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.

RNA World Revisited

  • Scripps Researchers ‘Evolve’ an RNA-Amplifying RNA Polymerase 
  • It’s Used for First Ever All-RNA Amplification Called “riboPCR”
  • TriLink Reagent Plays a Role in this Remarkably Selective in Vitro Evolution Method 
Prof. Gerald Joyce & Dr. David Horning. Photo by Madeline McCurry-Schmidt. Taken from scripps.edu

Prof. Gerald Joyce & Dr. David Horning. Photo by Madeline McCurry-Schmidt. Taken from scripps.edu

Those of you who regularly read my blog will recall an earlier posting on “the RNA World,” which was envisioned by Prof. Walter Gilbert in the 1980s as a prebiotic place billions of years ago when life began without DNA. That post recommended reading more about this intriguing hypothesis by consulting a lengthy review by Prof. Gerald Joyce. Now, Prof. Joyce and postdoc David Horning have advanced the hypothesis one step further by reporting the first ever amplification of RNA by an in vitro-selected RNA polymerase, thus providing significant supportive evidence for the RNA World. Following are their key findings, which were enabled in part by a TriLink reagent—read on to find out which one and how!

In Vitro Evolution of an RNA Polymerase

Horning & Joyce designed an in vitro selection method to chemically “evolve” an RNA polymerase capable of copying a relatively long RNA template with relatively high fidelity. The double emphasis on “relatively” takes into account that the RNA World would have many millions of years to evolve functionally better RNA polymerases capable of copying increasingly longer RNA templates with increasingly higher fidelity.

As depicted below, they started with a synthetic, highly structured ribozyme (black) wherein random mutations were introduced throughout the molecule at a frequency of 10% per nucleotide position to generate a population of 1014 (100,000,000,000,000) distinct variants to initiate the in vitro evolution process. Step 1 involved 5’-5’ click-mediated 1,2,3-trazole (Ø) attachment of an 11-nt RNA primer (magenta) partially complementary to a synthetic 41-nt RNA template (brown) encoding an aptamer that binds guanosine triphosphate (GTP). In Steps 2 and 3, the primer hybridizes to template and is extended by polymerization of A, G, C and U triphosphates (cyan).

Taken from Horning & Joyce, Proc. Natl. Acad. Sci., 2016

Taken from Horning & Joyce, Proc. Natl. Acad. Sci., 2016

GTP aptamer showing red and cyan sequences corresponding to above cartoon. Taken from Horning & Joyce, Proc. Natl. Acad. Sci., 2016

GTP aptamer showing red and cyan sequences corresponding to above cartoon. Taken from Horning & Joyce, Proc. Natl. Acad. Sci., 2016

Step 4 involves binding of aptameric structures to immobilized GTP (green), then photocleavage of the 1,2,3-triazole linkage in Step 5, followed by reverse transcription to cDNA and conventional PCR in Step 6 for transcription into ribozymes in Step 7. Twenty-four rounds of this evolution by selection were carried out, progressively increasing the stringency by increasing the length of RNA to be synthesized by decreasing the time allowed for polymerization. By the 24th round, the population could readily complete the GTP aptamer shown below. Subsequent cloning, sequencing and screening were then used to characterize the most active polymerase, which was designated “24-3.”

The TriLink “Connection”

2'-Azido-dUTP (aka 2'-azido-UTP)

2′-Azido-dUTP (aka 2′-azido-UTP)

The aforementioned in vitro evolution process actually involves tons of experimental details that interested readers will need to consult in the published paper, which is accompanied by an extensive Supporting Information section. In the latter, a subsection titled Primer Extension Reaction describes 3’ biotinylation of the template RNA strand (brown in above scheme) using TriLink “2’-azido-UTP” (more properly named 2’-azido-dUTP) and yeast poly(A) polymerase, followed by click connection of the RNA template’s 3’-terminal 2’-azido moiety to biotin-alkyne. This very clever functionalization of the RNA template strand allowed for subsequent capture of the double-stranded primer extension reaction products on streptavidin-coated beads, followed by elution of the desired nonbiotinylated strand for GTP aptamer selection (Step 4 above).

Properties of RNA Polymerase 24-3

Needless to say—but I will—enzymologists and RNA aficionados will undoubtedly be interested in musing over the kinetic and fidelity properties of RNA polymerase 24-3.

The rate of 24-3 polymerase catalyzed addition to a template-bound primer was measured using an 11-nt template that is cited extensively in the literature to evaluate various ribozymes. It was found that the average rate of primer extension by 24-3 is 1.2 nt/min, which is ∼100-fold faster than that of the starting ribozyme polymerase randomly mutagenized for in vitro selection.

The NTP incorporation fidelities of the starting and 24-3 ribozyme polymerases on this 11-nt test template, at comparable yields of product, are 96.6% and 92.0%, respectively. Horning & Joyce noted that the higher error rate of 24-3 is due primarily to an increased tendency for G•U wobble pairing.

Phenylalanyl tRNA. Taken from Horning & Joyce, Proc. Natl. Acad. Sci., 2016

Phenylalanyl tRNA. Taken from Horning & Joyce, Proc. Natl. Acad. Sci., 2016

Other longer RNA templates having various base compositions or intramolecular structures were also studied, with the stated “final test of polymerase generality” being use of 24-3 to synthesize yeast phenylalanyl tRNA from a 15-nt primer (in red right). The authors humorously describe the results as follows:

“Despite the stable and complex structure of the template, full-length tRNA was obtained in 0.07% yield after 72 h. This RNA product is close to the limit of what can be achieved with the polymerase, but is likely the first time a tRNA molecule has been synthesized by a ribozyme since the end of the RNA world, nearly four billion years ago.”

Exponential Amplification of RNA

PCR is the most widely used method for amplifying nucleic acids, and involves repeated cycles of heat denaturation and primer extension. The 24-3 RNA polymerase was used to carry out PCR-like amplification, but in an all-RNA system (named riboPCR by Horning & Joyce) using A, G, C, and U triphosphates and a 24-nt RNA template composed of two 10-nt primer-binding sites flanking the sequence AGAG. Somewhat special conditions were employed:

  • The concentration of Mg2+ was reduced to minimize spontaneous RNA cleavage
  • PEG8000 was used as a “molecular crowding” agent to improve ribozyme activity at the reduced Mg2+ concentration
  • Tetrapropylammonium chloride was added to lower the melting temperature of the duplex RNA

Under these conditions, 1 nM of the 24-nt RNA template was driven through >40 repeated thermal cycles, resulting in 98 nM newly synthesized template and 106 nM of its complement, corresponding to 100-fold amplification. Sequencing of the amplified products revealed that the central AGAG sequence was largely preserved, albeit with a propensity to mutate the third position from A to G, reflecting the low barrier to wobble pairing.

