N-of-1 patient: crafting personalised treatments for ultra-rare diseases with AntiSense Oligonucleotide (ASO) technology

The n-of-1 patient is that one person with a unique genetic mutation that causes an ultra-rare disease, designated as a disease with less than 30 patients in the whole world. The advent of affordable genomic sequencing has identified millions of n-of-1 patients, which is becoming a large and growing population with desperate needs.

Though a great progress is made in identifying n-of-1 patients, and ruling the genetic causes of their diseases; usually, drugs that work in patients with the common mutations, often do not work for these unique patients.

n-Lorem is a foundation created by Dr. Stanley Crooke, the founder, chairman and chief executive officer of Ionis Pharmaceuticals, a global leader in RNA-targeted therapy. This foundation was created to provide individualized treatments for patients with ultra-rare diseases using the technology developed at Ionis Pharmaceuticals.

The mission of n-Lorem is to use the versatility and specificity of antisense technology to kindly offer experimental antisense oligonucleotides (ASO) medicines to treat the n-of-1 patient. 

Antisense oligonucleotides (ASOs) are short, synthetic, single-stranded DNA-mimics that can alter the RNA, and consequently protein expression and function. Because they can manipulate the intermediate step between gene and protein translation – at the pre-mRNA level – ASOs can reduce, or restore, or modify protein expression by different mechanisms.

Very simply: DNA gets converted into mRNAASOs function in between the two. As such, if the DNA gene has a mutation and codes a dysfunctional mRNA, and consequentially a dysfunctional protein that causes a disease, an ASO can change that. The ASO has the correct complementary code to produce the precise mRNA, and automatically, the precise protein needed to perform the right function. By intervening in the step before protein gets translated, it makes sure that nothing goes wrong and that the mutated gene doesn’t go any further, preventing disease from happening.

Even though it only started one year ago, n-Lorem together with  Ionis Pharmaceuticals  have helped design and provide experimental ASOs for two unique patients: one with Batten’s disease and ataxia-telangiectasia (AT); the other one, with a FUS mutation in Amyotrophic Lateral Sclerosis (ALS). These have provided a tremendous opportunity to certify the n-Lorem concept and drive motivation forward.

Anyone can apply to n-Lorem for a potential treatment. The proposals are approved and prioritized based on certain criteria, such as the severity of the disease, feasibility of developing an ASO treatment for the genetic cause of the disease, degree of potential benefit vs. potential risks, practicality of treatment, availability of physician and institution to treat patient, and other intricacies of the condition. 

The unique patient needs to work with a physician that makes the connection to n-Lorem, who will then make an informed decision about whether a patient is appropriate to receive an experimental ASO treatment through a Commission.

It’s outstanding that the FDA reaction to n-Lorem has been very supportive; and, in fact, initial guidance has been put in place in January 2021 to reach more patients in need. 

Once regulatory permission has been given, an investigator-led clinical trial is initiated and the patient can receive their custom experimental ASO treatment at no personal cost and will all clinical support.

This cost-free individualized therapy is possible for Ionis Pharmaceuticals because of the inherent efficiency and versatility of the ASO technology. The knowledge of modern ASOs mechanisms and specific possible effectiveness in selected organs, with different possible routes of application, together with integrated safety databases, allows a dive for the treatment of unique patients. 

It’s honourable to use science to help the n-of-1 patient and their families. 

I hope for more Dr. Stanley Crooke’s…


RNA Viruses, such as the SARS-CoV-2HIV and Influenza, tend to pick up mutations rather quickly, once they are copied inside the cells of our bodies. This happens because the little cell workers that copy the RNA (called enzymes) are sloppy workers and prone to make errors. 

The SARS-CoV-2 virus genetic code has just 30,000 nucleotides blocks of RNA, or letters that can spell at least 29 genes1; and, the most common mutations are single-nucleotide changes between viruses from different people, that have little effect on the overall performance of the virus infection rate, but that allow researchers to track the spread by linking closely-related viruses2

In fact, sequencing data actually suggests that coronaviruses change more slowly than most other RNA viruses, because they have “proofreading” mechanisms that correct potentially fatal copying mistakes, accumulating only two single-letter mutations per month in its genome — a rate of change about half that of Influenza and one-quarter that of HIV2.

