Brian Naughton // Thu 12 July 2018 // Filed under biotech // Tags biotech alzheimers antibody

There have been a lot of results coming out from Alzheimer's trials recently, and a lot of discussion about the "amyloid hypothesis" and its role in the disease. In this post I'll review some of the evidence, and see how it relates to data from recent AD trial results from Merck and Biogen/Eisai. I mainly reference three good reviews that cover most of the basic facts and arguments around the amyloid hypothesis. Much of my additional data is from AlzForum, a fantastic resource for Alzheimer's news.



The basics

A simplified model of the amyloid hypothesis is that the cell-surface protein APP (Amyloid Precursor Protein) gets cleaved by BACE1 and γ-secretase and released as a 42 amino acid peptide, Aβ42; Aβ42 forms oligomers, then extracellular plaques in the brain; these oligomers and/or plaques somehow lead to intracellular Tau tangles which cause neuronal death.

One big question here is whether it's the plaques or oligomers that are the main trigger:

Several similar studies suggest that Aβ — particularly soluble oligomers of Aβ42 (Shankar et al, 2008) — can trigger AD‐type tau alterations

This model is nicely summarized by a diagram from NRD:

amyloid primer

As the diagram shows, the obvious drug targets are γ-secretase and BACE1 (to stop Aβ42 production), Aβ42 monomers/oligomers/plaques (to reduce plaque formation), Tau (to prevent Tau tangles).

There have been drugs targeting all of these processes. None have been successful:

The only approved drugs for Alzheimer's are fairly ineffectual cholinesterase inhibitors (and an accompanying NMDA receptor inhibitor). These drugs are usually thought of more as symptom relief than treatment.

Aβ42 Antibodies

Why do drug companies keep making Aβ42 antibodies after so many failures? In fact, there is quite a bit of variability in what these antibodies actually do. Ryan Watts, now CEO of Denali Therapeutics, gave an interview with AlzForum back in 2012 where he explained the difference between Genentech's crezenumab and other Aβ42 antibodies.

Q: How is crenezumab different from the other Aβ antibodies that are currently in Phase 2 and 3 trials?

A: We have a manuscript under review that describes its properties. Basically, crenezumab binds to oligomeric and fibrillar forms of Aβ with high affinity, and to monomeric Aβ with lower affinity. By comparison, solanezumab binds monomeric Aβ, and gantenerumab binds aggregated Aβ, as does bapineuzumab. Crenezumab binds all forms of the peptide. Crenezumab is engineered on an IgG4 backbone, which allows it to activate microglia just enough to promote engulfment of Aβ, but not so strongly as to induce inflammatory signaling through the p38 pathway and release of cytokines such as tumor necrosis factor α. Crenezumab is the only IgG4 anti-Aβ antibody in clinical development that I am aware of. We have not seen vasogenic edema in our Phase 1 trials, which was the first main hurdle for us to overcome.

Biogen describes the MOA of their aducanumab antibody like this:

Aducanumab is thought to target aggregated forms of beta amyloid including soluble oligomers and insoluble fibrils which can form into amyloid plaque in the brain of Alzheimer’s disease patients.

Denali Therapeutics

As an aside, Denali is not working on an Aβ42 inhibitor (perhaps for IP reasons since Ryan Watts was heavily involved in the development of crezenumab). Apart from their novel RIPK1 program, they are still pursuing BACE1 and Tau.

Our lead RIPK1 product candidate, DNL747, is a potent, selective and brain penetrant small molecule inhibitor of RIPK1 for Alzheimer’s disease and ALS. Microglia are the resident immune cells of the brain and play a significant role in neurodegeneration. RIPK1 activation in microglia results in production of a number of pro-inflammatory cytokines that can cause tissue damage.

Our three antibody programs are against known targets including aSyn, TREM2 and a bi-specific therapeutic agent against both BACE1 and Tau. Our BACE1 and Tau program is an example of combination therapy, which we believe holds significant promise in developing effective therapies in neurodegenerative diseases.



How does amyloid cause disease?