Amplification of a 20-nt template (without the central insert) was monitored in real time, using FRET from fluorescently labeled primers, and input template concentrations ranging from 10 nM to 1 pM. The resulting amplification profiles shown in the paper are typical for real-time PCR, shifted by a constant number of cycles per log-change in starting template concentration. A plot of cycle-to-threshold vs. logarithm of template concentration, also shown in the paper, was linear across the entire range of dilutions indicating exponential amplification of the template RNA with a per-cycle amplification efficiency of 1.3-fold.

Implications for the Ancient RNA World

It would be an injustice to Horning & Joyce if I would try to paraphrase their concluding discussion of this investigation, so here is what they say:

The vestiges of the late RNA world appear to be shared by all extant life on Earth, most notably in the catalytic center of the ribosome, but most features of RNA-based life likely were lost in the Archaean era. Whatever forms of RNA life existed, they must have had the ability to replicate genetic information and express it as functional molecules. The 24-3 polymerase is the first known ribozyme that is able to amplify RNA and to synthesize complex functional RNAs. To achieve fully autonomous RNA replication, these two activities must be combined and further improved to provide a polymerase ribozyme that can replicate itself and other ribozymes of similar complexity. Such a system could, under appropriate conditions, be capable of self-sustained Darwinian evolution and would constitute a synthetic form of RNA life.

Applications for Today’s World of Biotechnology

The aforementioned report by Horning & Joyce has received wide acclaim in the scientific press and world-wide public media as supporting the existence of a prebiotic RNA World, billions of years ago, from which life on Earth evolved.

While the academic part of my brain, if you will, fully appreciates the significance of these new insights on “living” RNA eons ago, the technical applications part of my brain is more piqued by possible practical uses of all-RNA copying or all-RNA riboPCR.

I, for one, plan to muse over possible applications of such all-RNA systems in today’s world of biotechnology, and hope that you do too, and are willing to share any ideas as comments here.

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.

Continue reading

Aptamers: Chemistry Bests Mother Nature’s Antibodies

• Discovered ~20 years ago, aptamer applications are booming
• Modified oligos and nucleotide triphosphates play pivotal roles
• World’s first chemical guided missile could be the answer to wiping out cancer
• Are antibodies passé?

Aptamers are nucleic acids (or peptides) that bind to a specific target molecule. RNA or DNA aptamers are usually created by selection from a large pool (aka library) of random sequences; however, natural RNA aptamers also exist in riboswitches. As discussed below, aptamers have been used for an impressively wide variety of applications in either basic research or, especially, health-related diagnostics and therapeutics. This remarkable utility is clearly reflected in the publication statistics—since their discovery in 1990, there have been ~11,000 publications indexed to DNA or RNA aptamers in SciFinder with a projected average rate of ~5 per day in 2013! More than 1,600 of these publications are patents, which is a stunning testament to the commercial potential of aptamers.

Most published authors: Analyzing these SciFinder aptamer publications by author gave the following top-5 ranking for number of publications indexed to aptamers…amazing productivity!

Tan, Weihong:  306
Ellington, Andrew D.:  173
Ikebukuro, Kazunori:  112
Famulok, Michael:  99
Sullenger, Bruce A.:  97

Trying to get what you want sometimes leads to getting what you need…
One concept, two labs, and a pair of seminal publications 

By remarkable coincidence in 1990, two labs independently published conceptually similar achievement of RNA selection in vitro—without using an RNA replicase, as in the past—but by quite different approaches.

Craig Tuerk and Larry Gold described in Science a procedure they cleverly named SELEX, which sounds a bit like select, and was an acronym for systematic evolution of ligands by exponential enrichment. This now classic paper has nearly 5,000 citations in Google Scholar. The authors noted that “[t]he method relies on mechanisms usually ascribed to the process of evolution, that is, variation, selection, and replication.” Briefly, as depicted in the figure below taken from this paper, a segment of RNA was transcribed from DNA template that had been synthesized so as to have eight contiguous, “randomized” positions (N = A, G, C and T) by means of “mixed couplings” using all four phosphoramidite reagents. This pool of 65,536 ( = 48) different RNAs was incubated with gp43 and the subset of RNAs selected by gp43 were then collected, reverse-transcribed into cDNA, amplified by PCR, and then transcribed into RNA for a second round of SELEX. After six rounds of SELEX, sequencing 20 clones of cDNA revealed that, in addition to the wild type 8-nt RNA sequence, a major variant mutated at 4-of-8 positions was also selected, along with several minor variants with fewer mutations.

gold

Taken from Tuerk and Gold in Science 1990.

Those interested in the scientific context of the above work, and the molecular biological interpretations, are encouraged to read the original paper, which is freely available as a pdf through a Google Scholar by searching for “Tuerk Gold 1990”. Here, however, are selected—pun intended—prescient comments by Tuerk and Gold in their concluding section simply entitled “Applications.”

• “Among many general applications of this technique, SELEX analyses can be used to determine the optimal binding sequences for any nucleic acid binding protein.”

• “Small molecules…can be bound to insoluble supports to partition RNAs that interact specifically with these substrates.”

• “We expect that, at the very least, nucleic acid ligands that inhibit replicative proteins of epidemiologically important infections can be likewise evolved. Other, more sophisticated effects of evolved RNA molecules on target activities may be possible.”

• “Finally, SELEX may be just the beginning of evolution in a test tube…[and] provide unpredictable and unimaginable molecular configurations of nucleic acids and proteins with any number of targeted functions.”

Andrew D. Ellington and Jack W. Szostak reported in Nature Methods the synthesis of large numbers of random sequence RNA molecules for binding to specific ligands to investigate fundamental questions related to formation of stable polynucleotide 3-dimensional structures in the context of theories of the origin and early evolution of life. Briefly, they synthesized ~150-nt DNAs comprised of central ~100-nt random sequence—via mixed phosphoramidite couplings (see above)—flanked by defined-sequence 5’ and 3’ ends as primer and restriction sites for cloning. As depicted below in a figure from this paper, transcribed random-sequences of RNA were applied to a column of agarose having an immobilized dye as a model ligand.

Taken from Ellington and Szostak in Nature 1990.

Taken from Ellington and Szostak in Nature 1990.