The problem is, that scientists can spot mutations faster than they can make sense of them, or what problems they may cause. Many mutations will have no consequence for the virus’s ability to spread or cause disease, because they do not alter the shape of a protein; whereas those mutations that do change proteins are more likely to harm the virus than improve it2. For example, in the beginning of the pandemic in Singapore, the ∆382 deletion made the infection of the virus milder3. On the contrary, the G614 variant showed a fitness advantage of infection, where individuals had a higher concentration of pseudotyped virions, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity4

If we think about it, the virus just wants to spread, but not actually kill – because, if it kills, it can no longer spread.

More recently, a new SARS-CoV-2 virus variant showed up in the UK, where multiple spike protein mutations are seen (deletion 69-70, deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H)5. Changes are also seen in other genomic regions, inclusively in the receptor binding domain (N501Y, “Nelly”). 

The unusually high number of spike protein mutations suggests that the variant has not emerged through gradual accumulation of mutations6. Instead, one possible explanation for the emergence of the variant, is prolonged SARS-CoV-2 infection in a single patient, potentially with reduced immunocompetence, similar to what has previously been described7,8. Such prolonged infection in immunocompromised patients can lead to accumulation of immune-escape mutations at a higher rate. 

This explanation is also suggested to the current SARS-CoV-2 virus variant found in Brazil (P.1)9, and in South Africa (501Y.V2)10

Unfortunately, this shows that the emergence of successful variants with similar properties is not so rare6; and, just like the need to develop new influenza vaccines every season, that also might be the case for SARS-CoV-2. The persistence of the pandemic, may enable accumulation of immunologically relevant mutations in the population, even as vaccines are developed. 

But, because science tries to be one step ahead, this is exactly what manufacturers are already working on, specifically the ones using mRNA technology that can quickly adapt their platforms to the current mutations seen.

Mutation luck
Mutation of luck


1          Naqvi, A. A. T. et al. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochim Biophys Acta Mol Basis Dis 1866, 165878-165878, doi:10.1016/j.bbadis.2020.165878 (2020).

2          Callaway, E. The coronavirus is mutating — does it matter? Nature 585, 174-177, doi:https://doi.org/10.1038/d41586-020-02544-6 (2020).

3          Young, B. E. et al. Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study. The Lancet 396, 603-611, doi:10.1016/S0140-6736(20)31757-8 (2020).

4          Korber, B. et al. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 182, 812-827.e819, doi:10.1016/j.cell.2020.06.043 (2020).

5          Andrew Rambaut, N. L., Oliver Pybus, Wendy Barclay4, Jeff Barrett5, Alesandro Carabelli6, et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations: COVID-19 genomics UK consortium. https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 December 2020 (2020).

6          ECDC. Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom. https://www.ecdc.europa.eu/sites/default/files/documents/SARS-CoV-2-variant-multiple-spike-protein-mutations-United-Kingdom.pdf December 2020 (2020).

7          Choi, B. et al. Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host. N Engl J Med 383, 2291-2293, doi:10.1056/NEJMc2031364 (2020).

8          McCarthy, K. R. et al. Natural deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape. bioRxiv, 2020.2011.2019.389916, doi:10.1101/2020.11.19.389916 (2020).

9          Kupferschmidt, K. New mutations raise specter of ‘immune escape’. Science 371, 329-330, doi:10.1126/science.371.6527.329 (2021).

10        Karim, S. S. A. The 2nd Covid-19 wave in South Africa. https://www.scribd.com/document/488618010/Full-Presentation-by-SSAK-18-Dec December 2020 (2020).

Moderna mRNA COVID-19 vaccine: how did they do it?

Moderna uses an efficient method to make large quantities of individual mRNAs with high purity, based on a technique developed in 1984 by D. Melton and colleagues at Harvard University and published in Nucleic Acids Research. In here bacteriophage polymerases were used to transcribe plasmid DNA and make purified RNAs. D. Melton went further and showed that he could transcribe a synthetic mRNA injected into frog oocytes, and get expression of b-globin (Krieg & Melton, Nucleic Acids Research, 1984). With this report, the protocol to make pure mRNAs was settled.

Today, at Moderna, they moved on from this idea to a GMP drug-product inside of a vial in under two months. In the case of the COVID-19 vaccine, they went from a sequence of the virus to having the material ready for a Phase I clinical trial in 45 days. 

