damage but this is the one path most aligned to abbreviated survival and transformation into AML.

In effect, my bone marrow is rusting and very slowly failing. The failure could speed with the acquisition of additional mutations or any other systemic inflammatory condition.

Anyway, 3 years ago my first retail hematologist told me "it's rare, you're fine, take aspirin and go home."

I couldn't accept that - this seemed bad. I decided that if I wanted to know the truth I needed to physically stand in front of the foremost expert in the world on the topic and ask them "what is the state-of-the-art?"

I came to this conclusion after about a year of reading all the most well-cited academic papers about AML, Myelofibrosis, and Essential Thrombocythemia. In particular, anything that mentioned MPL. There are virtually no papers mentioning MPL.

To put that in perspective: 500,000 patients in the US deal with the broad disease category. 5% of those are MPL, and 40% of those are the -K variant. So 10,000 people - which means anything targeting it would be well into orphan drug designation territory. I'd need to find a pretty niche researcher.

So, I laddered up the academic food chain using a little cash (donations), emails, airline tickets, and conference admission. ~2 years after my diagnosis I found myself in a closed-door session called the MPN Roundtable in Chicago with 100 of the foremost experts in the world. No cameras, no transcripts, just some of the greatest minds in the field earnestly debating the path forward to a cure.

I listen carefully to them, ask dumb questions, connect dots across research. I rehomed my care to an academic research hospital specializing in MPN research, and started funding research on the condition it includes my specific MPL mutation. Researchers happy oblige.

Cas12a2 was the keynote topic at this year's meeting and there was _very little_ dissent.

p1esk 14 minutes ago | parent | prev | next [-]

I’d also like to read about your experience.

ordinaryradical an hour ago | parent | prev [-]

Seconding this comment. I would love to read a write-up about your experience and how you’ve been trying to work on solutions for yourself. Stories like these are valuable to the field and inspiring to other folks dealing with a tough diagnosis.

acomjean 37 minutes ago | parent | prev | next [-]

We did whole genome crispr designs at my last university job. Can confirm that off target effects are an issue with cas9. Pattern matching across the genome to see if a design is unique takes some time. These were interesting pipelines to work on.

It’s only a matter of time before the next better thing shows up.

rozap an hour ago | parent | prev | next [-]

This is wild, have you written about it publicly, or can you expand on it here?

shevy-java an hour ago | parent | prev | next [-]

So how does Cas12a2 mitigate off-target effects?

If it were to work, gene therapy as-is would be possible. Which it is not, not even for those overpriced therapies. I have no doubt that sooner or later it will happen, as the problem space is finite, not infinite, but I simply don't see the correlation here.

> The implications of Cas12a2 on undruggable conditions that exhibit known driver mutation profiles is profound.

So what does this change exactly? Humans defined it as "undruggable conditions". You can reason this is an improvement, but I still see it in failure-territory. If it were to work, gene therapy would be an accurate - and affordable - technique. Which it is not right now.

> I am a layperson in this field (I'm a SWE, not in biotech), but I am happy to answer questions.

How does "answering questions" offset the technology being inferior right now?

GaggiX 2 hours ago | parent | prev [-]

I know nothing about this field, but I imagine the actual problem is how do you deliver the Cas12a2 protein to each individual cancer cell compare to a viral gene therapy?

spligak 2 hours ago | parent [-]

There are two major problems, delivery is one of them. Collateral damage of mass cell destruction leading to systemic inflammation is the other.

The approach I'm reviewing now uses lipid nanoparticles (LNPs) for delivery. It isn't great for targeting my bone marrow condition but its workable. The team hasn't optimized it at all, either. There are also viral delivery mechanisms that I haven't studied yet.

The collateral damage problem is the backpressure on the delivery problem. If you get really good at delivery, you can destroy A LOT of cells very quickly. The human body (usually) responds to these events by releasing a lot of pro-inflammatory cytokines. This can lead to cytokine storms or worse.

As you "get good" at killing the target cells, the net effect can turn bad. It will probably be a balancing act.

shevy-java an hour ago | parent | next [-]

Lipid nanoparticles are quite old as-is. How do you target cells specifically?

> If you get really good at delivery, you can destroy A LOT of cells very quickly.

You can destroy cells quickly. Ok. So the question is: how do you detect specifically only cancer cells via lipid nanoparticles? That was already a problem years ago with Herceptin. The rationale that is always used is that "we need to do something" for certain aggressive cancers. It has never been a super-effective technique, despite all the promo of how monoclonal antibodies are so accurate.

> As you "get good" at killing the target cells, the net effect can turn bad. It will probably be a balancing act.

That's already the status quo in the whole cancer field. I don't think that more than sloppy accuracy is acceptable for any gene therapy - and the off-target cleaving of CRISPR has always been the number #1 problem here.

cyberax an hour ago | parent [-]

> So the question is: how do you detect specifically only cancer cells via lipid nanoparticles?

You don't. Healthy cells will also get these nanoparticles, but without the triggering DNA sequence, the mRNA payload will remain inert and eventually will be degraded.

im3w1l an hour ago | parent | prev [-]

Naively, I would deal with this by deciding how many cells I want to kill each day and then figure out a dosing schedule that achieves that. Or maybe it's better to do one dose every few days. But yeah either way.