They chose six dyes that have “many possible hydrogen-bond donor and acceptor groups as well as planar surfaces for stacking interactions.” Bound RNAs were eluted and reverse transcribed for PCR amplification before another cycle of selection. After four to five cycles and sequencing, it was concluded that binding of selected RNAs is specific with regard to cross-reactivity of each selected pool for each column. However, each dye-binding pool was estimated to be a complex mixture of 102 – 105 different sequences, i.e. “there are many independent sequence ‘solutions’ to each ligand-binding ‘problem.’“

For some reason, reading this analogy of many solutions for one problem brought to mind these lyrics from the song in the Rolling Stones 1969 album Let It Bleed:

No, you can’t always get what you want
But if you try sometime, you just might find
You get what you need


Those interested in the details of clonal sequence information, etc. extracted from the results are encouraged to read the original paper, which is freely available as a pdf through a Google Scholar search for “Ellington Szostak 1990.” These authors went on to say that “[w]e have termed these individual RNA sequences ‘aptamers’, from the Latin ‘aptus’, to fit. Furthermore, they suggested that “it may be possible to isolate novel ribozymes from pools of random-sequence RNAs” using transition state analog affinity columns, by analogy with the isolation of catalytic antibodies.

The enabling power of aptamers

The vast body of literature covering basic research and numerous applications of nucleic acid aptamers is a stunning testament to the enabling power of these molecules, and the myriad of expanded types of aptamers and aptamer-generation methods. The Ellington Lab has provided a very useful tool for obtaining information about apatamers in the form of The Aptamer Database, which is a comprehensive, annotated repository for information about aptamers and in vitro selection. This searchable resource is provided to collect, organize and distribute all the known information regarding aptamer selection. For example, when I searched for “toxin” in Title Keywords, three citations were provided with active links, e.g. this 2006 article by Tang et al. in Electrophoresis: The DNA aptamers that specifically recognize ricin toxin are selected by two in vitro selection methods.

Additional search tools for aptamer-related publications, such as PubMed, Scirus, and SciFinder, readily provide access to whatever aspects may be of interest. In perusing this wealth of information, I came across the following items that I selected—pun intended (again!)—as representative examples of recently available literature for various categories.

Selections Methods:

Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer
Multiplexed microcolumn-based process for efficient selection of RNA aptamers
In vivo SELEX for Identification of Brain-penetrating Aptamers

Targeting Cells:

Development of an Efficient Targeted Cell-SELEX Procedure for DNA Aptamer Reagents
Selection of DNA Aptamers against Glioblastoma Cells with High Affinity and Specificity
• Rapid Identification of Cell-Specific, Internalizing RNA Aptamers with Bioinformatics Analyses of a Cell-Based Aptamer Selection

Therapeutics:

Nucleic acid aptamers: clinical applications and promising new horizon
Therapeutic RNA aptamers in clinical trials
An RNA Alternative to Human Transferrin: A New Tool for Targeting Human Cells

Diagnostics:

Development of an Aptamer-Based Concentration Method for the Detection of Trypanosoma cruzi in Blood
Harnessing aptamers for electrochemical detection of endotoxin

Food Safety:

Aptamer-Based Molecular Recognition of Lysergamine, Metergoline and Small Ergot Alkaloids
First report of the use of a saxitoxin?protein conjugate to develop a DNA aptamer to a small molecule toxin
Nucleic acid aptamers for capture and detection of Listeria spp

“World’s first chemical guided missile could be the answer to wiping out cancer”

This attention grabbing headline of an article in Deakin University Newsroom led me to contact Prof. Wei Duan regarding the current status of this promising research that he and his team first described in a Cancer Sci. 2011 publication entitled RNA aptamer against a cancer stem cell marker epithelial cell adhesion molecule. In this study, SELEX was used to identify a 40-base RNA aptamer that binds to epithelial cell adhesion molecule (EpCAM), which is overexpressed in most solid cancers and is reported to be a cancer stem cell marker. Interestingly, the aptamer was further truncated to 19 bases yet still interacts specifically with a number of live human cancer cells derived from breast, colorectal, and gastric cancers that express EpCAM, but not with those not expressing EpCAM. Importantly, this EpCAM RNA aptamer is efficiently internalized after binding to cell surface EpCAM. These authors believed that this is the first RNA aptamer against a cancer stem cell surface marker being developed, and that such cancer stem cell aptamers will greatly facilitate the development of novel targeted nanomedicine and molecular imaging agents for cancer theranostics.

Prof. Wei Duan, Director of Nanomedicine, Deakin University (Geelong, Victoria, Australia); taken from Deakin University website via Bing Images.

Prof. Wei Duan, Director of Nanomedicine, Deakin University (Geelong, Victoria, Australia); taken from Deakin University website via Bing Images.

As for the current status of this line of research, Prof. Duan provided me with the following comments. “With a few rare exceptions, most of the chemotherapy drugs and molecularly targeted agents in oncology clinics kill only non-cancer stem cells.  In order to improve the cancer treatment outcome, we must target cancer stem cells. Our lab has developed the world’s first RNA aptamer against cancer stem cell marker protein. We are currently working on novel treatment strategies by targeting cancer stem cells in vivo using our aptamers. For example, using cancer stem cell targeting aptamers, we can transform conventional chemotherapy drugs to robust cancer stem cell busters in xenograft tumour models.  With some smart engineering and strategic chemical modifications, we can now deliver siRNA into cancer stem cells in vivo to achieve an unprecedented %ID (percentage of injected dose). I believe that furture development of aptamer for cancer stem cell targeting will transform the way we think and approach cancer treatment.”

Expanding chemical modifications to an expanded genetic alphabet

Moving beyond sequence pools comprised of natural A, G, C, and T/U to chemically modified nucleotides in aptamers has been extensively investigated to either increase diversity of structural elements (e.g. hydrophobicity, polarity, 3D shape, etc.) to obtain improved binding, or improve biological properties (e.g. nuclease resistance, cellular uptake, etc.). Because of limitations in both enzyme activity and the modified NTPs readily available, the vast majority of modified aptamers have been developed using 2′ fluoro dC (fC) and 2′ fluoro dU (fU), although the 2′ amino and 2′ OMe analogs of the pyrimidines have also been used. More “exotic” modified dNTPs with pendant amino acid or hydrophobic moieties that have been investigated can be perused by clicking here for a 2012 review by Marcel Hollenstein entitled Nucleoside Triphosphates — Building Blocks for the Modification of Nucleic Acids.

