Advances in Nucleic Acid-Based Therapeutics Against Alzheimer’s

  • Dementia Develops in Someone in the World Every 3 Seconds
  • Nucleic Acid-Based Approaches for an Alzheimer’s Drug Are Advancing
  • Ionis Pharmaceuticals is First to Begin Clinical Trials with Antisense Oligonucleotide Targeting Tau

The concept of nucleic acid-based therapeutics, as originally conceived by Paul Zamecnik, goes back to his seminal publication in 1978 that I’ve blogged about previously. However, it wasn’t until the advent of automated synthesis of various types of modified oligonucleotide analogs that this “antisense” approach to drug development achieved critical mass of sustained attention. Since then, synthetic oligonucleotides and mechanisms of interference with mRNA expression have greatly expanded to now include a diverse “armory” of alternatives to combat diseases, including:

  • Antisense oligonucleotides (ASOs) that induce cleavage of mRNA by RNase H or other mechanisms
  • Short-interfering RNA (siRNA) that are incorporated into RISC that cleaves mRNA
  • Antagomirs that block microRNA (miR) binding to mRNA
  • Aptamers that bind to target proteins as drugs, or for targeted delivery of other types of drugs
  • Splice-switching oligonucleotides (SSOs) that hybridize with a pre-mRNA and disrupt normal splicing
  • Recently reported RNA-guided RNA-targeted CRISPR-Cas variants that can knockdown RNA systems much more specifically than siRNA

Investigating possible NA-based approaches to currently refractory, or other so-called ‘undruggable’ diseases, has attracted much needed interest from academics and pharma researchers, as well as implementation of GMP procedures. Recognizing this need, and the absence of a conventional drug to treat Alzheimer’s disease (AD)—the leading cause of dementia in adults—kindled my efforts to research the literature and write this blog.

What is AD?

Auguste Deter, who was a patient of German psychiatrist Alois Alzheimer, was the first described case of what became known as Alzheimer’s disease. Taken from Wikipedia.org

According to a U.S. National Institutes of Aging fact sheet, AD is an irreversible, progressive brain disorder that slowly destroys memory and thinking skills, and eventually the ability to carry out the simplest tasks. In most people with AD, symptoms first appear in their mid-60s. Statistics vary, but AD accounts for as much as ~80% of all dementia—an umbrella term for loss of cognitive functioning—which will develop in someone in the world every 3 seconds, and afflict close to 50 million people in 2017. This is based on estimates by Alzheimer’s Disease International.

Brains from bodies of deceased persons who had advanced AD exhibit overall “shrinkage,” macroscopically, compared to persons who did not show indications

Taken from fellowshipoftheminds.com

of AD. Microscopically, AD is characterized by accumulation of toxic “amyloid plaques,” which are sticky buildup that accumulate outside nerve cells, or neurons. Amyloid is a protein that is normally found throughout the body, but in AD the protein is cleaved by beta secretase (BACE1) and gamma secretase to yield amyloid beta (Aβ) peptides of 36–43 amino acids. Aβ molecules can aggregate to form flexible soluble oligomers that may exist in several forms. It is now believed that certain misfolded oligomers can induce other Aβ molecules to also take the misfolded oligomeric form, leading to a chain reaction akin to a prion infection.

Amyloid plaques. Taken from slideshare.net

Since 1993, when a variant of the apolipoprotein E (APOE) gene was found to be strongly associated with increased vascular and plaque Aβ deposits in late-stage AD patients, many researchers have probed APOE connections to Aβ. However, in September 2017 this investigative field was reportedly “stunned” by results published by Shi et al. showing that neurotoxic effects associated with APOE may result from a damaging immune response to a different protein named tau, encoded by the MAPT gene. This late-breaking scientific news is part of an ongoing story of AD molecular pathology that interested readers will want to follow.

“Tangles” of tau protein (green) are visible in a brain cell from someone who had Alzheimer’s disease. Taken from Underwood, Science (2017)

Recent Advances in Nucleic Acid-Based Drugs for AD

My strategy for researching this topic began with querying Google Scholar for “Alzheimer’s” articles since 2013 that are coupled with key words for each of the above nucleic acid-based drug modalities, namely, “antisense,” “siRNA,” etc. This led to literature ranked by Google Scholar according to citation counts. I then perused this information to select items for each of these modalities. I linked to the search results for readers interested in further digging into these topics.

Antisense Oligonucleotides

A report that caught my attention was by Lane et al. from Ionis (formerly Isis) Pharmaceuticals. This company (founded and still led by Stanley Crooke, about whom I’ve blogged) is widely acknowledged to be the leader in clinical development of antisense therapeutics. In a nutshell, Lane et al. hypothesized that, given the critical role for tau (see above) in transducing Aβ-linked neurotoxicity, reducing the synthesis of tau could have a therapeutic effect.

Ionis-MAPTRx, a 2′-O-methoxyethyl chimeric ASO, was found to reduce tau expression in transgenic mice and was tested in FDA/IND-enabling toxicology studies in rodents and non-human primates (NHPs). Intrathecal administration of the highest dose in NHPs resulted in a mean MAPT mRNA reduction of 77% in frontal cortex and 74% in hippocampus without dose-limiting side effects. Following up on this, I found that on October 13, 2017, Ionis announced initiation of a Clinical Study of Ionis-MAPTRx in patients with AD, thus earning a $10 million milestone payment from Biogen.

In another ASO approach, Farr et al. have further investigated their previously reported 20-mer phosphonothioate oligonucleotide (GAO) that had been shown to knockdown levels of glycogen synthase kinase (GSK)-3β, which is a multifunctional protein implicated in the pathological characteristics of AD, including neurofibrillary tangles, Aβ, and neurodegeneration. In the present study, they assessed the impact of peripherally administered GAO on learning and memory—measured by a T-maze (see picture)—in two different mouse models of AD, as well as knockdown of protein expression. GAO-treated mice showed improved acquisition and retention, along with decreased protein levels. They concluded that this study “supports peripherally administered GAO as a viable means to mediate GSK-3β activity within the brain and a possible treatment for AD.”