By one definition, the amyloid hypothesis "posits that the deposition of the amyloid-β peptide in the brain is a central event in Alzheimer's disease pathology". There are several ways that amyloid could cause AD. This diagram from a 2011 NRD review shows three options:

amyloid hypothesis

  • Aβ trigger: Aβ triggers the disease once it reaches a threshold, and once it starts, reducing Aβ levels does not help
  • Aβ threshold: Aβ triggers the disease once it reaches a threshold, but reducing Aβ levels back below the threshold does help
  • Aβ driver: Aβ causes Alzheimer's, and reducing Aβ levels at any time should ameliorate disease

Simplifying, if the Aβ trigger model is correct, then we don't expect anti-Aβ42 antibodies to work, except perhaps preventatively. If the Aβ driver model is correct, then these antibodies should work, at least partially.

From the same review:

A strong case can be made that the deposition of amyloid-β in the brain parenchyma is crucial for initiating the disease process, but there are no compelling data to support the view that, once initiated, the disease process is continuously driven by or requires amyloid-β deposition.

For this reason, after Aβ42 antibody trials fail, the stock answer from pharma is that they need to begin treatment earlier. Of course, the earlier you treat, the longer the trial takes, and the more you need new amyloid detection technologies like Florbetavir/PET to see what's going on. So it's probably natural that there is a gradual transition to ever earlier interventions and longer trials, even though this can also seem like excuse-making.



Evidence for the amyloid hypothesis

Despite all the failed drugs and holes in our understanding, the amyloid hypothesis remains durable due to the weight of evidence in its corner.

APP

Mutations in APP both cause and prevent Alzheimer's. Half of people with trisomy 21 (or any APP duplication, it seems) develop AD by the time they reach their fifties.

A protective variant found in APP also points to a causal relationship, and therapeutic potential (see Robert Plenge on allelic series).

We found a coding mutation (A673T) in the APP gene that protects against Alzheimer's disease and cognitive decline in the elderly without Alzheimer's disease. This substitution is adjacent to the aspartyl protease β-site in APP, and results in an approximately 40% reduction in the formation of amyloidogenic peptides in vitro. Carriers are about 7.5 times more likely than non-carriers to reach the age of 85 without suffering major cognitive decline

A cryoEM structure of Aβ42 fibril from 2017 gives us structural evidence for why APP mutations should be protective or damaging, suggesting that APP's effect on AD is via amyloid/Aβ42. amyloid

APOE

The APOE e4 allele strongly predisposes people to Alzheimer's. It's one of the strongest genetic associations known, besides Mendelian diseases. In 2018, Yadong Huang's team at the Gladstone Institiute used iPSCs to investigate the mechanism. Confusingly, they found that APOE is independently associated with both Aβ42 and Tau.

"ApoE4 in human neurons boosted production of Aβ40 and Aβ42"

"It does not do that in mouse neurons. Independent of its effect on Aβ, ApoE4 triggered phosphorylation and mislocalization of tau."

"Based on these data, we should lower ApoE4 to treat AD"

This research may also help explain why mouse models of Alzheimer's have often been misleading.

Other evidence

  • Mutations in PSEN1 and PSEN2 (components of gamma-secretase) cause Alzheimer's.
  • Other diseases are caused by mutations in amyloid-forming proteins. For example, there is a mutation that enables IAPP to form amyloid, which causes Familial British Dementia. In ALS, the aggregated form of SOD1 may be protective and the soluble form disease-causing.

    The formation of large aggregates is in competition with trimer formation, suggesting that aggregation may be a protective mechanism against formation of toxic oligomeric intermediates.



Criticism of the amyloid hypothesis

The main criticism of the antibody hypothesis is that we have been testing anti-amyloid drugs — especially antibodies against Aβ42 — for a long time now, and none of them have had any effect on disease progression.

Derek Lowe (and many of his commenters) has written especially skeptically on his blog:

Eli Lilly remains committed to plunging through this concrete wall headfirst. [...] our gamma-secretase inhibitor completely failed in 2010. Then we took our antibody, solanezumab into Phase III trials that failed in 2012. And found out in 2013 that our beta-secretase inhibitor failed.

Morgan Sheng, VP of Neuroscience at Genentech, is much more positive. In a recent interview in NRD he said:

Let me start by saying that I fully believe in the amyloid hypothesis, and I think it’s going to be vindicated completely within years. [...] phase III results from drugs like Eli Lilly’s solanezumab suggest these agents sort of work; they just don’t work very well

It seems like targeting Tau is an acceptable strategy to amyloid hypothesis skeptics because it's not targeting Aβ42, even though it's still part of the standard amyloid hypothesis model. Drugs that are based on the "amyloid hypothesis" and drugs that work by trying to reduce amyloid tend to get conflated in a confusing way.