Modified nucleotides used in SOMAmer™ selection (taken from Technical Note on SomaLogics website)

Modified nucleotides used in SOMAmer™ selection (taken from Technical Note on SomaLogics website)

Especially noteworthy, however, is SomaLogic’s development of novel SOMAmer™ (Slow Off-rate Modified Aptamer) protein-binding technology capable of measuring thousands of proteins in small volumes of biological samples with low limits of detection, a broad dynamic range, and high reproducibility. This approach, which was first published in 2010 in PLoS One, uses chemically-modified nucleotides shown below to mimic amino acid side chains together with new SELEX strategies. SOMAmers have already been developed for more than 1,100 different protein targets critical to normal and disease biology, with many more said to come soon.

More recently, a truly remarkable milestone in aptamer technology was reported earlier this year in Nature Biotechnology by Ichiro Hirao and coworkers at the RIKEN Systems and Structural Biology Center and TagCyx Biotechnologies in Japan. These investigators note that DNA aptamers produced with natural or modified natural nucleotides often lack the desired binding affinity and specificity to target proteins. They then describe a method for selecting DNA aptamers containing the four natural nucleotides and an unnatural nucleotide with the hydrophobic base Ds, which specifically pairs with the unnatural base Px during PCR, as depicted below and highlighted in an earlier related blog.

Taken from a news article in BioTechniques 2013 via Bing Images.

Taken from a news article in BioTechniques 2013 via Bing Images.

Up to three Ds nucleotides were incorporated in a random sequence library. Selection experiments against two human target proteins, vascular endothelial cell growth factor-165 (VEGF-165) and interferon-γ (IFN-γ), yielded DNA aptamers that bind with KD values of 0.65 pM and 0.038 nM, respectively, affinities that are >100-fold improved over those of aptamers containing only natural bases. The authors concluded that “[t]hese results show that incorporation of unnatural bases can yield aptamers with greatly augmented affinities, suggesting the potential of genetic alphabet expansion as a powerful tool for creating highly functional nucleic acids.

Verified Randomized Sequences

I highly recommend reading Ellington and coworkers Current Protocols in Nucleic Acid Chemistry (2009) for detailed guidance on design, synthesis, and amplification of DNA pools for in vitro selection. These experts note that the “quality of randomization” is critically dependent on various aspects of automated DNA chain assembly using empirically determined ratios of A, G, C and T phosphoramidites to generate each N. Completely random pools should theoretically have 25% base composition at each N position, and therefore an unbiased distribution of di-, tri-, etc. nucleotide sequences.

If you’re looking for a supplier for verified random sequences, check out TriLink Biotechnologies. TriLink is a leader in verified manufacturing of randomized sequences that are now offered as convenient, stocked DNA or RNA random-libraries having 20, 30 or 40 randomized Ns and restriction sites for use with corresponding PCR primers and biotin labeling if desired. The mix of individual bases has been optimized to ensure as close to a 1:1:1:1 ratio of bases (i.e. 25% base composition) as possible during oligo synthesis. Each lot is tested by enzymatic digest to determine overall base composition and to verify that it falls within TriLink’s rigorous specifications, ensuring lot-to-lot reproducibility.

To my knowledge, TriLink is the only supplier of randomized sequences that have been verified by high-throughput applications (aka next-generation sequencing) to more deeply analyze randomization. NeoVentures BioTechnology has independently sequenced 61 clones of a 40-N library to obtain base composition at each position and, importantly, tri-nucleotide distribution, as detailed in this white paper. By contrast, NeoVenture’s analysis of a sample from an anonymous vendor revealed substantial deviation from random base composition and, consequently, unacceptable skewing of tri-nucleotide distribution.

Does complete randomness matter? Experts say yes: Ellington and coworkers opine that “[c]ompletely random sequence pools are used to initiate selection experiments when no functional nucleic acid sequence or structural motif is known in advance.” Furthermore, they add, “completely random sequence pools explore a much wider swath of sequence space and are more useful for the isolation of novel binding species (aptamers) or catalytic species.” 

Commercial Landscape

In July 2013 a comprehensive and up-to-date report entitled Aptamers Market – Technology Trend Analysis By Applications – Therapeutics, Diagnostics, Biosensors, Drug Discovery, Biomarker Discovery, Research Applications with Market Landscape Analysis – Global Forecasts to 2018 was made available by Market Research.com for purchase. The following is included in the free abstract of this report.

• Aptamers is an emerging market, widely considered as a rival or substitute to antibodies in the scientific industry. It is poised to grow rapidly in various application areas, including therapeutics and diagnostics. The global aptamers market is valued to be $287 million in 2013 and is expected to reach $2.1 billion by 2018.
• The list of promising aptamers in the clinical trials pipeline estimates that these synthetic chemical antibodies will soon surpass monoclonal antibodies in therapeutics, diagnosis, and imaging. With technological merits over antibodies, the aptamers market is poised to grow at par with antibodies in the next 10-15 years.
• The advantages of chemically modified aptamers and low production cost compared to antibodies aid the growth of the market.
• There are ~60 biotech and pharmaceutical companies working on aptamers.

A review of nanotechnology and aptamers noted an important linkage between “expiration of the early patents…and a simultaneous decentralization of aptamer-technology commercialization”.

Given the range of applications, growth trajectory, and estimated market potential of aptamers, I’m guessing this is a field many of you currently are or will want to monitor.  I’ve put together a list of notable players to keep your eye on. These include, in alphabetical order: AM Biotechnologies, LLC (U.S.) Aptagen, LLC (U.S.) Aptamer Sciences, Inc. (S. Korea) Aptamer Solutions, Ltd. (U.K.) Base Pair Biotechnologies (U.S.), Bioapter S.L. (Spain), Integrated Biotechnologies, Inc. (U.S.), NeoVentures Biotechnology, Inc. (Canada), NOXXON Pharma AG (Germany), OTC Biotech (U.S.), Regado Biosciences, Inc. (U.S.), and TriLink BioTechnologies (U.S.)—hum, maybe I should have done this list in reverse alphabetical order.

What lies ahead?

Sorry, no crystal ball for science! Taken from wired.com via Bing Images

Sorry, no crystal ball for science! Taken from wired.com via Bing Images

I don’t believe in a crystal ball that can predict the future for aptamers, or anything else for that matter. After searching the literature for aptamers and keywords such “future”, “perspective”, “horizon” or other forward-looking terms, I decided that there wasn’t any publication that I could quote from and cite as providing insights as to new directions. Consequently, I’ll offer my half-thoughts on some things that might occur at some time in the future.