Taken from ratbehaviour.org

To learn about a T-maze, click here.

siRNA

SLN loaded with siRNA (green). Taken from precisionnanosystems.com

While there are several intriguing studies of ASOs associated with AD therapy, siRNA is much more common in the research and treatment of AD. The report that I found most interesting was published by Rassu et al. in 2017, and is titled Nose-to-brain delivery of BACE1 siRNA loaded in solid lipid nanoparticles for Alzheimer’s therapy. My interest stemmed from the focus on developing delivery technology to achieve “nose-to-brain” as a very convenient, non-invasive route for delivery using solid lipid nanoparticles (SLNs), which are viewed as promising technologies for drug-delivery.

In this report, the siRNA targeted the secretase BACE1, which has been widely investigated because of its involvement in forming neurotoxic Aβ peptides, as mentioned above. To increase the transcellular pathway in neuronal cells, a short cell-penetrating peptide derived from rabies virus glycoprotein known as RVG-9R was used, based on previous studies demonstrating that intravenous treatment with an RVG-9R-bound antiviral siRNA afforded robust protection against fatal viral encephalitis in mice. Building on this prior knowledge, Rassu et al. optimized the molar ratio of RVG-9R and BACE1 siRNA, and investigated chitosan-coated and uncoated SLNs as a nasal delivery system capable of exploiting both olfactory and trigeminal nerve pathways.

Taken from researchgate.net

The positive charges from protonated amino (NH2) groups of the coating formulation ensured muco-adhesiveness to the particles, and prolonged residence-time in the nasal cavity. They studied cellular transport of siRNA released from the SLNs using the Caco-2 cells, which is a human epithelial colorectal adenocarcinoma cell line, as a model for epithelial-like phenotypes. It was found that siRNA better permeates the monolayer when released from chitosan-coated SLNs vs. uncoated SLNs or “naked” siRNA.

Chitosan. Taken from Wikipedia.org

Antagomir

MicroRNA-146a (miR-146a) is upregulated in the brains of patients with AD and induces activation of tau (see above). To determine whether reducing miR-146a could ameliorate tau-related AD pathologies, Wang et al. assessed its levels and the use of a miR-146a inhibitor (antagomir) in a validated mouse model of AD. The antagomir and solvent control were delivered into the hippocampus of these mice at three months of age and memory was tested in all mice using several types of mazes (see above) before extracting brain samples for quantitative RT-PCR using measurements of miR-146a and protein targets. In a nutshell, the overall results demonstrated that improvement of memory by intrahippocampal miR-146a antagomir was associated with the predicted alterations in the tau-related neural pathway, confirming that inhibition of miR-146a expression has a therapeutic effect in this mouse model of AD. It was concluded that “this data support (sic) the concept that miR-146a antagomir is a potential efficacious therapeutic target for the tau pathology of AD.”

Aptamers

Aptamer A1 structure reported by Liang et al.

In a study published by Liang et al. in 2015, systematic evolution of ligands by exponential enrichment (SELEX) with random-sequence libraries was used to obtain a DNA aptamer (A1). That aptamer is pictured below, and has been shown to have high-affinity binding to purified human BACE1 extracellular domain. They subsequently confirmed that A1 exhibited a marked inhibitory effect on BACE1 activity in an AD cell model, based on decreased concentrations of Aβ fragments and BASE1 protein. These investigators concluded that “these findings support the preliminary feasibility of an aptamer evolved from a SELEX strategy to function as a potential BACE1 inhibitor. To our knowledge, this is the first study to acquire a DNA aptamer that exhibited binding specificity to BACE1 and inhibited its activity.”

Splice-Switching Oligonucleotides

According to Hinrich et al., apolipoprotein E receptor 2 (ApoER2), which is involved in long‐term potentiation, learning, and memory, has been proposed to be involved in AD, though a role for the receptor in the disease is not clear. ApoER2 signaling requires amino acids encoded by alternatively spliced exon 19. To test the role of deregulated ApoER2 splicing in AD, they designed a splice-switching oligonucleotide (SSO) that increases exon 19 splicing. Treatment of AD mice with a single dose of SSO corrected ApoER2 splicing for up to 6 months and improved synaptic function and learning and memory. They concluded that “these results reveal an association between ApoER2 isoform expression and AD, and provide preclinical evidence for the utility of SSOs as a therapeutic approach to mitigate AD symptoms by improving ApoER2 exon 19 splicing.”

CRISPR

Individuals heterozygous for the Swedish mutation of the amyloid precursor protein (APPswe) display an increased β-secretase cleavage leading to higher Aβ levels—both in brain and peripheral tissues, according to Gyorgy et al. They added that the mutation is a double base change adjacent to each other and has a dominant effect, which led them to hypothesize that the CRISPR system would selectively disrupt the mutated allele without affecting the wild-type (wt) allele.

In a nutshell, human APPswe fibroblasts and non-mutated control fibroblasts from subjects of the same family were grown in vitro, and then transfected with a Cas9 plasmid together with different guide RNAs (gRNAs) designed to bind either the mutated or non-mutated site with the mutation in the gRNA recognition sequence. Sanger sequencing was performed on cells that had been successfully transfected with CRISPR plasmids, and on such cells, both the APPswe mutant and wt alleles could be disrupted with gRNAs designed against the mutated and non-mutated sites, respectively. Moreover, these effects appeared to be highly specific as assayed by deep sequencing as they did not find any random mutations on the wt allele with the gRNA targeting the mutated site or vice versa.

This study reported in 2016 was said to “[provide] the first experimental evidence that the CRISPR/Cas9 method could be used to develop a novel treatment strategy against familial forms of Alzheimer’s disease caused by dominant mutations.”

Closing Comments

From the above sampling of publications reporting promising results for nucleic-acid-based therapeutic approaches to AD, I hope you will agree with me that it seems likely a clinically successful drug will prevail. What and when are uncertain, but I’m betting that something will be Ionis-MAPTRx , which is the most advanced clinical candidate to date.

Addendum

Taken from October 31, 2017 GEN

Alzheimer’s disease may move, cancer-like, from place to place in the body, lodging in the brain after originating in peripheral tissues, according to October 31, 2017 news in GEN. This cancer-like mobility was demonstrated through a technique called parabiosis—the surgical union of two specimens to allow them to share a blood supply, as shown here. This technique was used to keep pairs of mice together for several months, wherein normal mice, which don’t naturally develop AD, were joined to transgenic AD mice, modified to carry a mutant human gene that produces high levels of plaque-forming Aβ. It was reported that human Aβ originating from transgenic AD mice entered the circulation and accumulated in the brains of normal mice, forming cerebral amyloid angiopathy and Aβ plaques after a 12-month period of parabiosis.