Evidence against the amyloid hyothesis

Here I am mainly summarizing from a 2015 review. In this review, the author mainly disputes the "linear story" of the amyloid hypothesis and not the fact that Aβ plays some kind of role in AD.

  • Many people have plaque but no disease.

    The existence of this group of individuals (healthy, but amyloid positive) is a substantial challenge to the amyloid cascade hypothesis. It is clearly possible to have amyloid deposits without dementia; therefore amyloid is not sufficient to cause disease.

    Such individuals are not rare; rather, they account for a quarter to a third of all older individuals with normal or near-normal cognitive function.

  • Anti-Aβ42 antibodies can reduce plaque without alleviating the disease.

    The second test of the amyloid cascade hypothesis has also been done: amyloid has been removed from the brains of individuals with AD and from mice with engineered familial forms of the disease. Here the tests have been less definitive and the evidence is mixed.

  • Other drugs that should work (beta-secretase inhibitors, gamma-secretase inhibitors, BACE1 inhibitors, Tau inhibitors) don't appear to work.

  • Mutations in the Tau gene can cause dementia without plaques forming, so amyloid is not a necessary step in the process.

  • We do not understand AD pathology well. For example, what are the toxic species of Aβ and Tau? What is the connection between Aβ and tangle pathology? Do Tau tangles spread between neurons like prions?

  • There are other possible causes of AD. For example, certain infections could be causative.

Infection

Recent work showing an association between herpes virus and Alzheimer's could be thought of as supporting or disputing the amyloid hypothesis. In this model, the virus "seeds" amyloid plaque formation, which then sequesters the virus. The idea that amyloid plaques are protective is not entirely new, beginning with the "bioflocculant hypothesis" for Aβ, published in 2002.

[Robinson and Bishop] posited that Aβ’s aggregative 332 properties could make it ideal for surrounding and sequestering pathogenic agents in the brain

If herpes causes AD, then we'd expect to see evidence in epidemiological datasets. Both herpes infection and periodontitis appear to be associated with AD risk. Further, antiherpetic medications appear to reduce the risk of AD. A lot more could be done here with a large database of phenotypic information, like UK biobank...

Relatedly, a Bay Area company, Cortexyme, recently raised $76M to pursue an AD drug against a bacterial protease found in plaques.



Recent news

So what about the recent trial results? There were two major trials with new results this year: Merck's BACE1 inhibitor, verubecestat, and Biogen/Eisai's anti-Aβ42 antibody, BAN2401. Meanwhile the trial design for Biogen's aducanumab is being tweaked — not a good sign generally — and there should be new data on that later this year.

Verubecestat

After failing a Phase III in 2017 verubecestart had more bad news last month:

Treatment with verubecestat reduced the concentration of Aβ-40 and Aβ-42 in cerebrospinal fluid by 63 to 81%, which confirms that the drug had the intended action of reducing Aβ production. In the PET amyloid substudy, treatment with verubecestat reduced total brain amyloid load by a modest amount; the mean standardized uptake value ratio was reduced from 0.87 at baseline to 0.83 at week 78 in the 40-mg group. These results suggest that lowering Aβ in the cerebrospinal fluid is associated with some reduction in brain amyloid.

Notably, despite the drug working as intended, the reduction in brain amyloid was minimal. Hence, some people claim that amyloid removal has not been tested: gc tweet

Merck's Aβ42 antibody, BAN2401

New Phase II results for Merck's soluble protofibril antibody, BAN2401, were just released in July 2018. The results were hotly disputed because while the Bayesian analysis failed to show an effect, an alternative p-value based analysis (ANCOVA) showed positive results. I don't know exactly what the differences between the analyses were, but generally you would hope for agreement between the two, unless the effect was pretty marginal or just not real. The data pulled out in the tweet below shows how strange this situation is. Merck tweet

Given the ambivalent nature of the result, naturally some saw it as positive news, since there was at least something, while skeptics saw the opposite.