Overall, I think that applications of aptamers will out-pace antibodies based on inherently greater structural diversity that can be obtained chemically, as opposed to biologically, and with a much more limited set of amino acid/analog “building blocks”. Other advantages, as noted by Base Pair Biotechnologies, include more economical production—especially in GMP grade—flexible “fine tuning” for desired bio-distribution, stability or shelf-life.

High-throughput sequencing and related bioinformatics will likely continue to enable new and improved aptamer selection methods, as exemplified by the recent work of Hoon et al., who used one such approach to develop a novel method for selecting high-affinity DNA aptamers based on a single round of selection.

Aptamers—not antibodies—will advantageously be selected for small molecule targets to develop new or improved label-free electronic sensors, such as those reported by Ohno et al. for an aptamer-modified graphene field-effect transistor. Incidentally, ethanolamine (HOCH2CH2NH2), which is associated with several diseases and has only four non-hydrogen atoms, was reported by Mann et al. to be perhaps the smallest aptamer target so far.

Finally, I expect that molecular modeling will get faster, cheaper, better and more accessible to folks wanting an aptamer against a molecular target, and thereby enable more computationally guided aptamer selection. One example of advances in this direction can be found in a 2013 publication entitled Computational approaches to predicting the impact of novel bases on RNA structure and stability by Harrison et al.

What do you think? Your ideas or other comments on this post are welcomed.

Postscript:  Latest breaking aptamer news

News from Naples

conference

This first ever international meeting on Aptamers In Medicine Perspectives, which was supported in part by TriLink, brought together many experts in, and practitioners of aptamer technology whose presentations are listed in the Final Program. TriLink’s CEO, Rick Hogrefe was in attendance and provided the following insights:

“Dr. Hoinka, of the National Center for Biotechnology Information, described the use of a novel high- throughput (HT) SELEX method called HTSAptamotif, which is coupled to an NGS platform and probably a much bigger computer than most labs have, to crunch out sequence and motif patterns that allow you to rationally design your aptamer. It is reasonable to expect that some year all that will be needed to design the perfect aptamer will be the crystal structure of the target and your somewhat smarter smart phone. An iPhone app will be soon to follow, no doubt.”

Rick also observed that “[o]ne reoccurring topic of discussion was the advantages of using chemically synthesized aptamers versus those made by transcription. One of the main disadvantages of using long RNA aptamers (>60mer) is that they must be prepared by transcription. Methods are still in development to prepare these compounds economically and eventually at scale. Many researchers truncate their original sequence to something more manageable—a 19-mer was reported in one talk. The greatest fear regarding the use of enzymatic synthesis of aptamers was the removal of one very deleterious contamination—5’-triphosphate oligonucleotides, which are potent activators of RIG-I. This is done with a phosphatase after transcription. During the Q&A session that followed the talk of Dr. Zhou of John Rossi’s lab at the City of Hope, Dr. Sullenger said he very carefully studied this reaction and was unable to optimize it sufficiently to remove all the triphosphates from the aptamer. Another attendee believed that they were able to sufficiently remove the triphosphate. More work is needed to develop a good method to detect the presence of triphosphate modifications on long oligos.”

Rick’s concluding opinions are that “[o]verall, it is apparent that aptamers are not only here to stay, but are rapidly expanding into what may become the most universally applicable oligonucleotide technology to date. The excellent talks in this meeting covered much of the breadth of what aptamers are capable of doing. It is time to buy your random library kit from TriLink and start your own aptamer research. Most likely you will find an aptamer that fits the bill—and your target—perfectly.” 

Where are they now?

drgoldDr. Gold founded SELEX-based NeXagen, which later became NeXstar Pharmaceuticals. Gilead acquired NeXstar in 1999 and teamed up with (OSI) EyeTech to develop Macugen (aka Pegaptanib), which is an anti-angiogenic, chemically modified RNA aptamer for the treatment of neovascular (wet) age-related macular degeneration. Gold is the founder, chairman of the board, and CEO of SomaLogic, where he continues his work on aptamers. Dr. Gold was made a member of the American Academy of Arts and Sciences in 1993, and the National Academy of Sciences in 1995.

tuerkCraig Tuerk was a graduate student with Dr. Gold, and then worked at NeXagen (a SELEX-based company founded by Gold). Dr. Tuerk left NeXagen in 1994, many years before his co-invention of SELEX would ultimately lead to Macugen (see Gold above). He currently teaches biochemistry and genetics at Kentucky’s Morehead State University. The Tuerk Lab research interests include in vitro evolution strategies, combinatorial libraries and drug design.

szostakThe Szostak Lab is affiliated with the Center for Computational & Integrative Biology, Massachusetts General Hospital, the Department of Molecular Biology, Massachusetts General Hospital, the Department of Chemistry and Chemical Biology, Harvard University, the Department of Genetics, Harvard Medical School, and the Howard Hughes Medical Institute. The Nobel Prize in Physiology or Medicine 2009 was awarded jointly to Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak “for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase.”

ellingtonDr. Ellington received his graduate degree in Biochemistry and Molecular Biology from Harvard University (working with Dr. Steve Benner), and was a post-doctoral Fellow with Jack Szostak at Massachusetts General Hospital. He was an assistant faculty member at Indiana University in the Department of Chemistry until 1998, and has since been a full Professor in the Department of Chemistry and Biochemistry at the University of Texas at Austin. Throughout his career Dr. Ellington has worked on the directed evolution of molecules and organisms, and has developed both insights into the origin of life and applications in biotechnology. The Ellington Lab motto is “what evolves here changes the world.”

TagCyx Biotechnologies 

According to its website, TagCyx Biotechnologies “core technology, the ‘unnatural base pair system’, has been developed by Dr. Hirao, founder and CEO of TagCyx Biotechnologies, during the course of his research at ERATO project (Exploratory Research for Advanced Technology) of Japan Science and Technology Agency, followed by the research at the University of Tokyo, and presently at RIKEN. The ‘Unnatural base pair system’ is an innovative technology which enables the site-specific incorporation of functional component into DNA, RNA and proteins. TagCyx Biotechnologies was founded in March 2007 as a RIKEN authorized venture business, with the mission of dissemination and application of this technology to various fields.”

From the clever corporate name joining natural base pairs TA and GC with variable, unnatural base pair YX, we can expect to see more from this company in the future.