Advances in Aptamer Applications – Part 2

  • Top Cited Aptamer Publications Over the Past Three Years
  • Jerry’s Picks for Top 3 Aptamer Publications So Far This Year
  • TriLink Products Cited in Numerous Aptamer Publications

Aptamers are highly structured nucleic acids that bind to a specific target molecule. RNA or DNA aptamers are usually selected from a very large pool (aka library) of random sequences, and can be comprised of either natural and/or chemically modified nucleotides. My first blog on aptamers was titled Aptamers: Chemistry Bests Mother Nature’s Antibodies. This purposefully provocative claim was intended to emphasize the growing body of evidence that collectively indicates aptamers can perform better than antibodies in many applications.

NMR-derived structures of aptamers binding to either a large protein or small molecule. Taken from genelink .com

Because it has been nearly four years since that boastful blog in 2013, I thought it was time to survey aptamer applications published since then to comment on what has been trending or is otherwise notable. I found more than 1,500 articles in PubMed for 2014 through 2017 (estimate) that have the search term “aptamer” in the title or abstract. Given this huge number of publications, I used Google Scholar citation frequency as a numerical indicator of interest, importance and/or impact for these publications in each year. I also decided to focus on original publications that, by definition, excludes review articles. 

Top 3 Cited Publications in 2014

  1. Activatable fluorescence/MRI bimodal platform for tumor cell imaging via MnO2 nanosheet–aptamer nanoprobe (109 citations)

This Chinese team of researchers led by uber-prolific Weihong Tan, about whom I’ve previously blogged, designed a novel methodology for imaging tumor cells using quenched-fluorescent aptamers. In the presence of target cells, the binding of these “dark” aptamers to cell surface markers weakens the adsorption of aptamers on MnO2 nanosheets causing partial fluorescence recovery (i.e., unquenching), thus illuminating the target cells, as well as facilitating endocytosis into target cells. After endocytosis, reduction of MnO2 nanosheets by glutathione further activates the fluorescence signals and generates large amounts of Mn2+ ions as a contrast agent for magnetic resonance imaging (MRI).

Taken from pubs.rsc.org

  1. A phase II trial of the nucleolin-targeted DNA aptamer AS1411 in metastatic refractory renal cell carcinoma (88 citations)

Taken from mct.aacr.org

The anticancer mechanism of action for DNA aptamer AS1411, which has multiple G-quadruplex moieties that disrupt cancer cell replication following nucleolin-mediated uptake, is depicted below and detailed elsewhere. In this clinical study, it was found that AS1411 appears to have limited activity in patients with metastatic renal cell carcinoma. However, rare, dramatic and durable responses can be observed and toxicity is low. Further studies with AS1411 and other nucleolin-targeted compounds may benefit from efforts to discover predictive biomarkers for response.

  1. An aptamer-based dipstick assay for the rapid and simple detection of aflatoxin B1 (61 citations)

Aflatoxin B₁ structure. Taken from wikipedia.org

Aflatoxin B₁ (AFB1) produced by Aspergillus flavus and A. parasiticus is considered the most toxic aflatoxin and it is highly implicated in hepatocellular carcinoma in humans. In this work by Korean researchers, a rapid and simple dipstick assay based on an aptamer has been developed for determination of AFB1 contamination in food. The dipstick assay format was based on a competitive reaction of a biotin-modified aptamer specific to AFB1 between target and Cy5-modified DNA probes. Streptavidin and anti-Cy5 antibody as capture reagents were immobilized at test and control lines on a membrane of the dipstick assay. The method was confirmed to be specific to AFB1, and the entire process of the assay can be completed within 30 min.

Top 3 Cited Publications in 2015

  1. Aptamer-conjugated silver nanoparticles for electrochemical dual-aptamer-based sandwich detection of staphylococcus aureus (63 citations)

Taken from sciencedirect .com

Staphylococcus aureus (S. aureus) is one of the most important human pathogens and causes numerous illnesses. This report by Iranian researchers describes a sensitive and highly selective dual-aptamer-based sandwich immunosensor for the detection of S. aureus. As depicted below, a biotinylated primary anti-S.aureus aptamer was immobilized on streptavidin coated magnetic beads (MB), which serves as a capture probe. A secondary anti-S.aureus aptamer was conjugated to silver (Ag) nanoparticles such that, in the presence of target bacterium, a sandwich complex is formed on the MB surface and the electrochemical signal of Ag is measured by anodic stripping voltammetry.

  1. Aptamer-based fluorescence biosensor for chloramphenicol determination using upconversion nanoparticles (59 citations)

Chloramphenicol. Taken from Wikipedia .com

Chloramphenicol (CAP) shown below is a naturally occurring antibiotic that is artificially manufactured for use in veterinary and human medicine. Due to its adverse effects in humans, use of the antibiotic is restricted and, in Europe, ‘zero tolerance’ for CAP in food products has been legislated. In this report by Chinese researchers, detection of CAP uses aptamer-conjugated magnetic nanoparticles for both recognition and concentration, together with upconversion nanoparticles for detection. The method was validated for measurement of CAP in milk vs. a commercially available enzyme-linked immunosorbent assay (ELISA) method.

  1. A new aptamer/graphene interdigitated gold electrode piezoelectric sensor for rapid and specific detection of Staphylococcus aureus (48 citations)

Taken from mdpi .com

This work by Chinese investigators describes a novel aptamer/graphene interdigitated gold electrode piezoelectric sensor for detecting S. aureus by binding to the aptamer, which is immobilized on the graphene via the π–π stacking of DNA bases, as depicted below. When S. aureus is present, aptamer dissociates from the graphene and thus leads to change of oscillator frequency of the piezoelectric sensor.

Top 3 Cited Publications in 2016

  1. Aptamer–MIP hybrid receptor for highly sensitive electrochemical detection of prostate specific antigen (38 citations)

This study in the UK uses a thiolated DNA aptamer for prostate specific antigen (PSA) immobilized on the surface of a gold electrode. Controlled electropolymerization of dopamine around the complex served to create an imprint of the complex following removal of PSA. This molecularly imprinted polymer (MIP) cavity was found to act synergistically with the embedded aptamer to provide recognition properties superior to that of aptamer alone. A generalized depiction for producing a MIP is shown below.