This automated process starts with back-translation using Moderna’s proprietary computer algorithm, that has been defined over the years to pick the best mRNA sequence for the target in question. 

Then, the therapeutic mRNA is engineered to avoid the innate immune sensors that defend against RNA viruses and might destroy the vaccine. These defences come in to main types: Toll-like receptors (TLR) in the endoplasmic reticulum, and RIG-I/MDA-5-like receptors in the cytoplasm. 

To avoid TLRs, Moderna places modified nucleotides. This technique is based on a paper by Diebold and colleagues published in Science (2004), where the researchers took macrophages from mice and incubated them with different polymers (polyA, polyC, polyG, polyI, polyU), then checking for an IFN-alpha response. What they have seen was that the only polymer that created the IFN-alpha response was the one that contain Uridine (polyU), which seems to be the only nucleotide that is being recognized by the TLR-driven innate immune response. As such, at Moderna, mRNAs are engineered to replace all U’s with N1-methyl-pseudiuridine without affecting base-pairing, but avoiding TLR recognition. N1-methyl-pseudiuridine is a naturally occurring nucleotide that our bodies recognize as native.

Another problem though, is avoiding the creation of double-stranded RNA (dsRNA) to escape the RIG-I/MDA-5-like receptors. The state-of-the-art used in Moderna to avoid this trap, is HPLC purification to reduce dsRNA content. This is a technique based on Karikó & Weismann (2011, Nucleic Acids Research), that results in very little dsRNA in the end-product, and an avoidance of the innate immune response. The developed technique at Moderna has recently been published in Science Advances (June 2020), where Moderna scientists describe a highly sensitive assay to detect dsRNA and purify therapeutic mRNAs.

(It seems Moderna scientists are now going even further, and have reengineer T7 RNA polymerase not to produce dsRNA at all – although this has not been published yet)

The third step to make a good mRNA-drug, and a successful vaccine, is to find an efficient delivery method.  With that in mind, Moderna researchers looked back at work done by Wolff and colleagues in the 90s (Science, 1990, vol.247, 1465-1468), where they were able to directly inject RNA in the mouse skeletal mouse and have protein expression, with no special delivery system involved. 

In 2014, researchers at Moderna were able to go further, and measured with a Luciferase system, the in vivo expression of biologically active proteins in a dose-dependent manner, by injecting mice with Moderna’s naked mRNA. Nowadays, Moderna targets different tissues via multiple Routes of Administration with specific delivery vehicles (ROAs: direct injection in the heart or tumours, subcutaneous, intravenous, intramuscular). 

Most ROAs require mRNA encapsulation with Lipid nanoparticles (LNPs, 80-100nm). Each encased particle contains 2-6 molecules of mRNA, phospholipid cholesterol, a PEG lipid that keeps the lipid nanoparticles stable avoiding aggregation, and an ionizable lipid that at low pH interacts with the mRNA. These mRNA-LNPs are akin to endogenous lipid transport complexes, slightly bigger than Very-Low Density Lipoproteins (VLDLs), and seen as “friendly bubbly characters” by our bodies.

At Moderna, they empower a rational-structure LNP design by analysing and engineering each individual step of the component mixture, to enhance chemical/physical stability of mRNA-LNPs to allow an optimal biodistribution, cellular uptake, endosomal escape and protein expression. In comparison to the competitor LNPs in the field, which have a 1-2% delivery rate, Moderna’s LNPs can deliver 30% mRNA into cells. To date, Moderna has published two peer-revied articles describing these efforts and their applications in different ROAs (Sabis … Benenato, Mol Ther, 2018Hassett … Britto, Mol Ther Nuc Acids, 2019). 

Finally, there needs to be the right knowledge to engineer the best mRNA sequence for a particular purpose in order to make a good mRNA-drug or vaccine. 

So, there needs to be translation initiation fidelity, so that it always starts in the right place and there’s faithful decoding; and, also, the ribosome needs to stop in the right place. 

The mRNA needs to have a functional half-life, to function before it gets destroyed. 

Also, the therapeutics or vaccine needs to hit the correct cell type, which is achieved by putting “off-logic gates”, like microRNAs target sites in the 3’prime UTR, that cause the mRNA to be degraded in case it hits an undesired cell type.