Aducanumab

Aducanumab often seems like the most promising anti-Aβ antibody, and maybe the last chance for anti-Aβ antibodies to prove themselves. Back in 2015, Aducanumab showed some promising Phase Ib results. (I even wrote about it).

“They’re the most striking data we have seen with anything, period,” says [an AD trialist]

However, since then the many related trial failures, plus Biogen changing the trial design due to "variability", have left many people pessimistic. Perhaps BAN2401's recent results, however unsatisfying, show that an Aβ inhibitor is not just doomed to show no effect.

Conclusions

There doesn't actually seem to be much controversy about whether amyloid has a role in Alzheimer's; the genetic evidence is especially hard to dispute. I think the disagreement is more whether reducing Aβ plaques (or oligomers) can treat or prevent Alzheimer's. If the plaque is protective, then it's possible that reducing plaque may even worsen the disease.

There are also still plenty of unanswered disease mechanism questions, like whether it's oligomers or plaques that are causative, how Tau tangles cause neuronal death, and how tangles spread from neuron to neuron. Also, a 2018 paper suggests that Tau's function is the opposite of what we thought: instead of stabilizing microtubules, it keeps them dynamic.

One obvious question is why are there not more Tau-based drugs? Tau pathology is not a new idea and Tau's causal relationship with dementia is one of the least controversial parts of the AD story. In fact, there are now at least five Phase I trials underway, so these drugs might just be lagging behind Aβ42 antibodies by a few years. Certainly, Tau tangles being intracellular and in the brain makes drug development more complicated.

"Anti-tau antibodies don’t enter neurons and they don’t bind intracellular tau. We’ve invested a lot of careful rigorous work to try and understand this and I hope that the field will agree that we can put to rest that question"

(Crossing the blood-brain barrier is a problem for almost all AD drugs and especially antibodies — an interesting rule of thumb is that about 0.1% of antibody gets into the brain.)

Despite all the failures, I think the story is coming together and I'm pretty optimistic. We haven't actually tried that many ways of attacking the disease. I think that reducing plaque and/or oligomers very early could still work — mainly because we have seen the "drug" APP A673T working — meanwhile, reducing Tau tangles is arguably the most promising avenue of intervention, and it is yet to be properly tested.

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Brian Naughton // Mon 11 September 2017 // Filed under biotech // Tags biotech vc

Y Combinator recently announced that they want to do more biotech, specifically "health and synthetic biologies". This seems like a good thing in general, since there aren't too many incubators for biotech out there. IndieBio is the biggest, but they are completely focused on biotech, even providing lab space.

So what are YC actually investing in? Here are the biotech companies from the 2017 Winter and Summer batches (data from techcrunch: 1 2 3 4):