Taken from sigmaaldrich .com

  1. Aptamer-functionalized nanoparticles for surface immobilization-free electrochemical detection of cortisol in a microfluidic device (34 citations)

Taken from wikipedia.org

Monitoring the periodic diurnal variations in cortisol (aka hydrocortisone, show below) from small volume samples of serum or saliva is of great interest, due to the regulatory role of cortisol within various physiological functions and stress symptoms. This publication from China reports use of aptamer-functionalized gold nanoparticles pre-bound with electro-active triamcinolone for detection of cortisol based on its competitive binding to the aptamer by monitoring a signal from the displaced triamcinolone using square wave voltammetry at graphene-modified electrodes. The assay was benchmarked vs. ELISA and radioimmunoassays.

  1. Multifunctional aptamer-based nanoparticles for targeted drug delivery to circumvent cancer resistance (32 citations)

Taken from Liu et al. Biomaterials (2016)

In yet another publication from China, Liu et al. report use of a G-quadruplex nanostructure to target cancer cells by binding with nucleolin, in a manner analogous to that mentioned above. A second component is double-stranded DNA (dsDNA), which is rich in GC base pairs that can be applied for self-assembly with doxorubicin (Dox) for delivery to resistant cancer cells. These nanoparticles were found to effectively inhibit tumor growth with less cardiotoxicity.

Jerry’s Top 3 Publication Picks for 2017-to-Date

Here are my Top 3 “fav” aptamer articles published during the first half of 2017, and my reasons for these aptamer selections—pun intended. Interested readers can consult the original publication for technical details.

  1. Targeted delivery of CRISPR/Cas9 to prostate cancer by modified gRNA using a flexible aptamer-cationic liposome

CRISPR/Cas9 is unquestionably—in my opinion—the hottest topic in nucleic acid-based R&D these days, as I have previously blogged about. Off-target effects of CRISPR/Cas9 can be problematic, so using targeted delivery to cells of interest is an important approach for mitigating this problem. In this study, an aptamer-liposome-CRISPR/Cas9 chimera was designed to combine efficient delivery with adaptability to other situations. The chimera incorporated an RNA aptamer that specifically binds prostate cancer cells expressing the prostate-specific membrane antigen as a ligand, and the approach “provides a universal means of cell type-specific CRISPR/Cas9 delivery, which is a critical goal for the widespread therapeutic applicability of CRISPR/Cas9 or other nucleic acid drugs.”

  1. A cooperative-binding split aptamer assay for rapid, specific and ultra-sensitive fluorescence detection of cocaine in saliva

This report claims the first ever development of a split aptamer that achieves enhanced target-binding affinity through cooperative binding. In this instance, a split cocaine-binding aptamer incorporates two binding domains, such that target binding at one domain greatly increases the affinity of the second domain. This system afforded specific, ultra-sensitive, one-step fluorescence detection of cocaine in saliva without signal amplification. This limit of detection meets the standards recommended by the European Union’s Driving under the Influence of Drugs, Alcohol and Medicines program.

  1. Detection of organophosphorus pesticide–Malathion in environmental samples using peptide and aptamer based nanoprobes

Environmental contamination with pesticide residues has necessitated the development of rapid, easy and highly sensitive approaches for the detection of pesticides such as malathion, a toxic organophosphorus pesticide, widely used in agricultural fields. These Indian investigators employed an aptamer, cationic peptide and unmodified gold nanoparticles. The peptide, when linked to the aptamer renders the gold nanoparticles free and therefore, red in color. When the aptamer is associated with malathion, however, the peptide remains available to cause the aggregation of the nanoparticles and turn the suspension blue. The sensitivity was tested in real samples and the results implied the high practicability of the method.

Aptamer Publications in 2014-Present Citing TriLink Products

I was pleasantly surprised to find more than 250 publications on aptamers in Google Scholar citing the use of TriLink products since 2014. This volume of literature is way too large to summarize succinctly, so I decided to do a quick scan to select the following items that provide an indication of the broad diversity of applications partially enabled by TriLink products:

2’-F-UTP. Taken from trilinkbiotech .com

In closing, I should first mention that, while scanning the aptamer/TriLink publications mentioned above, it was evident that the most frequently cited TriLink products were 2’-F-CTP and 2’-F-UTP, which are incorporated into aptamers to impart nuclease resistance, as discussed on a TriLink webpage.

My second and last comment is that, as you may have noticed, there seems to be a high proportion of aptamer publications coming out of China and/or coauthored by Chinese investigators collaborating with researchers in other countries. This despite the fact that Chinese publications in Life Sciences are ~6-times fewer that those from the US, according to reliable statistics. I have no idea why this is so, but thought it’s an intriguing factoid.

As usual, your comments are welcomed.

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Evolving Polymerases to Do the Impossible

  • Polymerases Aren’t What They Used to Be! 
  • Scripps Team Evolves Polymerases That Read and Write With 2’-O-Methyl Ribonucleotides
  • Key Reagents for Romesberg’s “Molecular Moonshots” Are Supplied by TriLink BioTechnologies

Long-time devotees of these posts will likely remember a blog several years ago about Prof. Floyd Romesberg at the Department of Chemistry, The Scripps Research Institute who achieved a seemingly impossible feat. Namely, designing a new pair of complementary bases such that DNA replicating in E. coli would be comprised of six bases, thereby creating a six-base genetic code that is expanded from Nature’s four-base code.

Floyd E. Romesberg. Taken from utsandiego.com

More recently, Romesberg has cleverly outfoxed Nature once again, this time by evolving nucleic acid polymerases into mutant polymerases that can do what heretofore seemed impossible. He and his research team’s publication (Chen et al.) is a tour de force of experimental methodology that is not easily read, and is even harder to simply summarize in a short space like this blog. Consequently, I’ll first tell you what was accomplished, then give a short synopsis of principal new methodology, and close by commenting on the significance of this fascinating work.

Doing the Impossible

Romesberg’s lab successfully achieved what I think of as “multiple molecular moonshots,” wherein a Taq polymerase (which normally reads and writes DNA during PCR), was evolved by novel selection (SELEX) methods into mutant polymerases that are able to transcribe DNA into 2’-O-methyl (2’-OMe) RNA, and reverse transcribe 2’-OMe RNA into DNA for PCR/sequencing.