Incidentally, according to a press release earlier this year, Dai Nippon Printing Co., Ltd. and TagCyx Biotechnologies have jointly developed a printing ink with a highly effective anti-counterfeit feature, through the integration of artificial DNA that is extremely difficult to replicate. This artificial DNA based ink is virtually impossible for third parties to replicate, and as it makes it possible to achieve powerful judgments of authenticity, can be used in anti-counterfeiting efforts connected with high-value printing requiring strong security, such as bank notes or cash vouchers.

MRI by DNA aptamers in vivo

After writing this blog, Philip Liu and his coworkers at Massachusetts General Hospital published the first-ever demonstration of protein-guided magnetic resonance imaging (MRI) by DNA aptamers in vivo using, as a model system, transcription factor (TF) protein AP-1, a heteroduplex protein comprising members of Fos and Jun immediate early gene families that plays an essential role in modifying gene expression by signal transduction. This work was published in FASEB J. A preprint of this report—kindly provided to me by Dr. Liu—describes details for conjugation of TF AP-1 or control synthetic double-stranded phosphorothioate end-capped DNA aptamers to superparamagnetic iron oxide nanoparticles (SPIONs), gold, or fluorescein for imaging by MRI, transmission electron microscopy studies, and optical methods, respectively. The SPION-enabled MRI results revealed that neuronal AP-1 TF protein levels were elevated in neurons of live mice after amphetamine exposure, as expected, while transgenic mice with neuronal dominant-negative A-FOS mutant protein, which has no binding affinity for the AP-1 sequence, showed a completely null MRI signal. These investigators concluded that further clinical development is warranted.

Shortest aptamer yet?

Also after finishing this blog, an 11-mer aptamer was reported by Nadal et al. to have been obtained by truncation of an aptamer that specifically binds to β-conglutin (Lup an 1), an anaphylactic allergen. The highest affinity was observed with a truncation resulting in a G-quadruplex-containing 11-mer sequence that had an apparent equilibrium dissociation constant (KD) of 1.7 × 10-9 M. This 11-mer sequence was demonstrated to have high specificity for β-conglutin and showed no cross-reactivity to other lupin conglutins (α-, δ-, γ-conglutins) and closely related proteins such as gliadin.

Another Resource

Nucleic Acid Therapeutics can be searched for “aptamers” with other keywords for full-text access to numerous publications on various aspects of RNA or DNA aptamer selection, targeting, etc. and reviews thereof.

Language Trivia

The word “aptamer” is used regardless of what language you happen to be reading or speaking. The same is true for “blog”, although in German someone might instead use “digitale Netztagebücher”. Since even for German speakers that doesn’t exactly flow off the tongue, the latest edition of Duden—the German equivalent of the Oxford English Dictionary, completely unrelated to “dude”—added 5,000 new words, many of them in English, such as “blog” and “flashmob”, according to Anna Sauerbrey, a German, in the New York Times Op-Ed on September 26, 2013.

Nanomedicine: Using ‘Tiny Little FedEx Trucks’ to Target Breast Cancer Tumors

breastcancerlogo

As we enter October, national breast cancer awareness month, I thought it an appropriate time to review some of the latest advances in breast cancer research. Let’s start with a review of the latest statistics published by the NCI and a look at current treatments, then we’ll explore some of the most promising new research in this field.

According to the National Institutes of Health (NIH) National Cancer Institute (NCI) Cancer Topics for Breast Cancer, the projected statistics on breast cancer for women in the United States in 2013 are grim: 232,340 new cases and 39,620 deaths. Moreover, global statistics for breast cancer were estimated to be over 1.5 million new diagnoses and 500,000 deaths in 2010—with the majority of these being in low and middle income countries, which presents a major challenge of a different kind.

The NIH NCI website provides an informative online booklet entitled What You Need To Know About™ Breast Cancer to learn about breast cancer types, staging, treatment, and questions to ask the doctor. There is also NCI’s overview of Cancer Advances in Focus: Breast Cancer that provides the following perspectives for “today” and “tomorrow.”

Today

  • Among women diagnosed with breast cancer during the period from 1999 through 2006, 90% were expected to survive their disease at least 5 years. Among white women, the 5-year relative survival rate was 91%; among African American women, it was 78%. The increase in breast cancer survival seen since the mid-1970s has been attributed to both screening and improved treatment.
  • Breast-conserving surgery (lumpectomy) followed by local radiation therapy has replaced mastectomy as the preferred surgical approach for treating early-stage breast cancer.
  • Routine mammographic screening is an accepted standard for the early detection of breast cancer. The results of eight randomized trials, the NIH-ACS Breast Cancer Detection Demonstration Projects, and other research studies showed that mammographic screening can reduce the mortality from breast cancer.
  • Hormonal therapy with selective estrogen receptor modulators (SERMs), such as tamoxifen, and aromatase inhibitors is now standard in the treatment of women with estrogen receptor-positive breast cancer, both as adjuvant therapy and in the treatment of advanced disease. Estrogen receptor-positive breast cancer cells can be stimulated to grow by the hormone estrogen. SERMs interfere with this growth stimulation by preventing estrogen from binding to the estrogen receptor. In contrast, aromatase inhibitors block estrogen production by the body. Food and Drug Administration (FDA)-approved aromatase inhibitors include anastrozole, exemestane, and letrozole.
  • Tamoxifen and another SERM, raloxifene, have been approved by the FDA as treatments to reduce the risk of breast cancer in women who have an increased risk of developing the disease.
  • The monoclonal antibody trastuzumab is an accepted treatment for breast cancers that overproduce a protein called human epidermal growth factor receptor 2, or HER2. This protein is produced in abnormally high amounts by about 20% of breast tumors. Breast cancers that overproduce HER2 tend to be more aggressive and are more likely to recur. Trastuzumab targets the HER2 protein specifically, and this antibody, in conjunction with adjuvant chemotherapy, can lower the risk of recurrence of HER2-overproducing breast cancers by about 50% in comparison with chemotherapy alone.
  • Several breast cancer susceptibility genes have now been identified, including BRCA1, BRCA2, TP53, and PTEN/MMAC1. Approximately 60% of women with an inherited mutation in BRCA1 or BRCA2 will develop breast cancer sometime during their lives, compared with about 12% of women in the general population.