  • Darmiyan: Alzheimer's diagnostic
    We definitely need better Alzheimer's diagnostics, so this seems like a great thing. Usually these diagnostics are designed to help enroll prodromal patients in clinical trials (e.g., Avid), but this one seems to be for screening too, at least according to techcrunch. It's unclear to me what their technology is, though it appears to be MRI-based.
  • HelpWear: heart attack-detecting wearable
    This watch monitors heart palpitations, arrhythmias and heart attacks. I'd buy one if I were at risk... It will enter clinical trials in the "near future."
  • Oncobox: cancer genetic test
    This test appears to match cancer drugs to patients, so I guess it's similar to Foundation Medicine, though with "full DNA and RNA profiles". Usually, it's pretty expensive to do anything novel like this, since you have to convince doctors that it makes sense. So you need to fund a trial, or ten.
  • Forever Labs: autologous stem cells
    Pretty cool, but reminiscent of the whole cord blood thing. It also reminds me of the companies you can send your surplus teeth to (there are several!), which is an odd, but noninvasive, way to get stem cells from kids.
  • Cambridge Cancer Genomics: "next gen liquid biopsy, AI, smart genomics"
    This is quite a few buzzwords, especially for a British company. They say they are "applying our proprietary analysis to a tumour's genomic features", to help guide treatment. The team certainly looks solid, but similarly to Oncobox, they will likely need a bunch of money to prove this works.
  • Modern fertility: at-home fertility test
    These guys appear to be packaging a panel of useful fertility tests for home use. I don't think they have to invent anything new here, which is probably a good thing. It's "physician-ordered", which avoids FDA involvement (and is also a good phrase to search for in "DTC" genetic tests...)
  • BillionToOne: NIPT for developing countries
    (Disclaimer: I know these guys). This one makes sense to me. NIPT is a great technology that should be brought to every country.
  • PreDxion: blood test for the ER
    This appears to be a POC blood test. I don't doubt the need for new tests like this, but they'll need to go through FDA, which is a long road.
  • Clear Genetics: automated genetic counseling
    Automating genetic counseling is necessary because there are only a couple of thousand genetic counselors in the US and the tests are getting more common and more complex. It's a bit hard to believe genetic counseling is a $5B market in the US though, since that implies $2M+ revenue per genetic counselor.
  • Delee: a circulating tumor cell diagnostic
    I thought CTCs were done after On-Q-Ity but it's been a while and there's probably something new and interesting to do here. They've completed a small trial already, which is great.
  • AlemHealth: radiology imaging diagnostic
    Like BillionToOne, AlemHealth is bringing a known-useful technology to emerging markets. Perhaps surprisingly, I believe this kind of global radiology outsourcing is already common in the US (one large healthcare system sends images to Brazil and India, apparently).
  • Indee: CRISPR research tool
    This is apparently for "developing and manufacturing" cell therapies by gene editing. It sounds novel, cell therapies are here for the long-term, and there are dozens of CAR-T companies around to pay for it, so it could be cool.
  • InnaMed: home blood-testing device
    This seems to be a cartridge-based blood diagnostic, kind of like Cepheid, except for home use. I don't know if doctors like to bill for these visits or not, which can kill adoption, but if InnaMed can pull it off it seems like a great thing... Like PreDxion, they'll need FDA clearance.
  • Volt Health: electrical stimulation medical device
    This seems to be a topical neurostimulation device to treat incontinence. It looks like one of those electrical muscle stimulation belts for your abs. I instinctively like this because incontinence is one of those massive problems nobody wants to work on. Maybe the trial will be inexpensive too, since the risks seem low.

My sole criterion for a company to make the list was that it may involve FDA, CLIA/CAP, or similar. There may be omissions! — I just skimmed through the techcrunch articles.

In 2015, 18 out of 108 YC companies were labeled "biomedical". My criteria are stricter, and I count 14 out of 210 companies from 2017 as "biotech". This appears to be lower than — or at least not significantly higher than — the number in 2015, somewhat contradicting the YC quote.

Interestingly, the 2015 batch were also much more computation- and therapeutics-focused, including 20n, atomwise, Transcriptic and Notable Labs. Synbio leader Ginkgo was funded in 2014. 11 of the 14 biotechs from 2017 are diagnostics (including Clear Genetics), one is a therapy / medical device (Volt), one a research tool (Indee), and one a service I can't classify (Forever Labs).

It's a curious set of companies, surprisingly light on computation- or data-driven companies, which you'd think would be YC's strength. Also notably, I don't see any synthetic biology companies (arguably Indee?) and only Volt Health is therapeutic. By contrast, IndieBio has many (at least half?) synthetic biology companies, and several therapeutics.

Because the list is so diagnostics-focused, many of the companies on this list will need expensive trials to properly enter their markets. Perhaps the YC program is setting them up for a raise from traditional biotech VCs? I don't yet see what YC wants to do in biotech, but their statement about doing more is only a few months old, so it will be interesting to see what happens in 2018.

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Brian Naughton // Tue 27 June 2017 // Filed under biotech // Tags biotech drug development

I looked around for a broad review of this area, discussing classes of drug targets and therapies, but didn't really find anything. These are some notes I made in an effort to help understand the landscape.

Drug target types

Every drug has a "target", a biomolecule that the drug affects in humans. There are only a few options for targets.

  • Underexpressed protein
    Sometimes, a protein is lacking and needs to be upregulated or replaced. The solution, for extracellular proteins, can be as simple as injecting the missing protein. This may sound like it's an obscure element of drug development, but it's basically the foundation of biotech. Genzyme started out replacing the missing enzymes in Gaucher and Fabry disease; Genentech got their start with recombinant insulin, an underexpressed peptide; Amgen's first big drug was recombinant G-CSF (neupogen).