As depicted below, this was exemplified using a 60-mer DNA template and 18-mer 2’-OMe RNA primer to produce a fully-modified 48-mer 2’-OMe RNA by means of an evolved mPol and all four A, G, C and U 2’-OMe NTPs, which I’m proud to say were bought from TriLink BioTechnologies! This type of molecular evolution of a polymerase has no precedent.

DNA template   5’ ————————————- 3’

RNA primer                                 ←←← 3’ xxxxxx 5’

mPol ↓ 2’-OMe NTPs

Determining the fidelity of this seemingly impossible molecular transformation was addressed by achieving a feat of comparable impossibility! As depicted below, the aforementioned 48-mer 2’-OMe RNA product was hybridized to a DNA primer for reverse transcription into a 48-mer complementary DNA (cDNA) strand, using an evolved mPol, together with all four A, G, C and T unmodified dNTPS, which were also purchased from TriLink. This unprecedented conversion of 2’-OMe RNA into cDNA was followed by conventional PCR/sequencing, the results of which demonstrated relatively high fidelity.

2’-OMe template   5’ xxxxxxxxxxxxxxxxxxxxxxxxxxx 3’

DNA primer                                           ←←← 3’ —— 5’

mPol ↓ dNTPs

cDNA                        3’ ————————————– 5’

How They Did It

In the selection cycle shown below, (1) phage-display libraries were used to expose individual polymerases (Pol) on E. coli. cells in proximity to chemically attached primer/template complexes of interest, which are mixed with natural or modified triphosphates including biotin (green; B)-labelled UTP to extend the primer. (2) Phage that display active mutant polymerases (mPols) are isolated with streptavidin (SA) beads. After washing to remove nonspecific binders, phage cleaved from the beads are used to re-infect E. coli. (3) Heat-treated lysates of E. coli that express the recovered mPols are next subjected to plate-based screening using 96-well plates coated with primer/template complex and extension buffer that contained natural or modified triphosphates and B-UTP, incorporation of which is chromogenically detected. (4) Mutants that give rise to the most activity are selected for individual gel-based analysis, from which (5) promising candidates are selected for further diversification (e.g., by gene shuffling, as depicted) and then subjected to additional rounds of evolution.

Taken from Chen et al. Nature Chemistry (2017)

What is the Significance

In a previous blog, I’ve commented on increasing interest in the utility of aptamers, which are oligonucleotides that can specifically bind small molecules or motifs in proteins, and thus be used to build electronic sensors or studied as potential therapeutic agents rivaling antibodies. Therapeutic aptamers, like antisense oligonucleotides, require incorporation of chemical modifications to impart stability toward nucleases in blood or cellular targets.

Burmeister et al. have previously reported methods for mPol transcription of a DNA template into a fully modified, nuclease-resistant 23-mer 2’-OMe RNA aptamer—also using TriLink’s 2’-OMe NTPs! However, they encountered considerable experimental difficulties in generating this therapeutically promising 23-mer against vascular endothelial growth factor. These technical issues have now been surmounted by the mPol-evolution approaches in the present work by Romesberg’s team, which enabled improved access to longer 2’-OMe RNA aptamers with reasonable efficiency and fidelity.

Moreover, the present study is the first to evolve an mPol for reverse transcription of fully modified 2’-OMe RNA into DNA, which can then be amplified by PCR and/or sequenced, thereby opening the door for a variety of new analytical methods. Most importantly, the molecular mechanism by which these remarkable mPol activities was evolved, namely, the stabilization of an interaction between the “thumb and fingers domains,” may be general and thus useful for the optimization of other Pols. In that case, we can look forward to further advances in evolving other Pols to do the impossible—hopefully using modified nucleotide triphosphates from TriLink!

As usual, your comments are welcome.

Jerry’s Favs from the Recent OTS Meeting

  • 12th Annual OTS Meeting in Montreal Très Excitant!
  • RNAi Approach to Treating Preeclampsia Spurred by Researchers’ Personal Experiences
  • Ionis Video for Spinal Muscular Atrophy Amazes the Audience
  • 30 years later, PS-Modified Oligonucleotides Continue to be Enabling!
montreal

City line of Montreal. Taken from oligotherapeutics.org

The 12th Annual Meeting of the Oligonucleotide Therapeutics Society (OTS) held on September 25-28, 2016 in French-speaking Montreal, Quebec, Canada brought together hundreds of enthusiastic investigators from around the world. All attendees share a common interest in oligo-based therapeutics, and we gratefully say merci beaucoup to the organizers of this very well run event.

Commenting here on my “favs” is limited by space, and highly subjective—by intent—focusing on only several impressions that struck me as worth sharing. Readers interested in perusing all of the lecture titles and speaker biosketches can do so at this link, which also lists corporate sponsors—including TriLink—and connects with the regularly updated OTS website.

Jerry’s balcony view of OTS 2016 presentations at the Centre Mont-Royal venue

Jerry’s balcony view of OTS 2016 presentations at the Centre Mont-Royal venue

Before getting to my selected topics, I wish to congratulate the OTS Board of Directors and Scientific Advisory Council for their ongoing valuable contributions to this society, and continuing efforts to include participation by the new generation of young investigators, who I’m sure will collectively make exciting advances in the field of oligonucleotide therapeutics. It was pleasure for me to me meet some of these “next gen” scientists, and learn about their current work, which is quite sophisticated by comparison to what I and others did in the early—dare I say primitive—era of antisense oligonucleotide drug discovery.

Toward Treating Preeclampsia: Personalized Drug Developers’ Stories

Preeclampsia (PE) is a disorder that occurs during pregnancy, affects both the mother and the fetus, and is characterized by elevated blood pressure, swelling and protein in the urine. According to a Preeclampsia Foundation fact sheet, every minute somewhere in the world a woman dies in pregnancy or childbirth, which amounts to more than 500,000 deaths each year. In addition, PE causes ~15% of premature births in industrialized countries and is the number one reason doctors decide to deliver a baby early.

Dr. Melissa J. Moore is a professor in the RNA Therapeutics Institute and the Department of Biochemistry and Molecular Pharmacology at the University of Massachusetts Medical School. Taken from hhmi.org

Dr. Melissa J. Moore is a professor in the RNA Therapeutics Institute and the Department of Biochemistry and Molecular Pharmacology at the University of Massachusetts Medical School. Taken from hhmi.org

In her OTS lecture on clinical development of an RNA interference (RNAi) approach to treat PE, Dr. Melissa J. Moore (pictured below) introduced an attention-grabbing personal element when she revealed her bout with PE. Coincidentally, she discovered that her then attending physician, Dr. S. Ananth Karumanchi, had begun his quest for identifying PE-causality at the molecular level prompted by his daughter’s dangerously premature birth due to PE. This turned out to be a truncated kinase receptor abbreviated sFlt1, which Moore described as Karumanchi’s break-through discovery for possible development of PE therapeutics.