Tomorrow

  • We will use our rapidly increasing knowledge in the fields of cancer genomics and cell biology to develop more effective and less toxic treatments for breast cancer and to improve our ability to identify cancers that are more likely to recur. Moreover, we will use this knowledge to tailor breast cancer therapy to the individual patient.
  • We will use our increasing knowledge of the immune system to enhance the body’s ability to recognize and destroy cancer cells. The knowledge we have acquired thus far has facilitated the development of several promising breast cancer treatment vaccines that are currently under clinical evaluation.
  • We will use advanced technologies, including genomic technologies, to improve our ability to detect breast cancer at its earliest stages, when it is most treatable, and to better define individual risk for this disease.
  • We will strive to understand, address, and eliminate factors that contribute to the higher mortality from breast cancer experienced by African American women compared with women of other racial and ethnic groups.

Managing the Nation’s Cancer Research Portfolio

As a scientist and taxpayer, you’ll likely be very interested—as I was—in knowing much more about the specifics of what the NCI proposed for managing the Nation’s cancer research portfolio in 2013. This information is nicely laid out at an NCI website that includes a downloadable pdf version with programmatic details and a summary budget ($5.833 Billion).

ncir

National Cancer Institute Research Campus in Bethesda, MD (via Bing Images)

Among the details that I found particularly interesting is an introductory section called “Provocative Questions.” NCI launched an initiative late in 2010, seeking to go beyond the questions that are self-evident or that have been studied for many years. NCI “asked investigators to propose intriguing questions that need attention but might not otherwise get it or that have stumped us in the past but may be answered by new technologies. The initiative, which elicited a strong and exciting response from the research community, has recently funded its first 56 investigators.” In addition to a link therein for the Provocative Questions Project website, there is a link to a short video wherein NCI Director Harold Varmus, MD, discusses this project.

How do Normal v. Breast Cancer Cells Appear Microscopically?

Courtesy of NCI via Bing Images

Courtesy of NCI via Bing Images

From the descriptors given in the summary slide, provided by NCI, it is evident that breast cancer cell shape, size, and other properties reflect cellular dysfunctions, relative to normal cells, as is generally characteristic for other types of cancer. The accompanying high-resolution color enhanced scanning electron micrograph (SEM) of a breast cancer cell is visually stunning yet scary in view of the aforementioned death rate statistics.

A color enhanced scanning electron micrograph (SEM) of a breast cancer cell. Photograph: Science photo library (taken from theguardian.com via Bing Images)

A color enhanced scanning electron micrograph (SEM) of a breast cancer cell. Photograph: Science photo library (taken from theguardian.com via Bing Images)

Spotlight on an Expert

Prof. Esther H. Chang, MD PhD

Prof. Esther H. Chang, MD PhD

Prof. Esther H. Chang, MD PhD, is a member of the Departments of Oncology and Otolaryngology at the Lombardi Comprehensive Cancer Center of Georgetown University Medical Center. Before joining Georgetown University, Dr. Chang held positions at the National Cancer Institute (NCI), Stanford University, and the Uniformed Services University of Health Sciences. Currently, she is serving as the Interim President of the American Society for Nanomedicine and she is also an Executive Board Member of the International Society for Nanomedicine (ISNM) in Basel. Dr. Chang is the founding scientist of, as well as a Senior Consultant for, SynerGene Therapeutics, Inc. She has over 130 publications and has served as a member of a number of scientific advisory boards for NCI, NASA, the US Military Cancer Institute, and the Department of Energy.

I had the good fortune to become a collaborator of Dr. Esther H. Chang when she was working at the Uniformed Services University of Health Sciences, and I was literally across the street working at the FDA at NIH. We found that we shared a common interest in antisense therapeutics, which at that time (1980s) was a relatively new and—importantly—entirely novel drug development paradigm envisaged as affording more specific, less toxic anticancer agents. My lab could synthesize various chemically modified oligos, but had no molecular or cellular biology expertise. Dr. Chang’s lab at the time was working on Ras, which is a common oncogene in human cancer. We eventually published those initial collaborative investigations, and later reported a series of three papers on tumor-specific targeting and delivery of modified hybrid (DNA-RNA) anti-HER-2 siRNA analogs developed by TriLink (click here for details).

Dr. Chang’s achievements in specifically targeting tumors using antibody-fragment-tagged liposomal nanoparticles are indeed notable—and quotable—as outlined below.

“Tiny little FedEx trucks”

Tiny FedEx electric vehicles for delivery in Paris (Bing Images)

Tiny FedEx electric vehicles for delivery in Paris (Bing Images)

As scientists, we can appreciate the need to occasionally over simplify very complex technical concepts, and scientific jargon, in order to talk to nonscientists about our research. Consequently, I had to smile with appreciation when Dr. Chang referred to tumor cell-specific, targeted delivery of liposomal nanoparticles as involving “tiny little FedEx trucks” when interviewed on National Public Radio that can be listened to by clicking here.

Drug-carrying nanoparticles may be targeted to specific cell types. Illustration created by Amadeo Bachar for UCSD Center of Excellence in Nanomedicine; first published in Morachis et al., Pharm Rev 2012 (taken from Bing Images).

Dr. Chang’s use of this catchy metaphor is apropos for a couple of reasons. Just as trucks carry various types of cargo, liposomal nanoparticles (spheres pictured) can be loaded with various classes of therapeutic agents, ranging from traditional small-molecule entities to high-molecular weight genes, mRNAs, and mi/siRNA. Also, just as FedEx employs advanced technologies to locate ZIP-code intended-recipients, nanoparticles can utilize antibodies, fragments of antibodies (Y-shaped molecules pictured above) or other agents (ligands) for specific delivery to intended target cells via binding to cell surface receptors (pink molecules pictured above).

In an early publication entitled Tumor-targeted p53-gene therapy enhances the efficacy of conventional chemo/radiotherapy, Dr. Chang noted that a long-standing goal in gene therapy for cancer is a stable, low toxic, systemic gene delivery system that selectively targets tumor cells, including metastatic disease. In particular, ligand-directed tumor targeting of cationic liposome-DNA complexes (lipoplexes) showed promise for targeted gene delivery and systemic gene therapy. She demonstrated that Lipoplexes developed in her lab directed by ligands such as folate, transferrin or anti-transferrin receptor scFv antibody fragment, showed tumor-targeted gene delivery, expression, and anti-cancer effect in mouse models of human breast cancer, as well as prostate, head and neck cancers, seeming to meet these goals.

Based upon these promising results, this nanodelivery system has moved in human clinical trials. When I asked Dr. Chang about the status of such trials, and whether these results were applicable is some way to breast cancer, she offered the following comments:

“Tumor specificity is very crucial to a cancer therapy’s efficacy,” Chang asserts. “Because we have a targeting moiety, the nanocomplex will travel through the bloodstream and whenever it encounters a tumor cell — whether a primary tumor or metastasis — the nanoparticle will bind to it, enter the tumor cell and destroy it.”