At Moderna, they have all steps in place for a rapid development of mRNA as medicines:

  1. Efficient methods to make large quantities of individual mRNAs at high purity;
  2. Ability to avoid the innate immune sensors that defend against RNA viruses;
  3. Efficient delivery methods,
  4. Knowledge of how to engineer the best mRNA sequence for a particular purpose.

Besides proprietary algorithm to define the mRNA sequence and unique LNP design; one of the big differences between BioNTech/Pfizer vaccine and Moderna, is that Moderna does not use self-amplifying RNA in their vaccines. According to Dr Melissa Moore, Chief Scientific Officer at Moderna Therapeutics Inc., self-amplifying RNA first starts by building dsRNA which pushes-up the immune response against the vaccine, as such Moderna hasn’t gone down that road to avoid such road-blocks.

The important take-out message is not which vaccine we take.

With a mRNA vaccine, the cell is doing the protein itself, and the antigen-presenting cells are exhibiting it on their surface, which causes an activation of B and T cells.

This protects us and others from developing this devastating disease.

COVID-19 mRNA vaccine, the BNT162b2 candidate

The principle of mRNA therapeutics is to introduce therapeutic messenger (m) RNAs encoding the genetic information for a protein, into a cell of interest. The mRNA structure is designed to increase half-life, translation and protein functionality. 

The mRNA synthesis is made by in vitro transcription using a linear DNA template, which provides more than 500 copies of mRNA per template. They promote a transient expression of the encoded protein/antigen, and are degraded into nucleotides, without the formation of toxic metabolites. Since mRNA is highly sensitive, it gets degraded after a short-time, with no risk of genomic integration. 

This one process can be used to manufacture essentially any mRNA sequence. 

The raw reaction mixture has mRNA and all types of impurities, both process-related (T7 RNA polymerase, remaining building blocks, hydrolyzed DNA…), and product-related impurities (break-off transcripts, side products…), that need to be further purified with high affinity chromatographic methods.

Once purified RNA is obtained, the therapeutic is ready to deliver to the patient.

BioNTech together with their partner Pfizer and FosunPharma, managed to do all this in a record time of 84 days to develop a COVID-19 vaccine. 

Their scientists designed multiple antigen variants using the SARS-CoV-2 Spike (S) protein.

Next, they ran preclinical and toxicology evaluation tests in vitro and in vivo (e.g., in vitro expression data, antibody titers in animal models, pseudo-virus neutralization (pVN) assay in animal models), so they could discover the most active antigen and bring it into the clinic. Also, using their Good Manufacturing Practice (GMP) facilities they produced small scale batches for fast entry into the clinic to demonstrate safety, tolerability (i.e., low reactogenicity), and immunogenicity. 

Afterwards, they initiated clinical trials, where not one but four vaccine candidates were simultaneously studied, in order identify the safest and most effective candidate for further development. In parallel, there was already preparation of larger manufacturing batches of the candidate with the best output in the clinical studies; and, the identification of collaboration partners to develop and provide the vaccine worldwide (Pfizer, FosunPharma).

BioNTech and Pfizer studied three mRNA types during all Phase I/II studies, to evaluate safety and efficacy. The basis for such studies was that different types of mRNA vaccines lead to different responses. 

As such, vaccine prototype (1) was a Uridine mRNA (uRNA) with strong intrinsic adjuvant effect, strong antibody response, that stimulates the production of more CD8+T cells then CD4+T cells.

Vaccine prototype (2) was a Nucleoside-modified mRNA (modRNA), with a moderate intrinsic adjuvant effect, very strong antibody response, lower cytokine induction, that stimulates more CD4+T cells then CD8+T cells.

In the case of vaccine prototype (3), this was a Self-amplifying mRNA (saRNA) with long duration, and a higher likelihood for good efficacy antibody response with lower dosage. 

Early and constant interaction with the regulatory agencies (e.g.EMA) has allowed that BNT162b2 vaccine candidate raced to the finish line, being now the leading candidate from BioNTech & Pfizer; and, currently in review for conditional marketing authorization approval.

It is outstanding that if a new variant of the virus is required (e.g., due to a mutated virus sequence), a new GMP batch of a possible vaccine could be available within half of the time (around 42 days).

If there is a positive message out of these dark days, is that Science is there to save us from our doom. 

Let’s embrace Science.

mRNA vaccine