The condensed version of these two remarkably interwoven, PE-related personal stories—that you can hear first-hand from Moore on YouTube—was an agreement between Moore and Karumanchi to collaborate on discovering whether double-stranded short-interfering RNA (siRNA) targeting sFlt1 could be useful as an RNAi-based PE therapeutic agent.

Melissa Moore’s ultrasound sonogram. Taken from her YouTube video

Melissa Moore’s ultrasound sonogram. Taken from her YouTube video

Moore went on to gratefully acknowledge her colleague at the RNA Therapeutics Institute, Prof. Anastasia Khvorova, for setting up “by hook or by crook” the first non-profit academic facility for large-scale production of siRNA suitable for clinical development. This led to designing and producing a nuclease-resistant siRNA comprised of 2’-OMe/2’-F ribonuceosides and phosphorothioates at the ends, with an attached hydrophobic cholesterol moiety for improved delivery.

Even more impressive—at least to me—was Moore’s ability to access pregnant baboons in a non-human primate model of PE. This is inherently difficult due to issues involving non-human primates for any research, and is technically much more challenging compared to, for example, infectious disease models. Dr. Moore showed lots of compelling results from her model studies, and concluded her talk by saying that clinical studies were planned.

In closing this section, it’s worth noting that Moderna—a leading mRNA therapeutics company—has recently announced its appointment of Dr. Moore as Chief Scientific Officer of Moderna’s mRNA Research Platform.

Ionis Pharmaceuticals Drug Video for Spinal Muscular Atrophy Amazes the Audience

Dr. Stanley T. Crooke. Taken from ionispharma.com

Dr. Stanley T. Crooke. Taken from ionispharma.com

This year’s OTS Lifetime Achievement Award address by Dr. Stanley T. Crooke, founder and CEO of Ionis Phamaceuticals (formerly Isis Pharmaceuticals), was presented to an auditorium packed with attendees who, like me, greatly admire Crooke’s many scientific and commercial contributions to the field over the past decades. These currently include more than 450 (!) scientific publications and 38 drugs in the pipeline, with 3 finishing Phase III—very impressive and promising indeed!

Ionis’ impact on providing efficacious oligonucleotide-based therapies to patients was conveyed most powerfully—in my opinion—by a video about Cameron, an infant SMA patient who was born with Spinal Muscular Atrophy (SMA). According to an NIH fact sheet, SMA is a genetic disease that causes weakness and wasting of the voluntary muscles in the arms and legs of infants and children. These disorders are linked to an abnormal or missing gene known as the survival motor neuron gene 1 (SMN1), without which motor neurons in the spinal cord degenerate and die.

As detailed elsewhere by Chiriboga et al., Nusinersen (aka ISIS-SMNRx or ISIS 396443) is a 2’-O-(2-methoxyethyl) (MOE) phosphorothioate-modified antisense oligonucleotide (ASO) designed to alter splicing of SMN2 mRNA and increase the amount of functional SMN protein produced, thus compensating for the genetic defect in the SMN1 gene. The cartoon shown below depicts how this ASO targets an hnRNP-A1/A2–dependent splicing silencer in intron 7 of the SMN pre-mRNA. Nusinersen displaces hnRNP proteins from this silencer site on the SMN2 pre-mRNA, facilitating accurate splicing of SMN2 transcripts (e.g., increasing the synthesis of transcripts containing exon 7) and resulting in increased production of full-length SMN protein.

Taken from researchgate.org after Chiriboga et al.

Taken from researchgate.org after Chiriboga et al.

Ionis and its commercial partner Biogen announced in August 2016 that Nusinersen met the primary endpoint pre-specified for the interim analysis of ENDEAR, the Phase 3 trial evaluating Nusinersen in infantile-onset (Type 1) SMA. The analysis found that infants receiving Nusinersen experienced a statistically significant improvement in the achievement of motor milestones compared to those who did not receive treatment. In September, Biogen announced that it applied for Priority Review by the FDA that, if granted, would shorten the review period of Nusinersen following the Agency’s acceptance of the NDA filing by Ionis and Biogen.

Cameron at 2+ years enjoying the moment with his mom. Taken from YouTube

Cameron at 2+ years enjoying the moment with his mom. Taken from YouTube

The amazing effect of Nusinersen warranting this Priority Review is best appreciated—in my opinion—by watching a YouTube video showing the progress of Cameron during his treatment. When viewing this video, keep in mind that Cameron’s Type I SMA is typically evident at birth or within the first few months, and that symptoms include floppy limbs and trunk, feeble movements of the arms and legs, swallowing and feeding difficulties, and impaired breathing. Sadly, the prognosis is poor for babies with SMA Type I. Most die within the first two years. But not so for Cameron, shown below at 2+ years, thanks to Nusinersen!

Phosphorothioate-Modified Oligonucleotides Continue to be Enabling—30 Years On!

men

Left: Prof. Fritz Eckstein. Taken from oligotherapeutics.org Right: Prof. Wojciech J. Stec. Taken from cbmm.lodz.pl

That nuclease-resistant phosphorothioate (PS)-modified internucleotide linkages have had an enabling influence on all manner of oligo-based drug development is evident from the first-ever OTS Lifetime Achievement Award in 2015 being given to Prof. Fritz Eckstein for his pioneering and life-long work on PS linkages in DNA and RNA. Following Fritz’s lead, and aided by the availability of ABI’s DNA synthesizer, Prof. Wojciech J. Stec and yours truly published the first completely automated method for synthesis of fully or partially PS-modified DNA oligos in 1984. This opened the door for early antisense experiments with PS-modified oligos, which have continued now for 30 years!

Perhaps surprisingly, the ever evolving field of oligonucleotide therapeutics continues to rely on PS-modifications in a myriad of mechanistically distinct strategies, such as “classic” antisense to mRNA, siRNA, anti-miRNAs, modulators of RNA splicing, etc. In this regard, Dr. Crooke’s concluding remarks on his goal of deciphering the “code” for protein binding to chemically modified ASO, led me to muse about the negatively charged P-Smoiety in such binding of PS-containing ASO.