This tumor targeted nanomedicine delivering the p53 gene (SGT-53) has already completed a Phase I safety trial, the results of which were described in an article entitled Phase I Study of a Systemically Delivered p53 Nanoparticle in Advanced Solid Tumors published in May of this year. The purpose of this trial was to give back to cancer patients the tumor-busting p53 gene they have lost.

She continued, “We were very encouraged by the results since the patients handled SGT-53 very well.  Only minimal side effects occurred. Even more exciting, at the end of treatment the majority of patients showed at least stable disease. We were also able to demonstrate targeted delivery of SGT-53 to metastatic cancer, and not to normal cells. These agents are intended to increase the effects of standard therapies by sensitizing the tumor cells to their killing effects. Thus, cancer is less likely to recur. We have seen fantastic anti-cancer responses in animal models with breast cancer, and we have seen this treatment working in various types of solid tumors in patients. Therefore, we think it is very likely that it will also be successful in treating breast cancer.”

Regarding future development of this agent, Chang stated “Three Phase II clinical trials are imminent in patients with pancreatic cancer, glioblastoma and lung cancer. We hope to evaluate this agent in patients with breast cancer in the near future.”

More on Nanomedicine for Cancer Therapy

Researchers in nanomedicine (a term first used in the late 1990s) aim to develop a variety of revolutionary tools:

  • Drug carriers that focus drug action at the site of disease to limit side effects.
  • Vaccines that are more feasible for use in areas with limited health care access (more stable, less expensive, and with minimal adverse reactions).
  • Imaging agents that produce signal detectable from significant depths only in diseased tissues.
  • Scaffolds for culturing engineered tissues that mimic the corresponding extracellular matrix and enable modulation of development over time and real-time monitoring of their activity and biochemistry.

As with any scientific field, its boundaries blur with those of related fields, including pharmaceutics, bio- and materials engineering, nuclear medicine, tissue engineering, and many others.

Schematic of localized magnetic delivery (taken from Nature Nano 2009 via Bing Images)

Schematic of localized magnetic delivery (taken from Nature Nano 2009 via Bing Images)

Magnetically Triggered, Local On-Demand Release of Drugs

Tran & Wilson highlight a particularly fascinating approach in nanomedicine aimed at making controllable magnetic drug delivery possible for the treatment of breast cancer. They note that a recent study published by Kong et al. in Nano Letters documents the synthesis and performance of porous silica nanocapsules filled with magnetic nanoparticles as a controllable magnetic drug delivery vector. Under a remotely applied radiofrequency magnetic field, these nanocapsules demonstrate on-off switchable release of the internally loaded drug payload. Both in vitro and in vivo studies using mouse breast cancer cell models demonstrate that the magnetic targeting of these nanocapsules allows for deep tumor penetration and subsequent on-demand release of the drug cargo, significantly reducing tumor cell viability.

“Chemical Antibodies” – Improving Nature with RNA Aptamers

Earlier this year, Shigdar et al. reported the use of sensitive “chemical antibodies” for diagnosis in breast cancer. They state that Epithelial cell adhesion molecule (EpCAM) is expressed at low levels in a variety of normal human epithelial tissues, but is overexpressed in 70–90% of carcinomas. From a clinico-pathological point of view, this has both prognostic and therapeutic significance. EpCAM was first suggested as a therapeutic target for the treatment of epithelial cancers in the 1990s. However, following several immunotherapy trials, the results have been mixed. It has been suggested that this is due, at least in part, to an unknown level of EpCAM expression in the tumors being targeted. Thus, selection of patients who would benefit from EpCAM immunotherapy by determining EpCAM status in the tumor biopsies is currently undergoing vigorous evaluation. However, current EpCAM antibodies are not robust enough to be able to detect EpCAM expression in all pathological tissues. Shigdar et al. go on to report a newly developed EpCAM RNA aptamer, also known as a chemical antibody, which is not only specific but also more sensitive than current antibodies for the detection of EpCAM in formalin-fixed paraffin-embedded (FFPE) primary breast cancers.

Schematic of dye- or drug-containing nanoparticle targeted to cancer cells by Y-shaped RNA aptamers (taken from Chemical & Engineering News 2012 via Bing Images)

Schematic of dye- or drug-containing nanoparticle targeted to cancer cells by Y-shaped RNA aptamers (taken from Chemical & Engineering News 2012 via Bing Images)

Twenty-mer aptamers were chemically synthesized with 2′-fluoro- or 2′-O-methyl-pyrimidine bases, a 3′-inverted deoxythymidine, and 5′-fluorescent tags. One of these aptamers showed no non-specific staining or cross-reactivity with tissues that do not express EpCAM. They were able to reliably detect target proteins in breast cancer xenograft where an anti-EpCAM antibody showed limited or no reactivity. They conclude that these results show the potential of aptamers in the future of histopathological diagnosis and as a tool to guide targeted immunotherapy.

I hope you leave this blog inspired by the promising developments that have been made in the field of breast cancer research and optimistic about the strides we, as a research community, continue to make toward finding a cure.

Breaking News:  FDA backs Roche drug as first-of-a-kind therapy to treat breast cancer before surgery

On September 12th, the Washington Post reported online that the FDA’s panel of cancer experts voted 13-0, with one abstention, that the benefits of Perjeta (a monoclonal antibody developed at Genentech) as an initial treatment for breast cancer outweigh its risks. The recommendation is not binding, but sets the stage for the FDA to clear the drug as the first pharmaceutical option approved to shrink or eliminate tumors before surgery. “We are supporting the movement of a highly active drug for metastatic breast cancer to the first-line setting, with the hope that women with earlier stages of breast cancer will live longer and better,” said Dr. Mikkael Sekeres, an associate professor of medicine at the Cleveland Clinic. Doctors hope that using cancer drugs earlier could help shrink tumors, making them easier to remove. In some cases, that could allow women to keep their breasts, rather than having a full mastectomy.

Perjeta works by blocking signals inside cancer cells that would tell them to divide and grow Photo: Roche (taken from itv.com via Bing Images).  Differences between HER family receptors are described here.

Perjeta works by blocking signals inside cancer cells that would tell them to divide and grow Photo: Roche (taken from itv.com via Bing Images). Differences between HER family receptors are described here.

Taken from Bing Images

Taken from Bing Images