  • Overexpressed protein
    Sometimes, you are making too much protein and you need to dial it down. Many cancer targets are like this (e.g., HER2 amplification), though some are mutated too. This is one of the easiest scenarios for drug development, because all you have to do is knock the protein down with high specificity. It's much easier to break something than fix it.

  • Malfunctioning protein
    If you have a genetic disease, there's a good chance it's due to an absent or malfunctioning protein. Cystic fibrosis has over a thousand known causative mutations and most of these mutations cause misfolding. How do you fix a misfolded protein? It's always difficult and sometimes impossible. Vertex's CF drugs represent one unusual success story. Their latest drug, Orkambi, is actually two drugs in one: one that increases CFTR's activity (Kalydeco, a drug originally for the G551D mutation only), and the other helps the mutated CFTR fold properly.

  • Non-proteins
    There are things in the body besides proteins, for example, hormones, lipids, DNA. These are much less common targets for therapies, though amazingly gene therapy is starting to become feasible. (There are now two human gene therapies approved in Europe, and several veterinary gene therapies). According to a 2016 review in NRDD, FDA-approved drugs targeted non-proteins in only 28/695 cases.

Choice of Therapy

There are a plethora of options these days.

  • Small molecules
    • Chemical
      This is what most people mean by a drug. You use chemistry to make them: perhaps you have a large library of randomly generated chemicals that you screen against a target, or perhaps you design your drug and simulate target binding computationally. Computer-aided drug design (CADD) works sometimes and is improving quickly, partially thanks to deep learning.
    • Biological
      Unlike chemically-derived small molecules, you don't create these, you find them in organisms in the soil, the ocean, etc. These molecules are generally more complex structurally than regular small molecules, since they've had millions of years to evolve that complexity. Many drugs come from natural sources, especially antibiotics; the main issue is how to find them. We have already found much of the low-hanging fruit, like penicillin, many times over.
    • DNA-encoded
      It's obvious that you can use DNA to encode and evolve proteins. Less obviously, you can encode small molecules too, by chemically fusing DNA barcodes to your chemicals. These libraries are interesting because just like proteins, you can evolve them, but you retain the flexible chemistry of small molecules. DiCE Molecules, which launched last year, is doing this.
  • Proteins
    • Recombinant
      You can make almost any protein recombinantly in a microbe, then use that to replace a missing (extracellular) enzyme. Proteins are big, and get degraded quickly in the gut by proteases, so you usually have to inject them. (If ingesting proteins had drug-like effects, then eating would be more hazardous!) They are also usually too large to enter cells efficiently, further limiting their use as drugs.
    • Antibodies
      Antibodies are proteins, but with a specific template for interfacing with the immune system. They are very large and cannot enter cells, so they only target cell-surface or extracellular targets. That works extremely well for the 10-20% of proteins that are accessible that way. Antibodies are our closest thing to a magic bullet, and are among the most successful drugs of all time. You can evolve antibodies in mice, use phage display, or identify them in humans. There are several varieties: antibody fragments, nanobodies, BiTEs, etc.
    • Peptides
      Peptides are basically just short proteins. They are interesting potential drugs because they exhibit some of the properties of small molecules (small size, sometimes able to enter cells) and some of the properties of proteins (safe, easy to synthesize). Peptides are still rapidly degraded in the gut, so most are injected. Some of the limitations of peptides being proteins can be overcome by using peptidomimetics like D-peptides.
    • Peptides (DNA-encoded)
      Peptides are generally encoded by DNA anyway, but there is a nice way to evolve a library of peptides, analogous to DNA-encoded small molecules: the decades-old-but-still-futuristic phage display. You can use phage display to select for antibody fragment binding too.
    • Protein + nucleotide
      CRISPR/Cas9 is a gene editing technology combining an enzyme that cuts DNA (Cas9) and an guide RNA that defines the target. Cas9 is a sophisticated enzyme, so it is quite large and cannot enter cells unaided. That means to make Cas9 into a real therapy you need a way to deliver it. Older gene editing technologies like TALENs and Zinc Fingers also work well if they can be delivered, though they are much harder to program than Cas9.
    • Protein + small molecule
      Antibody-drug conjugates promise to combine the advantages of antibodies (targeting cells with high specificity) with small molecules (ability to enter cells). The canonical example is an antibody designed to find a cancer cell, then deliver an attached "warhead" small molecule to kill it. Stemcentrx is one of many companies working on ADCs.
  • Nucleotides
    • mRNA
      Instead of delivering proteins to cells, why not just deliver the instructions to make the protein? Unfortunately, just like proteins get degraded by proteases, RNA gets degraded by nucleases, so again it comes down to delivery. Like proteins, the body tolerates nucleotides very well. Moderna is developing several mRNA-based therapies.
    • Antisense RNA
      Antisense RNA binds to mRNA and interferes with translation. There have been two successful antisense RNA therapies recently: one for Crohn's (mongersen, which can be orally administered, since Crohn's is a disease of the gut), and one for SMA (nusinersen, which is injected into the CSF). Despite not being the coolest technology around, antisense RNA has had some amazing successes.
    • Aptamers
      Like antibodies, aptamers are evolved to bind their targets with high specificity, but instead of amino acids, they are made from DNA or RNA. Aptamers can be evolved using a simple process called SELEX (unfortunately IP-encumbered). As nucleotides, aptamers are degraded quickly and require special delivery mechanisms. The only approved aptamer therapy, Macugen, is for AMD and it's injected directly into the eye.
    • RNAi
      RNAi encompasses a few related systems that are difficult for me to differentiate: siRNA, shRNA, miRNA, piRNA. RNA interference is an extremely effective tool for modifying cell lines, but so far has been less effective as a therapy. Alnylam has several RNAi therapies in development.
    • Raw DNA/RNA
      Raw DNA or RNA with the right sequence will do gene editing at low frequency, even without a proper vector. You can also inject complete plasmids that get transcribed and translated (assuming some accompanying stress like electroporation). This is called a DNA vaccine, which is conceptually quite similar to an mRNA, except that DNA vaccines are injected with an adjuvant like Freund's adjuvant, to elicit an immune response to the resultant protein.
  • Cells
    Cell-based therapies are becoming increasingly important, especially for cancer treatment. In cancer, the idea is to train the immune system (usually T-cells) to attack cancer cells more efficiently. Since the vast majority of cancers are quashed by the immune system anyway, this makes a lot of sense. CAR-Ts — perhaps the best-known cell therapy for cancer — are T-cells that have been extracted and forced to express a cell-surface antibody fragment with specificity for a cancer, which forces the T-cell to engage the cancer. There's a lot more going on in cell-based therapy, like stem cell therapies, but I don't know too much about this.