Taken from zon.trilinkbiotech.com

Taken from zon.trilinkbiotech.com

My initial thought was that P-S likely enhances binding to positively charged amino acid moieties in proteins, due to greater polarizability vs. P-O, and that Sp or Rp P-Sstereochemistry may likely influence binding. Moreover, this spatial aspect of a binding “code” can now be studied using stereospecific synthesis of PS-ASO by either Stec’s OTP method or Wada’s oxazaphospholidine method. Time will tell—stay tuned!
As usual, your comments here are welcomed.

Highlights of 2015 Publications Using TriLink BioTechnologies Products

  • Publications Citing TriLink Products Exceed 6,000
  • TriLink Products Showed up at a Rate of One Publication per Work Day
  • Among These Customer Publications, Modified mRNA is Trending
Taken from thetrymovement.com

Taken from thetrymovement.com

From my college classes decades ago, I can still clearly recall—thankfully—many “ah ha” moments. Most importantly is when I crystalized to purity and then confirmed structure by NMR the first compound I synthesized in Organic Chemistry Lab. Another ah ha moment—but on a completely different level—was during a philosophy class when the professor partially paraphrased a quote by Aristotle as “we are what we do.” The full quote given above is even more thought provoking because it ties in the notion of excellence, which I took to heart then, and have attempted to live by ever since.

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Reflections on Advances in Medicinal Oligonucleotides

  • Oligos Are Not “Magic Bullets”
  • Oligos Have, Nevertheless, Enabled New Drug Paradigms
  • Oligos Continue to Attract Significant Corporate Investments

Reflections

The 10th Annual Meeting of the Oligonucelotide Therapeutics Society (OTS) is in full swing today in San Diego, CA where it began on Oct 12 and concludes on Oct 15. Having worked on antisense oligos since the early days (~30 years ago) participating in this meeting led me to several thoughts that I wish to share with you in this post.

First of all, contrary to many sceptics in those early days, the concept of using synthetic oligonucleotides as an entirely new class of medicinal agents has not only survived but also greatly expanded in terms of the biological target/mechanism of action and types of oligo constructs used—each with a seemingly endless array of chemical modifications to evaluate. In approximate chronological order of discovery, these targets and the types of oligos they have now come to include are listed below coincidentally, most of these are represented in the 2014 OTS agenda.

Target
mRNA
dsDNA
transcription factors
immunostimulation
proteins
splice junctions
RNA interference
Oligo Type
antisense
triplex
dsDNA decoys
CpG
aptamers
blockers
siRNA

 

 

 

 

 

Secondly, while it has been possible for oligo chemists to design and synthesize a plethora of modified oligos to achieve optimized nuclease stability, binding to target, etc., efficient delivery has remained the single most challenging problem to deal with. In talks on medicinal oligos, this situation is oftentimes eluded to as something to the effect of “there are only three remaining problems to solve: delivery, delivery, and delivery.”

Lastly, contrary to early hopes of being Dr. Ehrlich’s “magic bullets” (see caption below), oligos didn’t quite prove to be the new paradigm for a speedy concept-to-clinic solution. As all of us in the oligo world know, oligo-based therapeutics have encountered long and costly R&D timelines and clinical development paths typical of all other classes of therapeutic compounds.

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Hot Topic in Oligonucleotide Therapeutics: Nanomedicine

  • What is it?
  • Why is it Hot?
  • How do Nucleic Acids Fit in?

The upcoming Oligonucleotide Therapeutics Society (OTS) annual meeting on Oct 12-15 in San Diego has an agenda with a number of presentations that could each qualify as a hot topic to highlight in this blog post. While mulling over which to pick, the talk by Prof. Weihong Tan—an extraordinarily prolific researcher at the University of Florida—entitled DNA-based molecular medicine and nanomedicine triggered my decision to comment on nanomedicine because it’s at the nexus of multiple scientific disciplines and various aspects of medicine.

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30 Years of Automated Amidite DNA Oligos and Going Strong

Is this the most enabling biotechnology yet? I think so, what do you think?

A list of Historical Events for 1983 includes Michael Jackson’s “Thriller” album going to #1 and airing the final TV episode of “M*A*S*H” watched by a record 125 million viewers. Aside from this pop culture, 1983 was quite remarkable in the history of biotechnology. Two closely interconnected and unquestionably transformative events occurred: introduction of automated synthesis of DNA oligonucleotides (aka oligos) by Applied Biosystems, Inc. (ABI) and invention of PCR by Kary Mullis. My July 15th post gave scientific homage, if you will, to the enabling power of PCR and ended by noting that ready access to synthetic DNA oligos was, in effect, “enabling the enabler” and likewise deserves comment here.

Picks and shovels for the biotechnology gold rush

In recently published reflections entitled The Chemical Synthesis of DNA/RNA: Our Gift to Science, Prof. Marvin H. Caruthers gives a firsthand account of the initial development of the now well-known phosphoramidite (amidite) method for oligo synthesis with members of his research group at the University of Colorado at Boulder, notably, Serge Beaucage, Mark Matteucci, Bill Efcavitch, Curt Becker, and Lincoln McBride.

marvin

Prof. Marvin H. Caruthers, 2006 National Medal of Science Laureate (Bing Images).

These reflections go onto a very interesting backstory on founding ABI in Foster City, California to commercialize automated oligo synthesis using solid-phase amidite methodology, as pictured below. This, together with automated protein sequencers, peptide synthesizers, and related “tools”, were envisaged as enabling the then emerging field of biotechnology.

solidphase

Automated solid-phase phosphoramidite DNA oligonucleotide synthesis cycle (adapted from M. H. Caruthers, J. Biol. Chem. 2013, 288: 1420-1427).

ABI’s co-founder and first CEO, Sam Eletr, metaphorically referred to ABI’s tool-provider business model as making the “picks and shovels for the biotechnology gold rush.” Bill Efcavitch, Curt Becker, and Lincoln McBride joined ABI to do this, while Serge Beaucage went to Beckman (which introduced its amidite-based DNA oligo synthesizer shortly after ABI), and Mark Matteucci joined Genentech to do oligo synthesis. For further background on the history of this revolutionary technology, click here for a 1983 publication by Köster and coworkers on β-cyanoethyl (CE) phosphoramidites in oligo synthesis.

andre

Mr. Andre Marion (left) and Dr. Sam Eletr (right), who co-founded ABI in 1980 (Bing Images) as a company that would manufacture and sell “picks and shovels for the biotechnology gold rush,” are still very active in commercial biotechnology.

Transforming targeted drug development with antisense therapeutics

My small part in this story involved being chosen as one of the early-access test sites for ABI’s first amidite-based oligo synthesizer (while at FDA/NIH), and then joining ABI in 1986 to commercialize new applications. These applications included automated amidite RNA oligo synthesis and scale-up (1umol → 10umol →200umol) of DNA oligos.  We focused on modified oligos as potential antisense inhibitors of mRNA function, particularly methylphosphonate (PCH3) and phosphorothioate (PS) oligos, which at the time were gaining scientific attention—and new venture investments—as the “next big thing” for targeted drug development.

Continuing the historical evolution and impact of the commercialization of oligo synthesis…Lynx Therapeutics was subsequently spun-out of ABI in 1992 to pursue antisense therapeutics.  Today, this field is led by Isis Pharmaceuticals.  It’s been a few years now and these applications are indeed proving to be the next big thing, as demonstrated by ISIS’s recent announcement of FDA approval of KYNAMRO™ (mipomersen sodium or ISIS 301012) for the treatment of homozygous familial hypercholesterolemia.

kynamro

In this announcement, Stanley T. Crooke, MD, PhD, Chairman of the Board and CEO of Isis said that “KYNAMRO™ is the first systemic antisense drug to reach the market and is the culmination of two decades of work to create a new, more efficient drug technology platform.” The structure of ISIS 301012 is reported to be a hybrid RNA/DNA/RNA 20-mer that is fully PS-modified, and has five 2′-O-(2-methoxyethyl)-modified (2′-MOE) ribonucleosides at the 5′ and 3′ ends, ten 2′-deoxynucleosides in between; all cytosines are methylated at the C5 position: 5′-GCCTCAGTCTGCTTCGCACC-3′. PS and 2’-MOE modifications provide resistance to degradation by nucleases, while the central DNA segment allows RNase H-mediated cleavage of the mRNA target.

Congratulations to Dr. Crooke and to Isis for this milestone achievement for amidite chemistry! With over 25 other oligo drugs under active development in Phase 2 or higher, we expect to see the FDA approving more of these types of drugs in the near future. Click here for a survey and summary of these oligo drugs.

Stunning scalability:  billion-fold batch-size and million-fold parallelism

ABI’s original synthesis-scale for automated amidite DNA oligo assembly was 1umol, which was soon followed by 10umol and then 200umol batch-sizes. Far greater scalability was driven by the need for ever increasing amounts of oligos in preclinical animal experiments and subsequent clinical studies. Eventually, oligo drug commercialization required further investment in cost-effective process development. When I asked Dr. Yogesh Sanghvi, (formerly with Isis and founder/President of Rasayan, Inc.) about batch-size for oligo drug manufacturing, he said that “oligo synthesis scale has been increased to 750mmol using a solid-support method.“ Click here for his review of the current status of synthesis, chemical modifications, purification, and analysis of modified oligos for therapeutics.

By contrast to these very large single batch-sizes for manufacturing of an individual oligo drug, conventional gene synthesis and, especially, emerging applications in synthetic biology, require very small batch-sizes for manufacturing many thousands of different oligos. One way this has been achieved is through the use of multi-well plates for parallelized solid-phase synthesis of thousands of oligos at a time. Such approaches make “pennies per base” cost to customers a reality. If one assumes that ~1nmol and ~1mol single-batch scales are technically “doable,” then the scalability for solid-phase amidite synthesis is ~109-fold!

Fundamentally different strategies for producing huge numbers of tiny amounts of oligos employ massively parallelized array-based amidite synthesis, unblocking and cleavage from the array, and then either single-tube multiplex manipulations or use of water/oil picoliter-sized droplets.

Enabling never ending and expanding scope of science and technology

In this blog, I’ve explored the use of oligos in targeted drug development and the amazing diversity of manufacturing scales for oligos. These versatile enablers have also played—and continue to play—transformative roles in countless other areas of science and technology. Being a bit “PowerPoint-challenged” and squeezed for time, I opted for simply listing below various types of science and technology enabled in part by automated amidite DNA (and RNA) oligo synthesis. This list is not ordered in any way and it is not intended to be comprehensive, but it is quite an impressive list, nonetheless. There’s strong “entanglement,” so to speak, between DNA oligo synthesis and seemingly indispensable PCR (and other) amplification methods. Consequently, many of the listed items are “co-enabled” by oligo synthesis and amplification. Links to representative literature or websites are provided for readers who may be interested in more information.

Oligo synthesis: quo vadis?

There’s absolutely no doubt in my mind that currently available automated amidite oligo chain-assembly will continue to enable significant expansion of major nucleic acid-based applications beyond the types listed below. It’s less clear to me whether a non-amidite method will be invented to replace amidite chain-assembly for some applications and/or enable new applications for which amidite methodology is inadequate. Other chemical and/or enzymatic processes are conceivable, and there are likely some very creative minds musing over possible ways to outperform amidites relative to “faster, better, cheaper” oligo production, so never say never.

Comment on this list or any other content herein is welcomed.

List of science and technology enabled by oligos:  

sanofi

Sanofi’s newly launched facility for large-scale production of semi-synthetic artemisinin, a potent anti-malarial represents a further milestone in an anti-malarial drug partnership led by OneWorld Health, a non-profit drug development organisation, with funding from the Bill & Melinda Gates Foundation. Sanofi plans to have 60 tons per year capacity in 2014, which would meet at least a third of the annual global need for the drug (taken from European Biotechnology News via Bing Images). Click here for more on this facility and here for a 2013 Nature publication of the science.

triangles

DNA origami triangles, self-assembled in a single step from over 200 DNA strands. Each is a single 5 megadalton molecular complex, incorporating 15,000 nucleotides. ~120nm per edge, 1µm scan. Sample courtesy of Paul W.K. Rothemund, California Institute of Technology (taken from Asylum Research via Bing Images).

 

algae

Biodiesel can be made from algae; click here for advantages of using algae for biofuel production (taken from our-energy.com via Bing Images).