Delivery

The big advantage of small molecules over proteins and nucleotides — and a watchword for most of the novel therapies above — is delivery: small molecules can get across the gut and penetrate the cell membrane to bind with targets inside the cell. Proteins and nucleotides are degraded quickly, especially in the gut, and proteins are usually way too large to enter cells anyway.

There are exceptions to this rule, cases when cells are more accessible: for example, the eye is easier to access than most organs (e.g., the aptamer therapy, Macugen); if your target is in the gut then you may be able to deliver it orally (e.g., the antisense RNA therapy, mongersen); if you can apply your therapy ex vivo (especially retransplantable tissue like liver or bone marrow) then you no longer need a delivery vector (e.g., Provenge and other adoptive cell transfers, gene editing in embryos). Examining the pipelines of the new batch of gene editing and RNA therapy biotechs, we see that the diseases they tackle are very often in the bone marrow, liver or eye.

If your target is inside a cell, the cell cannot be extracted for treatment ex vivo, and you can't develop a good small molecule, then what can you do? Many of the modern protein or nucleotide-based therapeutics listed above need some some additional help to protect them from degradation, localize them to target cells, and penetrate the cell membrane. It could be argued that delivery technology has lagged behind drug technology generally. There are still no great options for delivery.

  • Viruses
    Viruses, especially AAV, are especially useful for nucleotide therapies like gene therapy. This makes sense when you consider that viruses are nanomachines, evolved over billions of years to target cells and inject nucleotides. However, since viruses are often immunogenic, there can be side-effects.
  • Nanoparticles / Liposomes
    In rare cases, liposomes have been used to deliver drugs, like cisplatin. We were recently surprised to learn that Moderna, the mRNA biotech, is using lipid-nanoparticles to deliver mRNA to cells. Virus-like particles (essentially noninfectious viruses) may combine the best of both worlds.

For a more detailed discussion on delivery methods, there's a good recent review in NRDD.

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